eaogorg.files.wordpress.com€¦ · Web viewGEOCHEMISTRY ARTICLES – October 2019. Analytical Chemistry. Mironov, N.A., Milordov, D.V., Abilova, G.R., Yakubova, S.G., Yakubov,

GEOCHEMISTRY ARTICLES – October 2019

Analytical Chemistry

Mironov, N.A., Milordov, D.V., Abilova, G.R., Yakubova, S.G., Yakubov, M.R., 2019. Methods for studying petroleum porphyrins (review). Petroleum Chemistry 59, 1077-1091.

Vieira, A.L., Nespeca, M.G., Pavini, W.D., Ferreira, E.C., Gomes Neto, J.A., 2019. A user-friendly Excel spreadsheet for dealing with spectroscopic and chromatographic data. Chemometrics and Intelligent Laboratory Systems 194, 103816.

Wu, L., Sun, R., Li, Y., Sun, C., 2019. Sample preparation and analytical methods for polycyclic aromatic hydrocarbons in sediment. Trends in Environmental Analytical Chemistry 24, e00074.

Zhakupbekova, A., Baimatova, N., Kenessov, B., 2019. A critical review of vacuum-assisted headspace solid-phase microextraction for environmental analysis. Trends in Environmental Analytical Chemistry 22, e00065.

Zhou, T., Che, G., Ding, L., Sun, D., Li, Y., 2019. Recent progress of selective adsorbents: From preparation to complex sample pretreatment. TrAC Trends in Analytical Chemistry 121, 115678.

GAS CHROMATOGRAPHY/GC×GC/GC-MS

Alam, M.S., Zeraati-Rezaei, S., Xu, H., Harrison, R.M., 2019. Characterization of gas and particulate phase organic emissions (C9–C37) from a diesel engine and the effect of abatement devices. Environmental Science & Technology 53, 11345-11352.

Moayedpour, S., Parastar, H., 2019. RMet: An automated R based software for analyzing GC-MS and GC×GC-MS untargeted metabolomic data. Chemometrics and Intelligent Laboratory Systems 194, 103866.

IMAGING: AFM

Abarghani, A., Gentzis, T., Shokouhimehr, M., Liu, B., Ostadhassan, M., 2020. Chemical heterogeneity of organic matter at nanoscale by AFM-based IR spectroscopy. Fuel 261, 116454.

Jubb, A.M., Hackley, P.C., Hatcherian, J.J., Qu, J., Nesheim, T.O., 2019. Nanoscale molecular fractionation of organic matter within unconventional petroleum source beds. Energy & Fuels 10, 9759-9766.

Li, Y., Yang, J., Pan, Z., Tong, W., 2020. Nanoscale pore structure and mechanical property analysis of coal: An insight combining AFM and SEM images. Fuel 260, 116352.

IMAGING: SEM, TEM, HIM

Chen, Q., Yan, X., Zhang, J., Li, W., Guo, Y., Hong, T., Wang, R., Pan, T., 2019. An alteration effect of weathering on pores in shale: A case study of the Niutitang Formation of Lower Cambrian in the northern Hunan province. Natural Gas Industry 39, 32-41.

Gao, F., Song, Y., Liang, Z., Li, Z., Yuan, Y., Zhang, Y., Chen, L., Guo, W., 2019. Development characteristics of organic pore in the continental shale and its genetic mechanism: a case study of Shahezi Formation shale in the Changling fault depression of Songliao Basin Acta Petrolei Sinica 40, 1030-1044.

Goral, J., Andrew, M., Olson, T., Deo, M., 2020. Correlative core- to pore-scale imaging of shales. Marine and Petroleum Geology 111, 886-904.


Maleke, M., Valverde, A., Gomez-Arias, A., Cason, E.D., Vermeulen, J.-G., Coetsee-Hugo, L., Swart, H., van Heerden, E., Castillo, J., 2019. Anaerobic reduction of europium by a Clostridium strain as a strategy for rare earth biorecovery. Scientific Reports 9, 14339.

Salge, T., Stosnach, H., Rosatelli, G., Hecht, L., Reimold, W.U., 2019. Evidence for shock-induced anhydrite recrystallization and decomposition at the UNAM-7 drill core from the Chicxulub impact structure. Meteoritics & Planetary Science 54, 2334-2356.

Sannomiya, T., Arai, Y., Nagayama, K., Nagatani, Y., 2019. Transmission electron microscope using a linear accelerator. Physical Review Letters 123, 150801.

Strullu-Derrien, C., Bernard, S., Spencer, A.R.T., Remusat, L., Kenrick, P., Derrien, D., 2019. On the structure and chemistry of fossils of the earliest woody plant. Palaeontology 62, 1015-1026.

Tripathy, A., Kumar, A., Srinivasan, V., Singh, K.H., Singh, T.N., 2019. Fractal analysis and spatial disposition of porosity in major Indian gas shales using low-pressure nitrogen adsorption and advanced image segmentation. Journal of Natural Gas Science and Engineering 72, 103009.

Wei, B., Zhang, X., Liu, J., Wu, R., Xiang, H., Xu, X., 2020. Supercritical CO2-EOR in an asphaltenic tight sandstone formation and the changes of rock petrophysical properties induced by asphaltene precipitation. Journal of Petroleum Science and Engineering 184, 106515.

Ye, L., Xuanlong, S., Guoli, H., Makeen, Y.M., Abdullah, W.H., Ayinla, H.A., Lihua, T., Rongsheng, Z., Xianli, D., 2019. Petrological and organic geochemical characteristics of oil sands from the Middle Jurassic Yan’an Formation in the southern Ordos Basin, China. Arabian Journal of Geosciences 12, 625.

IMAGING: X-RAY CT

Bartels, W.B., Rücker, M., Boone, M., Bultreys, T., Mahani, H., Berg, S., Hassanizadeh, S.M., Cnudde, V., 2019. Imaging spontaneous imbibition in full Darcy-scale samples at

pore-scale resolution by fast X-ray tomography. Water Resources Research 55, 7072-7085.


Lammel, D.R., Arlt, T., Manke, I., Rillig, M.C., 2019. Testing contrast agents to improve micro computerized tomography (μCT) for spatial location of organic matter and biological material in soil. Frontiers in Environmental Science 7, 153. doi: 110.3389/fenvs.2019.00153.

Lu, X., Armstrong, R.T., Mostaghimi, P., 2020. Analysis of gas diffusivity in coal using micro-computed tomography. Fuel 261, 116384.

Pickrell, J., 2019. How the earliest mammals thrived alongside dinosaurs. Nature 574, 468-472.


LIQUID CHROMATOGRAPHY/LC-MS/SFC

Ahmed, M.A., Felisilda, B.M.B., Quirino, J.P., 2019. Recent advancements in open-tubular liquid chromatography and capillary electrochromatography during 2014–2018. Analytica Chimica Acta 1088, 20-34.

Jin, G., Liu, Y., Xue, S., Meng, Y., Yan, J., Yang, F., Guo, Z., Zhu, J., Liang, X., 2019. Determination of three carotenoids in microalgae by matrix solid-phase dispersion extraction and high-performance liquid chromatography. Chromatographia 82, 1593-1601.

Spranger, T., van Pinxteren, D., Reemtsma, T., Lechtenfeld, O.J., Herrmann, H., 2019. 2D liquid chromatographic fractionation with ultra-high resolution MS analysis resolves a vast molecular diversity of tropospheric particle organics. Environmental Science & Technology 53, 11353-11363.

MASS SPECTROSCOPY/ICR-FTMS/ORBITRAP

Berg, S.M., Whiting, Q.T., Herrli, J.A., Winkels, R., Wammer, K.H., Remucal, C.K., 2019. The role of dissolved organic matter composition in determining photochemical reactivity at the molecular level. Environmental Science & Technology 53, 11725-11734.

Bianco, A., Riva, M., Baray, J.-L., Ribeiro, M., Chaumerliac, N., George, C., Bridoux, M., Deguillaume, L., 2019. Chemical characterization of cloudwater collected at Puy de Dôme by FT-ICR MS reveals the presence of SOA components. ACS Earth and Space Chemistry 3, 2076-2087.

Buckley, M., Recabarren, O.P., Lawless, C., García, N., Pino, M., 2019. A molecular phylogeny of the extinct South American gomphothere through collagen sequence analysis. Quaternary Science Reviews 224, 105882.

Guillemant, J., Albrieux, F., de Oliveira, L.P., Lacoue-Nègre, M., Duponchel, L., Joly, J.-F., 2019. Insights from nitrogen compounds in gas oils highlighted by high-resolution Fourier transform mass spectrometry. Analytical Chemistry 91, 12644-12652.

Kune, C., McCann, A., Raphaël, L.R., Arias, A.A., Tiquet, M., Van Kruining, D., Martinez, P.M., Ongena, M., Eppe, G., Quinton, L., Far, J., De Pauw, E., 2019. Rapid visualization of chemically related compounds using Kendrick mass defect as a filter in mass spectrometry imaging. Analytical Chemistry 91, 13112-13118.

Mekic, M., Liu, J., Zhou, W., Loisel, G., Cai, J., He, T., Jiang, B., Yu, Z., Lazarou, Y.G., Li, X., Brigante, M., Vione, D., Gligorovski, S., 2019. Formation of highly oxygenated multifunctional compounds from cross-reactions of carbonyl compounds in the atmospheric aqueous phase. Atmospheric Environment 219, 117046.

Morrison, E.S., Shields, M.R., Bianchi, T.S., Liu, Y., Newman, S., Tolic, N., Chu, R.K., 2020. Multiple biomarkers highlight the importance of water column processes in treatment wetland organic matter cycling. Water Research 168, 115153.

Palacio Lozano, D.C., Ramírez, C.X., Sarmiento Chaparro, J.A., Thomas, M.J., Gavard, R., Jones, H.E., Cabanzo Hernández, R., Mejia-Ospino, E., Barrow, M.P., 2020. Characterization of bio-crude components derived from pyrolysis of soft wood and its esterified product by ultrahigh resolution mass spectrometry and spectroscopic techniques. Fuel 259, 116085.

Qiu, J., Lü, F., Zhang, H., Liu, W., Chen, J., Deng, Y., Shao, L., He, P., 2020. UPLC Orbitrap MS/MS-based fingerprints of dissolved organic matter in waste leachate driven by waste age. Journal of Hazardous Materials 383, 121205.

Rogel, E., Witt, M., Moir, M.E., 2019. Effects of aging on asphaltene deposit composition using ultrahigh-resolution magnetic resonance mass spectrometry. Energy & Fuels 33, 9596-9603.


Stavitskaya, A.V., Konstantinova, M.L., Podmasteriev, V.V., Safieva, R.Z., 2019. Ultrahigh-resolution mass spectrometry analysis of ozonation products of petroleum nitrogen compounds. Petroleum Chemistry 59, 1147-1152.

Yu, Z., Liu, X., Chen, C., Liao, H., Chen, Z., Zhou, S., 2019. Analytical dataset on the molecular compositional changes of dissolved organic matter during hyperthermophilic composting. Data in Brief, 104588.

Zhang, Y.-Y., Wei, X.-Y., Lv, J.-H., Zong, Z.-M., 2020. Study on the oxygen forms in soluble portions from thermal dissolution and alkanolyses of the extraction residue from Baiyinhua lignite. Fuel 260, 116301.

Zheng, F., Chung, W., Palmisano, E., Dong, D., Shi, Q., Xu, Z., Chung, K.H., 2019. Molecular characterization of polar heteroatom species in oilsands bitumen-derived vacuum residue fractions by Fourier transform ion cyclotron resonance mass spectrometry. Petroleum Science 16, 1196-1207.

Zherebker, A., Podgorski, D.C., Kholodov, V.A., Orlov, A.A., Yaroslavtseva, N.V., Kharybin, O., Kholodov, A., Spector, V., Spencer, R.G.M., Nikolaev, E., Perminova, I.V., 2019. The molecular composition of humic substances isolated from yedoma permafrost and alas cores in the eastern Siberian Arctic as measured by ultrahigh resolution mass spectrometry. Journal of Geophysical Research: Biogeosciences 124, 2432-2445.

MASS SPECTROSCOPY/OTHER

Borisov, R.S., Kulikova, L.N., Zaikin, V.G., 2019. Mass spectrometry in petroleum chemistry (petroleomics) (review). Petroleum Chemistry 59, 1055-1076.

Chadwick, G.L., Jiménez Otero, F., Gralnick, J.A., Bond, D.R., Orphan, V.J., 2019. NanoSIMS imaging reveals metabolic stratification within current-producing biofilms. Proceedings of the National Academy of Sciences 116, 20716-20724.

Dufresne, M., Patterson, N.H., Norris, J.L., Caprioli, R.M., 2019. Combining salt doping and matrix sublimation for high spatial resolution MALDI imaging mass spectrometry of neutral lipids. Analytical Chemistry 91, 12928-12934.

He, H., Guo, Z., Wen, Y., Xu, S., Liu, Z., 2019. Recent advances in nanostructure/nanomaterial-assisted laser desorption/ionization mass spectrometry of low molecular mass compounds. Analytica Chimica Acta 1090, 1-22.


Velichko, N.V., Pinevich, A.V., 2019. Classification and identification tasks in microbiology: Mass spectrometric methods coming to the aid. Microbiology 88, 534-547.

Waller, S.E., Belousov, A., Kidd, R.D., Nikolić, D., Madzunkov, S.M., Wiley, J.S., Darrach, M.R., 2019. Chemical ionization mass spectrometry: Applications for the in situ measurement of nonvolatile organics at ocean worlds. Astrobiology 19, 1196-1210.

Xu, S., Shi, W., Yu, Q., Wang, X., 2019. Capillary introduction mass spectrometry coupled with selective cryotrapping for analysis of volatile compounds in water. Analytical Methods 11, 5237-5242.

Xue, J., Bai, Y., Liu, H., 2019. Recent advances in ambient mass spectrometry imaging. TrAC Trends in Analytical Chemistry 120, 115659.

Yao, Y.-N., Wu, L., Di, D., Yuan, Z.-C., Hu, B., 2019. Vibrating tip spray ionization mass spectrometry for direct sample analysis. Journal of Mass Spectrometry 54, 772-779.

Zhou, Y., Li, L., Jin, L., Zhu, J., Li, J., Li, Y., Fan, H., Hu, H., 2020. Effect of functional groups on volatile evolution in coal pyrolysis process with in-situ pyrolysis photoionization time-of-flight mass spectrometry. Fuel 260, 116322.

METABOLOMICS/LIPIDOMICS

Chamberlain, C.A., Rubio, V.Y., Garrett, T.J., 2019. Impact of matrix effects and ionization efficiency in non-quantitative untargeted metabolomics. Metabolomics 15, 135.

Hao, L., Zhu, Y., Wei, P., Johnson, J., Buchberger, A., Frost, D., Kao, W.J., Li, L., 2019. Metandem: An online software tool for mass spectrometry-based isobaric labeling metabolomics. Analytica Chimica Acta 1088, 99-106.

Jiang, J.-Y., Zhu, S., Zhang, Y., Sun, X., Hu, X., Huang, H., Ren, L.-J., 2019. Integration of lipidomic and transcriptomic profiles reveals novel genes and regulatory mechanisms of Schizochytrium sp. in response to salt stress. Bioresource Technology 294, 122231.

Li, X., Qu, C., Bian, Y., Gu, C., Jiang, X., Song, Y., 2019. New insights into the responses of soil microorganisms to polycyclic aromatic hydrocarbon stress by combining enzyme activity and sequencing analysis with metabolomics. Environmental Pollution 255, Part 2, 113312.

Liu, X., Zhou, L., Shi, X., Xu, G., 2019. New advances in analytical methods for mass spectrometry-based large-scale metabolomics study. TrAC Trends in Analytical Chemistry 121, 115665.


Nie, X., Hua, Q., Xu, P., Yang, C., 2020. Biological insights into non-model microbial hosts through stable-isotope metabolic flux analysis. Current Opinion in Biotechnology 64, 32-38.

Ware, T.B., Shin, M., Hsu, K.-L., 2019. Metabolomics analysis of lipid metabolizing enzyme activity. Methods in Enzymology 626, 407-428.

PUPPYOMICS

Hecht, E.E., Smaers, J.B., Dunn, W.D., Kent, M., Preuss, T.M., Gutman, D.A., 2019. Significant neuroanatomical variation among domestic dog breeds. The Journal of Neuroscience 39, 7748-7758.

Archaeological/Art Organic Chemistry

Carrión Marco, Y., Vives-Ferrándiz Sánchez, J., 2019. Rethinking the perishable: Identifying organic remains in metal objects at the Iron Age site of La Bastida de les Alcusses (Moixent, Spain). Journal of Archaeological Science: Reports 27, 101970.

Casabianca, T., Marinelli, E., Pernagallo, G., Torrisi, B., 2019. Radiocarbon dating of the Turin Shroud: New evidence from raw data. Archaeometry 61, 1223-1231.

Devièse, T., Ribechini, E., Querci, D., Higham, T., 2019. Assessing the efficiency of supercritical fluid extraction for the decontamination of archaeological bones prior to radiocarbon dating. Analyst 144, 6128-6135.

Drieu, L., Horgnies, M., Binder, D., Pétrequin, P., Pétrequin, A.M., Peche-Quilichini, K., Lachenal, T., Regert, M., 2019. Influence of porosity on lipid preservation in the wall of archaeological pottery. Archaeometry 61, 1081-1096.

Dunne, J., Rebay-Salisbury, K., Salisbury, R.B., Frisch, A., Walton-Doyle, C., Evershed, R.P., 2019. Milk of ruminants in ceramic baby bottles from prehistoric child graves. Nature 574, 246-248.

Fujii, H., Mazzitelli, J.-B., Adilbekov, D., Olmer, F., Mathe, C., Vieillescazes, C., 2019. FT-IR and GC–MS analyses of Dressel IA amphorae from the Grand Congloué 2 wreck. Journal of Archaeological Science: Reports 28, 102007.

Maggiano, C.M., White, C.D., Stern, R.A., Peralta, J.S., Longstaffe, F.J., 2019. Focus: Oxygen isotope microanalysis across incremental layers of human bone: Exploring archaeological reconstruction of short term mobility and seasonal climate change. Journal of Archaeological Science 111, 105028.

Niekus, M.J.L.T., Kozowyk, P.R.B., Langejans, G.H.J., Ngan-Tillard, D., van Keulen, H., van der Plicht, J., Cohen, K.M., van Wingerden, W., van Os, B., Smit, B.I., Amkreutz, L.W.S.W., Johansen, L., Verbaas, A., Dusseldorp, G.L., 2019. Middle Paleolithic complex technology and a Neandertal tar-backed tool from the Dutch North Sea. Proceedings of the National Academy of Sciences 116, 22081-22087.

Pacheco-Ruiz, R., Adams, J., Pedrotti, F., Grant, M., Holmlund, J., Bailey, C., 2019. Deep sea archaeological survey in the Black Sea – Robotic documentation of 2,500 years of human seafaring. Deep Sea Research Part I: Oceanographic Research Papers 152, 103087.

Spyrou, M.A., Keller, M., Tukhbatova, R.I., Scheib, C.L., Nelson, E.A., Andrades Valtueña, A., Neumann, G.U., Walker, D., Alterauge, A., Carty, N., Cessford, C., Fetz, H., Gourvennec, M., Hartle, R., Henderson, M., von Heyking, K., Inskip, S.A., Kacki, S., Key, F.M., Knox, E.L., Later, C., Maheshwari-Aplin, P., Peters, J., Robb, J.E., Schreiber, J., Kivisild, T., Castex, D., Lösch, S., Harbeck, M., Herbig, A., Bos, K.I., Krause, J., 2019. Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes. Nature Communications 10, 4470.

Zilhão, J., 2019. Tar adhesives, Neandertals, and the tyranny of the discontinuous mind. Proceedings of the National Academy of Sciences 116, 21966-21968.

Biochemistry

Amend, J.P., LaRowe, D.E., 2019. Minireview: demystifying microbial reaction energetics. Environmental Microbiology 21, 3539-3547.

Bajic, D., Sanchez, A., 2020. The ecology and evolution of microbial metabolic strategies. Current Opinion in Biotechnology 62, 123-128.

Bale, N.J., Palatinszky, M., Rijpstra, W.I.C., Herbold, C.W., Wagner, M., Sinninghe Damsté, J.S., 2019. Membrane lipid composition of the moderately thermophilic ammonia-oxidizing archaeon “Candidatus Nitrosotenuis uzonensis” at different growth temperatures. Applied and Environmental Microbiology 85, e01332-01319.

Bird, L.R., Dawson, K.S., Chadwick, G.L., Fulton, J.M., Orphan, V.J., Freeman, K.H., 2019. Carbon isotopic heterogeneity of coenzyme F430 and membrane lipids in methane-oxidizing archaea. Geobiology 17, 611-627.

Hajjar, G., Rizk, T., Akoka, S., Bejjani, J., 2019. Cholesterol, a powerful 13C isotopic biomarker. Analytica Chimica Acta 1089, 115-122.

Hua, Z.-S., Wang, Y.-L., Evans, P.N., Qu, Y.-N., Goh, K.M., Rao, Y.-Z., Qi, Y.-L., Li, Y.-X., Huang, M.-J., Jiao, J.-Y., Chen, Y.-T., Mao, Y.-P., Shu, W.-S., Hozzein, W., Hedlund, B.P., Tyson, G.W., Zhang, T., Li, W.-J., 2019. Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea. Nature Communications 10, 4574.

Podosokorskaya, O.A., Teplyuk, A.V., Zayulina, K.S., Kopitsyn, D.S., Dominova, I.N., Elcheninov, A.G., Toshchakov, S.V., Kublanov, I.V., 2019. The metabolism of thermophilic hydrolytic bacterium Thauera hydrothermalis strain Par-f-2 isolated from the West Siberian subsurface biosphere. Microbiology 88, 556-562.

Zeldes, B.M., Loder, A.J., Counts, J.A., Haque, M., Widney, K.A., Keller, L.M., Albers, S.-V., Kelly, R.M., 2019. Determinants of sulphur chemolithoautotrophy in the extremely thermoacidophilic Sulfolobales. Environmental Microbiology 21, 3696-3710.

Zhang, T., Yuan, D., Xie, J., Lei, Y., Li, J., Fang, G., Tian, L., Liu, J., Cui, Y., Zhang, M., Xiao, Y., Xu, Y., Zhang, J., Zhu, M., Zhan, S., Li, S., 2019. Evolution of the cholesterol biosynthesis pathway in animals. Molecular Biology and Evolution 36, 2548-2556.

Biodegradation

Che, S., Men, Y., 2019. Synthetic microbial consortia for biosynthesis and biodegradation: promises and challenges. Journal of Industrial Microbiology & Biotechnology 46, 1343-1358.

Chettri, B., Singh, A.K., 2019. Kinetics of hydrocarbon degradation by a newly isolated heavy metal tolerant bacterium Novosphingobium panipatense P5:ABC. Bioresource Technology 294, 122190.

Evans, M.V., Getzinger, G., Luek, J.L., Hanson, A.J., McLaughlin, M.C., Blotevogel, J., Welch, S.A., Nicora, C.D., Purvine, S.O., Xu, C., Cole, D.R., Darrah, T.H., Hoyt, D.W., Metz, T.O.,

Lee Ferguson, P., Lipton, M.S., Wilkins, M.J., Mouser, P.J., 2019. In situ transformation of ethoxylate and glycol surfactants by shale-colonizing microorganisms during hydraulic fracturing. The ISME Journal 13, 2690-2700.

Lillington, S.P., Leggieri, P.A., Heom, K.A., O’Malley, M.A., 2020. Nature’s recyclers: anaerobic microbial communities drive crude biomass deconstruction. Current Opinion in Biotechnology 62, 38-47.

Ra, T., Zhao, Y., Zheng, M., 2019. Comparative study on the petroleum crude oil degradation potential of microbes from petroleum-contaminated soil and non-contaminated soil. International Journal of Environmental Science and Technology 16, 7127-7136.

Roager, L., Sonnenschein, E.C., 2019. Bacterial candidates for colonization and degradation of marine plastic debris. Environmental Science & Technology 53, 11636-11643.

Song, N., Bai, L., Xu, H., Jiang, H.-L., 2020. The composition difference of macrophyte litter-derived dissolved organic matter by photodegradation and biodegradation: Role of reactive oxygen species on refractory component. Chemosphere 242, 125155.

Sun, X., Chu, L., Mercando, E., Romero, I., Hollander, D., Kostka, J.E., 2019. Dispersant enhances hydrocarbon degradation and alters the structure of metabolically active microbial communities in shallow seawater from the northeastern Gulf of Mexico. Frontiers in Microbiology 10, 2387. doi: 2310.3389/fmicb.2019.02387.

BIODEGRADATION PATHWAYS/GENOMICS

Bukliarevich, H.A., Charniauskaya, M.I., Akhremchuk, A.E., Valentovich, L.N., Titok, M.A., 2019. Effect of the structural and regulatory heat shock proteins on hydrocarbon degradation by Rhodococcus pyridinivorans 5Ap. Microbiology 88, 573-579.

Chen, D., Wu, S., Xue, H., Jiang, J., 2020. Stereoselective catabolism of compounds by microorganisms: Catabolic pathway, molecular mechanism and potential application. International Biodeterioration & Biodegradation 146, 104822.

Geiger, R.A., Junghare, M., Mergelsberg, M., Ebenau-Jehle, C., Jesenofsky, V.J., Jehmlich, N., von Bergen, M., Schink, B., Boll, M., 2019. Enzymes involved in phthalate degradation in sulphate-reducing bacteria. Environmental Microbiology 21, 3601-3612.

Kiamarsi, Z., Soleimani, M., Nezami, A., Kafi, M., 2019. Biodegradation of n-alkanes and polycyclic aromatic hydrocarbons using novel indigenous bacteria isolated from contaminated soils. International Journal of Environmental Science and Technology 16, 6805-6816.


Biofuels/Biomass/Bioengineering

Chatterjee, A., DeLorenzo, D.M., Carr, R., Moon, T.S., 2020. Bioconversion of renewable feedstocks by Rhodococcus opacus. Current Opinion in Biotechnology 64, 10-16.


Hendry, J.I., Bandyopadhyay, A., Srinivasan, S., Pakrasi, H.B., Maranas, C.D., 2020. Metabolic model guided strain design of cyanobacteria. Current Opinion in Biotechnology 64, 17-23.

Jang, S., Kim, M., Hwang, J., Jung, G.Y., 2019. Tools and systems for evolutionary engineering of biomolecules and microorganisms. Journal of Industrial Microbiology & Biotechnology 46, 1313-1326.

Karthikeyan, R., Singh, R., Bose, A., 2019. Microbial electron uptake in microbial electrosynthesis: a mini-review. Journal of Industrial Microbiology & Biotechnology 46, 1419-1426.

Khot, M., Raut, G., Ghosh, D., Alarcón-Vivero, M., Contreras, D., Ravikumar, A., 2020. Lipid recovery from oleaginous yeasts: Perspectives and challenges for industrial applications. Fuel 259, 116292.

Kim, G.B., Kim, W.J., Kim, H.U., Lee, S.Y., 2020. Machine learning applications in systems metabolic engineering. Current Opinion in Biotechnology 64, 1-9.

Lan, W., Luterbacher, J.S., 2019. A road to profitability from lignin via the production of bioactive molecules. ACS Central Science 5, 1642-1644.

Lee, J.-C., Lee, B., Heo, J., Kim, H.-W., Lim, H., 2019. Techno-economic assessment of conventional and direct-transesterification processes for microalgal biomass to biodiesel conversion. Bioresource Technology 294, 122173.

Mahajan, D., Sengupta, S., Sen, S., 2019. Strategies to enhance of microbial lipid production using metabolic engineering approach. Biocatalysis and Agricultural Biotechnology 22, 101321.


Tóth, S.Z., Yacoby, I., 2019. Paradigm shift in algal H2 production: Bypassing competitive processes. Trends in Biotechnology 37, 1159-1163.

Woo, J.E., Jang, Y.-S., 2019. Metabolic engineering of microorganisms for the production of ethanol and butanol from oxides of carbon. Applied Microbiology and Biotechnology 103, 8283-8292.

Yang, X., Liang, Q., Chen, Y., Wang, B., 2019. Alteration of methanogenic archaeon by ethanol contribute to the enhancement of biogenic methane production of lignite. Frontiers in Microbiology 10, 2323. doi: 2310.3389/fmicb.2019.02323.

Biogeochemistry

Armitage, D.W., Jones, S.E., 2019. How sample heterogeneity can obscure the signal of microbial interactions. The ISME Journal 13, 2639-2646.


Callefo, F., Maldanis, L., Teixeira, V.C., Abans, R.A.d.O., Monfredini, T., Rodrigues, F., Galante, D., 2019. Evaluating biogenicity on the geological record with synchrotron-based techniques. Frontiers in Microbiology 10, 2358. doi: 2310.3389/fmicb.2019.02358.

Conrad, R., Klose, M., Enrich-Prast, A., 2019. Acetate turnover and methanogenic pathways in Amazonian lake sediments. Biogeosciences Discussions 2019, 1-19.

Evans, T.W., Coffinet, S., Könneke, M., Lipp, J.S., Becker, K.W., Elvert, M., Heuer, V., Hinrichs, K.-U., 2019. Assessing the carbon assimilation and production of benthic archaeal lipid biomarkers using lipid-RIP. Geochimica et Cosmochimica Acta 265, 431-442.

Foster, J.S., Reid, R.P., Visscher, P.T., Dupraz, C., 2019. Editorial: Characterizing modern microbialites and the geobiological processes underlying their formation. Frontiers in Microbiology 10, 2299. doi: 2210.3389/fmicb.2019.02299.

Fuchsman, C.A., Palevsky, H.I., Widner, B., Duffy, M., Carlson, M.C.G., Neibauer, J.A., Mulholland, M.R., Keil, R.G., Devol, A.H., Rocap, G., 2019. Cyanobacteria and cyanophage contributions to carbon and nitrogen cycling in an oligotrophic oxygen-deficient zone. The ISME Journal 13, 2714-2726.

Haas, S., Desai, D.K., LaRoche, J., Pawlowicz, R., Wallace, D.W.R., 2019. Geomicrobiology of the carbon, nitrogen and sulphur cycles in Powell Lake: a permanently stratified water column containing ancient seawater. Environmental Microbiology 21, 3927-3952.

Klintzsch, T., Langer, G., Nehrke, G., Wieland, A., Lenhart, K., Keppler, F., 2019. Methane production by three widespread marine phytoplankton species: release rates, precursor compounds, and potential relevance for the environment. Biogeosciences 16, 4129-4144.

Lindsay, M.R., Colman, D.R., Amenabar, M.J., Fristad, K.E., Fecteau, K.M., Debes II, R.V., Spear, J.R., Shock, E.L., Hoehler, T.M., Boyd, E.S., 2019. Probing the geological source and biological fate of hydrogen in Yellowstone hot springs. Environmental Microbiology 21, 3816-3830.


Taubert, M., Grob, C., Crombie, A., Howat, A.M., Burns, O.J., Weber, M., Lott, C., Kaster, A.-K., Vollmers, J., Jehmlich, N., von Bergen, M., Chen, Y., Murrell, J.C., 2019. Communal metabolism by Methylococcaceae and Methylophilaceae is driving rapid aerobic methane oxidation in sediments of a shallow seep near Elba, Italy. Environmental Microbiology 21, 3780-3795.

Williams, B.T., Cowles, K., Bermejo Martínez, A., Curson, A.R.J., Zheng, Y., Liu, J., Newton-Payne, S., Hind, A.J., Li, C.-Y., Rivera, P.P.L., Carrión, O., Liu, J., Spurgin, L.G., Brearley, C.A., Mackenzie, B.W., Pinchbeck, B.J., Peng, M., Pratscher, J., Zhang, X.-H., Zhang, Y.-Z., Murrell, J.C., Todd, J.D., 2019. Bacteria are important dimethylsulfoniopropionate producers in coastal sediments. Nature Microbiology 4, 1815-1825.

Xie, R., Wu, D., Liu, J., Sun, T., Liu, L., Wu, N., 2019. Evolution of gas hydrates inventory and anaerobic oxidation of methane (AOM) after 40ka in the Taixinan Basin, South China Sea. Deep Sea Research Part I: Oceanographic Research Papers 152, 103084.

Zak, D., Roth, C., Unger, V., Goldhammer, T., Fenner, N., Freeman, C., Jurasinski, G., 2019. Unraveling the importance of polyphenols for microbial carbon mineralization in rewetted riparian peatlands. Frontiers in Environmental Science 7, 147. doi: 110.3389/fenvs.2019.00147.

BIOFILM/MICROBIAL INDUCED CORROSION



Inaba, Y., Xu, S., Vardner, J.T., West, A.C., Banta, S., 2019. Microbially influenced corrosion of stainless steel by Acidithiobacillus ferrooxidans supplemented with pyrite: importance of thiosulfate. Applied and Environmental Microbiology 85, e01381-01319.

Jin, P., Robbins, W., Bota, G., 2019. Effect of thiophenes on high-temperature corrosion by sulfidation and naphthenic acids. Energy & Fuels 33, 10365-10371.

Puglisi, E., Romaniello, F., Galletti, S., Boccaleri, E., Frache, A., Cocconcelli, P.S., 2019. Selective bacterial colonization processes on polyethylene waste samples in an abandoned landfill site. Scientific Reports 9, 14138.

MICROBIAL MEDIATION OF MINERAL FORMATION/DEGRADATION

Alibrahim, A., Al-Gharabally, D., Mahmoud, H., Dittrich, M., 2019. Proto-dolomite formation in microbial consortia dominated by Halomonas strains. Extremophiles 23, 765-781.

De Wever, A., Benzerara, K., Coutaud, M., Caumes, G., Poinsot, M., Skouri-Panet, F., Laurent, T., Duprat, E., Gugger, M., 2019. Evidence of high Ca uptake by cyanobacteria forming intracellular CaCO3 and impact on their growth. Geobiology 17, 676-690.

Lü, X., He, Q., Wang, Z., Cao, M., Zhao, J., Jiang, J., Zhao, R., Zhang, H., 2019. Calcium carbonate precipitation mediated by bacterial carbonic anhydrase in a karst cave: Crystal morphology and stable isotopic fractionation. Chemical Geology 530, 119331.

Maeda, A., Yoshimura, T., Araoka, D., Suzuki, A., Tamenori, Y., Fujita, K., Toyofuku, T., Ohkouchi, N., Kawahata, H., 2019. Magnesium isotopic composition of tests of large benthic foraminifers: Implications for biomineralization. Geochemistry, Geophysics, Geosystems 20, 4046-4058.

Minto, J.M., Lunn, R.J., El Mountassir, G., 2019. Development of a reactive transport model for field-scale simulation of microbially induced carbonate precipitation. Water Resources Research 55, 7229-7245.

Seknazi, E., Kozachkevich, S., Polishchuk, I., Bianco Stein, N., Villanova, J., Suuronen, J.-P., Dejoie, C., Zaslansky, P., Katsman, A., Pokroy, B., 2019. From spinodal decomposition to alternating layered structure within single crystals of biogenic magnesium calcite. Nature Communications 10, 4559.

Carbon Cycle

Black, B.A., Gibson, S.A., 2019. Deep carbon and the life cycle of large igneous provinces. Elements 15, 319-324.


Kamber, B.S., Petrus, J.A., 2019. The influence of large bolide impacts on Earth's carbon cycle. Elements 15, 313-318.

Le Moigne, F.A.C., 2019. Pathways of organic carbon downward transport by the oceanic biological carbon pump. Frontiers in Marine Science 6, 634. doi: 610.3389/fmars.2019.00634.


McKenzie, N.R., Jiang, H., 2019. Earth's outgassing and climatic transitions: The slow burn towards environmental “catastrophes”? Elements 15, 325-330.

Mikhail, S., Füri, E., 2019. On the origin(s) and evolution of Earth's carbon. Elements 15, 307-312.

Pedrosa-Pàmies, R., Conte, M.H., Weber, J.C., Johnson, R., 2019. Hurricanes enhance labile carbon export to the deep ocean. Geophysical Research Letters 46, 10484-10494.

Plank, T., Manning, C.E., 2019. Subducting carbon. Nature 574, 343-352.

Suarez, C.A., Edmonds, M., Jones, A.P., 2019. Earth catastrophes and their impact on the carbon cycle. Elements 15, 301-306.

Weber, T., Wiseman, N.A., Kock, A., 2019. Global ocean methane emissions dominated by shallow coastal waters. Nature Communications 10, 4584.

Wong, K., Mason, E., Brune, S., East, M., Edmonds, M., Zahirovic, S., 2019. Deep carbon cycling over the past 200 million years: A review of fluxes in different tectonic settings. Frontiers in Earth Science 7, 263. doi: 210.3389/feart.2019.00263.

Climate Change

Zhang, Y., Song, C., Band, L.E., Sun, G., 2019. No proportional increase of terrestrial gross carbon sequestration from the greening Earth. Journal of Geophysical Research: Biogeosciences 124, 2540-2553.

Carbon Sequestration

Newell, A.J., Pourmalek, A., Butcher, A.S., Shariatipour, S.M., 2019. The importance of lithofacies control on fluid migration in heterogeneous aeolian formations for geological CO2

storage: Lessons from observational evidence and modelling of bleached palaeoreservoirs at Salt Wash Graben, Utah. International Journal of Greenhouse Gas Control 91, 102841.

Yonkofski, C., Tartakovsky, G., Huerta, N., Wentworth, A., 2019. Risk-based monitoring designs for detecting CO2 leakage through abandoned wellbores: An application of NRAP’s WLAT and DREAM tools. International Journal of Greenhouse Gas Control 91, 102807.


Coal/Lignite/Peat Geochemistry

Kara-Gülbay, R., Yaylalı-Abanuz, G., Korkmaz, S., Erdoğan, M.S., Hoş-Çebi, F., Çevik, S., Ağırman-Aktürk, E., 2019. Organic matter type, maturity, depositional environmental characteristics, and liquid hydrocarbon potential of Late Carboniferous Kozlu bituminous coal and coaly shale beds (Zonguldak-Amasra Basin, NW Anatolia, Turkey): An application of biomarker geochemistry. Energy & Fuels 33, 9491-9509.


Okushita, K., Hata, Y., Sugimoto, Y., Takahashi, T., Kanehashi, K., 2019. Protonated nitrogen structure in 15N-labeled model coal investigated by solid-state 1H–15N double-CP NMR experiments under ultrafast magic-angle spinning. Energy & Fuels 33, 9419-9428.

Rajak, P.K., Singh, V.K., Singh, P.K., Singh, M.P., Singh, A.K., 2019. Environment of paleomire of lignite seams of Bikaner-Nagaur basin, Rajasthan (W. India): petrological implications. International Journal of Oil, Gas and Coal Technology 22, 218-245.

Su, X., Wang, Q., Zhou, F., Si, Q., Song, J., Lin, H., 2019. Characteristics of graphite-like crystallites in coal with increasing coalification. International Journal of Oil, Gas and Coal Technology 22, 368-388.

Wang, S., Chen, H., Zhang, X., 2020. Transformation of aromatic structure of vitrinite with different coal ranks by HRTEM in situ heating. Fuel 260, 116309.

Yu, K., Ju, Y., Shao, C., 2020. Structure characteristics and evolution mechanism of nanopore in transitional coal-bearing shale. Journal of Petroleum Science and Engineering 184, 106545.



COAL BED METHANE

Li, J., Lu, S., Zhang, P., Cai, J., Li, W., Wang, S., Feng, W., 2020. Estimation of gas-in-place content in coal and shale reservoirs: A process analysis method and its preliminary application. Fuel 259, 116266.


Moore, M.T., Vinson, D.S., Whyte, C.J., Eymold, W.K., Walsh, T.B., Darrah, T.H., 2018. Differentiating between biogenic and thermogenic sources of natural gas in coalbed methane reservoirs from the Illinois Basin using noble gas and hydrocarbon geochemistry, in: Lawson, M., Formolo, M.J., Eiler, J.M. (Eds.), From Source to Seep: Geochemical Applications in Hydrocarbon Systems. Geological Society, London, Special Publications 468. Geological Society, London, London, pp. 151-188.

Pajdak, A., Skoczylas, N., Dębski, A., Grzegorek, J., Maziarz, W., Kudasik, M., 2019. CO2 and CH4 sorption on carbon nanomaterials and coals – Comparative characteristics. Journal of Natural Gas Science and Engineering 72, 103003.

Vinson, D.S., Blair, N.E., Ritter, D.J., Martini, A.M., McIntosh, J.C., 2019. Carbon mass balance, isotopic tracers of biogenic methane, and therole of acetate in coal beds: Powder River Basin (USA). Chemical Geology 530, 119329.

Cosmochemistry/Planetary Geochemistry

Candian, A., 2019. A fresh mechanism for how buckyballs form in space. Nature 574, 490-491.

Codella, C., Ceccarelli, C., Lee, C.-F., Bianchi, E., Balucani, N., Podio, L., Cabrit, S., Gueth, F., Gusdorf, A., Lefloch, B., Tabone, B., 2019. The HH 212 interstellar laboratory:

Astrochemistry as a tool to reveal protostellar disks on solar system scales around a rising sun. ACS Earth and Space Chemistry 3, 2110-2121.

Czaplinski, E.C., Gilbertson, W.A., Farnsworth, K.K., Chevrier, V.F., 2019. Experimental study of ethylene evaporites under Titan conditions. ACS Earth and Space Chemistry 3, 2353-2362.

Davidson, J., Alexander, C.M.O.D., Stroud, R.M., Busemann, H., Nittler, L.R., 2019. Mineralogy and petrology of Dominion Range 08006: A very primitive CO3 carbonaceous chondrite. Geochimica et Cosmochimica Acta 265, 259-278.

Enrique-Romero, J., Rimola, A., Ceccarelli, C., Ugliengo, P., Balucani, N., Skouteris, D., 2019. Reactivity of HCO with CH3 and NH2 on water ice surfaces. A comprehensive accurate quantum chemistry study. ACS Earth and Space Chemistry 3, 2158-2170.

Gure, A.J., Sorenson, T., Dewey, J.C., Kraus, T., Eggleston, C.M., Parkinson, B.A., 2019. Photostationary state in photoelectrochemical generation of perchlorate: Relevance to Mars. ACS Earth and Space Chemistry 3, 2171-2174.

Khawaja, N., Postberg, F., Hillier, J., Klenner, F., Kempf, S., Nölle, L., Reviol, R., Zou, Z., Srama, R., 2019. Low-mass nitrogen-, oxygen-bearing, and aromatic compounds in Enceladean ice grains. Monthly Notices of the Royal Astronomical Society 489, 5231-5243.

López-Sepulcre, A., Balucani, N., Ceccarelli, C., Codella, C., Dulieu, F., Theulé, P., 2019. Interstellar formamide (NH2CHO), a key prebiotic precursor. ACS Earth and Space Chemistry 3, 2122-2137.

Moores, J.E., King, P.L., Smith, C.L., Martinez, G.M., Newman, C.E., Guzewich, S.D., Meslin, P.-Y., Webster, C.R., Mahaffy, P.R., Atreya, S.K., Schuerger, A.C., 2019. The methane diurnal variation and microseepage flux at Gale Crater, Mars as constrained by the ExoMars Trace Gas Orbiter and Curiosity observations. Geophysical Research Letters 46, 9430-9438.

Mougel, B., Moynier, F., Koeberl, C., Wielandt, D., Bizzarro, M., 2019. Identification of a meteoritic component using chromium isotopic composition of impact rocks from the Lonar impact structure, India. Meteoritics & Planetary Science 54, 2592-2599.

Muñoz Caro, G.M., Ciaravella, A., Jiménez-Escobar, A., Cecchi-Pestellini, C., González-Díaz, C., Chen, Y.-J., 2019. X-ray versus ultraviolet irradiation of astrophysical ice analogs leading to formation of complex organic molecules. ACS Earth and Space Chemistry 3, 2138-2157.

Oba, Y., Takano, Y., Naraoka, H., Watanabe, N., Kouchi, A., 2019. Nucleobase synthesis in interstellar ices. Nature Communications 10, 4413.

Sewiło, M., Charnley, S.B., Schilke, P., Taquet, V., Oliveira, J.M., Shimonishi, T., Wirström, E., Indebetouw, R., Ward, J.L., van Loon, J.T., Wiseman, J., Zahorecz, S., Onishi, T., Kawamura, A., Chen, C.H.R., Fukui, Y., Hamedani Golshan, R., 2019. Complex organic molecules in star-forming regions of the Magellanic Clouds. ACS Earth and Space Chemistry 3, 2088-2109.

ASTROBIOLOGY

Cohen, B.A., Malespin, C.A., Farley, K.A., Martin, P.E., Cho, Y., Mahaffy, P.R., 2019. In situ geochronology on Mars and the development of future instrumentation. Astrobiology 19, 1303-1314.

Ćirković, M.M., Vukotić, B., Stojanović, M., 2019. Persistence of technosignatures: A comment on Lingam and Loeb. Astrobiology 19, 1300-1302.

Corenblit, D., Darrozes, J., Julien, F., Otto, T., Roussel, E., Steiger, J., Viles, H., 2019. The search for a signature of life on Mars: A biogeomorphological approach. Astrobiology 19, 1279-1291.

Garschagen, L.S., Mancinelli, R.L., Moeller, R., 2019. Introducing Vibrio natriegens as a microbial model organism for microgravity research. Astrobiology 19, 1211-1220.

Hakkila, J., Nemiroff, R., 2019. Time-reversed gamma-ray burst light-curve characteristics as transitions between subluminal and superluminal motion. The Astrophysical Journal 883, 70.

Haqq-Misra, J., 2019. Does the evolution of complex life depend on the stellar spectral energy distribution? Astrobiology 19, 1292-1299.

Heinz, J., Waajen, A.C., Airo, A., Alibrandi, A., Schirmack, J., Schulze-Makuch, D., 2019. Bacterial growth in chloride and perchlorate brines: Halotolerances and salt stress responses of Planococcus halocryophilus. Astrobiology 19, 1377-1387.

Ilgrande, C., Defoirdt, T., Vlaeminck, S.E., Boon, N., Clauwaert, P., 2019. Media optimization, strain compatibility, and low-shear modeled microgravity exposure of synthetic microbial communities for urine nitrification in regenerative life-support systems. Astrobiology 19, 1353-1362.

Janjic, A., 2019. Assisted evolution in astrobiology—Convergence of ecology and evolutionary biology within the context of planetary colonization. Astrobiology 19, 1410-1417.

Lenardic, A., Seales, J., 2019. Different is more: The value of finding an inhabited planet that is far from Earth2.0. Astrobiology 19, 1398-1409.

Kahana, A., Schmitt-Kopplin, P., Lancet, D., 2019. Enceladus: First observed primordial soup could arbitrate origin-of-life debate. Astrobiology 19, 1263-1278.

Mateo-Marti, E., Galvez-Martinez, S., Gil-Lozano, C., Zorzano, M.-P., 2019. Pyrite-induced uv-photocatalytic abiotic nitrogen fixation: implications for early atmospheres and Life. Scientific Reports 9, 15311.

McLoughlin, N., Grosch, E.G., Vullum, P.E., Guagliardo, P., Saunders, M., Wacey, D., 2019. Critically testing olivine-hosted putative martian biosignatures in the Yamato 000593 meteorite—Geobiological implications. Geobiology 17, 691-707.

Mißbach, H., Steininger, H., Thiel, V., Goetz, W., 2019. Investigating the effect of perchlorate on flight-like gas chromatography–mass spectrometry as performed by MOMA on board the ExoMars 2020 rover. Astrobiology 19, 1339-1352.

Onstott, T.C., Ehlmann, B.L., Sapers, H., Coleman, M., Ivarsson, M., Marlow, J.J., Neubeck, A., Niles, P., 2019. Paleo-rock-hosted life on Earth and the search on Mars: A review and strategy for exploration. Astrobiology 19, 1230-1262.

Patty, C.H.L., ten Kate, I.L., Buma, W.J., van Spanning, R.J.M., Steinbach, G., Ariese, F., Snik, F., 2019. Circular spectropolarimetric sensing of vegetation in the field: Possibilities for the remote detection of extraterrestrial life. Astrobiology 19, 1221-1229.

Seto, M., Noguchi, K., Cappellen, P.V., 2019. Potential for aerobic methanotrophic metabolism on Mars. Astrobiology 19, 1187-1195.

Shotwell, R.F., Hays, L.E., Beaty, D.W., Goreva, Y., Kieft, T.L., Mellon, M.T., Moridis, G., Peterson, L.D., Spycher, N., 2019. Can an off-nominal landing by an MMRTG-powered spacecraft induce a special region on Mars when no ice is present? Astrobiology 19, 1315-1338.


Waltham, D., 2019. Intrinsic climate cooling. Astrobiology 19, 1388-1397.

Wordsworth, R., Kerber, L., Cockell, C., 2019. Enabling Martian habitability with silica aerogel via the solid-state greenhouse effect. Nature Astronomy 3, 898-903.

Environmental Geochemistry




Salim, F., Górecki, T., 2019. Theory and modelling approaches to passive sampling. Environmental Science: Processes & Impacts 21, 1618-1641.



Xu, S., Zhao, J., Yu, Q., Qiu, X., Sasaki, K., 2019. Effect of natural organic matter model compounds on the structure memory effect of different layered double hydroxides. ACS Earth and Space Chemistry 3, 2175-2189.

BIOREMEDIATION

Evans, M.V., Sumner, A.J., Daly, R.A., Luek, J.L., Plata, D.L., Wrighton, K.C., Mouser, P.J., 2019. Hydraulically fractured natural-gas well microbial communities contain genomic halogenation and dehalogenation potential. Environmental Science & Technology Letters 6, 585-591.

Fahid, M., Arslan, M., Shabir, G., Younus, S., Yasmeen, T., Rizwan, M., Siddique, K., Ahmad, S.R., Tahseen, R., Iqbal, S., Ali, S., Afzal, M., 2020. Phragmites australis in combination with hydrocarbons degrading bacteria is a suitable option for remediation of diesel-contaminated water in floating wetlands. Chemosphere 240, 124890.



Lusinier, N., Seyssiecq, I., Sambusiti, C., Jacob, M., Lesage, N., Roche, N., 2019. Biological treatments of oilfield produced water: A comprehensive review. SPE-195677-PA 24, 2135-2147.



DEEPWATER HORIZON/MACONDO/OTHER OIL SPILLS

Liu, Z., Callies, U., 2020. A probabilistic model of decision making regarding the use of chemical dispersants to combat oil spills in the German Bight. Water Research 169, 115196.

Meador, J.P., Nahrgang, J., 2019. Characterizing crude oil toxicity to early-life stage fish based on a complex mixture: Are we making unsupported assumptions? Environmental Science & Technology 53, 11080-11092.


Valencia-Agami, S.S., Cerqueda-García, D., Putzeys, S., Uribe-Flores, M.M., García-Cruz, U.N., Pech, D., Herrera-Silveira, J., Aguirre-Macedo, L.M., García-Maldonado, Q.J., 2019. Changes in the bacterioplankton community structure from southern Gulf of Mexico during a simulated crude oil spill at mesocosm scale. Microorganisms 7, 441.

Venera-Pontón, D.E., Schmidt, W.E., Fredericq, S., 2019. Population structure of the red macroalga Botryocladia occidentalis (Børgesen) Kylin (Rhodymeniaceae, Rhodymeniales) in the Gulf of Mexico Before the Deepwater Horizon oil spill. Frontiers in Marine Science 6, 652. doi: 610.3389/fmars.2019.00652.

MICROPLASTICS



OIL SAND PROCESS WATERS/TAILING PONDS

Mori, J.F., Chen, L.-X., Jessen, G.L., Rudderham, S.B., McBeth, J.M., Lindsay, M.B.J., Slater, G.F., Banfield, J.F., Warren, L.A., 2019. Putative mixotrophic nitrifying-denitrifying gammaproteobacteria implicated in nitrogen cycling within the ammonia/oxygen transition zone of an oil sands pit lake. Frontiers in Microbiology 10, 2435. doi: 2410.3389/fmicb.2019.02435.

UNCONVENTIONALSHALE GAS-CBM RESOURCES

Campa, M.F., Techtmann, S.M., Ladd, M.P., Yan, J., Patterson, M., Garcia de Matos Amaral, A., Carter, K.E., Ulrich, N., Grant, C.J., Hettich, R.L., Lamendella, R., Hazen, T.C., 2019. Surface water microbial community response to the biocide 2,2-dibromo-3-nitrilopropionamide, used in unconventional oil and gas extraction. Applied and Environmental Microbiology 85, e01336-01319.

Campa, M.F., Wolfe, A.K., Techtmann, S.M., Harik, A.-M., Hazen, T.C., 2019. Unconventional oil and gas energy systems: An unidentified hotspot of antimicrobial resistance? Frontiers in Microbiology 10, 2392. doi: 2310.3389/fmicb.2019.02392.

Evans, M.V., Getzinger, G., Luek, J.L., Hanson, A.J., McLaughlin, M.C., Blotevogel, J., Welch, S.A., Nicora, C.D., Purvine, S.O., Xu, C., Cole, D.R., Darrah, T.H., Hoyt, D.W.,

Metz, T.O., Lee Ferguson, P., Lipton, M.S., Wilkins, M.J., Mouser, P.J., 2019. In situ transformation of ethoxylate and glycol surfactants by shale-colonizing microorganisms during hydraulic fracturing. The ISME Journal 13, 2690-2700.

McAdams, B.C., Carter, K.E., Blotevogel, J., Borch, T., Hakala, J.A., 2019. In situ transformation of hydraulic fracturing surfactants from well injection to produced water. Environmental Science: Processes & Impacts 21, 1777-1786.

Mehta, N., Kocar, B.D., 2019. Geochemical conditions conducive for retention of trace elements and radionuclides during shale–fluid interactions. Environmental Science: Processes & Impacts 21, 1764-1776.

Evolution/Paleontology/Palynology

Abd El Gawad, E.A., Ghanem, M.F., Makled, W.A., Mousa, D.A., Lotfy, M.M., Temraz, M.G., Shehata, A.M., 2019. Source rock evaluation of subsurface Devonian–Carboniferous succession based on palyno-organic facies analysis in Faghur Basin, North Western Desert of Egypt: a division of the North Africa Paleozoic Basins. Arabian Journal of Geosciences 12, 655.

Beznosov, P.A., Clack, J.A., Lukševičs, E., Ruta, M., Ahlberg, P.E., 2019. Morphology of the earliest reconstructable tetrapod Parmastega aelidae. Nature 574, 527-531.


Chipman, A.D., Edgecombe, G.D., 2019. Developing an integrated understanding of the evolution of arthropod segmentation using fossils and evo-devo. Proceedings of the Royal Society B: Biological Sciences 286, 20191881.

Evans, S.D., Huang, W., Gehling, J.G., Kisailus, D., Droser, M.L., 2019. Stretched, mangled, and torn: Responses of the Ediacaran fossil Dickinsonia to variable forces. Geology 47, 1049-1053.

Frey, L., Coates, M., Ginter, M., Hairapetian, V., Rücklin, M., Jerjen, I., Klug, C., 2019. The early elasmobranch Phoebodus: phylogenetic relationships, ecomorphology and a new time-scale for shark evolution. Proceedings of the Royal Society B: Biological Sciences 286, 20191336.

Fröbisch, N.B., Witzmann, F., 2019. Early tetrapods had an eye on the land. Nature 574, 494-495.

Ginot, S., Goudemand, N., 2019. Conodont size, trophic level, and the evolution of platform elements. Paleobiology 45, 458-468.

Gurov, E.P., Permiakov, V.V., Koeberl, C., 2019. Remnants of paleoflora in impact melt rocks of the El'gygytgyn crater (Chukotka, Russia). Meteoritics & Planetary Science 54, 2532-2540.

Krings, M., 2019. Palaeolyngbya kerpii sp. nov., a large filamentous cyanobacterium with affinities to Oscillatoriaceae from the Lower Devonian Rhynie chert. PalZ 93, 377-386.


Pennisi, E., 2019. How life blossomed after the dinosaurs died. Science 366, 409.


Saleh, F., Antcliffe, J.B., Lefebvre, B., Pittet, B., Laibl, L., Perez Peris, F., Lustri, L., Gueriau, P., Daley, A.C., 2020. Taphonomic bias in exceptionally preserved biotas. Earth and Planetary Science Letters 529, 115873.


Wellman, C.H., Graham, L.E., Lewis, L.A., 2019. Filamentous green algae from the Early Devonian Rhynie chert. PalZ 93, 387-393.

Xiao, S., Chen, Z., Zhou, C., Yuan, X., 2019. Surfing in and on microbial mats: Oxygen-related behavior of a terminal Ediacaran bilaterian animal. Geology 47, 1054-1058.

Zhang, F., Xiao, S., Romaniello, S.J., Hardisty, D., Li, C., Melezhik, V., Pokrovsky, B., Cheng, M., Shi, W., Lenton, T.M., Anbar, A.D., 2019. Global marine redox changes drove the rise and fall of the Ediacara biota. Geobiology 17, 594-610.


ORIGINS OF LIFE/MICROBIAL GENOMICS

Becker, S., Feldmann, J., Wiedemann, S., Okamura, H., Schneider, C., Iwan, K., Crisp, A., Rossa, M., Amatov, T., Carell, T., 2019. Unified prebiotically plausible synthesis of pyrimidine and purine RNA ribonucleotides. Science 366, 76-82.

Bhowmik, S., Krishnamurthy, R., 2019. The role of sugar-backbone heterogeneity and chimeras in the simultaneous emergence of RNA and DNA. Nature Chemistry 11, 1009-1018.

Campbell, T.D., Febrian, R., McCarthy, J.T., Kleinschmidt, H.E., Forsythe, J.G., Bracher, P.J., 2019. Prebiotic condensation through wet–dry cycling regulated by deliquescence. Nature Communications 10, 4508.

Gözen, İ., 2019. A hypothesis for protocell division on the early Earth. ACS Nano 13, 10869-10871.


Hashizume, H., Theng, B.K.G., van der Gaast, S., Fujii, K., 2019. Formation of adenosine from adenine and ribose under conditions of repeated wetting and drying in the presence of clay minerals. Geochimica et Cosmochimica Acta 265, 495-504.

Hawbaker, N.A., Blackmond, D.G., 2019. Energy threshold for chiral symmetry breaking in molecular self-replication. Nature Chemistry 11, 957-962.


Hud, N.V., Fialho, D.M., 2019. RNA nucleosides built in one prebiotic pot. Science 366, 32-33.

Kitadai, N., Nishiuchi, K., 2019. Thermodynamic impact of mineral surfaces on amino acid polymerization: Aspartate dimerization on goethite. Astrobiology 19, 1363-1376.



Salcher, M.M., Schaefle, D., Kaspar, M., Neuenschwander, S.M., Ghai, R., 2019. Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae. The ISME Journal 13, 2764-2777.

HOMINID EVOLUTION

Channell, J.E.T., Vigliotti, L., 2019. The role of geomagnetic field intensity in late Quaternary evolution of humans and large mammals. Reviews of Geophysics 57, 709-738.

Cox, S.L., Ruff, C.B., Maier, R.M., Mathieson, I., 2019. Genetic contributions to variation in human stature in prehistoric Europe. Proceedings of the National Academy of Sciences 116, 21484-21492.

Faith, J.T., Rowan, J., Du, A., 2019. Early hominins evolved within non-analog ecosystems. Proceedings of the National Academy of Sciences 116, 21478-21483.

Scerri, E.M.L., Chikhi, L., Thomas, M.G., 2019. Beyond multiregional and simple out-of-Africa models of human evolution. Nature Ecology & Evolution 3, 1370-1372.

Warren, J.L.A., Ponce de León, M.S., Hopkins, W.D., Zollikofer, C.P.E., 2019. Evidence for independent brain and neurocranial reorganization during hominin evolution. Proceedings of the National Academy of Sciences 116, 22115-22121.

Fluid Inclusions

Lu, X., Zhao, M., Chen, Z., Li, X., Hu, H., Zhuo, Q., 2019. Recognition of hydrocarbon accumulation in Qigu oilfield and implications for exploration in the southern margin of Junggar Basin. Acta Petrolei Sinica 40, 1045-1058.

General Interest

Argüello-Luengo, J., González-Tudela, A., Shi, T., Zoller, P., Cirac, J.I., 2019. Analogue quantum chemistry simulation. Nature 574, 215-218.

Kittilä, A., Jalali, M.R., Evans, K.F., Willmann, M., Saar, M.O., Kong, X.Z., 2019. Field comparison of DNA-labeled nanoparticle and solute tracer transport in a fractured crystalline rock. Water Resources Research 55, 6577-6595.

Geology

Bartels, W.B., Rücker, M., Boone, M., Bultreys, T., Mahani, H., Berg, S., Hassanizadeh, S.M., Cnudde, V., 2019. Imaging spontaneous imbibition in full Darcy-scale samples at pore-scale resolution by fast X-ray tomography. Water Resources Research 55, 7072-7085.

Mazzini, A., Lupi, M., Sciarra, A., Hammed, M., Schmidt, S.T., Suessenberger, A., 2019. Concentric structures and hydrothermal venting in the Western Desert, Egypt. Frontiers in Earth Science 7, 266. doi: 210.3389/feart.2019.00266.

Xiao, C.-T., Wei, G.-Q., Song, Z.-Y., Xiao, Y.-P., Yang, W., Dong, M., Huang, Y.-F., Gao, D., 2019. Petrography and origin of the Lower Ordovician microbial carbonates in the Songzi Area of Hubei Province, middle Yangtze region, China. Petroleum Science 16, 956-971.

BOLIDE IMPACTS/CRATER GEOCHEMISTRY

Arp, G., Reimer, A., Simon, K., Sturm, S., Wilk, J., Kruppa, C., Hecht, L., Hansen, B.T., Pohl, J., Reimold, W.U., Kenkmann, T., Jung, D., 2019. The Erbisberg drilling 2011: Implications for the structure and postimpact evolution of the inner ring of the Ries impact crater. Meteoritics & Planetary Science 54, 2448-2482.

Baratoux, D., Niang, C.A.B., Reimold, W.U., Sapah, M.S., Jessell, M.W., Boamah, D., Faye, G., Bouley, S., Vanderheaghe, O., 2019. Bosumtwi impact structure, Ghana: Evidence for fluidized emplacement of the ejecta. Meteoritics & Planetary Science 54, 2541-2556.

Drake, H., Roberts, N.M.W., Heim, C., Whitehouse, M.J., Siljeström, S., Kooijman, E., Broman, C., Ivarsson, M., Åström, M.E., 2019. Timing and origin of natural gas accumulation in the Siljan impact structure, Sweden. Nature Communications 10, 4736.

El Kerni, H., Chennaoui Aoudjehane, H., Baratoux, D., Aoudjehane, M., Charrière, A., Ibouh, H., Rochette, P., Quesnel, Y., Uehara, M., Kenkmann, T., Wulf, G., Poelchau, M., Nguyen, V.B., Aboulahris, M., Makhoukhi, S., Aumaître, G., Bourlès, D., Keddadouche, K., 2019. Geological and geophysical studies of the Agoudal impact structure (Central

High Atlas, Morocco): New evidence for crater size and age. Meteoritics & Planetary Science 54, 2483-2509.


Hassler, S., Biller, S., Simonson, B.M., 2019. Petrography and sedimentology of the ~2490 Ma DS4 impact spherule layer revisited, Brockman Iron Formation (Hamersley Group, Western Australia). Meteoritics & Planetary Science 54, 2241-2253.

Hauser, N., Reimold, W.U., Cavosie, A.J., Crósta, A.P., Schwarz, W.H., Trieloff, M., Da Silva Maia de Souza, C., Pereira, L.A., Rodrigues, E.N., Brown, M., 2019. Linking shock textures revealed by BSE, CL, and EBSD with U-Pb data (LA-ICP-MS and SIMS) from zircon from the Araguainha impact structure, Brazil. Meteoritics & Planetary Science 54, 2286-2311.

Huber, M.S., Koeberl, C., Smith, F.C., Glass, B.P., Mundil, R., McDonald, I., 2019. Geochemistry of a confirmed Precambrian impact ejecta deposit: The Grænsesø spherule layer, South Greenland. Meteoritics & Planetary Science 54, 2254-2272.

Jourdan, F., Nomade, S., Wingate, M.T.D., Eroglu, E., Deino, A., 2019. Ultraprecise age and formation temperature of the Australasian tektites constrained by 40Ar/39Ar analyses. Meteoritics & Planetary Science 54, 2573-2591.


Koeberl, C., Ferrière, L., 2019. Libyan Desert Glass area in western Egypt: Shocked quartz in bedrock points to a possible deeply eroded impact structure in the region. Meteoritics & Planetary Science 54, 2398-2408.

Koeberl, C., Ivanov, B.A., 2019. Asteroid impact effects on Snowball Earth. Meteoritics & Planetary Science 54, 2273-2285.

Maierhofer, K., Koeberl, C., Brigham-Grette, J., 2019. Petrography and geochemistry of the impact to postimpact transition layer at the El'gygytgyn impact structure in Chukotka, Arctic Russia. Meteoritics & Planetary Science 54, 2510-2531.

Ozdemir, S., Schulz, T., van Acken, D., Luguet, A., Reimold, W.U., Koeberl, C., 2019. Meteoritic highly siderophile element and Re-Os isotope signatures of Archean spherule layers from the CT3 drill core, Barberton Greenstone Belt, South Africa. Meteoritics & Planetary Science 54, 2203-2216.

Pati, J.K., Poelchau, M.H., Reimold, W.U., Nakamura, N., Kuriyama, Y., Singh, A.K., 2019. Documentation of shock features in impactites from the Dhala impact structure, India. Meteoritics & Planetary Science 54, 2312-2333.

Prado, R.L., Espin Fenoll, I.C., Ullah, I., Miura, G.C.M., Crósta, A.P., Zanon dos Santos, R.P., Reimold, W.U., Elis, V.R., Imbernon, E., Riccomini, C., Diogo, L.A., 2019. Geophysical investigation of the Colônia structure, Brazil. Meteoritics & Planetary Science 54, 2357-2372.

Reimold, W.U., Crósta, A.P., Hasch, M., Kowitz, A., Hauser, N., Sanchez, J.P., Simões, L.S.A., de Oliveira, G.J., Zaag, P.T., 2019. Shock deformation confirms the impact origin for the Cerro do Jarau, Rio Grande do Sul, Brazil, structure. Meteoritics & Planetary Science 54, 2384-2397.


Schulz, T., Sackl, F., Fragner, E., Luguet, A., van Acken, D., Abate, B., Badjukov, D.D., Koeberl, C., 2020. The Zhamanshin impact structure, Kazakhstan: A comparative geochemical study of target rocks and impact glasses. Geochimica et Cosmochimica Acta 268, 209-229.

Siegert, S., Hecht, L., 2019. Heterogeneity of melts in impact deposits and implications for their origin (Ries suevite, Germany). Meteoritics & Planetary Science 54, 2409-2447.

Simonson, B.M., Beukes, N.J., Biller, S., 2019. Extending the paleogeographic range and our understanding of the Neoarchean Monteville impact spherule layer (Transvaal Supergroup, South Africa). Meteoritics & Planetary Science 54, 2217-2240.

Välja, R., Kirsimäe, K., Koeberl, C., Boamah, D., Kirs, J., 2019. Incipient devitrification of impact melt particles at Bosumtwi crater, Ghana: Implications for suevite cooling history and melt dispersion. Meteoritics & Planetary Science 54, 2557-2572.

Vasconcelos, M.A.R., Rocha, F.F., Crósta, A.P., Wünnemann, K., Güldemeister, N., Leite, E.P., Ferreira, J.C., Reimold, W.U., 2019. Insights about the formation of a complex impact structure formed in basalt from numerical modeling: The Vista Alegre structure, southern Brazil. Meteoritics & Planetary Science 54, 2373-2383.

Hydrates

Darnell, K.N., Flemings, P.B., DiCarlo, D., 2019. Nitrogen-driven chromatographic separation during gas injection into hydrate-bearing sediments. Water Resources Research 55, 6673-6691.

Ma, S., Zheng, J.-n., Tian, M., Tang, D., Yang, M., 2020. NMR quantitative investigation on methane hydrate formation characteristics under different driving forces. Fuel 261, 116364.

Mukumoto, K., Tsuji, T., Hendriyana, A., 2019. Large gas reservoir along the rift axis of a continental back-arc basin revealed by automated seismic velocity analysis in the Okinawa Trough. Geophysical Research Letters 46, 9583-9590.

Roostaie, M., Leonenko, Y., 2020. Analytical modeling of methane hydrate dissociation under thermal stimulation. Journal of Petroleum Science and Engineering 184, 106505.

Wei, L., Cook, A., Daigle, H., Malinverno, A., Nole, M., You, K., 2019. Factors controlling short-range methane migration of gas hydrate accumulations in thin coarse-grained layers. Geochemistry, Geophysics, Geosystems 20, 3985-4000.


Isotope Geochemistry


Colangelo-Lillis, J., Pelikan, C., Herbold, C.W., Altshuler, I., Loy, A., Whyte, L.G., Wing, B.A., 2019. Diversity decoupled from sulfur isotope fractionation in a sulfate-reducing microbial community. Geobiology 17, 660-675.

Eiler, J.M., Clog, M., Lawson, M., Lloyd, M., Piasecki, A., Ponton, C., Xie, H., 2018. The isotopic structures of geological organic compounds, in: Lawson, M., Formolo, M.J., Eiler, J.M. (Eds.), From Source to Seep: Geochemical Applications in Hydrocarbon Systems. Geological Society, London, Special Publications 468. Geological Society, London, London, p. 53.

Fogel, M.L., 2019. My stable isotope journey in biogeochemistry, geoecology, and astrobiology. Geochemical Perspectives 8, 105-281.

Freimuth, E.J., Diefendorf, A.F., Lowell, T.V., Bates, B.R., Schartman, A., Bird, B.W., Landis, J.D., Stewart, A.K., 2020. Contrasting sensitivity of lake sediment n-alkanoic acids and n-alkanes to basin-scale vegetation and regional-scale precipitation δ2H in the Adirondack Mountains, NY (USA). Geochimica et Cosmochimica Acta 268, 22-41.

Gao, Y., Casey, J.F., Bernardo, L.M., Yang, W., Bissada, K.K., 2018. Vanadium isotope composition of crude oil: effects of source, maturation and biodegradation, in: Lawson, M., Formolo, M.J., Eiler, J.M. (Eds.), From Source to Seep: Geochemical Applications in Hydrocarbon Systems. Geological Society, London, Special Publications 468. Geological Society, London, London, pp. 83-103.

Goldsmith, Y., Polissar, P.J., deMenocal, P.B., Broecker, W.S., 2019. Leaf wax δD and δ13C in soils record hydrological and environmental information across a climatic gradient in Israel. Journal of Geophysical Research: Biogeosciences 124, 2898-2916.

Goulden, S.K.E., Ohkouchi, N., Freeman, K.H., Chikaraishi, Y., Ogawa, N.O., Suga, H., Chadwick, O., Houlton, B.Z., 2019. Strong correspondence between nitrogen isotope composition of foliage and chlorin across a rainfall gradient: implications for paleo-reconstruction of the nitrogen cycle. Biogeosciences 16, 3869-3882.



McFarlin, J.M., Axford, Y., Masterson, A.L., Osburn, M.R., 2019. Calibration of modern sedimentary δ2H plant wax-water relationships in Greenland lakes. Quaternary Science Reviews 225, 105978.

Ni, Y., Liao, F., Yao, L., Gao, J., Zhang, D., 2019. Hydrogen isotope of natural gas from the Xujiahe Formation and its implications for water salinization in central Sichuan Basin, China. Journal of Natural Gas Geoscience 4, 215-230.


Pedentchouk, N., Turich, C., 2018. Carbon and hydrogen isotopic compositions of n-alkanes as a tool in petroleum exploration, in: Lawson, M., Formolo, M.J., Eiler, J.M. (Eds.), From Source to Seep: Geochemical Applications in Hydrocarbon Systems. Geological Society, London, Special Publications 468. Geological Society, London, London, pp. 105-125.

Suarez, C.A., Kohn, M.J., 2020. Caught in the act: A case study on microscopic scale physicochemical effects of fossilization on stable isotopic composition of bone. Geochimica et Cosmochimica Acta 268, 277-295.

CLUMPED ISOTOPES

Guo, W., 2020. Kinetic clumped isotope fractionation in the DIC-H2O-CO2 system: Patterns, controls, and implications. Geochimica et Cosmochimica Acta 268, 230-257.

Stolper, D.A., Lawson, M., Formolo, M.J., Davis, C.L., Douglas, P.M.J., Eiler, J.M., 2018. The utility of methane clumped isotopes to constrain the origins of methane in natural gas accumulations, in: Lawson, M., Formolo, M.J., Eiler, J.M. (Eds.), From Source to Seep: Geochemical Applications in Hydrocarbon Systems. Geological Society, London, Special Publications 468. Geological Society, London, London, pp. 23-52.


METHODS/INSTRUMENTATION

Mathematical Geochemistry/Phase Behavior

Agarwal, P., Klein, M.T., 2019. Generating data-driven models from molecular-level kinetic models: A kinetic model speedup strategy. Energy & Fuels 33, 10372-10379.

Heidariyan, H., Ehsani, M., Behbahani, T.J., Mohammadi, M., 2019. Experimental investigation and thermodynamic modeling of wax precipitation in crude oil using the multi-solid model and PC-SAFT EOS. Energy & Fuels 33, 9466-9479.

Law, J.C., Headen, T.F., Jiménez-Serratos, G., Boek, E.S., Murgich, J., Müller, E.A., 2019. Catalogue of plausible molecular models for the molecular dynamics of asphaltenes and resins obtained from quantitative molecular representation. Energy & Fuels 33, 9779-9795.

Mishra, A.K., Kumar, A., 2020. P-μ-T cubic equation of viscosity for hydrocarbons. Fluid Phase Equilibria 505, 112359.

Wang, Q., Pan, S., Bai, J., Chi, M., Cui, D., Wang, Z., Liu, Q., Xu, F., 2019. Theoretical study of structural and spatial properties of kerogen. Energy & Fuels 33, 9559-9569.

Zhang, Z., Guo, L., Zhang, H., Zhan, J.-H., 2019. Comparing product distribution and desulfurization during direct pyrolysis and hydropyrolysis of Longkou oil shale kerogen using reactive MD simulations. International Journal of Hydrogen Energy 44, 25335-25346.

Microbiology/Extremophiles


Babich, T.L., Safonov, A.V., Grouzdev, D.S., Andryuschenko, N.D., Zakharova, E.V., Nazina, T.N., 2019. Bacteria of the genus Shewanella from radionuclide-contaminated groundwater. Microbiology 88, 613-623.

Colombet, J., Billard, H., Viguès, B., Balor, S., Boulé, C., Geay, L., Benzerara, K., Menguy, N., Ilango, G., Fuster, M., Enault, F., Bardot, C., Gautier, V., Pradeep Ram, A.S., Sime-Ngando, T., 2019. Discovery of high abundances of aster-like nanoparticles in pelagic environments: Characterization and dynamics. Frontiers in Microbiology 10, 2376. doi: 2310.3389/fmicb.2019.02376.


Moeller, F.U., Webster, N.S., Herbold, C.W., Behnam, F., Domman, D., Albertsen, M., Mooshammer, M., Markert, S., Turaev, D., Becher, D., Rattei, T., Schweder, T., Richter, A., Watzka, M., Nielsen, P.H., Wagner, M., 2019. Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta. Environmental Microbiology 21, 3831-3854.

Needham, D.M., Poirier, C., Hehenberger, E., Jiménez, V., Swalwell, J.E., Santoro, A.E., Worden, A.Z., 2019. Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes. Philosophical Transactions of the Royal Society B: Biological Sciences 374, 20190086.

Needham, D.M., Yoshizawa, S., Hosaka, T., Poirier, C., Choi, C.J., Hehenberger, E., Irwin, N.A.T., Wilken, S., Yung, C.-M., Bachy, C., Kurihara, R., Nakajima, Y., Kojima, K., Kimura-Someya, T., Leonard, G., Malmstrom, R.R., Mende, D.R., Olson, D.K., Sudo, Y.,

Sudek, S., Richards, T.A., DeLong, E.F., Keeling, P.J., Santoro, A.E., Shirouzu, M., Iwasaki, W., Worden, A.Z., 2019. A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators. Proceedings of the National Academy of Sciences 116, 20574-20583.

Roux, S., Krupovic, M., Daly, R.A., Borges, A.L., Nayfach, S., Schulz, F., Sharrar, A., Matheus Carnevali, P.B., Cheng, J.-F., Ivanova, N.N., Bondy-Denomy, J., Wrighton, K.C., Woyke, T., Visel, A., Kyrpides, N.C., Eloe-Fadrosh, E.A., 2019. Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes. Nature Microbiology 4, 1895-1906.

Slobodkin, A.I., Slobodkina, G.B., 2019. Diversity of sulfur-disproportionating microorganisms. Microbiology 88, 509-522.

MICROBIAL ECOSYSTEMS


Evans, M.V., Getzinger, G., Luek, J.L., Hanson, A.J., McLaughlin, M.C., Blotevogel, J., Welch, S.A., Nicora, C.D., Purvine, S.O., Xu, C., Cole, D.R., Darrah, T.H., Hoyt, D.W., Metz, T.O., Lee Ferguson, P., Lipton, M.S., Wilkins, M.J., Mouser, P.J., 2019. In situ transformation of ethoxylate and glycol surfactants by shale-colonizing microorganisms during hydraulic fracturing. The ISME Journal 13, 2690-2700.




Lu, Y., Xia, X., Cheung, S., Jing, H., Liu, H., 2019. Differential distribution and determinants of ammonia oxidizing archaea sublineages in the oxygen minimum zone off costa Rica. Microorganisms 7, 453.

Lukhele, T., Selvarajan, R., Nyoni, H., Mamba, B.B., Msagati, T.A.M., 2019. Diversity and functional profile of bacterial communities at Lancaster acid mine drainage dam, South Africa as revealed by 16S rRNA gene high-throughput sequencing analysis. Extremophiles 23, 719-734.

Martin-Cuadrado, A.-B., Senel, E., Martínez-García, M., Cifuentes, A., Santos, F., Almansa, C., Moreno-Paz, M., Blanco, Y., García-Villadangos, M., del Cura, M.Á.G., Sanz-Montero, M.E., Rodríguez-Aranda, J.P., Rosselló-Móra, R., Antón, J., Parro, V., 2019.

Prokaryotic and viral community of the sulfate-rich crust from Peñahueca ephemeral lake, an astrobiology analogue. Environmental Microbiology 21, 3577-3600.

Mitzscherling, J., Horn, F., Winterfeld, M., Mahler, L., Kallmeyer, J., Overduin, P.P., Schirrmeister, L., Winkel, M., Grigoriev, M.N., Wagner, D., Liebner, S., 2019. Microbial community composition and abundance after millennia of submarine permafrost warming. Biogeosciences 16, 3941-3958.



Ranchou-Peyruse, M., Auguet, J.-C., Mazière, C., Restrepo-Ortiz, C.X., Guignard, M., Dequidt, D., Chiquet, P., Cézac, P., Ranchou-Peyruse, A., 2019. Geological gas-storage shapes deep life. Environmental Microbiology 21, 3953-3964.

Schmidt, R., Ulanova, D., Wick, L.Y., Bode, H.B., Garbeva, P., 2019. Microbe-driven chemical ecology: past, present and future. The ISME Journal 13, 2656-2663.

Trontelj, P., Borko, Š., Delić, T., 2019. Testing the uniqueness of deep terrestrial life. Scientific Reports 9, 15188.

Uritskiy, G., Getsin, S., Munn, A., Gomez-Silva, B., Davila, A., Glass, B., Taylor, J., DiRuggiero, J., 2019. Halophilic microbial community compositional shift after a rare rainfall in the Atacama Desert. The ISME Journal 13, 2737-2749.

Wang, Z., Juarez, D.L., Pan, J.-F., Blinebry, S.K., Gronniger, J., Clark, J.S., Johnson, Z.I., Hunt, D.E., 2019. Microbial communities across nearshore to offshore coastal transects are primarily shaped by distance and temperature. Environmental Microbiology 21, 3862-3872.

Wei, S., Cui, H., Zhang, Y., Su, X., Dong, H., Chen, F., Zhu, Y., 2019. Comparative evaluation of three archaeal primer pairs for exploring archaeal communities in deep-sea sediments and permafrost soils. Extremophiles 23, 747-757.

Yu, T., Zhang, M., Kang, D., Zhao, S., Ding, A., Lin, Q., Xu, D., Hong, Y., Wang, L., Zheng, P., 2019. Characteristics of microbial communities and their correlation with environmental substrates and sediment type in the gas-bearing formation of Hangzhou Bay, China. Frontiers in Microbiology 10, 2421. doi: 2410.3389/fmicb.2019.02421.

PETROLEUM DEGRADERS

Farhan Ul Haque, M., Crombie, A.T., Murrell, J.C., 2019. Novel facultative Methylocella strains are active methane consumers at terrestrial natural gas seeps. Microbiome 7, 134.



Lin, J.-H., Zhang, K.-C., Tao, W.-Y., Wang, D., Li, S., 2019. Geobacillus strains that have potential value in microbial enhanced oil recovery. Applied Microbiology and Biotechnology 103, 8339-8350.

Lusinier, N., Seyssiecq, I., Sambusiti, C., Jacob, M., Lesage, N., Roche, N., 2019. Biological treatments of oilfield produced water: A comprehensive review. SPE-195677-PA 24, 2135-2147.


Semenova, E.M., Sokolova, D.S., Grouzdev, D.S., Poltaraus, A.B., Vinokurova, N.G., Tourova, T.P., Nazina, T.N., 2019. Geobacillus proteiniphilus sp. nov., a thermophilic bacterium isolated from a high-temperature heavy oil reservoir in China. International Journal of Systematic and Evolutionary Microbiology 69, 3001-3008.

Paleoclimatology/Paleoceanography

Abshire, M.L., Romaniello, S.J., Kuzminov, A.M., Cofrancesco, J., Severmann, S., Riedinger, N., 2020. Uranium isotopes as a proxy for primary depositional redox conditions in organic-rich marine systems. Earth and Planetary Science Letters 529, 115878.

Ardenghi, N., Mulch, A., Koutsodendris, A., Pross, J., Kahmen, A., Niedermeyer, E.M., 2019. Temperature and moisture variability in the eastern Mediterranean region during Marine Isotope Stages 11–10 based on biomarker analysis of the Tenaghi Philippon peat deposit. Quaternary Science Reviews 225, 105977.

Beil, S., Kuhnt, W., Holbourn, A., Scholz, F., Oxmann, J., Wallmann, K., Lorenzen, J., Aquit, M., Chellai, E.H., 2019. Cretaceous Oceanic Anoxic Events prolonged by phosphorus cycle feedbacks. Climate of the Past Discussions 2019, 1-42.

Castro, J.M., de Gea, G.A., Quijano, M.L., Aguado, R., Froehner, S., Naafs, B.D.A., Pancost, R.D., 2019. Complex and protracted environmental and ecological perturbations during OAE 1a - Evidence from an expanded pelagic section from south Spain (Western Tethys). Global and Planetary Change 183, 103030.

Dumitru, O.A., Austermann, J., Polyak, V.J., Fornós, J.J., Asmerom, Y., Ginés, J., Ginés, A., Onac, B.P., 2019. Constraints on global mean sea level during Pliocene warmth. Nature 574, 233-236.

Elling, F.J., Gottschalk, J., Doeana, K.D., Kusch, S., Hurley, S.J., Pearson, A., 2019. Archaeal lipid biomarker constraints on the Paleocene-Eocene carbon isotope excursion. Nature Communications 10, 4519.

Filatova, N.I., 2019. A Jurassic anoxic event in the Pacific based on data from the West Kamchatka–Asian region. Doklady Earth Sciences 487, 894-897.


Grant, G.R., Naish, T.R., Dunbar, G.B., Stocchi, P., Kominz, M.A., Kamp, P.J.J., Tapia, C.A., McKay, R.M., Levy, R.H., Patterson, M.O., 2019. The amplitude and origin of sea-level variability during the Pliocene epoch. Nature 574, 237-241.

Łącka, M., Cao, M., Rosell-Melé, A., Pawłowska, J., Kucharska, M., Forwick, M., Zajączkowski, M., 2019. Postglacial paleoceanography of the western Barents Sea: Implications for alkenone-based sea surface temperatures and primary productivity. Quaternary Science Reviews 224, 105973.


Steinmann, J.W., Grammer, G.M., Brunner, B., Jones, C.K., Riedinger, N., 2020. Assessing the application of trace metals as paleoproxies and a chemostratigraphic tool in carbonate systems: A case study from the “Mississippian Limestone” of the midcontinent, United States. Marine and Petroleum Geology 112, 104061.

van der Boon, A., van der Ploeg, R., Cramwinckel, M.J., Kuiper, K.F., Popov, S.V., Tabachnikova, I.P., Palcu, D.V., Krijgsman, W., 2019. Integrated stratigraphy of the Eocene-Oligocene deposits of the northern Caucasus (Belaya River, Russia): Intermittent oxygen-depleted episodes in the Peri-Tethys and Paratethys. Palaeogeography, Palaeoclimatology, Palaeoecology 536, 109395.

Wang, T., Li, G., Aitchison, J.C., Ding, L., Sheng, J., 2019. Evolution of mid-Cretaceous radiolarians in response to oceanic anoxic events in the eastern Tethys (southern Tibet, China). Palaeogeography, Palaeoclimatology, Palaeoecology 536, 109369.

EXTINCTION EVENTS

Alvarez, S.A., Gibbs, S.J., Bown, P.R., Kim, H., Sheward, R.M., Ridgwell, A., 2019. Diversity decoupled from ecosystem function and resilience during mass extinction recovery. Nature 574, 242-245.

Carmichael, S.K., Waters, J.A., Königshof, P., Suttner, T.J., Kido, E., 2019. Paleogeography and paleoenvironments of the Late Devonian Kellwasser event: A review of its sedimentological and geochemical expression. Global and Planetary Change 183, 102984.

Moore, C.R., Brooks, M.J., Goodyear, A.C., Ferguson, T.A., Perrotti, A.G., Mitra, S., Listecki, A.M., King, B.C., Mallinson, D.J., Lane, C.S., Kapp, J.D., West, A., Carlson, D.L., Wolbach, W.S., Them, T.R., Harris, M.S., Pyne-O’Donnell, S., 2019. Sediment cores from White Pond, South Carolina, contain a platinum anomaly, pyrogenic carbon peak, and coprophilous spore decline at 12.8 ka. Scientific Reports 9, 15121.

Schobben, M., van de Schootbrugge, B., Wignall, P.B., 2019. Interpreting the carbon isotope record of mass extinctions. Elements 15, 331-337.

Thackeray, J.F., Scott, L., Pieterse, P., 2019. The Younger Dryas interval at Wonderkrater (South Africa) in the context of a platinum anomaly. Palaeontologia africana 54, 30-35.

Vajda, V., McLoughlin, S., Mays, C., Frank, T.D., Fielding, C.R., Tevyaw, A., Lehsten, V., Bocking, M., Nicoll, R.S., 2020. End-Permian (252 Mya) deforestation, wildfires and flooding—An ancient biotic crisis with lessons for the present. Earth and Planetary Science Letters 529, 115875.

Wei, H., Tang, Z., Yan, D., Wang, J., Roberts, A.P., 2019. Guadalupian (Middle Permian) ocean redox evolution in South China and its implications for mass extinction. Chemical Geology 530, 119318.

Whittle, R.J., Witts, J.D., Bowman, V.C., Crame, J.A., Francis, J.E., Ineson, J., 2019. Nature and timing of biotic recovery in Antarctic benthic marine ecosystems following the Cretaceous–Palaeogene mass extinction. Palaeontology 62, 919-934.

Petroleum Systems

Lawson, M., Formolo, M.J., Summa, L., Eiler, J.M., 2018. Geochemical applications in petroleum systems analysis: new constraints and the power of integration, in: Lawson, M., Formolo, M.J., Eiler, J.M. (Eds.), From Source to Seep: Geochemical Applications in Hydrocarbon Systems. Geological Society, London, Special Publications 468. Geological Society, London, London, pp. 1-21.

EXPLORATION

Du, J., Li, X., Bao, H., Xu, W., Wang, Y., Huang, J., Wang, H., Wanyan, R., Wang, J., 2019. Geological conditions of natural gas accumulation and new exploration areas in the Mesoproterozoic to Lower Paleozoic of Ordos Basin, NW China. Petroleum Exploration and Development 46, 866-882.

Jiang, Y., Zhao, K., Imber, J., Chen, L., Hu, H., 2020. Recognizing the internal structure of normal faults in clastic rocks and its impact on hydrocarbon migration: A case study from Nanpu Depression in the Bohai Bay Basin, China. Journal of Petroleum Science and Engineering 184, 106492.

Li, Y., Chang, X., Zhang, J., Xu, Y., Gao, D., 2019. Genetic mechanism of heavy oil in the Carboniferous volcanic reservoirs of the eastern Chepaizi Uplift, Junggar Basin. Arabian Journal of Geosciences 12, 648.


Ren, C., He, F., Gao, X., Wu, D., Yao, W., Tian, J., Guo, H., Huang, Y., Wang, L., Feng, H., Li, J., 2019. Prediction of exploration targets based on integrated analyses of source rock and simulated hydrocarbon migration direction: a case study from the gentle slope of Shulu Sag, Bohai Bay Basin, northern China. Geosciences Journal 23, 977-989.

Zhao, W., Hu, S., Guo, X., Li, J., Cao, Z., 2019. New concepts for deepening hydrocarbon exploration and their application effects in the Junggar Basin, NW China. Petroleum Exploration and Development 46, 856-865.

GENERATION & EXPULSION

Abd El Gawad, E.A., Ghanem, M.F., Lotfy, M.M., Mousa, D.A., Temraz, M.G., Shehata, A.M., 2019. Burial and thermal history simulation of the subsurface Paleozoic source rocks in Faghur basin, north Western Desert, Egypt: Implication for hydrocarbon generation and expulsion history. Egyptian Journal of Petroleum 28, 261-271.


Fang, R., Littke, R., Zieger, L., Baniasad, A., Li, M., Schwarzbauer, J., 2019. Changes of composition and content of tricyclic terpane, hopane, sterane, and aromatic biomarkers throughout the oil window: A detailed study on maturity parameters of Lower Toarcian Posidonia Shale of the Hils Syncline, NW Germany. Organic Geochemistry 138, 103928.

Kuang, W., Lu, M., Yeboah, I., Qian, G., Duan, X., Yang, J., Chen, D., Zhou, X., 2019. A comprehensive kinetics study on non-isothermal pyrolysis of kerogen from Green River oil shale. Chemical Engineering Journal 377, 120275.

Liu, J., Liu, Q., Zhu, D., Meng, Q., Huang, X., 2019. The function and impact of deep fluid on the organic matter during the hydrogeneration and evolution process. Journal of Natural Gas Geoscience 4, 231-244.

Liu, K., Ostadhassan, M., Hackley, P.C., Gentzis, T., Zou, J., Yuan, Y., Carvajal-Ortiz, H., Rezaee, R., Bubach, B., 2019. Experimental study on the impact of thermal maturity on shale microstructures using hydrous pyrolysis. Energy & Fuels 33, 9702-9719.

Liu, Y., Wu, Y., Xia, Y., Xing, L., Tian, C., Lei, T., 2019. The methylation of aromatic nuclei — I: Implications for the geochemical evolution of gas. International Journal of Coal Geology 215, 103302.

Song, H., Bao, J., Wen, Z., Cheng, D., 2019. Comparative study of aromatic hydrocarbons in bitumens and expelled oils generated by hydrous pyrolysis of coal. International Journal of Coal Geology 215, 103303.

Xie, L., Sun, Y., Uguna, C.N., Li, Y., Snape, C.E., Meredith, W., 2019. Thermal cracking of oil under water pressure up to 900 bar at high thermal maturities: 2. Insight from light hydrocarbon generation and carbon isotope fractionation. Energy & Fuels 33, 9546-9558.

Yu, F., Sun, P., Zhao, K.a., Ma, L., Tian, X., 2020. Experimental constraints on the evolution of organic matter in oil shales during heating: Implications for enhanced in situ oil recovery from oil shales. Fuel 261, 116412.


OIL & GAS


Borisova, L.S., 2019. The origin of asphaltenes and main trends in evolution of their composition during lithogenesis. Petroleum Chemistry 59, 1118-1123.

Byrne, D.J., Barry, P.H., Lawson, M., Ballentine, C.J., 2018. Noble gases in conventional and unconventional petroleum systems, in: Lawson, M., Formolo, M.J., Eiler, J.M. (Eds.), From Source to Seep: Geochemical Applications in Hydrocarbon Systems. Geological Society, London, Special Publications 468. Geological Society, London, London, pp. 127-149.

Byrne, D.J., Barry, P.H., Lawson, M., Ballentine, C.J., 2020. The use of noble gas isotopes to constrain subsurface fluid flow and hydrocarbon migration in the East Texas Basin. Geochimica et Cosmochimica Acta 268, 186-208.


Fursenko, E.A., Kim, N.S., 2019. Geochemistry of condensates of Maloyamal’skoe Field (Yamal Peninsula, Western Siberia). Petroleum Chemistry 59, 1138-1146.



Ma, W., Han, W., Hou, L., Tao, S., Tao, X., Chang, X., 2019. Geochemical characteristics, genetic types and sources of natural gas in the Yingjisu Depression, Tarim Basin, China. International Journal of Coal Geology 215, 103300.


Nekhaev, A.I., Maksimov, A.L., 2019. Diamondoids in oil and gas condensates (review). Petroleum Chemistry 59, 1108-1117.



Wu, X., Ni, C., Chen, Y., Zhu, J., Li, K., Zeng, H., 2019. Source of the Upper Paleozoic natural gas in the Dingbei area, Ordos Basin, China. Journal of Natural Gas Geoscience 4, 183-190.

Xiao, H., Li, M., Wang, W., You, B., Liu, X., Yang, Z., Liu, J., Chen, Q., Uwiringiyimana, M., 2019. Identification, distribution and geochemical significance of four rearranged hopane series in crude oil. Organic Geochemistry 138, 103929.


Yu, Q., Xu, G., Liang, H., Xu, F., Liang, J., Wang, D., 2019. A research into the crude oil geochemistry and oil-source correlation by means of gas chromatography and gas chromatography–mass spectrometry: a case study of the Laizhou Bay Sag, Bohai Bay Basin, China. Arabian Journal of Geosciences 12, 634.


SOURCE ROCKS



Abd El Gawad, E.A., Ghanem, M.F., Makled, W.A., Mousa, D.A., Lotfy, M.M., Temraz, M.G., Shehata, A.M., 2019. Source rock evaluation of subsurface Devonian–

Carboniferous succession based on palyno-organic facies analysis in Faghur Basin, North Western Desert of Egypt: a division of the North Africa Paleozoic Basins. Arabian Journal of Geosciences 12, 655.

Ali, M., Darwish, M., Essa, M.A., Abdelhady, A., 2019. Comparison of the Dakhla Formation source rock potential between Komombo Basin and Gebel Duwi, Upper Egypt. Arabian Journal of Geosciences 12, 613.

Alizadeh, B., Seyedali, S.R., Habibnia, B., 2019. Organic geochemical characteristics of Middle to Late Eocene Shahbazan Formation in Dezful Embayment, SW Iran: A case study from Qaleh-Nar oilfield. Petroleum Science and Technology 37, 2322-2329.

Awan, R.S., Liu, C., Gong, H., Dun, C., Tong, C., Chamssidini, L.G., 2020. Paleo-sedimentary environment in relation to enrichment of organic matter of Early Cambrian black rocks of Niutitang Formation from Xiangxi area China. Marine and Petroleum Geology 112, 104057.

Bushnev, D.A., Burdel’naya, N.S., Mokeev, M.V., 2019. Results of 13C NMR and FTIR spectroscopy of kerogen from the Upper Devonian Domanik of the Timan–Pechora Basin. Geochemistry International 57, 1173-1184.

Cui, J., Zhu, R., Li, S., Qi, Y., Shi, X., Mao, Z., 2019. Development patterns of source rocks in the depression lake basin and its influence on oil accumulation: Case study of the Chang 7 member of the Triassic Yanchang Formation, Ordos Basin, China. Journal of Natural Gas Geoscience 4, 191-204.


Jarzyna, J.A., Krakowska, P.I., Puskarczyk, E., Wawrzyniak-Guz, K., Zych, M., 2019. Total organic carbon from well logging - statistical approach, Polish shale gas formation case study. International Journal of Oil, Gas and Coal Technology 22, 140-162.


Kayukova, G.P., Mikhailova, A.N., Morozov, V.P., Musin, R.Z., Vandyukova, I.I., Sotnikov, O.S., Remeev, M.M., 2019. Comparative study of changes in the composition of organic matter of rocks from different sampling-depth intervals of domanik and domankoid deposits of the Romashkino oilfield. Petroleum Chemistry 59, 1124-1137.

Liu, X., Li, S., Zhang, J., Li, X., Zhao, S., Dai, L., Wang, G., 2019. Meso-Neoproterozoic strata and target source rocks in the North China Craton: A review. Precambrian Research 334, 105458.

Pearson, C.A., Philp, R.P., 2019. Geochemical characterization of the Upper Mississippian Goddard Formation, Noble Ranch Group, and related oils in the Anadarko Basin of Oklahoma. American Association of Petroleum Geologists Bulletin 103, 2545-2571.

Wang, J., Gao, Z., Kang, Z., Zhu, D., Liu, Q., Ding, Q., Liu, Z., 2020. Geochemical characteristics, hydrocarbon potential and depositional environment of the Yangye Formation source rocks in Kashi sag, southwestern Tarim Basin, NW China. Marine and Petroleum Geology 112, 104084.


Wang, T., David, J., 2019. Deep resistivity “turnover” effect at oil generation “peak” in the Woodford Shale, Anadarko Basin, USA. Petroleum Science 16, 972-980.

Zhang, J., Zhou, L., Zhou, J., Xiao, D., Han, G., Zhao, M., Fu, L., Li, H., Lou, D., Wang, H., 2019. Control of the Mesozoic tectonic movement on the hydrocarbon generation and evolution of Upper Paleozoic coal-measure source rocks in the Huanghua Depression, Bohai Bay Basin. Natural Gas Industry 39, 1-10.

Zhang, K., Liu, R., Liu, Z., Li, B., Han, J., Zhao, K., 2020. Influence of volcanic and hydrothermal activity on organic matter enrichment in the Upper Triassic Yanchang Formation, southern Ordos Basin, Central China. Marine and Petroleum Geology 112, 104059.

Zhao, X., Zhou, L., Pu, X., Jin, F., Shi, Z., Xiao, D., Han, W., Jiang, W., Zhang, W., Wang, H., 2019. Favorable formation conditions and enrichment characteristics of lacustrine facies shale oil in faulted lake basin: a case study of Member 2 of Kongdian Formation in Cangdong sag, Bohai Bay Basin Acta Petrolei Sinica 40, 1013-1029.

Zou, C., Pan, S., Horsfield, B., Yang, Z., Hao, S., Liu, E., Zhang, L., 2019. Oil retention and intrasource migration in the organic-rich lacustrine Chang 7 shale of the Upper Triassic Yanchang Formation, Ordos Basin, central China. American Association of Petroleum Geologists Bulletin 103, 2627-2663.

UNCONVENTIONALS



Dong, Y., Ju, B., Zhang, S., Tian, Y., Ma, S., Liu, N., Lu, G., 2020. Microscopic mechanism of methane adsorption in shale: Experimental data analysis and interaction potential simulation. Journal of Petroleum Science and Engineering 184, 106544.

Edilbi, A.N.F., Mohammed, K.F., Sadeq, Z.H., Aldalawy, A.A., Zebari, B.G.A., Pirouei, M., Suramairy, R., Ali, J.A., 2019. Source rock potential and reservoir characterization of the Lower Cretaceous Sarmord Formation in selected sections in Kurdistan Region-Iraq. Arabian Journal of Geosciences 12, 647.



Fang, C., Yang, Y., Sun, S., Qiao, R., 2020. Low salinity effect on the recovery of oil trapped by nanopores: A molecular dynamics study. Fuel 261, 116443.

Fang, Y., Yang, E., Cui, X., 2019. Study on distribution characteristics and displacement mechanism of microscopic residual oil in heterogeneous low permeability reservoirs. Geofluids 2019, 9752623.



Hwang, J., Pini, R., 2019. Supercritical CO2 and CH4 uptake by illite-smectite clay minerals. Environmental Science & Technology 53, 11588-11596.

Jiang, Y., Fu, Y., Xie, J., Dong, D., Zhou, K., Cheng, X., Qi, L., Zhang, H., Chen, C., Ma, T., Gu, Y., 2019. Development trend of marine shale gas reservoir evaluation and a suitable comprehensive evaluation system Natural Gas Industry 39, 1-9.

Jiao, F., 2019. Re-recognition of “unconventional” in unconventional oil and gas. Petroleum Exploration and Development 46, 847-855.


Kang, Y., Rao, Q., Zhao, Q., Wang, H., 2019. Exploration and development potential of the low-maturity continental shale gas in the Fuxin Basin. Natural Gas Industry B 6, 435-443.


Li, S., Sang, Q., Dong, M., Luo, P., 2019. Determination of inorganic and organic permeabilities of shale. International Journal of Coal Geology 215, 103296.


Planková, B., Lísal, M., 2020. Molecular dynamics of aqueous salt solutions in clay nanopores under the thermodynamic conditions of hydraulic fracturing: Interplay between solution structure and molecular diffusion. Fluid Phase Equilibria 505, 112355.

Qu, Z.G., Yin, Y., Wang, H., Zhang, J.F., 2020. Pore-scale investigation on coupled diffusion mechanisms of free and adsorbed gases in nanoporous organic matter. Fuel 260, 116423.

Sharma, S., Agrawal, V., Akondi, R.N., 2020. Role of biogeochemistry in efficient shale oil and gas production. Fuel 259, 116207.

Shu, Y., Lu, Y., Chen, L., Wang, C., Zhang, B., 2020. Factors influencing shale gas accumulation in the lower Silurian Longmaxi formation between the north and South Jiaoshiba area, Southeast Sichuan Basin, China. Marine and Petroleum Geology 111, 905-917.

Song, X., Zhang, C., Shi, Y., Li, G., 2019. Production performance of oil shale in-situ conversion with multilateral wells. Energy 189, 116145.



Yuan, Y., Rezaee, R., Al-Khdheeawi, E.A., Hu, S.-Y., Verrall, M., Zou, J., Liu, K., 2019. Impact of composition on pore structure properties in shale: Implications for micro-/mesopore volume and surface area prediction. Energy & Fuels 33, 9619-9628.

Zhou, F., Su, H., Liang, X., Meng, L., Yuan, L., Li, X., Liang, T., 2019. Integrated hydraulic fracturing techniques to enhance oil recovery from tight rocks. Petroleum Exploration and Development 46, 1065-1072.

Precambrian Geochemistry

Colwyn, D.A., Sheldon, N.D., Maynard, J.B., Gaines, R., Hofmann, A., Wang, X., Gueguen, B., Asael, D., Reinhard, C.T., Planavsky, N.J., 2019. A paleosol record of the evolution of Cr redox cycling and evidence for an increase in atmospheric oxygen during the Neoproterozoic. Geobiology 17, 579-593.



Nutman, A.P., Bennett, V.C., Friend, C.R.L., Kranendonk, M.V., 2019. The Eoarchean legacy of Isua (Greenland) worth preserving for future generations. Earth-Science Reviews 198, 102923.



Ward, J.F., Verdel, C., Campbell, M.J., Leonard, N., Duc Nguyen, A., 2019. Rare earth element geochemistry of Australian Neoproterozoic carbonate: Constraints on the Neoproterozoic oxygenation events. Precambrian Research 335, 105471.

ORGANICS/MICROFOSSILS/MICROBIAL EVOLUTION

Adachi, N., Ezaki, Y., Liu, J., Watabe, M., Sonoda, H., Altanshagai, G., Enkhbaatar, B., Dorjnamjaa, D., 2019. Late Ediacaran Boxonia-bearing stromatolites from the Gobi-Altay, western Mongolia. Precambrian Research 334, 105470.

Agić, H., Högström, A.E.S., Moczydłowska, M., Jensen, S., Palacios, T., Meinhold, G., Ebbestad, J.O.R., Taylor, W.L., Høyberget, M., 2019. Organically-preserved multicellular eukaryote from the early Ediacaran Nyborg Formation, Arctic Norway. Scientific Reports 9, 14659.

Baumgartner, R.J., Van Kranendonk, M.J., Wacey, D., Fiorentini, M.L., Saunders, M., Caruso, S., Pages, A., Homann, M., Guagliardo, P., 2019. Nano−porous pyrite and organic matter in 3.5-billion-year-old stromatolites record primordial life. Geology 47, 1039-1043.



Fakhraee, M., Katsev, S., 2019. Organic sulfur was integral to the Archean sulfur cycle. Nature Communications 10, 4556.

Gigler, G.M., Sośnicka, M., Erasmus, R., Schapira, J., Kinnaird, J.A., 2020. Microfossils or pseudofossils? Cu-Co sulphide microfeatures in the Neoproterozoic Katangan Supergroup, Democratic Republic of Congo. Precambrian Research 336, 105481.



Osterhout, J.T., Czaja, A.D., Bartley, J.K., Fralick, P.W., 2019. Preservation of carbon isotopes in kerogen from thermally altered Mesoproterozoic lacustrine microbialites. Canadian Journal of Earth Sciences 56, 1017-1026.

PALEOCLIMATOLOGY/PALEOCEANOGRAPHY


Lajoinie, M.F., Sial, A., Ballivián Justiniano, C.A., Cingolani, C.A., Recio, C., Etcheverry, R.O., Basei, M., Lanfranchini, M.E., 2019. First geochronological constraint for the Palaeoproterozoic Lomagundi-Jatuli δ13C anomaly in the Tandilia Belt basement (Argentina), Río de la Plata Craton. Precambrian Research 334, 105477.

Xu, L., Frank, A.B., Lehmann, B., Zhu, J., Mao, J., Ju, Y., Frei, R., 2019. Subtle Cr isotope signals track the variably anoxic Cryogenian interglacial period with voluminous manganese accumulation and decrease in biodiversity. Scientific Reports 9, 15056.


CRUSTAL EVOLUTION

Production/Engineering Geochemistry

Agarwal, P., Sahasrabudhe, M., Khandalkar, S., Saravanan, C., Klein, M.T., 2019. Molecular-level kinetic modeling of a real vacuum gas oil hydroprocessing refinery system. Energy & Fuels 33, 10143-10158.



Ma, Z.-H., Wei, X.-Y., Liu, G.-H., Liu, Z.-Q., Liu, F.-J., Zong, Z.-M., 2019. Insight into the compositions of the soluble/insolube portions from the acid/base extraction of five fractions distilled from a high temperature coal tar. Energy & Fuels 33, 10099-10107.

Malkin, A.Y., 2019. Oil as an object of rheology (review). Petroleum Chemistry 59, 1092-1107.

Malta, J.Á.M.S.C., Calabrese, C., Nguyen, T.-B., Trusler, J.P.M., Vesovic, V., 2020. Measurements and modelling of the viscosity of six synthetic crude oil mixtures. Fluid Phase Equilibria 505, 112343.


Morozova, A.V., Volkova, G.I., 2019. Effect of the petroleum resin structure on the properties of a petroleum-like system. Petroleum Chemistry 59, 1153-1160.

Xie, J., Jia, T., Gong, S., Liu, N., Nie, G., Pan, L., Zhang, X., Zou, J.-J., 2020. Synthesis and thermal stability of dimethyl adamantanes as high-density and high-thermal-stability fuels. Fuel 260, 116424.

Yashchenko, I.G., Polishchuk, Y.M., 2019. Classification approach to assay of crude oils with different physicochemical properties and quality parameters. Petroleum Chemistry 59, 1161-1168.


ASPHALTENES


Ghadimi, M., Ghaedi, M., Malayeri, M.R., Amani, M.J., 2020. A new approach to model asphaltene induced permeability damage with emphasis on pore blocking mechanism. Journal of Petroleum Science and Engineering 184, 106512.


Rogel, E., Moir, M.E., Hurt, M., Miao, T., Lee, E., 2019. Asphaltene and maltene adsorption into graphene. Energy & Fuels 33, 9538-9545.



Xue, H., Zhang, J., Han, S., Sun, M., Yan, X., Li, H., 2019. Effect of asphaltenes on the structure and surface properties of wax crystals in waxy oils. Energy & Fuels 33, 9570-9584.

Yuan, J., Elektorowicz, M., Chen, Z., Segun, G.A., Vakili, M., Zhong, L., Wang, B., Zhu, J., Wu, Y., 2019. Simulation and computer modeling of asphaltene in different solvents on oil-water interfaces using a molecular dynamic methodology. Journal of Molecular Graphics and Modelling 93, 107450.

INTERFACES/EOR

Al-Saedi, H.N., Long, Y., Flori, R.E., Bai, B., 2019. Coupling smart seawater flooding and CO2 flooding for sandstone reservoirs: Smart seawater alternating CO2 flooding (SMSW-AGF). Energy & Fuels 33, 9644-9653.

Alafnan, S., Aljawad, M., Alismail, F., Almajed, A., 2019. Enhanced recovery from gas condensate reservoirs through renewable energy sources. Energy & Fuels 33, 10115-10122.



Mohammadi, M., Mahani, H., 2020. Direct insights into the pore-scale mechanism of low-salinity waterflooding in carbonates using a novel calcite microfluidic chip. Fuel 260, 116374.

Saha, R., Sharma, A., Uppaluri, R.V.S., Tiwari, P., 2019. Interfacial interaction and emulsification of crude oil to enhance oil recovery. International Journal of Oil, Gas and Coal Technology 22, 1-15.

Sakthivel, S., Adebayo, A., Kanj, M.Y., 2019. Experimental evaluation of carbon dots stabilized foam for enhanced oil recovery. Energy & Fuels 33, 9629-9643.

Shang, X., Bai, Y., Sun, J., Dong, C., 2019. Performance and displacement mechanism of a surfactant/compound alkaline flooding system for enhanced oil recovery. Colloids and Surfaces A: Physicochemical and Engineering Aspects 580, 123679.



Wang, Z., Lin, M., Xiang, Y., Zeng, T., Dong, Z., Zhang, J., Yang, Z., 2019. Zr-induced thermostable polymeric nanospheres with double-cross-linked architectures for oil recovery. Energy & Fuels 33, 10356-10364.



Zhou, X., Kamal, M.S., 2019. Experimental study on the relationship between carbonate reservoir quality index and dynamic parameters of chemical solutions for oil recovery practice. Energy & Fuels 33, 9747-9758.

HEAVY OIL PRODUCTION

Abdelfatah, E., Berton, P., Rogers, R.D., Bryant, S.L., 2019. Low-temperature bitumen recovery from oil-sand reservoirs using ionic liquids. SPE-195677-PA 24, 2409-2422.


Recent Sediments

Amaro, T., Danovaro, R., Matsui, Y., Rastelli, E., Wolff, G.A., Nomaki, H., 2019. Possible links between holothurian lipid compositions and differences in organic matter (OM) supply at the western Pacific abyssal plains. Deep Sea Research Part I: Oceanographic Research Papers 152, 103085.

Bale, N.J., Hennekam, R., Hopmans, E.C., Dorhout, D., Reichart, G.-J., van der Meer, M., Villareal, T.A., Sinninghe Damsté, J.S., Schouten, S., 2019. Biomarker evidence for nitrogen-fixing cyanobacterial blooms in a brackish surface layer in the Nile River plume during sapropel deposition. Geology 47, 1088-1092.

Bao, R., Zhao, M., McNichol, A., Wu, Y., Guo, X., Haghipour, N., Eglinton, T.I., 2019. On the origin of aged sedimentary organic matter along a river-shelf-deep ocean transect. Journal of Geophysical Research: Biogeosciences 124, 2582-2594.




Jahnke, L.L., Des Marais, D.J., 2019. Carbon isotopic composition of lipid biomarkers from an endoevaporitic gypsum crust microbial mat reveals cycling of mineralized organic carbon. Geobiology 17, 643-659.

Louca, S., Astor, Y.M., Doebeli, M., Taylor, G.T., Scranton, M.I., 2019. Microbial metabolite fluxes in a model marine anoxic ecosystem. Geobiology 17, 628-642.

Rahayu, Y.P., Solihuddin, T., Kusumaningtyas, M.A., Afi Ati, R.N., Salim, H.L., Rixen, T., Hutahaean, A.A., 2019. The sources of organic matter in seagrass sediments and their contribution to carbon stocks in the Spermonde Islands, Indonesia. Aquatic Geochemistry 25, 161-178.

Versteegh, G.J.M.V., 2, A J. P. Houben3,4, and KA. F. Zonneveld2 , Houben, A.J.P., Zonneveld, K.A.F., 2019. Better molecular preservation of organic matter in an oxic than in a sulphidic depositional environment: evidence from of Thalassiphora pelagica (Dinoflagellata, Eocene) cysts. Biogeosciences Discussions 2019, 1-24.


Wu, W., Xu, Y., Hou, S., Dong, L., Liu, H., Wang, H., Liu, W., Zhang, C., 2019. Origin and preservation of archaeal intact polar tetraether lipids in deeply buried sediments from the South China Sea. Deep Sea Research Part I: Oceanographic Research Papers 152, 103107.

Xiao, W., Wang, Y., Liu, Y., Zhang, X., Shi, L., Xu, Y., 2019. Predominance of hexamethylated 6-methyl branched glycerol dialkyl glycerol tetraethers in the Mariana Trench: Source and environmental implication. Biogeosciences Discussions 2019, 1-36.


Zhou, J., Wu, J., Ma, L., Abuduwaili, J., 2019. Late Quaternary environmental change record in biomarker lipid compositions of Lake Ebinur sediments, Northwestern China. International Journal of Earth Sciences 108, 2361-2371.

Zirks, E., Krom, M.D., Zhu, D., Schmiedl, G., Goodman-Tchernov, B.N., 2019. Evidence for the presence of oxygen-depleted sapropel intermediate water across the Eastern Mediterranean during sapropel S1. ACS Earth and Space Chemistry 3, 2287-2297.

ATMOSPHERIC GEOCHEMISTRY

Bianco, A., Riva, M., Baray, J.-L., Ribeiro, M., Chaumerliac, N., George, C., Bridoux, M., Deguillaume, L., 2019. Chemical characterization of cloudwater collected at Puy de

Dôme by FT-ICR MS reveals the presence of SOA components. ACS Earth and Space Chemistry 3, 2076-2087.

Bryan, N.C., Christner, B.C., Guzik, T.G., Granger, D.J., Stewart, M.F., 2019. Abundance and survival of microbial aerosols in the troposphere and stratosphere. The ISME Journal 13, 2789-2799.

Leglise, J., Müller, M., Piel, F., Otto, T., Wisthaler, A., 2019. Bulk organic aerosol analysis by proton-transfer-reaction mass spectrometry: An improved methodology for the determination of total organic mass, O:C and H:C elemental ratios, and the average molecular formula. Analytical Chemistry 91, 12619-12624.


Mohr, C., Thornton, J.A., Heitto, A., Lopez-Hilfiker, F.D., Lutz, A., Riipinen, I., Hong, J., Donahue, N.M., Hallquist, M., Petäjä, T., Kulmala, M., Yli-Juuti, T., 2019. Molecular identification of organic vapors driving atmospheric nanoparticle growth. Nature Communications 10, 4442.

Schneider, S.R., Collins, D.B., Lim, C.Y., Zhu, L., Abbatt, J.P.D., 2019. Formation of secondary organic aerosol from the heterogeneous oxidation by ozone of a phytoplankton culture. ACS Earth and Space Chemistry 3, 2298-2306.


Zhou, B., Zhao, Y., Dai, Q., 2019. Application of comprehensive multiphase NMR to characterize organic matter in clay and atmospheric particulates. ACS Earth and Space Chemistry 2, 2276-2286.

HYDROSPHERE GEOCHEMISTRY


Bif, M.B., Siqueira, L., Hansell, D.A., 2019. Warm events induce loss of resilience in organic carbon production in the northeast Pacific Ocean. Global Biogeochemical Cycles 33, 1174-1186.

King, A.C.F., Thomas, E.R., Pedro, J.B., Markle, B., Potocki, M., Jackson, S.L., Wolff, E., Kalberer, M., 2019. Organic compounds in a Sub-Antarctic ice core: A potential suite of sea ice markers. Geophysical Research Letters 46, 9930-9939.

Lee, B.J., Kim, J., Hur, J., Choi, I.H., Toorman, E.A., Fettweis, M., Choi, J.W., 2019. Seasonal dynamics of organic matter composition and its effects on suspended sediment flocculation in river water. Water Resources Research 55, 6968-6985.


Omanović, D., Santinelli, C., Marcinek, S., Gonnelli, M., 2019. ASFit - An all-inclusive tool for analysis of UV–Vis spectra of colored dissolved organic matter (CDOM). Computers & Geosciences 133, 104334.

Romera-Castillo, C., Álvarez, M., Pelegrí, J.L., Hansell, D.A., Álvarez-Salgado, X.A., 2019. Net additions of recalcitrant dissolved organic carbon in the deep Atlantic Ocean. Global Biogeochemical Cycles 33, 1162-1173.

Rosset, T., Binet, S., Antoine, J.-M., Lerigoleur, E., Rigal, F., Gandois, L., 2019. Drivers of seasonal and event scale DOC dynamics at the outlet of mountainous peatlands revealed by high frequency monitoring. Biogeosciences Discussions 2019, 1-33.

Savenko, A.V., Pokrovsky, O.S., 2019. Distribution of dissolved matter in the Yenisei estuary and adjacent Kara Sea areas and its inter-annual variability. Geochemistry International 57, 1201-1212.


SOIL GEOCHEMISTRY

Dearing Crampton-Flood, E., Tierney, J.E., Peterse, F., Kirkels, F.M.S.A., Sinninghe Damsté, J.S., 2020. BayMBT: A Bayesian calibration model for branched glycerol dialkyl glycerol tetraethers in soils and peats. Geochimica et Cosmochimica Acta 268, 142-159.


Matiasek, S.J., Hernes, P.J., 2019. The chemical fingerprint of solubilized organic matter from eroded soils and sediments. Geochimica et Cosmochimica Acta 267, 92-112.

Sangok, F.E., Sugiura, Y., Maie, N., Melling, L., Nakamura, T., Ikeya, K., Watanabe, A., 2020. Variations in the rate of accumulation and chemical structure of soil organic matter in a coastal peatland in Sarawak, Malaysia. CATENA 184, 104244.

Sengupta, A., Indivero, J., Gunn, C., Tfaily, M.M., Chu, R.K., Toyoda, J., Bailey, V.L., Ward, N.D., Stegen, J.C., 2019. Spatial gradients in the characteristics of soil-carbon fractions are associated with abiotic features but not microbial communities. Biogeosciences 16, 3911-3928.




Remote Sensing-Hydrocarbon Seepage

Corrick, A.J., Hall, P.A., Gong, S., McKirdy, D.M., Selby, D., Trefry, C., Ross, A.S., 2020. A second type of highly asphaltic crude oil seepage stranded on the South Australian coastline. Marine and Petroleum Geology 112, 104062.


Leifer, I., 2019. A synthesis review of emissions and fates for the Coal Oil Point marine hydrocarbon seep field and California marine seepage. Geofluids 2019, 4724587.

Nelson, C.S., Campbell, K.A., Nyman, S.L., Greinert, J., Francis, D.A., Hood, S.D., 2019. Genetic link between Miocene seafloor methane seep limestones and underlying carbonate conduit concretions at Rocky Knob, Gisborne, New Zealand. New Zealand Journal of Geology and Geophysics 62, 318-340.

Pletnev, S.P., Romanova, A.V., Wu, Y., Annin, V.K., Utkin, I.V., Vereshchagina, O.F., 2019. Holocene methane emissions in the southwestern Sea of Okhotsk: Evidence from carbon isotopes in benthic foraminifera shells. Doklady Earth Sciences 488, 1081-1083.


Xu, A., Chen, Z., Qu, Y., Tian, Y., Shu, C., Zheng, X., Li, G., Yan, W., Zhao, M., 2019. Cold-water corals in a cold seep area on the northern continental slopes of the South China sea and their isotopic characteristics. Deep Sea Research Part I: Oceanographic Research Papers 152, 103043.

LAWSON, M., FORMOLO, M.J., EILER, J.M. (EDS.), 2018. FROM SOURCE TO SEEP: GEOCHEMICAL APPLICATIONS IN HYDROCARBON SYSTEMS. GEOLOGICAL SOCIETY, LONDON, SPECIAL PUBLICATIONS 468.








Abstracts


http://www.sciencedirect.com/science/article/pii/S0016236119318083

This study aims to differentiate between bacteria-algae interactions and thermal maturation, at the same time, shed light on the hydrocarbon generation pathways based on chemical changes at the submicron scale. For this goal, samples were taken from the lower shale member of the Bakken Formation in Willison Basin at the early and peak thermal maturity stages and analyzed with surface probes. Sample selection was based on bulk geochemical screening, organic petrology and fluorescence emission of the liptinite group macerals and solid bitumen reflectance. Submicron scale chemical heterogeneity resulting from biodegradation and different thermal maturity pathways was documented and compared using AFM-based Nano-IR spectroscopy. A significant chemical heterogeneity was noticed within unaltered telalginite and bacterially degraded Tasmanites, and also between solid bitumen particles that were adjacent to the telalginite at the same stage of maturity. Results suggest that separate pathways of maturation took place in the neighboring solid bitumen particles based on their infrared spectroscopic data. It was also found that thermal maturity progression reduced chemical heterogeneity in the organic matter particles. During bacterial degradation, Tasmanites lost its fluorescence emission while its relative chemical heterogeneity increased compared to the unaltered telalginite, a feature that has been reported at such a very fine scale of measurement. This study will ultimately improve our understanding of the processes that may result in hydrocarbon generation from organic matter.



Paleozoic Zeitoun, Desouqy and Dhiffah formations represent source rocks to hydrocarbon in Faghur basin, north Western Desert, Egypt. They are characterized by a sufficient amount of organic matter belonging to kerogen type III and mixed type II/III, which are in maturation stage. A 1D-basin modeling was performed by using geological and geochemical data of the Paleozoic source rocks from five wells in Faghur basin, north Western Desert, Egypt. These data used in 1D basin modeling for constructing and understanding of burial and thermal geo-histories of Faghur basin and for simulating and predicting the timing of petroleum and expulsion for the Paleozoic source rocks in the studied wells. Burial and thermal history models indicate that the Zeitoun Formation entered onset of oil generation in the studied wells during Late Cretaceous (100.10–91.65 my) with transformation ratio (TR) 10–25, peak oil during Late Cretaceous (91.65–79.30 my) with TR 25–50 and late oil stage at Late Cretaceous (79.30 my-0) to present day with TR 50–60.45. Desouqy Formation entered onset of oil generation also during Late Cretaceous (94.43–73.60 my) with TR 10–25 in the studied wells, peak oil during Late cretaceous (73.60–62.40 my) with TR 25–50 and Late oil stage during Late Cretaceous to present day (62.40 my-0) with TR 50–61.82. Dhiffah Formation entered onset of oil generation in the studied wells during Early to Late Cretaceous (102.11–92.27 my) with TR 10–25, peak oil during Late Cretaceous (92.27–86.40 my) with TR 25–50 and late oil stage at Late Cretaceous to present day (86.40 my-0) with TR 50–67.27. No cracking oil to gas in the studied Paleozoic source rocks in the studied wells. These basin modeling results also suggest that the

Paleozoic source rocks act as an effective source rock where a significant amount of petroleum is expected to be generated and expelled to any nearby prospect reservoir rocks in the Faghur basin.

Abd El Gawad, E.A., Ghanem, M.F., Makled, W.A., Mousa, D.A., Lotfy, M.M., Temraz, M.G., Shehata, A.M., 2019. Source rock evaluation of subsurface Devonian–Carboniferous succession based on palyno-organic facies analysis in Faghur Basin, North Western Desert of Egypt: a division of the North Africa Paleozoic Basins. Arabian Journal of Geosciences 12, 655.

https://doi.org/10.1007/s12517-019-4802-5

The Paleozoic rocks in North Africa are prolific with source rocks that contribute petroleum to giant fields especially in Algeria and Libya. The coeval subsurface source rocks from the Devonian and Carboniferous in the Western Desert of Egypt have been evaluated in the present study. The rocks from Zeitoun, Desouqy, and Dhiffah formations have been evaluated based on integration of the palynofacies, organic geochemical analysis, and well logging. The study depends on samples from five wells that are Buchis-1X, Phiops-1X, Siwa-D-1X, Tayim West-1X, and WKAL C-1XST. The distribution of palynofacies categories are statistically investigated by the principal component analysis (PCA) that specified the proximal-distal environmental trends by the values of component 1 that attributed to the terrestrial organic sources. The analyses revealed mostly poor, fair to good organic enrichments and poor to fair source potential in the studied rocks. The samples are mostly thermally mature, uncontaminated, and of gas prone type III and mixed oil/gas prone type II/III kerogen. The geological conditions that lead to the large difference in the hydrocarbon source potentiality between western North Africa and source rocks evaluated in this study from Egypt have been discussed. It is suggested that these differences resulted from the larger thickness of Paleozoic rocks and the increase in burial depths of the depocenters in the western side that lead to higher maturity levels that are responsible for the organic conversions and hydrocarbon expulsion.

Abdelfatah, E., Berton, P., Rogers, R.D., Bryant, S.L., 2019. Low-temperature bitumen recovery from oil-sand reservoirs using ionic liquids. SPE Journal 24, 2409-2422.

https://doi.org/10.2118/197070-PA

Steam injection is widely used for bitumen recovery. However, steam is not efficient for shallow or thin reservoirs because of heat loss in the wellbore or to surrounding formations. Numerous alternatives have been proposed, including the addition of solvents and replacement of steam with volatile solvents. Here, we describe a new technology that combines nonvolatile ionic liquids (ILs) and waterflooding for bitumen recovery that can deliver high recovery at ambient temperature.

Different ILs were designed for complete dispersal/dissolution of bitumen at ambient temperature. The designed ILs were tested in coreflood experiments with high-grade oil-sand ore from Alberta. Two different scenarios were tested: continuous injection of ILs at different injection rates and injection of a slug of ILs followed by water injection. Different slug volumes were tested at a constant injection rate. After ILs injection, the oil sand was removed from the column, and the remaining bitumen was quantified using a modified Dean-Stark method. Viscosity and solid-content measurements of the recovered samples at breakthrough were conducted.

Bitumen recovery by the designed ILs can be thought of as a solution mining process. Tuning the physical and chemical properties of the ILs is the most important aspect of achieving the desired interaction with the oil-sand system. Properties of the designed IL depend on the selected cation and anion, and the strength of their intermolecular interaction. Primary amines mixed with the oleic acid

chosen for IL1 form a viscous IL that can recover bitumen, leaving a slight amount of bitumen behind, but a large pressure gradient. Changing the cation to tertiary amines produces significantly less-viscous ILs, which completely recover the bitumen in the oil-sand column. Moreover, the cation can be tailored to significantly minimize the fines (clay) migration and viscosity of the recovered bitumen and to provide compatibility with an aqueous phase. In all cases, these recoveries are significant, compared with the currently used technologies.

This work proves that bitumen recovery from oil sand is possible at low temperatures by means of a process analogous to solution mining with the design of the proper ILs, in contrast to viscosity-reduction processes achieved by thermal methods. The properties of these ILs can be tuned for different recovery mechanisms. Thus, this work establishes the basis for developing a new class of in-situ recovery processes with high recovery efficiencies and low environmental impact.

Abshire, M.L., Romaniello, S.J., Kuzminov, A.M., Cofrancesco, J., Severmann, S., Riedinger, N., 2020. Uranium isotopes as a proxy for primary depositional redox conditions in organic-rich marine systems. Earth and Planetary Science Letters 529, 115878.

http://www.sciencedirect.com/science/article/pii/S0012821X19305709

In marine sediments, authigenic uranium (U) enrichments and U isotope compositions are important tools for interpreting changes in redox conditions, however, their use as paleoproxies requires a comprehensive understanding of the dominant processes that contribute to sediments becoming enriched or depleted. This study focuses on the U content and 238U/235U ratio of organic-rich surface sediments from the Namibian continental margin, where high productivity results in an expanded oxygen minimum zone (OMZ). The investigated core sample sites are located on the shelf, shelf break, and slope where bottom water redox conditions vary from anoxic to suboxic to oxic, respectively. While all cores have relatively high total organic carbon (TOC) contents (up to 12 wt.%), each location displays a unique U to TOC relationship. Shelf sediment exhibit a fair correlation between U and TOC, while the shelf break and slope sediments show a pronounced decoupling of U and TOC. On the Namibia continental margin, particle-rich nepheloid layers transport organic-rich deposits from within the OMZ, through oxic water, to be redeposited on the slope. Due to the sensitivity of U to changes in redox conditions, this lateral movement results in the release of the reduced U phases back into the water column through oxidation while transporting the partially remineralized organic carbon to the slope. Oxidation of U during transport does not alter the average primary 238U/235U isotopic signature in redeposited sediment, and the combination of high TOC, low U content and high δ238U values may become a useful tool for the identification of the boundaries of ancient OMZs.

Adachi, N., Ezaki, Y., Liu, J., Watabe, M., Sonoda, H., Altanshagai, G., Enkhbaatar, B., Dorjnamjaa, D., 2019. Late Ediacaran Boxonia-bearing stromatolites from the Gobi-Altay, western Mongolia. Precambrian Research 334, 105470.


A couplet comprising a Boxonia-bearing stromatolite unit and phosphatic layers occurs widely at the base of the Zuun-Arts Formation in the Zavkhan Terrane of Gobi-Altay Province, western Mongolia. The stromatolite unit is late Ediacaran in age and forms bioherms of several kilometres in lateral extent. The stromatolites consist of two parts: the lower columnar Boxonia stromatolites (ca. 7 m thick) change abruptly into the upper domed stromatolites (ca. 4.5 m thick) in the Bayan Gol Gorge. The columnar stromatolites are made up of columnar structures (2–6 cm in diameter), formed by the

accumulation of upward-convex laminae, and partly protrude laterally to form bridges between neighbouring columns. In contrast, the domed stromatolites (30–60 cm in width) are composed of accumulations of low convex laminae. Both types of stromatolite are characterized by alternating darker and lighter laminae, which consist of peloids, two types of micritic clot, homogeneous lime mud, and spar-filled fenestral fabrics. These stromatolites are inferred to have been deposited in a subtidal setting below the wave base, with no evidence of sediment displacement by strong currents. The stratigraphic transition from columnar to domed growth forms reflects deepening of the basin. The change in column diameter observed within the columnar stromatolites might reflect fluctuations in microbial activity. The appearance of inter-columnar bridges in the columnar stromatolites might indicate more active colonization of microbial mats, which expanded into the inter-columnar areas. Neither type of stromatolite includes microbial remains, such as filamentous or coccoidal cells. However, the various micritic components of the stromatolites (clots, peloids, and homogeneous lime mud) originated from in situ precipitation through microbial activity, and reflected differences in the timing and intensity of microbial calcification and degradation. These stromatolites, including the variety of micritic components, may provide clues to the variations in microbial metabolic activity and degradation processes that were associated with stromatolite formation.


https://doi.org/10.1021/acs.energyfuels.9b02250

Strategies to reduce the computer time to access the information in molecular-level kinetic models (MLKMs) were evaluated. A triglyceride hydroprocessing MLKM was used to generate data sets for small ranges of input parameters simulating three output parameters. The data sets were used to generate multilinear regression, polynomial regression, decision tree regression, gradient boosting regression, and artificial neural network data-driven model (DDM) representations of the MLKM. All of the DDMs were able to predict results very quickly (≪1 s). The predictive accuracy for the DDMs was compared to the polynomial regression, gradient boosting regression, and artificial neural network models, providing the best models over the entire range of the input parameters selected. However, in narrow input parameter ranges, multiple multilinear models and decision tree models also provide good accuracy, with the added benefit of easily understood parameters and faster solution times. Additionally, multilinear regression models had much lower data requirements than the decision tree regression and artificial neural network models. The major downside to all of the DDMs was shown to be the great loss in accuracy once the input parameters exceed the range of the input parameters in the data sets used to optimize the DDMs. This suggests that the extrapolation capability of the DDMs is very low, and as such, new data should be generated from the MLKM every time predictions are required outside the range of the underlying DDM data.

Agarwal, P., Sahasrabudhe, M., Khandalkar, S., Saravanan, C., Klein, M.T., 2019. Molecular-level kinetic modeling of a real vacuum gas oil hydroprocessing refinery system. Energy & Fuels 33, 10143-10158.


A molecular-level kinetic model was constructed for a vacuum gas oil hydroprocessing unit. The feedstock molecule selection was based on typical arrangements of structural attributes in crude oil. Based on the fundamental hydroprocessing chemistry, a reaction network was developed for the feedstock molecules including 5747 reactions distributed among 12 core types of reactions. The final molecular model contained 1532 unique species up to 45 carbons encompassing molecules up to five

aromatic rings with heteroatoms. To determine the initial condition of the feedstock, a statistical approach was applied by using probability density functions (PDFs) characterizing the molecules in terms of their structural attributes. Experimental feed measurements were used to determine the values of the PDF parameters. A library containing 21 sets of PDF parameters representing the range of the feed measurements was established and used to determine the starting point for optimization. Simulated feed properties showed excellent agreement with experimental values. For the kinetic model, the reactor system was divided into a series of 19 pseudo plug flow reactors (PFRs), one for each catalyst layer, interspersed with the appropriate quench streams. Each pseudo-PFR was modeled using a side-by-side reaction and vapor–liquid equilibrium approach. The activity of each type of catalyst and the deactivation due to coking and metal deposition were included in the simulation. Quantitative structure/reactivity correlations were used to greatly reduce the number of parameters in the model. The parameters were optimized using a simulated annealing algorithm so that the model results corresponded to the measured reactor effluent. The optimized model showed good agreement with the experimental measurements. To simplify the day-to-day running of the kinetic model while still allowing developers to change and study the model in more advanced applications, a user-friendly application was developed.

Agić, H., Högström, A.E.S., Moczydłowska, M., Jensen, S., Palacios, T., Meinhold, G., Ebbestad, J.O.R., Taylor, W.L., Høyberget, M., 2019. Organically-preserved multicellular eukaryote from the early Ediacaran Nyborg Formation, Arctic Norway. Scientific Reports 9, 14659.

https://doi.org/10.1038/s41598-019-50650-x

Eukaryotic multicellularity originated in the Mesoproterozoic Era and evolved multiple times since, yet early multicellular fossils are scarce until the terminal Neoproterozoic and often restricted to cases of exceptional preservation. Here we describe unusual organically-preserved fossils from mudrocks, that provide support for the presence of organisms with differentiated cells (potentially an epithelial layer) in the late Neoproterozoic. Cyathinema digermulense gen. et sp. nov. from the Nyborg Formation, Vestertana Group, Digermulen Peninsula in Arctic Norway, is a new carbonaceous organ-taxon which consists of stacked tubes with cup-shaped ends. It represents parts of a larger organism (multicellular eukaryote or a colony), likely with greater preservation potential than its other elements. Arrangement of open-ended tubes invites comparison with cells of an epithelial layer present in a variety of eukaryotic clades. This tissue may have benefitted the organism in: avoiding overgrowth, limiting fouling, reproduction, or water filtration. C. digermulense shares characteristics with extant and fossil groups including red algae and their fossils, demosponge larvae and putative sponge fossils, colonial protists, and nematophytes. Regardless of its precise affinity, C. digermulense was a complex and likely benthic marine eukaryote exhibiting cellular differentiation, and a rare occurrence of early multicellularity outside of Konservat-Lagerstätten.

Ahmed, M.A., Felisilda, B.M.B., Quirino, J.P., 2019. Recent advancements in open-tubular liquid chromatography and capillary electrochromatography during 2014–2018. Analytica Chimica Acta 1088, 20-34.


This review critically discusses the developments on open-tubular liquid chromatography (OT-LC) and open-tubular capillary electrochromatography (OT-CEC) during 2014–2018. An appropriate Scopus search revealed 5 reviews, 4 theoretical papers on open-tubular format chromatography, 29 OT-LC articles, 68 OT-CEC articles and 4 OT-LC/OT-CEC articles, indicating a sustained interest in these areas. The open-tubular format typically uses a capillary column with inner walls that are coated

with an ample layer or coating of solid stationary phase material. The ratio between the capillary internal diameter and coating thickness (CID/CT) is ideally ≤ 100 for appropriate chromatographic retention. We, therefore, approximated the CID/CT ratios and found that 22 OT-LC papers have CID/CT ratios ≤100. The other 7 OT-LC papers have CID/CT ratio >100 but have clearly demonstrated chromatographic retention. These 29 papers utilised reversed phase or ion exchange mechanisms using known or innovative solid stationary phase materials (e.g. metal organic frameworks), stationary pseudophases from ionic surfactants or porous supports. On the other hand, we found that 68 OT-CEC papers, 7 OT-LC papers and 4 OT-LC & OT-CEC papers have CID/CT ratios >100. Notably, 44 papers (42 OT-CEC and 2 OT-LC & OT-CEC) did not report the retention factor and/or effective electrophoretic mobility of analytes. Considering all covered papers, the most popular activity was on the development of new chromatographic materials as coatings. However, we encourage OT-CEC researchers to not only characterise changes in the electroosmotic flow but also verify the interaction of the analytes with the coating. In addition, the articles reported were largely driven by stationary phase or support development and not by practical applications.

Al-Saedi, H.N., Long, Y., Flori, R.E., Bai, B., 2019. Coupling smart seawater flooding and CO2 flooding for sandstone reservoirs: Smart seawater alternating CO2 flooding (SMSW-AGF). Energy & Fuels 33, 9644-9653.


Petroleum engineers continue to seek cost-effective improved oil recovery (IOR) methods to increase recovery efficiency, especially in heavy oil accumulations. Currently, smart water, low-salinity (LS) water, and CO2 are the most economically viable IOR methods according to the abundance of resources. The purpose of this work is to flood Bartlesville sandstone cores saturated with heavy oil successively with seawater, “smart” seawater, and finally CO2, with the aim of obtaining an optimum combination of these relatively low-cost methods. The core-flood experiments achieved promising results that could inform traditional enhanced oil recovery (EOR) methods for heavy oil. Several core-flooding scenarios were run, but the optimum scenario was 8 PV of seawater, 8 PV of smart seawater with depleted Ca2+, and 10 PV of miscible CO2. The seawater alone produced only ∼20% of original oil in place (OOIP); the smart seawater produced an additional 12.9% of OOIP; and the final miscible CO2 step produced 64.52% of OOIP, for a total of 96.77% of OOIP. There appears to be a synergistic effect of these methods. Other cases investigated also incorporated one LS water and three “smart” seawater cases. When LS water was injected instead of smart seawater, the total oil recovery was slightly lower than that of the smart seawater case. We found that the significant oil recovery was due to the LS water effect and not from the synergic effect of LS water and CO2. This conclusion is based on the solubility of CO2 in LS water being higher than that in smart seawater, which redirects CO2 to dissolve in heavy crude oil and results in increased oil recovery. Using the same compositions of brines that were used in the core-flood experiments, contact angle measurements and spontaneous imbibition tests on the same core materials were performed. The results of contact angle and spontaneous imbibition confirmed a wettability alteration of the rock surface toward more water wetness using our new EOR process. This combination technology can mitigate the CO2 flooding problems (gravity override, viscous channeling, and early breakthrough) and improve CO2 sweep efficiency by incorporating smart seawater, which itself has the ability to increase oil recovery by altering the wettability toward more water wetness and reducing the solubility of CO2 in the injected water, which redirects it to heavy crude oil.

Alafnan, S., Aljawad, M., Alismail, F., Almajed, A., 2019. Enhanced recovery from gas condensate reservoirs through renewable energy sources. Energy & Fuels 33, 10115-10122.


Natural gas is a rapidly growing source of energy, supplying more than a quarter of the global demand for power. Gas condensate is one type of natural gas resource in which liquid dropout can occur as the pressure decreases throughout the lifetime of the reservoir. This behavior can severely affect the productivity of the reservoir. Chemical and mechanical treatments are applied to repair such damage and restore the productivity of the well. While these types of approaches can yield some success, there is a need for more proactive strategies to eliminate this problem and minimize interference. In this research, we present a dynamic evaluation of the use of an integrated downhole heating system, where renewable energy serves as a source of downhole heating for more sustainable productivity throughout the gas condensate reservoir lifetime. The downhole heating efficiency is significantly influenced by the production rate because some portion of heat is removed with the produced gas. For that purpose, surface and subsurface calculations are coupled to investigate the limitations and the power requirements of renewable energy sources. Our study presents an integrated engineering analysis through simultaneous solving of mass and heat transfer equations coupled with surface renewable energy requirement. The presented study demonstrates the viable feasibility of this method for avoiding gas condensate problems and enhancing ultimate recovery.


https://doi.org/10.1021/acs.est.9b03053

Particulate and vapor phase emissions in the diluted exhaust of a light-duty diesel engine designed for Euro 5 application have been sampled. The engine was operated in three modes, and samples were collected from the exhaust without aftertreatment but also with aftertreatment by an exhaust oxidation catalyst and particle filter. The samples were analyzed by two-dimensional gas chromatography with time-of-flight mass spectral detection. The results show overall removal efficiencies for the organic compound mass by the combination of oxidation catalyst and particle filter of 50, 56, and 74% for the high-speed/high-load, low-speed/low-load, and high-speed/low-load conditions respectively. The results are clearly indicative of substantial repartitioning of the particulate and vapor components within the abatement devices and show an apparently reduced efficiency for the removal of high-molecular-weight alkanes under high-speed/high-load conditions relative to lower-molecular-weight compounds, although this may be due to alkane formation by thermocracking of other species. A notable feature is the presence of oxygenated compounds in the emissions, which are not present in the fuel. These are increased under high-speed/high-load conditions, and the results suggest the formation in the aftertreatment devices as well as in the combustion process.

Ali, M., Darwish, M., Essa, M.A., Abdelhady, A., 2019. Comparison of the Dakhla Formation source rock potential between Komombo Basin and Gebel Duwi, Upper Egypt. Arabian Journal of Geosciences 12, 613.

https://doi.org/10.1007/s12517-019-4833-y

The Campanian-Maastrichtian Dakhla Formation consists mainly of dark gray, laminated shale with siltstone and sandstone inter-beds containing highly organic matter and is a potential source rock. The main objectives of the present research are to correlate the geochemical characteristics of the Dakhla Formation east and west of the River Nile in Upper Egypt and to discuss the main reasons for their variations. Fifty-nine samples were collected from the Komombo Basin and examined along with 230

published ditch and core samples from Gebel Duwi. These data indicate that the quality of the Dakhla source rock potentially varies from fair to good in the Komombo Basin with TOC 0.46–2.66 wt.% and good to excellent in Gebel Duwi with TOC of 2.1–14 wt.%. Additionally, the Dakhla Formation kerogen is type III and type I/II kerogen in the Komombo Basin and Gebel Duwi, respectively; the organic matter of the Dakhla Formation in the Komombo Basin is mostly of terrigenous origin, while in Gebel Duwi, it is mostly of marine origin. Based on vitrinite reflectance (%Ro) and Tmax values, the analyzed samples of Dakhla source rock are in the immature to early mature stage for oil and gas generation in both areas where the Tmax values have a range of 422–444 °C in the Komombo Basin and 412–435 °C in the Gebel Duwi area, while %Ro values range from 0.43 to 0.78% in the Komombo Basin.

Alibrahim, A., Al-Gharabally, D., Mahmoud, H., Dittrich, M., 2019. Proto-dolomite formation in microbial consortia dominated by Halomonas strains. Extremophiles 23, 765-781.

https://doi.org/10.1007/s00792-019-01135-2

Microbes can be found in hypersaline environments forming diverse populations with complex ecological interactions. Microbes in such environments were found to be involved in the formation of minerals including dolomite, a mineral of economic importance and whose origin has been long-debated. Various reports on in vitro experiments using pure cultures provided evidence for the microbial role in dolomite formation. However, culturing experiments have been limited in scope and do not fully address the possible interactions of the naturally occurring microbial communities; consequently, the ability of microbes as a community to form dolomite has been investigated in this study. Our experiments focused on examining the microbial composition by culturing aerobic heterotrophs from the top hypersaline sediments of Al-Khiran sabkha in Kuwait, a modern dolomite-forming environment. The objectives of this study were to assess the ability of two microbial consortia to form dolomite using enrichment culture experiments, mineralogy, and metagenomics. Proto-dolomite was formed by a microbial community dominated by Halomonas strains whereby degradation of the extracellular polymeric substances (EPS) was observed and the pH changed from 7.00 to 8.58. Conversely, proto-dolomite was not observed within a microbial community dominated by Clostridiisalibacter in which EPS continuously accumulated and the pH slightly changed from 7.00 to 7.29.

Alizadeh, B., Seyedali, S.R., Habibnia, B., 2019. Organic geochemical characteristics of Middle to Late Eocene Shahbazan Formation in Dezful Embayment, SW Iran: A case study from Qaleh-Nar oilfield. Petroleum Science and Technology 37, 2322-2329.

https://doi.org/10.1080/10916466.2018.1522335

In a first attempt, Middle to Late Eocene Shahbazan Formation as a possible source rock in Dezful Embayment was geochemically investigated. Maturity indicators derived from Rock-Eval pyrolysis (Tmax and PI) and gas chromatography (CPI) show that the organic matter, which dominated by a mixed type II/III kerogen, is thermally mature and has already entered the oil window. A fair to good petroleum-generative potential is suggested by moderate to relatively high values of total organic carbon (TOC) and potential yield (S1+S2). Deposition of Shahbazan Formation under low-oxygen condition, which is represented by low pristane/phytane ratio (<1), conduced to preservation of organic matter. This is in accordance with considerable TOC contents, ranging from 1.01 to 1.72 wt%. The relation between pristane/nC17 and phytane/nC18 as well as terrigenous/aquatic ratio (∼1) represent the mixed marine and terrestrially sourced organic matter. Based on the results obtained from this study, Shahbazan Formation could have been acted as a prolific oil and gas source rock.

Alvarez, S.A., Gibbs, S.J., Bown, P.R., Kim, H., Sheward, R.M., Ridgwell, A., 2019. Diversity decoupled from ecosystem function and resilience during mass extinction recovery. Nature 574, 242-245.

https://doi.org/10.1038/s41586-019-1590-8

The Chicxulub bolide impact 66 million years ago drove the near-instantaneous collapse of ocean ecosystems. The devastating loss of diversity at the base of ocean food webs probably triggered cascading extinctions across all trophic level and caused severe disruption of the biogeochemical functions of the ocean, and especially disrupted the cycling of carbon between the surface and deep sea. The absence of sufficiently detailed biotic data that span the post-extinction interval has limited our understanding of how ecosystem resilience and biochemical function was restored; estimates of ecosystem ‘recovery’ vary from less than 100 years to 10 million years. Here, using a 13-million-year-long nannoplankton time series, we show that post-extinction communities exhibited 1.8 million years of exceptional volatility before a more stable equilibrium-state community emerged that displayed hallmarks of resilience. The transition to this new equilibrium-state community with a broader spectrum of cell sizes coincides with indicators of carbon-cycle restoration and a fully functioning biological pump. These findings suggest a fundamental link between ecosystem recovery and biogeochemical cycling over timescales that are longer than those suggested by proxies of export production, but far shorter than the return of taxonomic richness. The fact that species richness remained low as both community stability and biological pump efficiency re-emerged suggests that ecological functions rather than the number of species are more important to community resilience and biochemical functions.

Amaro, T., Danovaro, R., Matsui, Y., Rastelli, E., Wolff, G.A., Nomaki, H., 2019. Possible links between holothurian lipid compositions and differences in organic matter (OM) supply at the western Pacific abyssal plains. Deep Sea Research Part I: Oceanographic Research Papers 152, 103085.


Deep-sea benthic communities depend on the export of organic matter (OM) from the surface ocean. However, the effects of the pelagic-benthic coupling and the specific link between changing seasonal OM inputs and physiological changes of the mega-benthic community remain unclear. In this study, we identified differences in OM quality and quantity at two abyssal seafloor sites in the western Pacific Ocean and noted possible links between overlying primary production and the lipid composition of several deep-sea holothurian species. Phytopigment concentrations of the surface sediment were up to 16-times greater at the high productivity area (39°N) than at the oligotrophic area (1°N). Total carbohydrate and protein concentrations were also significantly higher at 39°N than 1°N, although to a lesser extent than for phytopigments. Holothurian abundances were almost 40 times higher at 39°N than 1° N. Significant differences were detected in the fatty acid (FA) compositions of the holothurian tissues in terms of proportions of the main food source indices (phytoplankton, zooplankton and bacterial FA), suggesting different food sources in the two areas. Phytodetritus and bacteria were the most dominant dietary sources at 39°N and 1°N, respectively. Stable carbon and nitrogen isotopic compositions did not contradict the FA data indicating that holothurians fed on both phytodetritus and bacteria from the sediments.

Overall, our results show that high densities of abyssal holothurians at 39°N is linked with the high quality of the sedimentary OM associated with the net primary production at the surface. Further, the differences in phytodetritus inputs may lead to a different lipid composition as a consequence of different feeding habits, although there may be some other mechanisms behind. This study provides

fundamental knowledge on lipid compositions of abyssal holothurians in relation to oceanic settings, thus improves our understanding of the ecosystem functioning in abyssal plains.

Amend, J.P., LaRowe, D.E., 2019. Minireview: demystifying microbial reaction energetics. Environmental Microbiology 21, 3539-3547.

https://doi.org/10.1111/1462-2920.14778

Summary The biology literature is rife with misleading information on how to quantify catabolic reaction energetics. The principal misconception is that the sign and value of the standard Gibbs energy (ΔGr

0) define the direction and energy yield of a reaction; they do not. ΔGr0 is one part of the

actual Gibbs energy of a reaction (ΔGr), with a second part accounting for deviations from the standard composition. It is also frequently assumed that ΔGr

0 applies only to 25 °C and 1 bar; it does not. ΔGr

0 is a function of temperature and pressure. Here, we review how to determine ?Gr as a function of temperature, pressure and chemical composition for microbial catabolic reactions, including a discussion of the effects of ionic strength on ?Gr and highlighting the large effects when multi-valent ions are part of the reaction. We also calculate ?Gr for five example catabolisms at specific environmental conditions: aerobic respiration of glucose in freshwater, anaerobic respiration of acetate in marine sediment, hydrogenotrophic methanogenesis in a laboratory batch reactor, anaerobic ammonia oxidation in a wastewater reactor and aerobic pyrite oxidation in acid mine drainage. These examples serve as templates to determine the energy yields of other catabolic reactions at environmentally relevant conditions.

Ardenghi, N., Mulch, A., Koutsodendris, A., Pross, J., Kahmen, A., Niedermeyer, E.M., 2019. Temperature and moisture variability in the eastern Mediterranean region during Marine Isotope Stages 11–10 based on biomarker analysis of the Tenaghi Philippon peat deposit. Quaternary Science Reviews 225, 105977.


The Mediterranean region is highly sensitive to climate change, particularly with regard to warming and increasing aridity. Understanding its past climate history during periods similar to the Holocene is key to understand the long-term dynamics that accompany anthropogenic climate change. Marine Isotope Stage (MIS) 11 (ca. 424–367 ka BP) is considered one of the best Holocene analogues. Despite detailed insight from Atlantic marine records and European continental records, MIS 11 temperature and rainfall evolution in the Mediterranean remains poorly understood.

We present a detailed record of MIS 11–10 climate change at Tenaghi Philippon, a telmatic peatland in NE Greece. We use microbial membrane lipids (brGDGTs), the δD of n-C29 (δDwax) and distribution of n-alkanes derived from plant leaf waxes, and levoglucosan concentrations to reconstruct changes in temperature, rainfall sources and vegetation burning. Glacial-interglacial temperature patterns indicate strong Atlantic influence in the Eastern Mediterranean region.

Low δDwax values and high temperatures indicate a predominance of Atlantic-sourced winter precipitation during MIS 11, and vice versa during MIS 10. The latter is attributed to a suppression of the Mediterranean storm track, probably due to a persistent high-pressure cell over most of the European continent, mainly in response to an extended ice cover during the glacial. The levoglucosan record is consistent with rapid change to drier conditions and increased vegetation burning from MIS 11 to 10. Millennial-scale oscillations allow to characterise cooling episodes previously recorded at

other sites, with conditions of decreased winter precipitation, while suggesting increased seasonality during the interglacial optimum.

Argüello-Luengo, J., González-Tudela, A., Shi, T., Zoller, P., Cirac, J.I., 2019. Analogue quantum chemistry simulation. Nature 574, 215-218.

https://doi.org/10.1038/s41586-019-1614-4

Computing the electronic structure of molecules with high precision is a central challenge in the field of quantum chemistry. Despite the success of approximate methods, tackling this problem exactly with conventional computers remains a formidable task. Several theoretical and experimental attempts have been made to use quantum computers to solve chemistry problems, with early proof-of-principle realizations done digitally. An appealing alternative to the digital approach is analogue quantum simulation, which does not require a scalable quantum computer and has already been successfully applied to solve condensed matter physics problems. However, not all available or planned setups can be used for quantum chemistry problems, because it is not known how to engineer the required Coulomb interactions between them. Here we present an analogue approach to the simulation of quantum chemistry problems that relies on the careful combination of two technologies: ultracold atoms in optical lattices and cavity quantum electrodynamics. In the proposed simulator, fermionic atoms hopping in an optical potential play the role of electrons, additional optical potentials provide the nuclear attraction, and a single-spin excitation in a Mott insulator mediates the electronic Coulomb repulsion with the help of a cavity mode. We determine the operational conditions of the simulator and test it using a simple molecule. Our work opens up the possibility of efficiently computing the electronic structures of molecules with analogue quantum simulation.


https://doi.org/10.1038/s41396-019-0463-3

Microbial community data are commonly subjected to computational tools such as correlation networks, null models, and dynamic models, with the goal of identifying the ecological processes structuring microbial communities. A major assumption of these methods is that the signs and magnitudes of species interactions and vital rates can be reliably parsed from observational data on species’ (relative) abundances. However, we contend that this assumption is violated when sample units contain any underlying spatial structure. Here, we show how three phenomena—Simpson’s paradox, context-dependence, and nonlinear averaging—can lead to erroneous conclusions about population parameters and species interactions when samples contain heterogeneous mixtures of populations or communities. At the root of this issue is the fundamental mismatch between the spatial scales of species interactions (micrometers) and those of typical microbial community samples (millimeters to centimetres). These issues can be overcome by measuring and accounting for spatial heterogeneity at very small scales, which will lead to more reliable inference of the ecological mechanisms structuring natural microbial communities.

Arp, G., Reimer, A., Simon, K., Sturm, S., Wilk, J., Kruppa, C., Hecht, L., Hansen, B.T., Pohl, J., Reimold, W.U., Kenkmann, T., Jung, D., 2019. The Erbisberg drilling 2011: Implications for the structure and postimpact evolution of the inner ring of the Ries impact crater. Meteoritics & Planetary Science 54, 2448-2482.

https://doi.org/10.1111/maps.13293

The 26 km diameter Nördlinger Ries is a complex impact structure with a ring structure that resembles a peak ring. A first research drilling through this “inner crystalline ring” of the Ries was performed at the Erbisberg hill (SW Ries) to better understand the internal structure and lithology of this feature, and possibly reveal impact‐induced hydrothermal alteration. The drill core intersected the slope of a 22 m thick postimpact travertine mound, before entering 42 m of blocks and breccias of crystalline rocks excavated from the Variscan basement at >500 m depth. Weakly shocked gneiss blocks that show that shock pressure did not exceed 5 GPa occur above polymict lithic breccias of shock stage Ia (10–20 GPa), with planar fractures and planar deformation features (PDFs) in quartz. Only a narrow zone at 49.20–50.00 m core depth exhibits strong mosaicism in feldspar and {102} PDFs in quartz, which are indicative of shock stage Ib (20–35 GPa). Finally, 2 m of brecciated Keuper sediments at the base of the section point to an inverse layering of strata. While reverse grading of clast sizes in lithic breccias and gneiss blocks is consistent with lateral transport, the absence of diaplectic glass and melt products argues against dynamic overthrusting of material from a collapsing central peak, as seen in the much larger Chicxulub structure. Indeed, weakly shocked gneiss blocks are rather of local provenance (i.e., the transient crater wall), whereas moderately shocked polymict lithic breccias with geochemical composition and 87Sr/86Sr signature similar to Ries suevite were derived from a position closer to the impact center. Thus, the inner ring of the Ries is formed by moderately shocked polymict lithic breccias likely injected into the transient crater wall during the excavation stage and weakly shocked gneiss blocks of the collapsing transient crater wall that were emplaced during the modification stage. While the presence of an overturned flap is not evident from the Erbisberg drilling, a survey of all drillings at or near the inner ring point to inverted strata throughout its outer limb. Whether the central ring of the Ries represents remains of a collapsed central peak remains to be shown. Postimpact hydrothermal alteration along the Erbisberg section comprises chloritization, sulfide veinlets, and strong carbonatization. In addition, a narrow zone in the lower parts of the polymict lithic breccia sequence shows a positive Eu anomaly in its carbonate phase. The surface expression of this hydrothermal activity, i.e., the travertine mound, comprises subaerial as well as subaquatic growth phases. Intercalated lake sediments equivalent to the early parts of the evolution of the central crater basin succession confirm a persistent impact‐generated hydrothermal activity, although for less time than previously suggested.

Awan, R.S., Liu, C., Gong, H., Dun, C., Tong, C., Chamssidini, L.G., 2020. Paleo-sedimentary environment in relation to enrichment of organic matter of Early Cambrian black rocks of Niutitang Formation from Xiangxi area China. Marine and Petroleum Geology 112, 104057.


Early Cambrian organic-rich black rocks are extensively distributed in the southern China. In this study, we have discussed the relation of paleo-sedimentary environments with enrichment of organic matter. Based on TOC data, we divided the Niutitang Formation into three parts (Upper, Middle, and Lower). The amount of total organic carbon in the Lower (1.55 wt %) and the Upper part (1.35 wt %) of Niutitang Formation is significantly smaller than the Middle part (8.0 wt %) which suggest initial transgression, and regression stages of the sea level respectively. The Middle part from both sections (Longbizui and Sancha) contains higher TOC content, which is a clue of intense transgression stage of sea level with high bio-productivity. Kerogen type index (KTI) using different macerals specify the organic matter in these black rock series is mainly type-I with a minor amount of type-II1. Moreover, these black rocks were deposited in weak to moderately restricted hydrographic conditions. The heterogenic mineral composition was also observed in these black rocks, including quartz, clay, gypsum, pyrite, barite, dolomite, and plagioclase. Quartz content in the Middle part is relatively higher than the Upper, and the Lower part displays a strong positive relation with TOC which

suggests the main source of quartz during deposition of the Middle part was biogenic quartz. During Early Cambrian period due to extension between the Yangtze and the Cathaysian plate, the hydrothermal fluids rich in uranium, vanadium, molybdenum, zinc, barium, etc. from the deeper part of the earth crust and entered the ocean basin through extensional remnant fissures and cracks, and due to upwelling phenomena entered to the shelf area. These nutrient-rich deep crustal fluids at the surface of the sea enhanced the evolution and breeding of planktons and other marine life; meanwhile, it upsurges the bio-productivity. Additionally, it creates bottom water hypoxia, which is favourable for the preservation of organic matter in the sedimentary rocks. The main factors responsible for the enrichment of organic matter in these Early Cambrian black rock series of Niutitang Formation were a hydrographic restriction, hydrothermal activities, and paleo-redox conditions, respectively.

Babich, T.L., Safonov, A.V., Grouzdev, D.S., Andryuschenko, N.D., Zakharova, E.V., Nazina, T.N., 2019. Bacteria of the genus Shewanella from radionuclide-contaminated groundwater. Microbiology 88, 613-623.

https://doi.org/10.1134/S0026261719040039

Decommissioned surface repositories of liquid radioactive waste remain a potential source of groundwater pollution. Establishment of biogeochemical barriers results in decreased migration of both radioactive and toxic macro-components of the waste. The article presents the results of studying the composition of the microbial community of groundwater sampled in the area of a surface repository for liquid radioactive waste. High-throughput sequencing of the 16S rRNA genes revealed the dominant and minor components of the community, among which were found bacteria of the genus Shewanella. Isolated pure cultures of Shewanella putrefaciens J1-6-2-2 and A-4-3 and Shewanella xiamenensis DCB2-1 were capable of reducing nitrate ions to dinitrogen, which resulted in a decrease in the redox potential of the medium and contributed to reduction and deposition of pertechnetate, uranyl, and chromate ions. In the presence of organic substrates the strains formed biofilms on a number of natural materials (vermiculite, pearlite, schungite, etc.) with high sorption characteristics for cesium, strontium, uranium, and technetium. Analysis of the genome of strain DCB2-1 revealed a cluster of genes homologous to those determining biofilm formation in the well-known strain Shewanella oneidensis MR-1. The isolated strains may be used for introduction into subsurface horizons and enrichment of the natural microbial community in order to create a biogeochemical barrier for purification of groundwater from nitrate ions and immobilization of radioactive waste components.



Free-living microbes are generally capable of growing on multiple different nutrients. Some of those nutrients are used simultaneously, while others are used sequentially. The pattern of nutrient preferences and co-utilization defines the metabolic strategy of a microorganism. Metabolic strategies can substantially affect ecological interactions between species, but their evolution and distribution across the tree of life remain poorly characterized. We discuss how the confluence of better computational models of genotype-phenotype maps and high-throughput experimental tools can help us fill gaps in our knowledge and incorporate metabolic strategies into quantitative predictive models of microbial consortia.

Bale, N.J., Hennekam, R., Hopmans, E.C., Dorhout, D., Reichart, G.-J., van der Meer, M., Villareal, T.A., Sinninghe Damsté, J.S., Schouten, S., 2019. Biomarker evidence for nitrogen-fixing cyanobacterial blooms in a brackish surface layer in the Nile River plume during sapropel deposition. Geology 47, 1088-1092.

https://doi.org/10.1130/G46682.1

Sapropels are organic-rich sediment layers deposited in the eastern Mediterranean Sea during precession minima, resulting from an increase in export productivity and/or preservation. Increased freshwater delivery from the African continent resulted in stratification, causing deepwater anoxia, while nutrient input stimulated productivity, presumably at the deep chlorophyll maximum. Previous studies have suggested that during sapropel deposition, nitrogen fixation was widespread in the highly stratified surface waters, and that cyanobacteria symbiotic with diatoms (diatom-diazotroph associations, DDAs) were responsible. Here we analyzed sapropel S5 sediments for heterocyst glycolipids (HGs) from three locations in the eastern Mediterranean. HG biomarkers can differentiate between those heterocystous cyanobacteria that are free living (found predominately in freshwater or brackish environments) and those that are from DDAs (found in marine settings). In our primary core, from a location which would have been influenced by the Nile River outflow, we detected a HG with a pentose (C5) head group specific for DDAs. However, HGs with a hexose (C6) head group, specific to free-living cyanobacteria, were present in substantially (up to 60×) higher concentration. These data suggest that at our study location, free-living cyanobacteria were the dominant diazotrophs, rather than DDAs. The C6 HGs increased substantially at the onset of sapropel S5 deposition, suggesting that substantial seasonal cyanobacterial blooms were associated with a brackish surface layer flowing from the Nile into the eastern Mediterranean. Two additional S5 sapropels were analyzed, one also from the Nile delta region and one from the region between Libya and southwestern Crete. Overall, comparison of the HG distribution in the three S5 sapropels provides evidence that all three locations were initially influenced by surface salinities that were sufficiently low to support free-living heterocystous cyanobacteria. While free-living heterocystous cyanobacteria continued to outnumber DDAs during sapropel deposition at the two Nile-influenced sites, DDAs, indicators of persistent marine salinities, were the dominant diazotrophs in the upper part of the sapropel at the more westerly site. These results indicate that N2 fixation by free-living cyanobacteria offers an important additional mechanism to stimulate productivity in regions with strong river discharge during sapropel deposition.

Bale, N.J., Palatinszky, M., Rijpstra, W.I.C., Herbold, C.W., Wagner, M., Sinninghe Damsté, J.S., 2019. Membrane lipid composition of the moderately thermophilic ammonia-oxidizing archaeon “Candidatus Nitrosotenuis uzonensis” at different growth temperatures. Applied and Environmental Microbiology 85, e01332-19.

http://aem.asm.org/content/85/20/e01332-19.abstract

Abstract: “Candidatus Nitrosotenuis uzonensis” is the only cultured moderately thermophilic member of the thaumarchaeotal order Nitrosopumilales (NP) that contains many mesophilic marine strains. We examined its membrane lipid composition at different growth temperatures (37°C, 46°C, and 50°C). Its lipids were all membrane-spanning glycerol dialkyl glycerol tetraethers (GDGTs), with 0 to 4 cyclopentane moieties. Crenarchaeol (cren), the characteristic thaumarchaeotal GDGT, and its isomer (crenʹ) were present in high abundance (30 to 70%). The GDGT polar headgroups were mono-, di-, and trihexoses and hexose/phosphohexose. The ratio of glycolipid to phospholipid GDGTs was highest in the cultures grown at 50°C. With increasing growth temperatures, the relative contributions of cren and crenʹ increased, while those of GDGT-0 to GDGT-4 (including isomers) decreased. TEX86 (tetraether index of tetraethers consisting of 86 carbons)-derived temperatures were

much lower than the actual growth temperatures, further demonstrating that TEX86 does not accurately reflect the membrane lipid adaptation of thermophilic Thaumarchaeota. As the temperature increased, specific GDGTs changed relative to their isomers, possibly representing temperature adaption-induced changes in cyclopentane ring stereochemistry. Comparison of a wide range of thaumarchaeotal core lipid compositions revealed that the “Ca. Nitrosotenuis uzonensis” cultures clustered separately from other members of the NP order and the Nitrososphaerales (NS) order. While phylogeny generally seems to have a strong influence on GDGT distribution, our analysis of “Ca. Nitrosotenuis uzonensis” demonstrates that its terrestrial, higher-temperature niche has led to a lipid composition that clearly differentiates it from other NP members and that this difference is mostly driven by its high crenʹ content.

Importance: For Thaumarchaeota, the ratio of their glycerol dialkyl glycerol tetraether (GDGT) lipids depends on growth temperature, a premise that forms the basis of the widely applied TEX86 paleotemperature proxy. A thorough understanding of which GDGTs are produced by which Thaumarchaeota and what the effect of temperature is on their GDGT composition is essential for constraining the TEX86 proxy. “Ca. Nitrosotenuis uzonensis” is a moderately thermophilic thaumarchaeote enriched from a thermal spring, setting it apart in its environmental niche from the other marine mesophilic members of its order. Indeed, we found that the GDGT composition of “Ca. Nitrosotenuis uzonensis” cultures was distinct from those of other members of its order and was more similar to those of other thermophilic, terrestrial Thaumarchaeota. This suggests that while phylogeny has a strong influence on GDGT distribution, the environmental niche that a thaumarchaeote inhabits also shapes its GDGT composition.

Bao, R., Zhao, M., McNichol, A., Wu, Y., Guo, X., Haghipour, N., Eglinton, T.I., 2019. On the origin of aged sedimentary organic matter along a river-shelf-deep ocean transect. Journal of Geophysical Research: Biogeosciences 124, 2582-2594.

https://doi.org/10.1029/2019JG005107

To assess the influences of carbon sources and transport processes on the 14C age of organic matter (OM) in continental margin sediments, we examined a suite of samples collected along a river‐shelf‐deep ocean transect in the East China Sea (ECS). Ramped pyrolysis‐oxidiation was conducted on suspended particulate matter in the Yangtze River and on surface sediments from the ECS shelf and northern Okinawa Trough. 14C ages were determined on OM decomposition products within different temperature windows. These measurements suggest that extensive amounts of pre‐old (i.e., millennial age) organic carbon (OC) are subject to degradation within and beyond the Yangtze River Delta, and this process is accompanied by an exchange of terrestrial and marine OM. These results, combined with fatty acid concentration data, suggest that both the nature and extent of OM preservation/degradation as well as the modes of transport influence the 14C ages of sedimentary OM. Additionally, we find that the age of (thermally) refractory OC increases during across‐shelf transport and that the age offset between the lowest and highest temperature OC decomposition fractions also increases along the shelf‐to‐trough transect. Amplified interfraction spread or 14C heterogeneity is the greatest in the Okinawa Trough. Aged sedimentary OM across the transect may be a consequence of several reasons including fossil OC input, selective degradation of younger OC, hydrodynamic sorting processes, and aging during lateral transport. Consequently, each of them should be considered in assessing the 14C results of sedimentary OM and its implications for the carbon cycle and interpretation of sedimentary records.

Baratoux, D., Niang, C.A.B., Reimold, W.U., Sapah, M.S., Jessell, M.W., Boamah, D., Faye, G., Bouley, S., Vanderheaghe, O., 2019. Bosumtwi impact structure, Ghana: Evidence for fluidized emplacement of the ejecta. Meteoritics & Planetary Science 54, 2541-2556.


The about 10.5 km diameter Bosumtwi impact crater is one of the youngest large impact structures on Earth. The crater rim is readily noticed on topographic maps or in satellite imagery. It defines a circular basin filled by water (Lake Bosumtwi) and lacustrine sediments. The morphology of this impact structure is also characterized by a circular plateau extending beyond the rim and up to 9–10 km from the center of the crater (about 2 crater radii). This feature comprises a shallow ring depression, also described as an annular moat, and a subdued circular ridge at its outer edge. The origin of this outermost feature could so far not be elucidated based on remote sensing data only. Our approach combines detailed topographic analysis, including roughness mapping, with airborne radiometric surveys (mapping near‐surface K, Th, U concentrations) and field observations. This provides evidence that the moat and outer ring are features inherited from the impact event and represent the partially eroded ejecta layer of the Bosumtwi impact structure. The characteristics of the outer ridge indicate that ejecta emplacement was not purely ballistic but requires ejecta fluidization and surface flow. The setting of Bosumtwi ejecta can therefore be considered as a terrestrial analog for rampart craters, which are common on Mars and Venus, and also found on icy bodies of the outer solar system (e.g., Ganymede, Europa, Dione, Tethys, and Charon). Future studies at Bosumtwi may therefore help to elucidate the mechanism of formation of rampart craters.

Bartels, W.B., Rücker, M., Boone, M., Bultreys, T., Mahani, H., Berg, S., Hassanizadeh, S.M., Cnudde, V., 2019. Imaging spontaneous imbibition in full Darcy-scale samples at pore-scale resolution by fast X-ray tomography. Water Resources Research 55, 7072-7085.

https://doi.org/10.1029/2018WR024541

Abstract Spontaneous imbibition is a process occurring in a porous medium which describes wetting phase replacing nonwetting phase spontaneously due to capillary forces. This process is conventionally investigated by standardized, well-established spontaneous imbibition tests. In these tests, for instance, a rock sample is surrounded by wetting fluid. The following cumulative production of nonwetting phase versus time is used as a qualitative measure for wettability. However, these test results are difficult to interpret, because many rocks do not show a homogeneous but a mixed wettability in which the wetting preference of a rock varies from location to location. Moreover, during the test the flow regime typically changes from countercurrent to cocurrent flow and no phase pressure or pressure drop can be recorded. To help interpretation, we complement Darcy-scale production curves with X-ray imaging to describe the differences in imbibition processes between water-wet and mixed-wet systems. We found that the formation of a spontaneous imbibition front occurs only for water-wet systems; mixed-wet systems show localized imbibition events only. The asymmetry of the front depends on the occurrence of preferred production sites, which influences interpretation. Fluid layers on the outside of mixed-wet samples increase connectivity of the drained phase and the effect of buoyancy on spontaneous imbibition. The wider implication of our study is the demonstration of the capability of benchtop laboratory equipment to image a full Darcy-scale experiment while at the same time obtaining pore-scale information, resolving the natural length and time scale of the underlying processes.

Baumgartner, R.J., Van Kranendonk, M.J., Wacey, D., Fiorentini, M.L., Saunders, M., Caruso, S., Pages, A., Homann, M., Guagliardo, P., 2019. Nano−porous pyrite and organic matter in 3.5-billion-year-old stromatolites record primordial life. Geology 47, 1039-1043.

https://doi.org/10.1130/G46365.1

Stromatolites of the ∼3.5 billion-year-old Dresser Formation (Pilbara Craton, Western Australia) are considered to be some of Earth’s earliest convincing evidence of life. However, uniquely biogenic interpretations based on surface outcrops are precluded by weathering, which has altered primary mineralogy and inhibited the preservation of microbial remains. Here, we report on exceptionally preserved, strongly sulfidized stromatolites obtained by diamond drilling from below the weathering profile. These stromatolites lie within undeformed hydrothermal-sedimentary strata and show textural features that are indicative of biogenic origins, including upward-broadening and/or upward-branching digitate forms, wavy to wrinkly laminae, and finely laminated columns that show a thickening of laminae over flexure crests. High-resolution textural, mineralogical, and chemical analysis reveals that the stromatolites are dominated by petrographically earliest, nano-porous pyrite that contains thermally mature, N-bearing organic matter (OM). This nano-porous pyrite is consistent with a formation via sulfidization of an originally OM-dominated matrix. Evidence for its relationship with microbial communities are entombed OM strands and filaments, whose microtexture and chemistry are consistent with an origin as mineralized biofilm remains, and carbon isotope data of extracted OM (δ13COM = −29.6‰ ± 0.3‰ VPDB [Vienna Peedee belemnite]), which lie within the range of biological matter. Collectively, our findings provide exceptional evidence for the biogenicity of some of Earth’s oldest stromatolites through preservation of OM, including microbial remains, by sulfidization.

Becker, S., Feldmann, J., Wiedemann, S., Okamura, H., Schneider, C., Iwan, K., Crisp, A., Rossa, M., Amatov, T., Carell, T., 2019. Unified prebiotically plausible synthesis of pyrimidine and purine RNA ribonucleotides. Science 366, 76-82.

http://science.sciencemag.org/content/366/6461/76.abstract

Abstract: Theories about the origin of life require chemical pathways that allow formation of life’s key building blocks under prebiotically plausible conditions. Complex molecules like RNA must have originated from small molecules whose reactivity was guided by physico-chemical processes. RNA is constructed from purine and pyrimidine nucleosides, both of which are required for accurate information transfer, and thus Darwinian evolution. Separate pathways to purines and pyrimidines have been reported, but their concurrent syntheses remain a challenge. We report the synthesis of the pyrimidine nucleosides from small molecules and ribose, driven solely by wet-dry cycles. In the presence of phosphate-containing minerals, 5′-mono- and diphosphates also form selectively in one-pot reactions. The pathway is compatible with purine synthesis, allowing the concurrent formation of all Watson-Crick bases.

Editor's Summary: Conditions right for making nucleosides. In the absence of biological catalysts and metabolism, can atmospheric and geochemical processes provide the substrates and conditions required for production of biological molecules? Becker et al. devised an abiotic synthetic scheme that allows for accumulation of both purine and pyrimidine nucleoside mono- and diphosphates (see the Perspective by Hud and Fialho). A key starting material for this chemistry, hydroxylamine and/or hydroxylamine disulfonate, can form under plausible early atmospheric conditions. Cycles between wet and dry conditions provide the environments necessary to complete formation of purine and pyrimidine bases essentially in one pot.

Beil, S., Kuhnt, W., Holbourn, A., Scholz, F., Oxmann, J., Wallmann, K., Lorenzen, J., Aquit, M., Chellai, E.H., 2019. Cretaceous Oceanic Anoxic Events prolonged by phosphorus cycle feedbacks. Climate of the Past Discussions 2019, 1-42.

https://www.clim-past-discuss.net/cp-2019-118/

Oceanic Anoxic Events (OAEs) document major perturbations of the global carbon cycle with repercussions on the Earth’s climate and ocean circulation that are relevant to understand future climate trends. Here, we compare sedimentation patterns, nutrient cycling, organic carbon accumulation and carbon isotope variability across Cretaceous Oceanic Anoxic Events OAE1a and OAE2 in two drill cores with unusually high sedimentation rates from the Vocontian Basin (southern France) and Tarfaya Basin (southern Morocco). OAE1a and OAE2 exhibit remarkable similarities in the evolution of their δ13C excursion with long-lasting negative carbon isotope excursions preceding the onset of both anoxic events, supporting the view that OAEs were triggered by massive emissions of volcanic CO2 into the atmosphere. Based on analysis of cyclic sediment variations, we estimated the duration of the individual phases within the carbon isotope excursions. For both events, we identify: (1) a precursor phase lasting ~ 430 kyr and ~ 130 kyr, (2) an onset phase of ~ 390 and ~ 70 kyr, (3) a peak phase of ~ 600 and ~ 90 kyr, (4) a plateau phase of ~ 1400 and ~ 200 kyr and (5) a recovery phase of ~ 630 and ~ 440 kyr, respectively. The total duration of the positive carbon isotope excursion is estimated as 3400 kyr and 790 kyr and that of the main carbon accumulation phase as 980 kyr and 180 kyr, for OAE1a and OAE 2 respectively. The extended duration of the peak, plateau and recovery phases requires fundamental changes in global nutrient cycles either (1) through excess nutrient inputs to the oceans by increasing continental weathering and river discharge or (2) through nutrient-recycling from the marine sediment reservoir. We investigated the role of phosphorus on the development of carbon accumulation by analysing phosphorus speciation across OAE2 and the mid-Cenomanian Event (MCE) in the Tarfaya Basin. The ratios of organic carbon and total nitrogen to reactive phosphorus (Corg/Preact and Ntotal/Preact) prior to OAE2 and the MCE hover close to or below the Redfield ratio characteristic of marine organic matter. Decreases in reactive phosphorus resulting in Corg/Preact and Ntotal/Preact above the Redfield ratio during the later phase of OAE2 and the MCE indicate leakage from the sedimentary column into the water column under the influence of intensified and expanded oxygen minimum zones. These results suggest that a positive feedback loop, rooted in the benthic phosphorus cycle, contributed to increased marine productivity and carbon burial over an extended period of time during OAEs.



Dissolved organic matter (DOM) composition influences its ability to form photochemically produced reactive intermediates (PPRI). While relationships have been established between bulk DOM properties and triplet DOM (3DOM) and singlet oxygen (1O2) quantum yields, contradictory evidence exists for hydroxyl radical (•OH) and hydroxylating species. Furthermore, little is known about these relationships at the molecular level. We evaluated DOM composition and photochemical reactivity of water samples from a wastewater treatment plant and the St. Louis River in Minnesota and Wisconsin, U.S.A. Bulk characterization using ultraviolet–visible spectroscopy demonstrates that color and apparent size of DOM decrease downstream, while molecular composition analysis using Fourier-transform ion cyclotron resonance mass spectrometry reveals that saturation and chemodiversity is highest near Lake Superior. 3DOM quantum yield coefficients and 1O2 quantum yields increase downstream and correlate strongly with saturated formulas. Similar results are

observed for carbon-normalized photodegradation rate constants of atorvastatin, carbamazepine, and venlafaxine, which react primarily with 3DOM and 1O2. In contrast, •OH quantum yields are lowest downstream and correlate with less saturated, more oxygenated DOM, suggesting that 3DOM is not its major precursor. Mixed relationships are observed for DEET, which reacts with multiple PPRI. Molecular-level compositional data reveal insights into the differing formation pathways of individual PPRI, but information about specific contaminants is needed to predict their photochemical fate.

Beznosov, P.A., Clack, J.A., Lukševičs, E., Ruta, M., Ahlberg, P.E., 2019. Morphology of the earliest reconstructable tetrapod Parmastega aelidae. Nature 574, 527-531.

https://doi.org/10.1038/s41586-019-1636-y

The known diversity of tetrapods of the Devonian period has increased markedly in recent decades, but their fossil record consists mostly of tantalizing fragments. The framework for interpreting the morphology and palaeobiology of Devonian tetrapods is dominated by the near complete fossils of Ichthyostega and Acanthostega; the less complete, but partly reconstructable, Ventastega and Tulerpeton have supporting roles. All four of these genera date to the late Famennian age (about 365–359 million years ago)—they are 10 million years younger than the earliest known tetrapod fragments, and nearly 30 million years younger than the oldest known tetrapod footprints. Here we describe Parmastega aelidae gen. et sp. nov., a tetrapod from Russia dated to the earliest Famennian age (about 372 million years ago), represented by three-dimensional material that enables the reconstruction of the skull and shoulder girdle. The raised orbits, lateral line canals and weakly ossified postcranial skeleton of P. aelidae suggest a largely aquatic, surface-cruising animal. In Bayesian and parsimony-based phylogenetic analyses, the majority of trees place Parmastega as a sister group to all other tetrapods.

Bianco, A., Riva, M., Baray, J.-L., Ribeiro, M., Chaumerliac, N., George, C., Bridoux, M., Deguillaume, L., 2019. Chemical characterization of cloudwater collected at Puy de Dôme by FT-ICR MS reveals the presence of SOA components. ACS Earth and Space Chemistry 3, 2076-2087.

https://doi.org/10.1021/acsearthspacechem.9b00153

Secondary organic aerosols (SOA) produced in the atmosphere from sequential oxidation of biogenic or anthropogenic volatile organic compounds (VOC) represent a significant part of the atmospheric organic aerosol. Aerosol particles can act as cloud condensation nuclei or can be scavenged by cloud droplets, where organic carbon undergo chemical and biological transformations. Due to its high complexity, a nontargeted analysis by FT-ICR MS (Fourier-transform ion cyclotron resonance mass spectrometry) has been used to characterize the dissolved organic matter at a molecular level. SOA compounds have been detected in six aqueous samples collected in 2017 at the Puy de Dôme station (PUY, France). SOA tracers, produced by VOC oxidation in environmental chambers or in ambient air and characterized in previous studies by mass spectrometry, were searched by FT-ICR MS in cloudwaters. Results clearly indicate the presence of oxidation products of isoprene, α- and β-pinene, and other monoterpenes and sesquiterpenes. Interestingly, a significant number of assigned molecular formulas are attributed to brown carbon and nitroaromatics. Seasonal variabilities are also observed for organonitrates and organosulfates.

Bif, M.B., Siqueira, L., Hansell, D.A., 2019. Warm events induce loss of resilience in organic carbon production in the northeast Pacific Ocean. Global Biogeochemical Cycles 33, 1174-1186.

https://doi.org/10.1029/2019GB006327

Abstract Between 2013 and 2016, a series of warm events induced by ocean atmosphere oscillations negatively impacted productivity in the northeast Pacific Ocean. For two consecutive winters (2013?2014 and 2014?2015), suppressed wind stress and warm near-surface ocean temperature anomalies restricted vertical mixing between the surface and underlying nutrient-enriched waters. Here we assess historical data of sea surface temperature and sea level pressure, along with nearly a decade of biogeochemical float data to evaluate the impact of these warm events on organic carbon production. The first stratified winter experienced little apparent impact on the magnitude of net organic carbon production in the growing season relative to prior years, suggesting an immediate resilience from reduced new nutrients, apparently depending on recycled iron. However, the subsequent winter experienced virtually zero net production; a loss of resilience, perhaps due to net iron removal with export, was evident. We find that consistently enhanced winter stratification decreased carbon production much more so than a single warm winter. This study highlights the sensitivity of marine productivity to ocean atmosphere oscillations, reducing deep ocean carbon sequestration with prolonged ocean warming and stratification.


https://doi.org/10.1111/gbi.12354

Archaeal ANaerobic MEthanotrophs (ANME) facilitate the anaerobic oxidation of methane (AOM), a process that is believed to proceed via the reversal of the methanogenesis pathway. Carbon isotopic composition studies indicate that ANME are metabolically diverse and able to assimilate metabolites including methane, methanol, acetate, and dissolved inorganic carbon (DIC). Our data support the interpretation that ANME in marine sediments at methane seeps assimilate both methane and DIC, and the carbon isotopic compositions of the tetrapyrrole coenzyme F430 and the membrane lipids archaeol and hydroxy‐archaeol reflect their relative proportions of carbon from these substrates. Methane is assimilated via the methyl group of CH3‐tetrahydromethanopterin (H4MPT) and DIC from carboxylation reactions that incorporate free intracellular DIC. F430 was enriched in 13C (mean δ13C = −27‰ for Hydrate Ridge and −80‰ for the Santa Monica Basin) compared to the archaeal lipids (mean δ13C = −97‰ for Hydrate Ridge and −122‰ for the Santa Monica Basin). We propose that depending on the side of the tricarboxylic acid (TCA) cycle used to synthesize F430, its carbon was derived from 76% DIC and 24% methane via the reductive side or 57% DIC and 43% methane via the oxidative side. ANME lipids are predicted to contain 42% DIC and 58% methane, reflecting the amount of each assimilated into acetyl‐CoA. With isotope models that include variable fractionation during biosynthesis for different carbon substrates, we show the estimated amounts of DIC and methane can result in carbon isotopic compositions of − 73‰ to − 77‰ for F430 and − 105‰ for archaeal lipids, values close to those for Santa Monica Basin. The F430 δ13C value for Hydrate Ridge was 13C‐enriched compared with the modeled value, suggesting there is divergence from the predicted two carbon source models.

Black, B.A., Gibson, S.A., 2019. Deep carbon and the life cycle of large igneous provinces. Elements 15, 319-324.

https://doi.org/10.2138/gselements.15.5.319

Carbon is central to the formation and environmental impact of large igneous provinces (LIPs). These vast magmatic events occur over geologically short timescales and include voluminous flood basalts, along with silicic and low-volume alkaline magmas. Surface outgassing of CO2 from flood basalts may average up to 3,000 Mt per year during LIP emplacement and is subsidized by fractionating magmas deep in the crust. The large quantities of carbon mobilized in LIPs may be sourced from the convecting mantle, lithospheric mantle and crust. The relative significance of each potential carbon source is poorly known and probably varies between LIPs. Because LIPs draw on mantle reservoirs typically untapped during plate boundary magmatism, they are integral to Earth's long-term carbon cycle.


https://doi.org/10.1134/S0965544119100025

The review discusses the achievements of the last 5 years in the field of using mass spectrometry for the analysis of crude oils and some oil refining products. The presented materials are systematized according to properties of the analyzed compounds and ionization techniques used. The capabilities and disadvantages of existing approaches are discussed.


https://doi.org/10.1134/S0965544119100037

The composition and structure of bitumenoid asphaltenes of modern and fossil sediments has been studied using a set of instrumental methods (elemental and X-ray diffraction analyses, visible spectroscopy, NMR spectroscopy, EPR, electron microscopy), which made it possible to trace the evolution of the asphaltenes from their generation in diagenesis to degradation and transformation into kerogen under high catagenesis conditions. In diagenesis, protoasphaltenes are formed, which turn into asphaltenes as a result of catagenetic transformations. In apocatagenesis under severe thermobaric conditions at great depths, despite an overall decrease in bituminosity, the amount of hydrocarbons increases as a result of degradation of asphaltenes: molecules of organic compounds (occluded hydrocarbons) could be trapped and preserved in large cavities of the macromolecular structure of asphaltenes. Three generations of asphaltenes have been distinguished: early diagenetic (protoasphaltenes of modern sediments), mesocatagenetic (asphaltenes formed in the main catagenesis zone), and late catagenetic (asphaltenes produced under conditions of high temperatures and pressures).

Bryan, N.C., Christner, B.C., Guzik, T.G., Granger, D.J., Stewart, M.F., 2019. Abundance and survival of microbial aerosols in the troposphere and stratosphere. The ISME Journal 13, 2789-2799.

https://doi.org/10.1038/s41396-019-0474-0

Bioaerosol transport in the atmosphere disperses microbial species between continents, affects human and plant health, and may influence hydrologic cycling. However, there have been few quantitative observations of bioaerosols at altitudes more than a few kilometers above the surface. Lack of data on bioaerosol distributions in the atmosphere has impeded efforts to assess the aerial dissemination of microbes and their vertical extent in the biosphere. In this study, a helium balloon payload system was used to sample microbial cells and dust particles in air masses as high as 38 km above sea level

over three locations in the southwestern United States. The cell concentrations at altitudes between 3 and 29 km were highly similar (2–5 × 105 cells m−3) and approximately threefold lower than those observed in the convective boundary layer (CBL; 1 × 106 cells m−3), decreasing to 8 × 104 cells m−3 at 35–38 km. The detection of adenosine triphosphate (ATP) and recovery of bacteria possessing extreme tolerance to desiccation and shortwave ultraviolet radiation confirmed that certain microorganisms have the capacity to persist at lower altitudes of the stratosphere. Our data and related calculations provide constraints on the upper altitudinal boundary for microbial habitability in the biosphere.



The extant elephants are only a small fraction of the diverse order of proboscideans that once roamed the planet, whereas the extinct gomphotheres represent the largest and most diverse of these enigmatic groups that survived into the Quaternary. However, their relationship to the living elephantids and the other extinct elephantiformes, such as the mastodons, remains debated. To begin to address this we have used proteomic analysis to sequence the collagen surviving in sub-fossil Notiomastodon bone from the site of Pilauco in Chile. Through the genus-level information retrieved, phylogenetic analyses of the near-complete (85–90%) sequences that were recovered surprisingly revealed a closer relationship between the South American gomphothere (Notiomastodon) and the American mastodon (Mammut) than to the elephantids (Loxodonta, Elephas and Mammuthus), as most commonly proposed; a finding that was consistent across all phylogenetic analyses used, including bayesian, parsimony and máximum likelihood approaches. These results demonstrate the potential information that can be recovered using the ever-increasing applications of proteomics to palaeobiology, particularly for improving our understanding of the evolution of extinct species in a manner consistent with the latest DNA-based approaches.

Bukliarevich, H.A., Charniauskaya, M.I., Akhremchuk, A.E., Valentovich, L.N., Titok, M.A., 2019. Effect of the structural and regulatory heat shock proteins on hydrocarbon degradation by Rhodococcus pyridinivorans 5Ap. Microbiology 88, 573-579.

https://doi.org/10.1134/S0026261719050023

The role of heat shock proteins in ability of Rhodococcus pyridinivorans 5Ap to degrade hydrocarbons at different temperatures was studied. The presence of the Сpn60.1–Сpn10 chaperons and of the Hrc regulatory protein was found to be required for hexadecane degradation at 42°C. When genetic determinants responsible for synthesis of these proteins were inactivated, the efficiency of hexadecane degradation decreased 1.7 and 2.7 times, respectively. Mutations in the cpn and hrcA genes did not affect the viability of R. pyridinivorans 5Ар: the original strain and the mutants exhibited the same growth rates at all temperatures in the minimal medium with succinate and in full-strength medium. In the absence of the Сpn60.1–Сpn10 heat shock proteins, the growth rate at 42°C decreased in the case of minimal agar media with kerosene, diesel fuel, acetone, naphthalene, 2-methylnaphthalene, or phenanthrene.

Bushnev, D.A., Burdel’naya, N.S., Mokeev, M.V., 2019. Results of 13C NMR and FTIR spectroscopy of kerogen from the Upper Devonian Domanik of the Timan–Pechora Basin. Geochemistry International 57, 1173-1184.

https://doi.org/10.1134/S0016702919110028

A series of kerogen samples from organic carbon rich rocks of middle Frasnian–early Famennian age from the Timan–Pechora basin was studied by Rock-Eval pyrolysis, solid-state 13C NMR spectroscopy, and Fourier transform infrared (FTIR) spectroscopy. In addition, we determined the spectral characteristics of kerogen isolated from the Domanikites of the early catagenetic stage artificially matured in an autoclave under hydrous conditions. In general, the trends of transformation of the kerogen structure during natural and experimental maturation are identical. The kerogen subjected to experimental maturation is characterized by an increase in the concentration of terminal methyl groups relative to methylene units. Artificial kerogen maturation results in a more rapid rearrangement of aromatic clusters and accumulation of bridgehead and protonated carbon compared with natural maturation.


http://sp.lyellcollection.org/content/468/1/127.abstract

Petroleum systems represent complex multiphase subsurface environments. The properties of the noble gases as conservative physical tracers allow them to be used to gain insight into the physical behaviour occurring within hydrocarbon systems. This can be used to better understand the mechanisms of hydrocarbon migration, residence time of fluids, and measurement of the scale of the subsurface fluid system involved in the transport and trapping of the hydrocarbon phase. The noble gases in the subsurface derive from different sources with distinct isotopic compositions, allowing them to be resolved in any crustal fluid. We discuss the processes within petroleum systems that incorporate the noble gases from each of these sources into hydrocarbon accumulations. The dominant mechanism controlling the introduction of air-derived noble gases into petroleum systems is via subsurface groundwater, and this records key information about the interaction of the petroleum system with the hydrogeological regime. Radiogenic noble gases accumulate over time, recording information about the age and relative timing of processes within the petroleum system. We review the conceptual framework and quantitative models describing these processes using examples from previous studies, and discuss both their current limitations and the potential for their application to unconventional hydrocarbon systems.

Byrne, D.J., Barry, P.H., Lawson, M., Ballentine, C.J., 2020. The use of noble gas isotopes to constrain subsurface fluid flow and hydrocarbon migration in the East Texas Basin. Geochimica et Cosmochimica Acta 268, 186-208.

http://www.sciencedirect.com/science/article/pii/S001670371930643X

The migration of hydrocarbons from source-rock to reservoir is a critical stage in petroleum system evolution. However, as migration occurs along confined pathways over geologically rapid timescales it is challenging to place quantitative constraints on migration behaviour in terms of interaction with other basinal fluids, flux, and lengthscales associated with this process. Due to their inert nature,

noble gases are ideal tracers of fluid provenance and physical processes in a variety of subsurface systems, and thus can serve as a potential geochemical indicator of migration distance. The recent proliferation of unconventional hydrocarbon production (i.e., production directly from source-rocks) allows for the analysis of fluids from these strata. Here we present noble gas data from natural gas samples produced from 27 related conventional and unconventional wells within the East Texas basin. These data enable characterisation of fluids during migration from source-rock to conventional reservoir. Unconventional gases and fluids are produced from the Haynesville shale (n = 8), and conventional gases and fluids are sourced from the overlying Cotton Valley (n = 5), Travis Peak (n = 9), and James Lime (n = 5) formations. Samples consist primarily of methane (>70%), with small contributions from longer-chain hydrocarbons, and other gases including CO2 and N2. Atmosphere-derived 36Ar, which is introduced into natural gas accumulations via interaction with groundwater during hydrocarbon generation and migration, is consistently higher in samples that have undergone a greater migration distance from the source interval. Thus, calculated volume ratios of gas-water interaction (Vg/Vw) show a far greater incidence of groundwater interaction in migrated samples. Radiogenically-produced 40Ar is also consistently elevated in migrated samples, despite these reservoirs being located in geologically younger strata. We derive the representative volume of rock required to produce the observed radiogenic 40Ar in each sample and show that samples that have migrated further have acquired radiogenic isotopes from larger volumes of rock. Furthermore, our volumetric parameters derived from atmospheric and radiogenic isotopes are consistent with a simple conceptual model of migration. We quantitatively apply this model to demonstrate that migration occurs along relatively localised pathways. Helium (3He/4He) and argon (40Ar/36Ar) isotopes are correlated and show elevated amounts of mantle-derived 3He and radiogenic 40Ar in migrated samples. We interpret this to represent mixing between a pristine source-rock signature and an endmember characterised by elevated 3He/4He and 40Ar/36Ar, likely representative of mantle-enriched groundwater circulating in the wider hydrogeological basin. Finally, we use an advection-diffusion model to show that enriched mantle 3He in the shallower strata and towards the southern edge of the basin can be explained by influx of mantle helium along the fault-bounded southern edge of the basin over timescales of millions of years. Together these approaches represent the first complete noble gas based characterization of a hydrocarbon system, sampling migration from source-rock to trap. We show conclusively that both atmospheric and radiogenic noble gases are entrained in the hydrocarbon phase during migration and that concentrations scale proportionally with migration distance, as greater volumes of groundwater and host rock are encountered.


https://www.frontiersin.org/article/10.3389/fmicb.2019.02358

The biogenicity problem of geological materials is one of the most challenging ones in the field of paleo and astrobiology. As one goes deeper in time, the traces of life become feeble and ambiguous, blending with the surrounding geology. Well-preserved metasedimentary rocks from the Archaean are relatively rare, and in very few cases contain structures resembling biological traces or fossils. These putative biosignatures have been studied for decades and many biogenicity criteria have been developed, but there is still no consensus for many of the proposed structures. Synchrotron-based techniques, especially on new generation sources, have the potential for contributing to this field of research, providing high sensitivity and resolution that can be advantageous for different scientific problems. Exploring the X-ray and matter interactions on a range of geological materials can provide insights on morphology, elemental composition, oxidation states, crystalline structure, magnetic properties, and others, which can measurably contribute to the investigation of biogenicity of putative

biosignatures. Here, we provide an overview of selected synchrotron-based techniques that have the potential to be applied in different types of questions on the study of biosignatures preserved in the geological record. The development of 3rd and recently 4th generation synchrotron sources will favor a deeper understanding of the earliest records of life on Earth and also bring up potential analytical approaches to be applied for the search of biosignatures in meteorites and samples returned from Mars in the near future.

Campa, M.F., Techtmann, S.M., Ladd, M.P., Yan, J., Patterson, M., Garcia de Matos Amaral, A., Carter, K.E., Ulrich, N., Grant, C.J., Hettich, R.L., Lamendella, R., Hazen, T.C., 2019. Surface water microbial community response to the biocide 2,2-dibromo-3-nitrilopropionamide, used in unconventional oil and gas extraction. Applied and Environmental Microbiology 85, e01336-19.


Abstract: Production of unconventional oil and gas continues to rise, but the effects of high-density hydraulic fracturing (HF) activity near aquatic ecosystems are not fully understood. A commonly used biocide in HF, 2,2-dibromo-3-nitrilopropionamide (DBNPA), was studied in microcosms of HF-impacted (HF+) versus HF-unimpacted (HF−) surface water streams to (i) compare the microbial community response, (ii) investigate DBNPA degradation products based on past HF exposure, and (iii) compare the microbial community response differences and similarities between the HF biocides DBNPA and glutaraldehyde. The microbial community responded to DBNPA differently in HF-impacted versus HF-unimpacted microcosms in terms of the number of 16S rRNA gene copies quantified, alpha and beta diversity, and differential abundance analyses of microbial community composition through time. The differences in microbial community changes affected degradation dynamics. HF-impacted microbial communities were more sensitive to DBNPA, causing the biocide and by-products of the degradation to persist for longer than in HF-unimpacted microcosms. A total of 17 DBNPA by-products were detected, many of them not widely known as DBNPA by-products. Many of the brominated by-products detected that are believed to be uncharacterized may pose environmental and health impacts. Similar taxa were able to tolerate glutaraldehyde and DBNPA; however, DBNPA was not as effective for microbial control, as indicated by a smaller overall decrease of 16S rRNA gene copies/ml after exposure to the biocide, and a more diverse set of taxa was able to tolerate it. These findings suggest that past HF activity in streams can affect the microbial community response to environmental perturbation such as that caused by the biocide DBNPA.

Importance: Unconventional oil and gas activity can affect pH, total organic carbon, and microbial communities in surface water, altering their ability to respond to new environmental and/or anthropogenic perturbations. These findings demonstrate that 2,2-dibromo-3-nitrilopropionamide (DBNPA), a common hydraulic fracturing (HF) biocide, affects microbial communities differently as a consequence of past HF exposure, persisting longer in HF-impacted (HF+) waters. These findings also demonstrate that DBNPA has low efficacy in environmental microbial communities regardless of HF impact. These findings are of interest, as understanding microbial responses is key for formulating remediation strategies in unconventional oil and gas (UOG)-impacted environments. Moreover, some DBNPA degradation by-products are even more toxic and recalcitrant than DBNPA itself, and this work identifies novel brominated degradation by-products formed.

Campa, M.F., Wolfe, A.K., Techtmann, S.M., Harik, A.-M., Hazen, T.C., 2019. Unconventional oil and gas energy systems: An unidentified hotspot of antimicrobial resistance? Frontiers in Microbiology 10, 2392. doi: 10.3389/fmicb.2019.02392.


Biocides used in unconventional oil and gas (UOG) practices, such as hydraulic fracturing, control microbial growth. Unwanted microbial growth can cause gas souring, pipeline clogging, and microbial-induced corrosion of equipment and transportation pipes. However, optimizing biocide use has not been a priority. Moreover, biocide efficacy has been questioned because microbial surveys show an active microbial community in hydraulic fracturing produced and flowback water. Hydraulic fracturing produced and flowback water increases risks to surface aquifers and rivers/lakes near the UOG operations compared with conventional oil and gas operations. While some biocides and biocide degradation products have been highlighted as chemicals of concern because of their toxicity to humans and the environment, the selective antimicrobial pressure they cause has not been considered seriously. This perspective article aims to promote research to determine if antimicrobial pressure in these systems is cause for concern. UOG practices could potentially create antimicrobial resistance hotspots under-appreciated in the literature, practice, and regulation arena, hotspots that should not be ignored. The article is distinctive in discussing antimicrobial resistance risks associated with UOG biocides from a biological risk, not a chemical toxicology, perspective. We outline potential risks and highlight important knowledge gaps that need to be addressed to properly incorporate antimicrobial resistance emergence and selection into UOG environmental and health risk assessments.

Campbell, T.D., Febrian, R., McCarthy, J.T., Kleinschmidt, H.E., Forsythe, J.G., Bracher, P.J., 2019. Prebiotic condensation through wet–dry cycling regulated by deliquescence. Nature Communications 10, 4508.

https://doi.org/10.1038/s41467-019-11834-1

Wet–dry cycling is widely regarded as a means of driving condensation reactions under prebiotic conditions to generate mixtures of prospective biopolymers. A criticism of this model is its reliance on unpredictable rehydration events, like rainstorms. Here, we report the ability of deliquescent minerals to mediate the oligomerization of glycine during iterative wet–dry cycles. The reaction mixtures evaporate to dryness at high temperatures and spontaneously reacquire water vapor to form aqueous solutions at low temperatures. Deliquescent mixtures can foster yields of oligomerization over ten-fold higher than non-deliquescent controls. The deliquescent mixtures tightly regulate their moisture content, which is crucial, as too little water precludes dissolution of the reactants while too much water favors hydrolysis over condensation. The model also suggests a potential reason why life evolved to favor the enrichment of potassium: so living systems could acquire and retain sufficient water to serve as a solvent for biochemical reactions.

Candian, A., 2019. A fresh mechanism for how buckyballs form in space. Nature 574, 490-491.

https://www.nature.com/articles/d41586-019-03139-6

The spectroscopic fingerprints of buckyballs have been observed in space, but questions remain about how these large molecules form. Laboratory experiments have revealed a possible mechanism.

A long-standing mystery in astronomical spectroscopy concerns diffuse interstellar bands, a family of absorption features seen in the spectra of the interstellar medium of the Milky Way and of other galaxies. First observed almost 100 years ago, the origin of any of the bands was unknown until 2015, when four of them were assigned1 to the cation of buckministerfullerene (C60

+; the uncharged molecule is often referred to simply as fullerene, or colloquially as a buckyball). Fullerene and its analogue, C70, are by far the biggest molecules detected in space, raising the question of how such large species can form in those rarified conditions. Researchers have suggested that fullerene forms in

the outflows of old, carbon-rich stars known as asymptotic giant branch stars2 — the temperatures and densities of these outflows promote chemistry similar to that of combustion. This could lead to the formation of soot, which can contain fullerene-like structures. Writing in Astrophysical Journal Letters, Bernal et al.3 propose a very different formation route for fullerene.

The carbon atoms in fullerene are arranged in the shape of a football, a molecular structure that is remarkably stable but also difficult to construct. Fullerene has been made in the laboratory in experiments designed to probe the chemistry that occurs in carbon-rich stars: carbon in the form of graphite was vaporized into a high-density helium flow, producing carbon clusters4. The discovery that fullerene was among the reaction products led to the award of the Nobel Prize in Chemistry to Harry Kroto, Richard Smalley and Robert Curl in 1996.

However, the range of temperatures required to create fullerene in this way is quite specific2; outside that range, molecules known as polycyclic aromatic hydrocarbons (PAHs) are produced instead. These molecules are 2D sections of a single layer of graphite (a graphene sheet), decorated with hydrogen atoms. Subsequent experiments5,6 have shown that PAHs that contain more than 60 carbon atoms are converted into fullerenes when exposed to sufficient ultraviolet irradiation.

The first astronomical source in which fullerene was detected was the star Tc 17. Puzzlingly, however, the emission associated with fullerene came from a location far away from the star and its ultraviolet photons, whereas the PAH emissions were closer to the star. On the basis of the previously reported laboratory experiments, this is the opposite of what should happen if fullerene forms from PAHs in this source8. So how can the locations of the emissions be explained?

Bernal and co-workers now report that fullerene also forms readily from silicon carbide (SiC), which has been proposed to be the first carbonaceous material to condense out of old, carbon-rich stars9. The authors rapidly heated grains of the crystalline form of SiC that is found in highest abundance in meteorites10, and irradiated them with xenon ions, mimicking the heating caused by shock waves around old stars.

Using a transmission electron microscope to image the surfaces of the samples down to the subnanometre scale, the scientists observed that the grain material had altered notably as a result of its treatment (Fig. 1). Silicon atoms had percolated to the outer layers of the grains, leaving behind what looked like sheets of carbon atoms in a hexagonal ‘chicken-wire’ arrangement — that is, graphene sheets.

The transformation of the outer layers of SiC into graphene sheets at high temperatures had been reported11 previously for a different form of SiC from that studied by Bernal and colleagues. However, Bernal et al. also observed the formation of hemispherical structures with diameters similar to that of fullerene. Their work thus provides a convincing new mechanism for the formation of fullerene in evolved stars.

Bernal et al. report another piece of evidence supporting the idea that SiC grains are rapidly heated and bombarded with ions in evolved stars. They have identified a fragment of the Murchison meteorite — a highly studied meteorite that is rich in organic compounds — in which the ratio of carbon-12 to carbon-13 isotopes is typical of material from an old, carbon-rich star. This indicates that the fragment was not produced during or after the formation of the meteorite, but instead is stardust that originated in an old star. The fragment has a core of SiC surrounded by graphene sheets. However, previous analyses12 of graphite-containing stardust found evidence only of titanium carbide cores, rather than SiC cores. This raises the question of how common SiC cores are in graphite-containing stardust.

The rapid heating of SiC grains in the presence of hydrogen can lead to the formation of PAHs13. Bernal and colleagues’ findings therefore suggest that the thermal conversion of SiC to graphene sheets in evolved stars could be the first step in the formation of large carbon-containing molecules in general: subsequent (or simultaneous) exposure of the graphene to atomic hydrogen produces PAHs, whereas ion bombardment produces fullerene. Alternatively, PAH molecules might be molecular intermediates in the formation of carbon soot, which can then be broken down by ultraviolet irradiation to make PAHs again14.

The efficiency of Bernal and colleagues’ fullerene-forming mechanism is unknown, raising the question of how many SiC grains are needed to account for the observed abundance of fullerene molecules in space. If there aren’t enough grains, then a further mechanism will be required to explain the abundance of fullerene. By contrast, if there are too many SiC grains, what happens to the ‘excess’ fullerene molecules produced, given that they are notoriously difficult to degrade? More experiments and detailed modelling of the formation of fullerene and of other carbon-containing large molecules from SiC grains are needed to understand this process, and to quantify its importance in old stars.

The launch of the James Webb Space Telescope in 2021 will provide powerful new tools for studying old stars, among other astronomical objects. Observations of fullerene-containing sources7,8 such as Tc 1 will be able to constrain the regions in which SiC grains, fullerene and PAHs are present, providing more clues about how large molecules are actually formed. Further analysis and modelling of the routes involved will eventually allow astronomers to suggest the identities of the other mysterious molecules responsible for the diffuse interstellar bands.

References1. Campbell, E. K., Holz, M., Gerlich, D. & Maier, J. P. Nature 523, 322–323 (2015).2. Jäger, C., Huisken, F., Mutschke, H., Llamas Jansa, I. & Henning, T. Astrophys. J. 696, 706–712

(2009).3. Bernal, J. J. et al. Astrophys. J. 883, L43 (2019).4. Kroto, H. W., Heath, J. R., O’Brien, S. C., Curl, R. F. & Smalley, R. E. Nature 318, 162–163

(1985).5. Berné, O. & Tielens, A. G. G. M. Proc. Natl Acad. Sci. USA 109, 401–406 (2012).6. Zhen, J., Castellanos, P., Paardekooper, D. M., Linnartz, H. & Tielens, A. G. G. M. Astrophys. J.

797, L30 (2014).7. Cami, J., Bernard-Salas, J., Peeters, E. & Male, S. E. Science 329, 1180–1182 (2010).8. Cami, J., Peeters, E., Bernard-Salas, J., Doppmann, G. & De Buizer, J. Galaxies 6, 101 (2018).9. Frenklach, M., Carmer, C. S. & Feigelson, E. D. Nature 339, 196–198 (1989).10. Daulton, T. L. et al. Science 296, 1852–1855 (2002).11. Mishra, N., Boeckl, J., Motta, N. & Iacopi, F. Phys. Status Solidi A 213, 2277–2289 (2016).12. Croat, K. T., Bernatowicz, T. J. & Daulton, T. L. Elements 10, 441–446 (2014).13. Merino, P. et al. Nature Commun. 5, 3054 (2014).14. Cherchneff, I., Barker, J. R. & Tielens, A. G. G. M. Astrophys. J. 401, 269–287 (1992).

Carmichael, S.K., Waters, J.A., Königshof, P., Suttner, T.J., Kido, E., 2019. Paleogeography and paleoenvironments of the Late Devonian Kellwasser event: A review of its sedimentological and geochemical expression. Global and Planetary Change 183, 102984.


The Late Devonian (383-359 Ma) was a time of prolonged climate instability with catastrophic perturbation of global marine ecosystems at the Frasnian-Famennian (F-F) and the Devonian-

Carboniferous (D-C) boundaries. The causes and mechanisms of anoxia and extinction at the F-F interval are not clearly delineated, and alternative explanations for virtually every aspect of this interval are still intensely debated. In many (but not all) locations, the F-F interval is characterized by two dark, organic-rich lithologies: the Lower and Upper Kellwasser beds (as originally described in Germany) that represent a stepwise ocean anoxia and extinction sequence. The Upper and Lower Kellwasser anoxia event beds are often collectively termed the Kellwasser Event, and the termination of this sequence is within the Upper Kellwasser Event at the F-F boundary. Current knowledge is limited by significant sampling bias, as most previous studies sampled epicontinental seaways or passive continental shelves, primarily from localities across Europe and North America. Together these formed a single equatorial continent with a rising mountain chain during the Late Devonian. Our understanding of the Kellwasser Event is thus based on data and observations from a restricted set of paleoenvironments that may not represent the complete range of Late Devonian environments and oceanic conditions. In the last decade, new methodologies and research in additional paleoenvironments around the world confirm that the Kellwasser Event was global in scope, but also that its expression varies with both paleoenvironment and paleogeography. Studying the many differing geochemical and lithological expressions of the Kellwasser Event using a) a wide variety of paleoenvironments, b) a multiproxy approach, and c) placement of results into the broader context of Late Devonian marine biodiversity patterns is vital for understanding the true scope of ocean anoxia, and determining the causes of the marine biodiversity crisis at the F-F boundary.

Carrión Marco, Y., Vives-Ferrándiz Sánchez, J., 2019. Rethinking the perishable: Identifying organic remains in metal objects at the Iron Age site of La Bastida de les Alcusses (Moixent, Spain). Journal of Archaeological Science: Reports 27, 101970.


The use of certain perishable materials for handicraft, such as wood, has been underestimated in archaeological investigation due to their poor preservation. Its study through indirect evidence (other non-perishable materials, ethnographic sources) is partial, and does not account for the real importance of wood in domestic, craft and ritual contexts in past societies. In this review we reclaim the use of wood as a co-constitutive material of objects by focusing on Iron Age tools, weapons and carpentry elements from a case-study in the Western Mediterranean. We also suggest the adoption of protocols for sampling and analysing the remains of wood adhered to metal objects, which may contribute to increase our knowledge about the use of this raw material in the past.

Casabianca, T., Marinelli, E., Pernagallo, G., Torrisi, B., 2019. Radiocarbon dating of the Turin Shroud: New evidence from raw data. Archaeometry 61, 1223-1231.

https://doi.org/10.1111/arcm.12467

In 1988, three laboratories performed a radiocarbon analysis of the Turin Shroud. The results, which were centralized by the British Museum and published in Nature in 1989, provided ?conclusive evidence? of the medieval origin of the artefact. However, the raw data were never released by the institutions. In 2017, in response to a legal request, all raw data kept by the British Museum were made accessible. A statistical analysis of the Nature article and the raw data strongly suggests that homogeneity is lacking in the data and that the procedure should be reconsidered.

Castro, J.M., de Gea, G.A., Quijano, M.L., Aguado, R., Froehner, S., Naafs, B.D.A., Pancost, R.D., 2019. Complex and protracted environmental and ecological perturbations during OAE 1a - Evidence from

an expanded pelagic section from south Spain (Western Tethys). Global and Planetary Change 183, 103030.


The early Aptian Oceanic Anoxic Event (OAE) 1a represents a major perturbation in the global carbon cycle associated with significant environmental, biotic and sedimentary changes. The signature of this event is a global negative followed by a positive stable carbon isotope excursion (CIE), associated with the input of light-carbon into the climate system and subsequent widespread deposition of organic-rich sediments. This study uses biostratigraphy, C-isotope stratigraphy, biomarkers, and elemental geochemistry to stratigraphically and geochemically characterize OAE 1a at an expanded pelagic marine section from the western Tethys.

The high-resolution δ13Corg analysis of the section highlights several successive negative CIEs during the onset of OAE 1a (isotope segment C3), pointing to rapid changes in global carbon cycling. The biomarker data indicate that the organic matter is thermally mature and is mainly of marine origin. The biomarker assemblage together with records of redox-sensitive trace elements suggest that sedimentation took place under generally well oxygenated waters punctuated by three short episodes of sea floor anoxia/dysoxia. The two first episodes of anoxia/dysoxia correlate with enhanced organic productivity during the main negative C-isotope excursion that represents the onset of the OAE 1a. They occurred at the final part of C-isotope negative excursions, likely as a response to C-release, increased temperatures and associated hydrological change and weathering, which resulted in increased fertilization-driven oxygen consumption. This was followed by the positive carbon isotope excursion, due to the burial of OM outpacing carbon input. The third episode of anoxia-dysoxia, which occurred later during the major positive C-isotope excursion, is not associated with fertilization, and perhaps instead reflects a general progressive depletion of oxygen during OAE 1a, linked to stagnation of marine waters. Interestingly, although the environmental parameters return to pre-OAE values at the end of the event, a biotic (especially microbial) perturbation persisted after OAE 1a. Our results suggest that instability in environmental conditions was the main feature during OAE 1a in the western Tethys with notable changes extending from the onset to the post-OAE 1a interval.


https://doi.org/10.1073/pnas.1912498116

Significance: Electricity-producing bacteria are potential power sources, fermentation platforms, and desalination systems, if current densities could be increased. These organisms form conductive biofilms on electrodes, allowing new cell layers to contribute to current production until a limit is reached, but the biological underpinning of this limit is not well-understood. We investigated the limitation behind this phenomenon using stable isotope probing and nanoscale secondary ion mass spectrometry, showing active cells are restricted to layers closest to the electrode. This metabolic observation fundamentally changes our understanding of electron flow and cell growth within current-producing biofilms and provides constraints on the physical structure of natural communities reliant on this process for growth. We predict improvements in biofilm conductivity will yield higher current-producing systems.

Abstract: Metal-reducing bacteria direct electrons to their outer surfaces, where insoluble metal oxides or electrodes act as terminal electron acceptors, generating electrical current from anaerobic

respiration. Geobacter sulfurreducens is a commonly enriched electricity-producing organism, forming thick conductive biofilms that magnify total activity by supporting respiration of cells not in direct contact with electrodes. Hypotheses explaining why these biofilms fail to produce higher current densities suggest inhibition by formation of pH, nutrient, or redox potential gradients; but these explanations are often contradictory, and a lack of direct measurements of cellular growth within biofilms prevents discrimination between these models. To address this fundamental question, we measured the anabolic activity of G. sulfurreducens biofilms using stable isotope probing coupled to nanoscale secondary ion mass spectrometry (nanoSIMS). Our results demonstrate that the most active cells are at the anode surface, and that this activity decreases with distance, reaching a minimum 10 µm from the electrode. Cells nearest the electrode continue to grow at their maximum rate in weeks-old biofilms 80-µm-thick, indicating nutrient or buffer diffusion into the biofilm is not rate-limiting. This pattern, where highest activity occurs at the electrode and declines with each cell layer, is present in thin biofilms (<5 µm) and fully grown biofilms (>20 µm), and at different anode redox potentials. These results suggest a growth penalty is associated with respiring insoluble electron acceptors at micron distances, which has important implications for improving microbial electrochemical devices as well as our understanding of syntrophic associations harnessing the phenomenon of microbial conductivity.

Chamberlain, C.A., Rubio, V.Y., Garrett, T.J., 2019. Impact of matrix effects and ionization efficiency in non-quantitative untargeted metabolomics. Metabolomics 15, 135.

https://doi.org/10.1007/s11306-019-1597-z

Introduction: LC–MS-based untargeted metabolomics has become increasingly popular due to the vast amount of information gained in a single analysis. Many studies utilize metabolomics to profile metabolic changes in various representative biofluids, tissues, or other sample types. Most analyses are performed measuring changes in the metabolic pool of a single biological matrix due to an altered phenotype, such as disease versus normal. Measurements in such experiments are typically highly reproducible with little variation due to analytical and technological advancements in mass spectrometry. With the expanded application of metabolomics into various non-analytical scientific disciplines, the emergence of studies comparing the signal intensities of specific analytes across different biological matrices (e.g. plasma vs. urine) is becoming more common, but the matrix effect between sample types is often neglected. Additionally, the practice of comparing the signal intensities of different analytes and correlating to relative abundance is also increasingly prevalent, but the response ratio between analytes due to differences in ionization efficiency is not always accounted for in data analysis. This report serves to communicate and raise awareness of these two well-recognized issues to prevent improper data interpretation in the field of metabolomics.

Objectives: We demonstrate the impact of matrix effects and ionization efficiency with labeled analytical standards in human plasma, serum, and urine and describe how the direct comparison of non-quantitative signal intensities between biofluids, as well as between different analytes in the same biofluid, in untargeted metabolomics is inaccurate without proper response corrections.

Methods: Human plasma, serum, and urine (n = 4 technical replicates per biofluid) were spiked with a panel of labeled internal standards all at identical concentrations, simultaneously extracted, and analyzed by UHPLC-HRMS. Signal intensities were compared for demonstration of the impact of matrix effects in untargeted metabolomics. A neat mixture of two co-eluting, structurally-similar labeled standards at the same concentration was also analyzed to demonstrate the effect of ionization efficiency on signal intensity.

Results: Despite being spiked at identical concentrations, labeled standards we examined in this study showed significant differences in their signal intensities between biofluids, as well as from each other in the same biofluid, due to matrix effects. Co-eluting standards were also found to yield significantly different signal intensities at identical concentrations due to differences in ionization efficiency.

Conclusions: Due to the presence of matrix effects in untargeted, non-quantitative metabolomics, the signal intensity of any single analyte cannot be directly compared to the signal intensity of that same analyte (or any other analyte) between any two different matrices. Due to differences in ionization efficiency, the signal intensity of any single analyte cannot be directly compared to the signal intensity of any other analyte, even in the same matrix.

Channell, J.E.T., Vigliotti, L., 2019. The role of geomagnetic field intensity in late Quaternary evolution of humans and large mammals. Reviews of Geophysics 57, 709-738.

https://doi.org/10.1029/2018RG000629

Abstract: It has long been speculated that biological evolution was influenced by ultra‐violet radiation (UVR) reaching the Earth's surface, despite imprecise knowledge of the timing of both UVR flux and evolutionary events. The past strength of Earth's dipole field provides a proxy for UVR flux because of its role in maintaining stratospheric ozone. The timing of Quaternary evolutionary events has become better constrained by fossil finds, improved radiometric dating, use of dung fungi as proxies for herbivore populations, and improved ages for nodes in human phylogeny from human mitochrondrial DNA (mtDNA) and Y‐chromosomes. The demise of Neanderthals at ~41 ka can now be closely tied to the intensity minimum associated with the Laschamp magnetic excursion, and the survival of anatomically modern humans (AMHs) can be attributed to differences in the aryl hydrocarbon receptor (AhR) that has a key role in the evolutionary response to UVR flux. Fossil occurrences and dung‐fungal proxies in Australia indicate that episodes of Late Quaternary extinction (LQE) of mammalian megafauna occurred close to the Laschamp and Blake magnetic excursions. Fossil and dung fungal evidence for the age of the LQE in North America (and Europe) coincide with a prominent decline in geomagnetic field intensity at ~13 ka. Over the last ~200 kyr, phylogeny based on mtDNA and Y‐chromosomes in modern humans yield nodes and bifurcations in evolution corresponding to geomagnetic intensity minima which supports the proposition that UVR reaching Earth's surface influenced mammalian evolution with the loci of extinction controlled by the geometry of stratospheric ozone depletion.

Plain Language Summary: The strength of Earth's magnetic field in the past, recorded by rocks and sediments, provides a proxy for past flux of ultra‐violet radiation (UVR) to Earth's surface due to the role of the field in modulating stratigraphic ozone. About 40 thousand years ago, mammalian fossils in Australia and Eurasia record an important die‐off of large mammals that included Neanderthals in Europe. In the Americas and Europe, a large mammalian die‐off appears to have occurred ~13 thousand years ago. Both die‐offs can be linked to minima in Earth's magnetic field strength implying that UVR flux variations to Earth's surface influenced mammalian evolution. For the last ~200 thousand years, estimates of the timing of branching episodes in the human evolutionary tree, from modern and fossil DNA and Y‐chromosomes, can be linked to minima in field strength which implies a long‐term role for UVR in human evolution. New fossil finds, improved fossil dating, knowledge of the past strength of Earth's magnetic field, and refinements in the human evolutionary tree, are sharpening the focus on a possible link between UVR arriving at the Earth's surface, magnetic field strength, and events in mammalian evolution.

Chatterjee, A., DeLorenzo, D.M., Carr, R., Moon, T.S., 2020. Bioconversion of renewable feedstocks by Rhodococcus opacus. Current Opinion in Biotechnology 64, 10-16.


The production of fuels and chemicals from renewable feedstocks is necessary for a fossil fuel independent economy. Lignin and other industrial wastes represent sustainable, non-food feedstocks that can be tapped for microbe-based bioproduction. Rhodococcus opacus is a gram-positive bacterium capable of catabolizing a broad range of feedstocks, and recent technological advances have further established its potential for lignin and industrial waste valorization. In the process of developing R. opacus as a platform for bioproduction, metabolic profiling has elucidated its native mechanisms of bioconversion, adaptive evolution has enhanced its tolerance towards inhibitory feedstocks, and genetic engineering has enabled it to produce novel products, such as wax esters, free fatty acids, and long chain hydrocarbons. Here, we present recent examples of broad feedstock utilization and value-added chemical production by R. opacus, demonstrating its potential as an industrially relevant strain.


https://doi.org/10.1007/s10295-019-02211-4

Functional differentiation and metabolite exchange enable microbial consortia to perform complex metabolic tasks and efficiently cycle the nutrients. Inspired by the cooperative relationships in environmental microbial consortia, synthetic microbial consortia have great promise for studying the microbial interactions in nature and more importantly for various engineering applications. However, challenges coexist with promises, and the potential of consortium-based technologies is far from being fully harnessed. Thorough understanding of the underlying molecular mechanisms of microbial interactions is greatly needed for the rational design and optimization of defined consortia. These knowledge gaps could be potentially filled with the assistance of the ongoing revolution in systems biology and synthetic biology tools. As current fundamental and technical obstacles down the road being removed, we would expect new avenues with synthetic microbial consortia playing important roles in biological and environmental engineering processes such as bioproduction of desired chemicals and fuels, as well as biodegradation of persistent contaminants.

Chen, D., Wu, S., Xue, H., Jiang, J., 2020. Stereoselective catabolism of compounds by microorganisms: Catabolic pathway, molecular mechanism and potential application. International Biodeterioration & Biodegradation 146, 104822.


Stereoisomeric compounds, including chemical pesticides and pharmaceuticals, are used worldwide in public health, industrial, and agricultural settings. Different stereoisomers of stereoisomeric compounds usually show different biological activities and stereoselective toxicities and experience different environmental fates. Due to their stereoselective effect and toxicity, investigations of the stereoselective catabolism of stereoisomeric compounds by microorganisms in environments are of great concern. Stereoselective enzymes responsible for the catabolism of stereoisomeric compounds have been proven to have great potential in the biological production of chirally pure chemicals. In this review, the microbial resources and their catabolic pathways involved in the stereoselective catabolism of stereoisomeric compounds, with emphasis on chiral pesticides (phenoxypropanoic acid

herbicides, lactofen, napropamide, synthetic pyrethroids, hexachlorocyclohexane and organophosphate pesticides) and some other xenobiotics (organohalides and polycyclic aromatic hydrocarbons), are summarized. The molecular mechanisms underlying stereoselective catalysis by enzymes based on structural resolution are expatiated. Furthermore, potential applications of stereoselective enzymes for the production of chirally pure chemicals are also introduced.


http://www.cngascn.com:81/ngi_wk/EN/abstract/abstract18894.shtml

In carrying out shale gas exploration in new areas and new strata, outcrop samples are usually adopted for reservoir evaluation, but uncertainty exists when the pore systems in underground shale are evaluated based on the pore structures of weathered outcrop samples. What’s more, how weathering alters shale pores is not figured out yet. In order to clarify the influence of weathering on the pores in black shale, this paper conducted comprehensive characterization and comparative analysis on the outcrop samples of different weathering levels and downhole core samples from the Niutitang Formation of Lower Cambrian in northern Hunan province using Ar-ion milling, field emission scanning electron microscope and gas adsorption techniques. Then, the alteration effect of weathering on the pores in black shale was discussed. And the following research results were obtained. First, the dissolution pores of carbonate mineral/feldspar, inter-crystal pores within pyrite aggregates, organic matter-hosted pores and micro-fractures are more developed in outcropping shale than in underground shale. Second, with the increase of weathering degree, the shale porosity increases and the specific surface area decreases firstly and then increases. Third, the weathering effect of shale mineral occurs in a certain order. The dissolution of unstable minerals and the oxidation of pyrite happen first, the oxidation of organic matter takes the second place, and the last is the loosening and breaking of matrix minerals. Fourth, the weathering degree of shale can be classified into three levels, i.e., weak, medium and high. The secondary pores in the shale of weak weathering level are mainly derived from the dissolution of carbonate minerals and feldspar and the oxidation of pyrite, and its porosity is up to 12%. The organic matter in the shale of medium weathering level is mostly oxidized, so its porosity is up to 30%. The shale of high weathering level mainly undergoes the loosening of matrix minerals (e.g. clay) and the gradual development of micro-fractures until rocks break. In conclusion, the research results are conducive to the application of outcrop research in shale gas reservoir evaluation and provide support for the shale gas exploration in new areas and new strata.

Chettri, B., Singh, A.K., 2019. Kinetics of hydrocarbon degradation by a newly isolated heavy metal tolerant bacterium Novosphingobium panipatense P5:ABC. Bioresource Technology 294, 122190.


This study report kinetics of PAHs and crude oil degradation by a newly isolated multiple heavy metal tolerant Novosphingobium panipatense P5:ABC. The isolate showed hydrocarbon degrading enzyme activities namely alkane hydroxylase, catechol 1,2-dioxygenase and catechol 2,3-dioxygenase. The level of C23O activity was 9.63 times higher than C12O thus suggesting active involvement of meta-cleavage pathway. The data of biodegradation of hydrocarbons fitted well to the first order kinetic model. The degradation rate was highest for phenanthrene followed by crude oil, and fluoranthene. We have further reported the estimate of fundamental kinetic parameters, half-saturation constant (Ks) and maximum degradation rates (Vmax) for biodegradation of phenanthrene

and fluoranthene. Overall characterization underscores the potential of Novosphingobium in bioremediation of crude oil polluted sites.

Chipman, A.D., Edgecombe, G.D., 2019. Developing an integrated understanding of the evolution of arthropod segmentation using fossils and evo-devo. Proceedings of the Royal Society B: Biological Sciences 286, 20191881.

https://doi.org/10.1098/rspb.2019.1881

Segmentation is fundamental to the arthropod body plan. Understanding the evolutionary steps by which arthropods became segmented is being transformed by the integration of data from evolutionary developmental biology (evo-devo), Cambrian fossils that allow the stepwise acquisition of segmental characters to be traced in the arthropod stem-group, and the incorporation of fossils into an increasingly well-supported phylogenetic framework for extant arthropods based on genomic-scale datasets. Both evo-devo and palaeontology make novel predictions about the evolution of segmentation that serve as testable hypotheses for the other, complementary data source. Fossils underpin such hypotheses as arthropodization originating in a frontal appendage and then being co-opted into other segments, and segmentation of the endodermal midgut in the arthropod stem-group. Insights from development, such as tagmatization being associated with different modes of segment generation in different body regions, and a distinct patterning of the anterior head segments, are complemented by palaeontological evidence for the pattern of tagmatization during ontogeny of exceptionally preserved fossils. Fossil and developmental data together provide evidence for a short head in stem-group arthropods and the mechanism of its formation and retention. Future breakthroughs are expected from identification of molecular signatures of developmental innovations within a phylogenetic framework, and from a focus on later developmental stages to identify the differentiation of repeated units of different systems within segmental precursors.

Ćirković, M.M., Vukotić, B., Stojanović, M., 2019. Persistence of technosignatures: A comment on Lingam and Loeb. Astrobiology 19, 1300-1302.

https://doi.org/10.1089/ast.2019.2052

In a recent article in this journal, Lingam and Loeb developed an excellent heuristic for searches for biosignatures versus technosignatures. We consider two ways in which their approach could be extended and sharpened, with focus on durability of technosignatures. We also note an important consequence of the adopted heuristic that offers strong support to the ideas of the Dysonian Search for ExtraTerrestrial Intelligence (SETI).

Codella, C., Ceccarelli, C., Lee, C.-F., Bianchi, E., Balucani, N., Podio, L., Cabrit, S., Gueth, F., Gusdorf, A., Lefloch, B., Tabone, B., 2019. The HH 212 interstellar laboratory: Astrochemistry as a tool to reveal protostellar disks on solar system scales around a rising sun. ACS Earth and Space Chemistry 3, 2110-2121.


The investigation of star-forming regions has enormously benefited from the recent advent of the ALMA interferometer working in the millimeter- and submillimeter-wavelength spectral windows. More specifically, the unprecedented combination of high-sensitivity and high-angular resolution provided by ALMA allows one to shed light on the jet/disk systems associated with a Sun-like mass protostar. In this context, astrochemistry also possesses the possibility to analyze complex spectra

obtained using large bandwidths: several interstellar complex organic molecules (iCOMs; C-bearing species with at least six atoms) have been detected and imaged around protostars, often thanks to a large number of rotational–vibrational lines. This in turn boosted the study of the astrochemistry at work during the earliest phases of star formation paving the way to the chemical complexity in planetary systems where Life could emerge. There is mounting evidence that the observations of iCOMs (e.g., CH3CHO or NH2CHO) can be used as unique tools to shed light on Solar System scales (<50 au) on the molecular content of protostellar disk. The increase of iCOMs abundance occur only under very selective physical conditions, such as those associated low-velocity shocks found where the infalling envelope is impacting the rotating accretion disk. The imaging of these regions with simpler molecules such as CO or CS is indeed paradoxically hampered by their high abundances and consequently high line opacities which do not allow the observers to disentangle all the emitting components at these small scales. In this respect, we review the state-of-the art of the ALMA analysis about the standard Sun-like star forming region in Orion named HH 212, associated with a pristine jet-disk protostellar system. We enrich the discussion with unpublished ALMA data sets, showing (i) how all of the physical components involved in the formation of a Sun-like star can be revealed only by observing different molecular tracers, and (ii) how the observation of iCOMs emission, observed to infer the chemical composition of star-forming regions, can be used also as a unique tracer to image protostellar disks on Solar System scales, that is, where planets will eventually form.

Cohen, B.A., Malespin, C.A., Farley, K.A., Martin, P.E., Cho, Y., Mahaffy, P.R., 2019. In situ geochronology on Mars and the development of future instrumentation. Astrobiology 19, 1303-1314.

https://doi.org/10.1089/ast.2018.1871

We review the in situ geochronology experiments conducted by the Mars Science Laboratory mission's Curiosity rover to understand when the Gale Crater rocks formed, underwent alteration, and became exposed to cosmogenic radiation. These experiments determined that the detrital minerals in the sedimentary rocks of Gale are ∼4 Ga, consistent with their origin in the basalts surrounding the crater. The sedimentary rocks underwent fluid-moderated alteration 2 Gyr later, which may mark the closure of aqueous activity at Gale Crater. Over the past several million years, wind-driven processes have dominated, denuding the surfaces by scarp retreat. The Curiosity measurements validate radiometric dating techniques on Mars and guide the way for future instrumentation to make more precise measurements that will further our understanding of the geological and astrobiological history of the planet.

Colangelo-Lillis, J., Pelikan, C., Herbold, C.W., Altshuler, I., Loy, A., Whyte, L.G., Wing, B.A., 2019. Diversity decoupled from sulfur isotope fractionation in a sulfate-reducing microbial community. Geobiology 17, 660-675.


The extent of fractionation of sulfur isotopes by sulfate‐reducing microbes is dictated by genomic and environmental factors. A greater understanding of species‐specific fractionations may better inform interpretation of sulfur isotopes preserved in the rock record. To examine whether gene diversity influences net isotopic fractionation in situ, we assessed environmental chemistry, sulfate reduction rates, diversity of putative sulfur‐metabolizing organisms by 16S rRNA and dissimilatory sulfite reductase (dsrB) gene amplicon sequencing, and net fractionation of sulfur isotopes along a sediment transect of a hypersaline Arctic spring. In situ sulfate reduction rates yielded minimum cell‐specific sulfate reduction rates < 0.3 × 10−15 moles cell−1 day−1. Neither 16S rRNA nor dsrB diversity indices correlated with relatively constant (38‰–45‰) net isotope fractionation (ε34Ssulfide‐sulfate). Measured

ε34S values could be reproduced in a mechanistic fractionation model if 1%–2% of the microbial community (10%–60% of Deltaproteobacteria) were engaged in sulfate respiration, indicating heterogeneous respiratory activity within sulfate‐reducing populations. This model indicated enzymatic kinetic diversity of Apr was more likely to correlate with sulfur fractionation than DsrB. We propose that, above a threshold Shannon diversity value of 0.8 for dsrB, the influence of the specific composition of the microbial community responsible for generating an isotope signal is overprinted by the control exerted by environmental variables on microbial physiology.

Colombet, J., Billard, H., Viguès, B., Balor, S., Boulé, C., Geay, L., Benzerara, K., Menguy, N., Ilango, G., Fuster, M., Enault, F., Bardot, C., Gautier, V., Pradeep Ram, A.S., Sime-Ngando, T., 2019. Discovery of high abundances of aster-like nanoparticles in pelagic environments: Characterization and dynamics. Frontiers in Microbiology 10, 2376. doi: 10.3389/fmicb.2019.02376.


This study reports the discovery of Aster-Like Nanoparticles (ALNs) in pelagic environments. ALNs are pleomorphic, with three dominant morphotypes which do not fit into any previously defined environmental entities [i.e., ultramicro-prokaryotes, controversed nanobes, and non-living particles (biomimetic mineralo-organic particles, natural nanoparticles or viruses)] of similar size. Elemental composition and selected-area electron diffraction patterns suggested that the organic nature of ALNs may prevail over the possibility of crystal structures. Likewise, recorded changes in ALN numbers in the absence of cells are at odds with an affiliation to until now described viral particles. ALN abundances showed marked seasonal dynamics in the lakewater, with maximal values (up to 9.0 ± 0.5 × 107 particles·mL−1) reaching eight times those obtained for prokaryotes, and representing up to about 40% of the abundances of virus-like particles. We conclude that (i) aquatic ecosystems are reservoirs of novel, abundant, and dynamic aster-like nanoparticles, (ii) not all virus-like particles observed in aquatic systems are necessarily viruses, and (iii) there may be several types of other ultra-small particles in natural waters that are currently unknown but potentially ecologically important.

Colwyn, D.A., Sheldon, N.D., Maynard, J.B., Gaines, R., Hofmann, A., Wang, X., Gueguen, B., Asael, D., Reinhard, C.T., Planavsky, N.J., 2019. A paleosol record of the evolution of Cr redox cycling and evidence for an increase in atmospheric oxygen during the Neoproterozoic. Geobiology 17, 579-593.


Atmospheric oxygen levels control the oxidative side of key biogeochemical cycles and place limits on the development of high‐energy metabolisms. Understanding Earth's oxygenation is thus critical to developing a clearer picture of Earth's long‐term evolution. However, there is currently vigorous debate about even basic aspects of the timing and pattern of the rise of oxygen. Chemical weathering in the terrestrial environment occurs in contact with the atmosphere, making paleosols potentially ideal archives to track the history of atmospheric O2 levels. Here we present stable chromium isotope data from multiple paleosols that offer snapshots of Earth surface conditions over the last three billion years. The results indicate a secular shift in the oxidative capacity of Earth's surface in the Neoproterozoic and suggest low atmospheric oxygen levels (<1% PAL pO2) through the majority of Earth's history. The paleosol record also shows that localized Cr oxidation may have begun as early as the Archean, but efficient, modern‐like transport of hexavalent Cr under an O2‐rich atmosphere did not become common until the Neoproterozoic.

Conrad, R., Klose, M., Enrich-Prast, A., 2019. Acetate turnover and methanogenic pathways in Amazonian lake sediments. Biogeosciences Discussions 2019, 1-19.

https://www.biogeosciences-discuss.net/bg-2019-411/

Lake sediments in Amazonia are a significant source of CH4, a potential greenhouse gas. Previous studies of sediments using 13C analysis found that the contribution of hydrogenotrophic versus aceticlastic methanogenesis to CH4 production was relatively high. Here, we determined the methanogenic pathway in the same sediments (n = 6) by applying [14C]bicarbonate or [2-14C]acetate, and confirmed the high relative contribution (50–80 %) of hydrogenotrophic methanogenesis. The respiratory index (RI) of [2-14C]acetate, which is 14CO2 relative to 14CH4 + 14CO2, divided the sediments into two categories, i.e., those with an RI < 0.2 being consistent with the operation of aceticlastic methanogenesis, and those with an RI > 0.4 showing that a large percentage of the acetate-methyl was oxidized to CO2 rather than reduced to CH4. Hence, part of the acetate was probably converted to CO2 plus H2 via syntrophic oxidation, thus enhancing hydrogenotrophic methanogenesis. This happened despite the presence of potentially aceticlastic Methanosaetaceae in all the sediments. Alternatively, acetate may have been oxidized with a constituent of the sediment organic matter (humic acid) serving as oxidant. Indeed, apparent acetate turnover rates were larger than CH4 production rates except in those sediments with a R < 0.2. Our study demonstrates that CH4 production in Amazonian lake sediments was not simply caused by a combination of hydrogenotrophic and aceticlastic methanogenesis, but probably involved additional acetate turnover.

Corenblit, D., Darrozes, J., Julien, F., Otto, T., Roussel, E., Steiger, J., Viles, H., 2019. The search for a signature of life on Mars: A biogeomorphological approach. Astrobiology 19, 1279-1291.

https://doi.org/10.1089/ast.2018.1969

Geological evidence shows that life on Earth evolved in line with major concomitant changes in Earth surface processes and landforms. Biogeomorphological characteristics, especially those involving microorganisms, are potentially important facets of biosignatures on Mars and are generating increasing interest in astrobiology. Using Earth as an analog provides reasons to suspect that past or present life on Mars could have resulted in recognizable biogenic landforms. Here, we discuss the potential for, and limitations of, a biogeomorphological approach to identifying the subsets of landforms that are modulated or created through biological processes and thus present signatures of life on Mars. Subsets especially involving microorganisms that are potentially important facets of biosignatures on Mars are proposed: (i) weathering features, biocrusts, patinas, and varnishes; (ii) microbialites and microbially induced sedimentary structures (MISS); (iii) bioaccumulations of skeletal remains; (iv) degassing landforms; (v) cryoconites; (vi) self-organized patterns; (vii) unclassified non-analog landforms. We propose a biogeomorphological frequency histogram approach to identify anomalies/modulations in landform properties. Such detection of anomalies/modulations will help track a biotic origin and lead to the development of an integrative multiproxy and multiscale approach combining morphological, structural, textural, and geochemical expertise. This perspective can help guide the choice of investigation sites for future missions and the types and scales of observations to be made by orbiters and rovers.

Corrick, A.J., Hall, P.A., Gong, S., McKirdy, D.M., Selby, D., Trefry, C., Ross, A.S., 2020. A second type of highly asphaltic crude oil seepage stranded on the South Australian coastline. Marine and Petroleum Geology 112, 104062.


Strandings of semi-solid to solid asphaltic bitumen along the coastline of South Australia have been reported as far back as the late 1800s. Hitherto only a single variety, now referred to as asphaltite, has been attributed to seepage from the nearby Bight Basin. The geochemistry of the asphaltites suggest they were derived from a marine source rock deposited under anoxic or euxinic conditions, most likely a Cretaceous ocean anoxic event, and were generated within the early/main oil window. Here we identify a new type of semi-solid asphaltic bitumen collected following a severe storm event in 2016. Termed asphaltic tars, these viscous oils bear a strong geochemical resemblance to the asphaltites. Both oil types have high asphaltene contents, identical n-alkane carbon isotopic profiles and near identical source-specific sterane distributions. However, several notable geochemical variations can distinguish these new strandings from the asphaltites. The most notable of these differences include heavier bulk sulphur isotopic composition, extremely high abundances of Re and Os with distinct 187Re/188Os and 187Os/188Os values and thermal maturity parameters consistent with generation in the late oil window. The differences in sulphur isotopic composition and Re-Os systematics could be considered evidence that despite their other source-specific similarities, the asphaltic tars originated from a different source rock. However, alteration of these two parameters can occur due to thermochemical sulphate reduction. Conclusive identification of this alteration process typically relies on further diagnostic parameters which are unfortunately not available in the case of coastal oil strandings. This introduces uncertainty to the correlation of these two types of asphaltic oil. In either scenario, the similarities between these two types of oil suggest their source rock(s) contained highly comparable organic matter inputs. We therefore attribute the origin of these new asphaltic tar strandings to natural seepage from the offshore Bight Basin.

Cox, S.L., Ruff, C.B., Maier, R.M., Mathieson, I., 2019. Genetic contributions to variation in human stature in prehistoric Europe. Proceedings of the National Academy of Sciences 116, 21484-21492.


Significance: Measurements of prehistoric human skeletal remains provide a record of changes in height and other anthropometric traits over time. Often, these changes are interpreted in terms of plastic developmental response to shifts in diet, climate, or other environmental factors. These changes can also be genetic in origin, but, until recently, it has been impossible to separate the effects of genetics and environment. Here, we use ancient DNA to directly estimate genetic changes in phenotypes and to identify changes driven not by genetics, but by environment. We show that changes over the past 35,000 y are largely predicted by genetics but also identify specific shifts that are more likely to be environmentally driven.

Abstract: The relative contributions of genetics and environment to temporal and geographic variation in human height remain largely unknown. Ancient DNA has identified changes in genetic ancestry over time, but it is not clear whether those changes in ancestry are associated with changes in height. Here, we directly test whether changes over the past 38,000 y in European height predicted using DNA from 1,071 ancient individuals are consistent with changes observed in 1,159 skeletal remains from comparable populations. We show that the observed decrease in height between the Early Upper Paleolithic and the Mesolithic is qualitatively predicted by genetics. Similarly, both skeletal and genetic height remained constant between the Mesolithic and Neolithic and increased between the Neolithic and Bronze Age. Sitting height changes much less than standing height—consistent with genetic predictions—although genetics predicts a small post-Neolithic increase that is not observed in skeletal remains. Geographic variation in stature is also qualitatively consistent with genetic predictions, particularly with respect to latitude. Finally, we hypothesize that an observed decrease in genetic heel bone mineral density in the Neolithic reflects adaptation to the decreased mobility indicated by decreased femoral bending strength. This study provides a model for interpreting phenotypic changes predicted from ancient DNA and demonstrates how they can be combined with

phenotypic measurements to understand the relative contribution of genetic and developmentally plastic responses to environmental change.

Cui, J., Zhu, R., Li, S., Qi, Y., Shi, X., Mao, Z., 2019. Development patterns of source rocks in the depression lake basin and its influence on oil accumulation: Case study of the Chang 7 member of the Triassic Yanchang Formation, Ordos Basin, China. Journal of Natural Gas Geoscience 4, 191-204.


During the Mesozoic, the T-J1 oil system of the Ordos Basin, whilst the degree of oil enrichment, main production layer, and source rock distribution exhibit strong regional differences, no systematic study has been conducted to investigate these differences. At this time, the total organic carbon abundance and vertical distribution of the eight long core wells in different areas of the basin within the Chang 7 member source layers were calculated by means of the ΔLogR method. According to the industrial oil well and the low production well, the favorable oil distribution areas of the Chang 8, Chang 7, and Chang 6 reservoirs are demarcated. The current study confirmed five distribution styles and strong regional differences in the longitudinal direction of source rocks. To be more specific, the Jiyuan area in the northwestern part of the lake basin is dominated by the bottom rich type and the full section rich type. The northeastern Shaanxi region is mainly dominated by the middle rich type and the top rich type. Meanwhile, the central area of the basin is mainly the interlayered type, and the southwestern Longdong region is mainly the bottom rich type. The comprehensive analysis of source rock type and oil favorable zone revealed that source rock type has a controlling effect on the crude oil distribution. The bottom rich type and full section rich type dominate the Jiyuan area and multiple layer oil production. In northern Shaanxi, the top rich type and middle rich type accumulate on the upper portion. Also, the Chang 6 reservoir was the main production layer. The bottom rich type of the Longdong area accumulates under the source, while the Chang 8 reservoir is the main production layer. The central parts of the lake basin are dominated by the interlayered type with multiple layers of production oil. The close relationship between the distribution pattern of source rocks and oil accumulation indicates an improvement on the distribution law of the continental lake with significance practical implication on the optimization of the field of near-source-in-source oil and gas exploration.

Czaplinski, E.C., Gilbertson, W.A., Farnsworth, K.K., Chevrier, V.F., 2019. Experimental study of ethylene evaporites under Titan conditions. ACS Earth and Space Chemistry 3, 2353-2362.


Titan has an abundance of lakes and seas, as confirmed by Cassini. Major components of these liquid bodies include methane (CH4) and ethane (C2H6); however, evidence indicates that minor components such as ethylene (C2H4) may also exist in the lakes. As the lake levels drop, 5 μm-bright deposits, resembling evaporite deposits on earth, are left behind. Here, we provide saturation values, evaporation rates, and constraints on ethylene evaporite formation by using a Titan simulation chamber capable of reproducing Titan surface conditions (89–94 K, 1.5 bar N2). Experimental samples were analyzed using Fourier transform infrared spectroscopy, mass, and temperature readings. Ethylene evaporites form more quickly in a methane solvent than in an ethane solvent or in a mixture of methane/ethane. We measured an average evaporation rate of (2.8 ± 0.3) × 10–4 kg m–2 s–

1 for methane and an average upper limit evaporation rate of <5.5 × 10–6 kg m–2 s–1 for ethane. Additionally, we observed red shifts in ethylene absorption bands at 1.630 and 2.121 μm and the persistence of a methane band at 1.666 μm.

Darnell, K.N., Flemings, P.B., DiCarlo, D., 2019. Nitrogen-driven chromatographic separation during gas injection into hydrate-bearing sediments. Water Resources Research 55, 6673-6691.

https://doi.org/10.1029/2018WR023414

Hydrates are solid phases composed of water cages enclosing gas molecules that may host large quantities of recoverable natural gas and may serve to sequester CO2 on geological time scales. Most hydrate studies focus on hydrates containing a single gas component, such as CH4 or CO2. Yet, there are several settings in which multiple components form hydrate mixtures, or mixed hydrates, including a subsurface injection technique that claims to simultaneously recover CH4 and sequester CO2 called “guest molecule exchange.” Here, we combine multicomponent phase behavior for hydrate‐forming systems with a multiphase fluid flow simulator to understand the evolution of hydrate and nonhydrate phases during subsurface injection. We simulate various scenarios for systems composed of H2O, CH4, CO2, and N2. Our study probes the impact of injection composition, initial reservoir composition, and transport of each component through the model domain. We observe chromatographic separation from the combined effect of compositional partitioning in each phase, variable flow speed of each phase, and compositional dependence of phase stabilities. We show that N2 drives chromatographic separation to create a CH4‐free zone and a CO2‐free zone that are connected by a continuous N2‐dominated vapor phase. While our results are theoretical and should be validated experimentally, they imply that guest molecule exchange acts as two sequential processes rather than as a simultaneous process. Furthermore, they show that injections into reservoirs with and without free water have vastly different behaviors, which has implications for the interpretation of the guest molecule exchange field test and various laboratory studies.

Davidson, J., Alexander, C.M.O.D., Stroud, R.M., Busemann, H., Nittler, L.R., 2019. Mineralogy and petrology of Dominion Range 08006: A very primitive CO3 carbonaceous chondrite. Geochimica et Cosmochimica Acta 265, 259-278.


Here we report the relative degrees of thermal metamorphism for five Antarctic Ornans-like carbonaceous (CO) chondrites, including Dominion Range (DOM) 08006, as determined from the Cr-content of their FeO-rich (ferroan) olivine. These five CO3 chondrites complete the previously poorly-defined CO3.00 to 3.2 chondrite metamorphic trend. DOM 08006 appears to be a highly primitive CO chondrite of petrologic type 3.00. We report the detailed mineralogy and petrography of DOM 08006 using a coordinated, multi-technique approach.

The interchondrule matrix in DOM 08006 consists of unequilibrated mixtures of silicate, metal, and sulfide minerals and lacks Fe-rich rims on silicates indicating that DOM 08006 has only experienced minimal, if any, thermal metamorphism. This is also reflected by the Co/Ni ratios of Ni-rich and Ni-poor metal, a sensitive indicator of thermal metamorphism, and the presence of euhedral chrome-spinel grains, which typically become subhedral to anhedral during progressive metamorphism. DOM 08006 matrix shows minor evidence for aqueous alteration and while the presence of magnetite surrounding metal in chondrules indicates that there has been some interaction with fluid, much metal remains and none of the sulfides analyzed show evidence of being formed by aqueous alteration. Furthermore, the plagioclase of ∼50% of chondrules analyzed show resolvable excess silica indicating that these chondrules have experienced minimal, if any, reprocessing in the CO parent body.

Noble gas data for DOM 08006 show that it contains the highest concentrations of trapped 36Ar and 132Xe of all CO chondrites analyzed to date, further indicating that DOM 08006 is the most primitive CO chondrite known. The cosmic ray exposure age of DOM 08006 is estimated to be ∼19 Ma.

The minimally altered nature of DOM 08006 demonstrates that it is an extremely important sample for providing valuable insight into early Solar System conditions. At a total weight of 667 g, a significant amount of material is available for a wide array of future studies.

De Wever, A., Benzerara, K., Coutaud, M., Caumes, G., Poinsot, M., Skouri-Panet, F., Laurent, T., Duprat, E., Gugger, M., 2019. Evidence of high Ca uptake by cyanobacteria forming intracellular CaCO3 and impact on their growth. Geobiology 17, 676-690.


Several species of cyanobacteria biomineralizing intracellular amorphous calcium carbonates (ACC) were recently discovered. However, the mechanisms involved in this biomineralization process and the determinants discriminating species forming intracellular ACC from those not forming intracellular ACC remain unknown. Recently, it was hypothesized that the intensity of Ca uptake (i.e., how much Ca was scavenged from the extracellular solution) might be a major parameter controlling the capability of a cyanobacterium to form intracellular ACC. Here, we tested this hypothesis by systematically measuring the Ca uptake by a set of 52 cyanobacterial strains cultured in the same growth medium. The results evidenced a dichotomy among cyanobacteria regarding Ca sequestration capabilities, with all strains forming intracellular ACC incorporating significantly more calcium than strains not forming ACC. Moreover, Ca provided at a concentration of 50 μM in BG‐11 was shown to be limiting for the growth of some of the strains forming intracellular ACC, suggesting an overlooked quantitative role of Ca for these strains. All cyanobacteria forming intracellular ACC contained at least one gene coding for a mechanosensitive channel, which might be involved in Ca influx, as well as at least one gene coding for a Ca2+/H+ exchanger and membrane proteins of the UPF0016 family, which might be involved in active Ca transport either from the cytosol to the extracellular solution or the cytosol toward an intracellular compartment. Overall, massive Ca sequestration may have an indirect role by allowing the formation of intracellular ACC. The latter may be beneficial to the growth of the cells as a storage of inorganic C and/or a buffer of intracellular pH. Moreover, high Ca scavenging by cyanobacteria biomineralizing intracellular ACC, a trait shared with endolithic cyanobacteria, suggests that these cyanobacteria should be considered as potentially significant geochemical reservoirs of Ca.

Dearing Crampton-Flood, E., Tierney, J.E., Peterse, F., Kirkels, F.M.S.A., Sinninghe Damsté, J.S., 2020. BayMBT: A Bayesian calibration model for branched glycerol dialkyl glycerol tetraethers in soils and peats. Geochimica et Cosmochimica Acta 268, 142-159.


Accurate temperature records for the deep geological past are a vital component of paleoclimate research. Distributional changes of branched glycerol dialkyl glycerol tetraether (brGDGT) lipids in geological archives including paleosoils are a promising indicators to infer past continental air temperatures. However, the ‘orphan’ status of the brGDGTs, the potential effect of temperature-independent parameters on their relative distribution, and the uneven geographical distribution of the soils used for calibration contribute to the high uncertainty of brGDGT-based transfer functions (root mean squared error, RMSE: ±5 °C). Here, we expand the soil dataset from the previous calibration(s) with new and published soil data. We use Bayesian statistics to calibrate the relationship of the 5-

methyl brGDGTs (MBT′5Me) and mean annual air temperature (MAAT). The addition of soils from warm (>28 °C) environments from India substantially increases the upper limit of the Bayesian calibration (BayMBT) from 25 to 29 °C, aiding in the generation of temperature records for past greenhouse climates, such as the Eocene. The BayMBT model also effectively minimizes the structured MAAT residuals prevalent in previous calibrations, therefore giving the opportunity to explore confounding factors on the calibration. We formulate a set of alternative calibration models to test the effect of specific environmental parameters and show that soils at mid-latitudes with temperature seasonalities >20 °C are not well described by the BayMBT model. We find that the MBT′5Me index is best correlated to the average temperature of all months >0 °C, called the BayMBT0 model. This finding supports the hypothesis that brGDGT production ceases or slows down in the winter months. However, a persistent feature of the BayMBT model and previous calibrations is the significant scatter at mid-latitudes, which is speculatively linked with a possible increase in diversity of microbial brGDGT-producing communities in these locations.

Devièse, T., Ribechini, E., Querci, D., Higham, T., 2019. Assessing the efficiency of supercritical fluid extraction for the decontamination of archaeological bones prior to radiocarbon dating. Analyst 144, 6128-6135.

http://dx.doi.org/10.1039/C9AN00859D

Bone is one of the main sample types used for building chronologies in archaeology. It is also used in other research areas such as palaeodiet and palaeoenvironmental studies. However, for results to be accurate, samples must be free of exogenous carbon. Contamination can originate from a wide range of sources in the post-depositional environment but may also occur during excavation and post excavation activities (i.e. with the application of conservation materials) or during laboratory handling. Efficient procedures to remove contamination are therefore crucial prior to radiocarbon or stable isotope measurements. This work describes the development of an innovative sample pretreatment for bones, based on using supercritical CO2, which shows unique solvation properties. The effectiveness of supercritical fluid extraction (SFE) to remove conservation materials was compared with that obtained when applying a routine extraction based on the use of organic solvents (methanol, acetone and chloroform). The chemical composition of the bone samples before and after the two pre-treatments was then investigated using analytical pyrolysis-based techniques: EGA-MS (Evolved Gas Analysis-Mass Spectrometry) and Py-GC/MS (Pyrolysis-Gas Chromatography coupled with Mass Spectrometry). Collagen samples extracted from the same bones, prepared with the two cleaning protocols, were also radiocarbon dated by Accelerator Mass Spectrometry (AMS). The results of this study show that SFE is an efficient alternative method because it was as effective as the established treatment protocol. It removes contaminants such as conservation materials from bone samples with a minimum of handling and can be used routinely in radiocarbon dating laboratories. This work also demonstrates that analytical pyrolysis is not only a very efficient method to identify contaminants in bones but also to assess the effectiveness of the pretreatment prior to the radiocarbon measurement of the samples.

Dong, Y., Ju, B., Zhang, S., Tian, Y., Ma, S., Liu, N., Lu, G., 2020. Microscopic mechanism of methane adsorption in shale: Experimental data analysis and interaction potential simulation. Journal of Petroleum Science and Engineering 184, 106544.


The adsorbed methane in shale determines the geological reserves of shale gas and production of the well. Therefore, it is of great importance to clarify the microscopic mechanism of methane adsorption

in shale for evaluating the geological condition and formulating exploitation plan. In this study, the experimental data and the simulation result were combined to research the microscopic mechanism of methane adsorption in shale. The experimental data for 99 groups of low-temperature nitrogen adsorption and methane isothermal adsorption were collected, to calculate the number of adsorption layers of methane in shale at the micro-level. The surface, microfracture and micropore structures of the organic matter in shale were constructed by graphite structure with the hydroxyl group. Thereafter, they were used to simulate the interaction potential of the organic matter on methane molecules and the adsorption layer's number by using the theory of intermolecular interaction potential field. Furthermore, the effects of different fracture widths and pore diameters on methane adsorption were analyzed and verified. The results show that the adsorption capacity of methane in shale is related to shale's structure, and the order of the adsorption capacity is surface < microfracture < micropore. Meanwhile, the multilayer adsorption can occur in microfractures with a width of 1.44–1.59 nm and micropores with a diameter of 1.49–1.83 nm, whereas the surface structure just can be the monolayer adsorption. These quantitatively results establish a foundation for the development of adsorption theory for methane in the shale.


https://doi.org/10.1038/s41467-019-12728-y

Fractured rocks of impact craters may be suitable hosts for deep microbial communities on Earth and potentially other terrestrial planets, yet direct evidence remains elusive. Here, we present a study of the largest crater of Europe, the Devonian Siljan structure, showing that impact structures can be important unexplored hosts for long-term deep microbial activity. Secondary carbonate minerals dated to 80 ± 5 to 22 ± 3 million years, and thus postdating the impact by more than 300 million years, have isotopic signatures revealing both microbial methanogenesis and anaerobic oxidation of methane in the bedrock. Hydrocarbons mobilized from matured shale source rocks were utilized by subsurface microorganisms, leading to accumulation of microbial methane mixed with a thermogenic and possibly a minor abiotic gas fraction beneath a sedimentary cap rock at the crater rim. These new insights into crater hosted gas accumulation and microbial activity have implications for understanding the astrobiological consequences of impacts.

Drieu, L., Horgnies, M., Binder, D., Pétrequin, P., Pétrequin, A.M., Peche-Quilichini, K., Lachenal, T., Regert, M., 2019. Influence of porosity on lipid preservation in the wall of archaeological pottery. Archaeometry 61, 1081-1096.

https://doi.org/10.1111/arcm.12479

Porosity of archaeological pottery is a key parameter used to assess its ability to trap lipids during the use of the pot and to preserve them over time. Mercury intrusion porosimetry and gas chromatography were used to study the distribution of porosity and the preservation of lipids in different chrono-cultural contexts. The data obtained show that the porosity pattern, related to the raw materials and the savoir-faire of the potters, influences the amount of lipids accumulated in the pottery. A significant overall porosity together with a high level of small pores is generally favourable for the preservation of lipids, but variations related to the environmental context are observed.



Based on field outcrop investigation, interpretation and analysis of drilling and seismic data, and consulting on a large number of previous research results, the characteristics of ancient marine hydrocarbon source rocks, favorable reservoir facies belts, hydrocarbon migration direction and reservoir-forming law in the Ordos Basin have been studied from the viewpoints of North China Craton breakup and Qilian-Qinling oceanic basin opening and closing. Four main results are obtained: (1) Controlled by deep-water shelf-rift, there are three suites of source rocks in the Ordos Basin and its periphery: Mesoproterozoic, Lower Cambrian and Middle-Upper Ordovician. (2) Controlled by littoral environment, paleo-uplift and platform margin, four types of reservoirs are developed in the area: Mesoproterozoic– Lower Cambrian littoral shallow sea quartz sandstone, Middle-Upper Cambrian–Ordovician weathering crust and dolomitized reservoir, and Ordovician L-shape platform margin reef and beach bodies. (3) Reservoir-forming assemblages vary greatly in the study area, with “upper generation and lower storage” as the main pattern in the platform, followed by “self-generation and self-storage”. There are both “upper generation and lower storage” and “self-generation and self-storage” in the platform margin zone. In addition, in the case of communication between deep-large faults and the Changchengian system paleo-rift trough, there may also exist a “lower generation and upper reservoir” combination between the platform and the margin. (4) There are four new exploration fields including Qingyang paleo-uplift pre-Carboniferous weathering crust, L-shape platform margin zone in southwestern margin of the basin, Ordovician subsalt assemblage in central and eastern parts of the basin, and Mesoproterozoic–Cambrian. Among them, pre-Carboniferous weathering crust and L-shape platform margin facies zone are more realistic replacement areas, and Ordovician subsalt assemblage and the Proterozoic-Cambrian have certain potential and are worth exploring.

Dufresne, M., Patterson, N.H., Norris, J.L., Caprioli, R.M., 2019. Combining salt doping and matrix sublimation for high spatial resolution MALDI imaging mass spectrometry of neutral lipids. Analytical Chemistry 91, 12928-12934.

https://doi.org/10.1021/acs.analchem.9b02974

The combination of sodium salt doping of a tissue section along with the sublimation of the matrix 2,5-dihydrobenzoic acid (DHB) was found to be an effective coating for the simultaneous detection of neutral lipids and phospholipids using matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry in positive ionization mode. Lithium, sodium, and potassium acetate were initially screened for their ability to cationize difficult to analyze neutral lipids such as cholesterol esters, cerebrosides, and triglycerides directly from a tissue section. The combination of sodium salt and DHB sublimation was found to be an effective cation/matrix combination for detection of neutral lipids. Further experimental optimizations revealed that sodium carbonate or sodium phosphate followed by DHB sublimation increases the signal intensity of the neutral lipids studied depending on the specific lipid family and tissue type by 10-fold to 140-fold compared with that of previously published methods. Application of sodium carbonate tissue doping and DHB sublimation resulted in crystal sizes ≤2 μm. We were thus able to image a mouse brain cerebellum at a high spatial resolution and detected 37 cerebrosides in a single run using a MALDI-TOF instrument. The combination of sodium doping and DHB sublimation offer a targeted and sensitive approach for the detection of neutral lipids that do not typically ionize well under normal MALDI conditions.

Dumitru, O.A., Austermann, J., Polyak, V.J., Fornós, J.J., Asmerom, Y., Ginés, J., Ginés, A., Onac, B.P., 2019. Constraints on global mean sea level during Pliocene warmth. Nature 574, 233-236.

https://doi.org/10.1038/s41586-019-1543-2

Reconstructing the evolution of sea level during past warmer epochs such as the Pliocene provides insight into the response of sea level and ice sheets to prolonged warming. Although estimates of the global mean sea level (GMSL) during this time do exist, they vary by several tens of metres hindering the assessment of past and future ice-sheet stability. Here we show that during the mid-Piacenzian Warm Period, which was on average two to three degrees Celsius warmer than the pre-industrial period, the GMSL was about 16.2 metres higher than today owing to global ice-volume changes, and around 17.4 metres when thermal expansion of the oceans is included. During the even warmer Pliocene Climatic Optimum (about four degrees Celsius warmer than pre-industrial levels), our results show that the GMSL was 23.5 metres above the present level, with an additional 1.6 metres from thermal expansion. We provide six GMSL data points, ranging from 4.39 to 3.27 million years ago, that are based on phreatic overgrowths on speleothems from the western Mediterranean (Mallorca, Spain). This record is unique owing to its clear relationship to sea level, its reliable U–Pb ages and its long timespan, which allows us to quantify uncertainties on potential uplift. Our data indicate that ice sheets are very sensitive to warming and provide important calibration targets for future ice-sheet models.

Dunne, J., Rebay-Salisbury, K., Salisbury, R.B., Frisch, A., Walton-Doyle, C., Evershed, R.P., 2019. Milk of ruminants in ceramic baby bottles from prehistoric child graves. Nature 574, 246-248.

https://doi.org/10.1038/s41586-019-1572-x

The study of childhood diet, including breastfeeding and weaning, has important implications for our understanding of infant mortality and fertility in past societies1. Stable isotope analyses of nitrogen from bone collagen and dentine samples of infants have provided information on the timing of weaning2; however, little is known about which foods were consumed by infants in prehistory. The earliest known clay vessels that were possibly used for feeding infants appear in Neolithic Europe, and become more common throughout the Bronze and Iron Ages. However, these vessels—which include a spout through which liquid could be poured—have also been suggested to be feeding vessels for the sick or infirm3,4. Here we report evidence for the foods that were contained in such vessels, based on analyses of the lipid ‘fingerprints’ and the compound-specific δ13C and Δ13C values of the major fatty acids of residues from three small, spouted vessels that were found in Bronze and Iron Age graves of infants in Bavaria. The results suggest that the vessels were used to feed infants with milk products derived from ruminants. This evidence of the foodstuffs that were used to either feed or wean prehistoric infants confirms the importance of milk from domesticated animals for these early communities, and provides information on the infant-feeding behaviours that were practised by prehistoric human groups.

Edilbi, A.N.F., Mohammed, K.F., Sadeq, Z.H., Aldalawy, A.A., Zebari, B.G.A., Pirouei, M., Suramairy, R., Ali, J.A., 2019. Source rock potential and reservoir characterization of the Lower Cretaceous Sarmord Formation in selected sections in Kurdistan Region-Iraq. Arabian Journal of Geosciences 12, 647.

https://doi.org/10.1007/s12517-019-4765-6

The Sarmord Formation is underlain by the most important source rocks and overlain by several major reservoirs in the Kurdistan Region. Two sections including a subsurface (well from Kirkuk oilfield) and a surface (outcrop at Bekhme Gorge) of the Sarmord Formation were studied to identify and describe the role of the Sarmord Formation within petroleum systems in the region. Thus, organic geochemistry and petrophysical characteristics of the Sarmord Formation have been studied using Rock-Eval, log data, core analysis and thin section studies. Results showed different lithologies between the studied sections of the Sarmord Formation; an intercalating of yellowish-gray marl (calcareous mudstone) and dark brownish to dark-gray shale was observed at outcrop, and subsurface section was mostly composed of clays with a composition of limestone and dolomite. The source rock potential of the shale layers of the Sarmord Formation reveals that the total organic carbon (TOC wt%) of subsurface section is 0.22 wt% on average which is regarded as poor organic carbon content. The average of Tmax value is 426 °C that shows the formation is thermally immature. The capability of formation in generating of hydrocarbons is poor at subsurface section. Whereas the surface (outcrop) samples show fair to good content of organic carbon (0.83 TOC wt% on average), and they are thermally mature (Tmax is 440 °C on average). The hydrocarbon generative potential of outcrop seems to be poor to good. The petrophysical study of the subsurface section displays low porosity and permeability (0.04% and 0.04 mD on average respectively). These values are generally considered as poor reservoir quality. Likewise, measurement values of porosity and permeability from outcrop are 6.425% and 0.108 mD on average, respectively, showing poor reservoir quality. The microscopic study also shows that the matrix material is largely comprised of lime mud and allomicrite types, and its porosity types (particularly of vague and fracture types) indicate the low percentage of porosity (not exceeding 1%). On the other hand, presence of bitumen seeps along fractures at the outcrop section may reveal that the formation can be regarded as a fractured-reservoir.



Organic compounds are ubiquitous in the Earth's surface, sediments and many rocks, and preserve records of geological, geochemical and biological history; they are also critical natural resources and major environmental pollutants. The naturally occurring stable isotopes of volatile elements (D, 13C, 15N, 17,18O, 33,34,36S) provide one way of studying the origin, evolution and migration of geological organic compounds. The study of bulk stable isotope compositions (i.e. averaged across all possible molecular isotopic forms) is well established and widely practised, but frequently results in non-unique interpretations. Increasingly, researchers are reading the organic isotopic record with greater depth and specificity by characterizing stable isotope ‘structures’ – the proportions of site-specific and multiply substituted isotopologues that contribute to the total rare-isotope inventory of each compound. Most of the technologies for measuring stable isotope structures of organic molecules have been only recently developed and to date have been applied only in an exploratory way. Nevertheless, recent advances have demonstrated that molecular isotopic structures provide distinctive records of biosynthetic origins, conditions and mechanisms of chemical transformation during burial, and forensic fingerprints of exceptional specificity. This paper provides a review of this young field, which is organized to follow the evolution of molecular isotopic structure from biosynthesis, through diagenesis, catagenesis and metamorphism.

El Kerni, H., Chennaoui Aoudjehane, H., Baratoux, D., Aoudjehane, M., Charrière, A., Ibouh, H., Rochette, P., Quesnel, Y., Uehara, M., Kenkmann, T., Wulf, G., Poelchau, M., Nguyen, V.B.,

Aboulahris, M., Makhoukhi, S., Aumaître, G., Bourlès, D., Keddadouche, K., 2019. Geological and geophysical studies of the Agoudal impact structure (Central High Atlas, Morocco): New evidence for crater size and age. Meteoritics & Planetary Science 54, 2483-2509.


Since the discovery of shatter cones (SCs) near the village of Agoudal (Morocco, Central High Atlas Mountains) in 2013, the absence of one or several associated circular structures led to speculation about the age of the impact event, the number, and the size of the impact crater or craters. Additional constraints on the crater size, age, and erosion rates are obtained here from geological, structural, and geophysical mapping and from cosmogenic nuclide data. Our geological maps of the Agoudal impact site at the scales of 1:30,000 (6 km2) and 1:15,000 (2.25 km2) include all known occurrences of SCs in target rocks, breccias, and vertical to overturned strata. Considering that strata surrounding the impact site are subhorizontal, we argue that disturbed strata are related to the impact event. Three types of breccias have been observed. Two of them (br1‐2 and br2) could be produced by erosion–sedimentation–consolidation processes, with no evidence for impact breccias, while breccia (br1) might be impact related. The most probable center of the structure is estimated at 31°59′13.73ʺN, 5°30′55.14ʺW using the concentric deviation method applied to the orientation of strata over the disturbed area. Despite the absence of a morphological expression, the ground magnetic and electromagnetic surveys reveal anomalies spatially associated with disturbed strata and SC occurrences. The geophysical data, the structural observations, and the area of occurrence of SCs in target rocks are all consistent with an original size of 1.4–4.2 km in diameter. Cosmogenic nuclide data (36Cl) constrain the local erosion rates between 220 ± 22 m Ma−1 and 430 ± 43 m Ma−1. These erosion rates may remove the topographic expression of such a crater and its ejecta in a time period of about 0.3–1.9 Ma. This age is older than the Agoudal iron meteorite age (105 ± 40 kyr). This new age constraint excludes the possibility of a genetic relationship between the Agoudal iron meteorite fall and the formation of the Agoudal impact site. A chronolgy chart including the Atlas orogeny, the alternation of sedimentation and erosion periods, and the meteoritic impacts is presented based on all obtained and combined data.

Elling, F.J., Gottschalk, J., Doeana, K.D., Kusch, S., Hurley, S.J., Pearson, A., 2019. Archaeal lipid biomarker constraints on the Paleocene-Eocene carbon isotope excursion. Nature Communications 10, 4519.

https://doi.org/10.1038/s41467-019-12553-3

A negative carbon isotope excursion recorded in terrestrial and marine archives reflects massive carbon emissions into the exogenic carbon reservoir during the Paleocene-Eocene Thermal Maximum. Yet, discrepancies in carbon isotope excursion estimates from different sample types lead to substantial uncertainties in the source, scale, and timing of carbon emissions. Here we show that membrane lipids of marine planktonic archaea reliably record both the carbon isotope excursion and surface ocean warming during the Paleocene-Eocene Thermal Maximum. Novel records of the isotopic composition of crenarchaeol constrain the global carbon isotope excursion magnitude to −4.0 ± 0.4‰, consistent with emission of >3000 Pg C from methane hydrate dissociation or >4400 Pg C for scenarios involving emissions from geothermal heating or oxidation of sedimentary organic matter. A pre-onset excursion in the isotopic composition of crenarchaeol and ocean temperature highlights the susceptibility of the late Paleocene carbon cycle to perturbations and suggests that climate instability preceded the Paleocene-Eocene Thermal Maximum.

Enrique-Romero, J., Rimola, A., Ceccarelli, C., Ugliengo, P., Balucani, N., Skouteris, D., 2019. Reactivity of HCO with CH3 and NH2 on water ice surfaces. A comprehensive accurate quantum chemistry study. ACS Earth and Space Chemistry 3, 2158-2170.


Interstellar complex organic molecules (iCOMs) can be loosely defined as chemical compounds with at least six atoms in which at least one is carbon. The observations of iCOMs in star-forming regions have shown that they contain an important fraction of carbon in a molecular form, which can be used to synthesize more complexes, even biotic molecules. Hence, iCOMs are major actors in the increasing molecular complexity in space, and they might have played a role in the origin of terrestrial life. Understanding how iCOMs are formed is relevant for predicting the ultimate organic chemistry reached in the interstellar medium. One possibility is that they are synthesized on the interstellar grain icy surfaces, via recombination of previously formed radicals. The present work focuses on the reactivity of HCO with CH3/NH2 on the grain icy surfaces, investigated by means of quantum chemical simulations. The goal is to carry out a systematic study using different computational approaches and models for the icy surfaces. Specifically, DFT computations have been benchmarked with CASPT2 and CCSD(T) methods, and the ice mantles have been mimicked with cluster models of 1, 2, 18, and 33 H2O molecules, in which different reaction sites have been considered. Our results indicate that the HCO + CH3/NH2 reactions, if they actually occur, have two major competitive channels: the formation of iCOMs CH3CHO/NH2CHO or the formation of CO + CH4/NH3. These two channels are either barrierless or present relatively low (≤10 kJ/mol equal to about 1200 K) energy barriers. Finally, we briefly discuss the astrophysical implications of these findings.


https://doi.org/10.1038/s41396-019-0466-0

In the last decade, extensive application of hydraulic fracturing technologies to unconventional low-permeability hydrocarbon-rich formations has significantly increased natural-gas production in the United States and abroad. The injection of surface-sourced fluids to generate fractures in the deep subsurface introduces microbial cells and substrates to low-permeability rock. A subset of injected organic additives has been investigated for their ability to support biological growth in shale microbial community members; however, to date, little is known on how complex xenobiotic organic compounds undergo biotransformations in this deep rock ecosystem. Here, high-resolution chemical, metagenomic, and proteomic analyses reveal that widely-used surfactants are degraded by the shale-associated taxa Halanaerobium, both in situ and under laboratory conditions. These halotolerant bacteria exhibit surfactant substrate specificities, preferring polymeric propoxylated glycols (PPGs) and longer alkyl polyethoxylates (AEOs) over polyethylene glycols (PEGs) and shorter AEOs. Enzymatic transformation occurs through repeated terminal-end polyglycol chain shortening during co-metabolic growth through the methylglyoxal bypass. This work provides the first evidence that shale microorganisms can transform xenobiotic surfactants in fracture fluid formulations, potentially affecting the efficiency of hydrocarbon recovery, and demonstrating an important association between injected substrates and microbial growth in an engineered subsurface ecosystem.


https://doi.org/10.1021/acs.estlett.9b00473

Organohalides are routinely detected in fluid produced from hydraulically fractured oil and natural-gas wells, yet the origin and fate of these compounds remain largely unknown. Because few organohalides are disclosed as fracturing fluid additives, one suspected formation mechanism is the reaction of geogenic halides oxidized by injected additives with natural or anthropogenic organic carbon. However, the potential role of microorganisms in organohalide cycling is currently unknown. Here, we uncover the microorganisms and enzymatic systems that contribute to organohalide transformations during hydraulic fracturing through nontarget organohalide chemical analysis and metagenomics. Twenty organohalide compounds were identified in fluid samples produced from two Marcellus Shale natural-gas wells, comprising five structural classes. Genes encoding halogenation and dehalogenation mechanisms were identified in metagenomes assembled from produced fluids collected from four Appalachian Basin natural-gas wells. Metagenomic results show the presence of non-heme chloroperoxidases, enzymes that generate peracetic acid, which can react with dissolved halides to form highly oxidizing hypohalous acid, a halogenation agent for geogenic or anthropogenic organic matter. Microbial organohalide transformation/mineralization could proceed through hydrolytic dehalogenation, with enzymes inferred to operate on haloacetates, haloacids, and haloalkanes of varying carbon chain lengths, some of which are present in these wells. These results indicate that microorganisms may play an underappreciated role in direct and indirect organohalide transformations in hydraulically fractured oil and gas systems.

Evans, S.D., Huang, W., Gehling, J.G., Kisailus, D., Droser, M.L., 2019. Stretched, mangled, and torn: Responses of the Ediacaran fossil Dickinsonia to variable forces. Geology 47, 1049-1053.

https://doi.org/10.1130/G46574.1

Dickinsonia is one of the oldest macroscopic metazoans in the fossil record. Determining the biological characters of this extinct taxon is critical to our understanding of the early evolution of life. Preservation of abundant specimens from the Ediacara Member (Rawnsley Quartzite), South Australia, in a variety of taphonomic states allows the unparalleled opportunity to compare the biomechanical responses of Dickinsonia tissue to various forces with those typical of modern organisms. Dickinsonia are found as lifted, transported, folded, rolled, ripped, and expanded or contracted individuals, while maintaining diagnostic morphology. This suite of characters indicates that Dickinsonia was composed of material that was flexible, difficult to rip, and capable of elastic and plastic deformation. While none of these traits are diagnostic of a single biomaterial component, we find many similarities with modern biopolymers, particularly collagen, keratin, and elastin. Maintenance of significant relief following complete tearing suggests that Dickinsonia was composed of relatively thick tissues, signifying higher oxygen requirements than previously hypothesized. The ability to be transported and still be preserved as recognizable fossils is unique amongst the Ediacara Biota and demonstrates that Dickinsonia was a taphonomic elite. Combined with discovery in multiple environmental settings, this indicates that the absence of Dickinsonia represents the likely extinction of this organism prior to the Nama assemblage, possibly due to a decrease in the global availability of oxygen in the latest Ediacaran.



Distributional patterns of intact polar lipids (IPLs) suggest that archaea are abundant in marine subsurface sediments. However, the production of archaeal lipids remains largely unresolved. We performed a lipid radioisotope probing (lipid-RIP) experiment using 14C-bicarbonate and 2-14C-acetate with surface and methanogenic marine sediments from the Rhone delta (Mediterranean Sea) to investigate mechanisms of carbon assimilation and to assess biomass production of benthic archaea. The direct determination of carbon assimilation rates into diagnostic IPLs in the experiments with 14C-bicarbonate were up to 9 times higher than in the incubations with 2-14C-acetate, implying that autotrophy is an important carbon pathway for the benthic archaea in the Rhone delta sediments. Production rates of polyglycosidic archaeols (AR) were one to two orders of magnitude higher than those of mono- and polyglycosidic glycerol dialkyl glycerol tetraethers (GDGTs), suggesting that the former IPLs are good biomarkers for active benthic archaea in marine sediments. In contrast, the low production rates of the monoglycosidic AR and GDGTs, indicate that a large fraction of these IPLs may represent fossil sedimentary remains from the water column. Unexpectedly, the lipid production rates of AR and GDGT core lipids (CLs) were similar to those of polyglycosidic IPLs. Considering the relatively short period of incubation (21 days), this suggests that CLs may be actively synthesized by benthic archaea in marine sediments and are not exclusively formed from the degradation of IPL precursors.

Fahid, M., Arslan, M., Shabir, G., Younus, S., Yasmeen, T., Rizwan, M., Siddique, K., Ahmad, S.R., Tahseen, R., Iqbal, S., Ali, S., Afzal, M., 2020. Phragmites australis in combination with hydrocarbons degrading bacteria is a suitable option for remediation of diesel-contaminated water in floating wetlands. Chemosphere 240, 124890.


The presence of diesel in the water could reduce the growth of plant and thus phytoremediation efficacy. The toxicity of diesel to plant is commonly explained; because of hydrocarbons in diesel accumulate in various parts of plants, where they disrupt the plant cell especially, the epidemis, leaves, stem and roots of the plant. This study investigated the effect of bacterial augmentation in floating treatment wetlands (FTWs) on remediation of diesel oil contaminated water. A helophytic plant, Phragmites australis (P. australis), was vegetated on a floating mat to establish FTWs for the remediation of diesel (1%, w/v) contaminated water. The FTWs was inoculated with three bacterial strains (Acinetobacter sp. BRRH61, Bacillus megaterium RGR14 and Acinetobacter iwoffii AKR1), possessing hydrocarbon degradation and plant growth-enhancing capabilities. It was observed that the FTWs efficiently removed hydrocarbons from water, and bacterial inoculation further enhanced its hydrocarbons degradation efficacy. Diesel contaminated water samples collected after fifteen days of time interval for three months and were analyzed for pollution parameters. The maximum reduction in hydrocarbons (95.8%), chemical oxygen demand (98.6%), biochemical oxygen demand (97.7%), total organic carbon (95.2%), phenol (98.9%) and toxicity was examined when both plant and bacteria were employed in combination. Likewise, an increase in plant growth was seen in the presence of bacteria. The inoculated bacteria showed persistence in the water, root and shoot of P. australis. The study concluded that the augmentation of hydrocarbons degrading bacteria in FTWs is a better option for treatment of diesel polluted water.

Faith, J.T., Rowan, J., Du, A., 2019. Early hominins evolved within non-analog ecosystems. Proceedings of the National Academy of Sciences 116, 21478-21483.


Significance: Testing ecological hypotheses of human evolution requires an understanding of the ancient plant and animal communities within which our ancestors lived. Though present-day ecosystems provide the baseline for reconstructing the ecological context of human evolution, the extent to which modern ecosystems are representative of past ones is unknown. Through analyses of a fossil dataset spanning the last 7 Myr, we show that eastern African communities of large-bodied mammalian herbivores differed markedly from those today until ∼700,000 y ago. Because large herbivores are ecosystem engineers and shape biotic communities in ways that impact a wide variety of species, this implies that the vast majority of early human evolution transpired in the context of ecosystems that functioned unlike any known today.

Abstract: Present-day African ecosystems serve as referential models for conceptualizing the environmental context of early hominin evolution, but the degree to which modern ecosystems are representative of those in the past is unclear. A growing body of evidence from eastern Africa’s rich and well-dated late Cenozoic fossil record documents communities of large-bodied mammalian herbivores with ecological structures differing dramatically from those of the present day, implying that modern communities may not be suitable analogs for the ancient ecosystems of hominin evolution. To determine when and why the ecological structure of eastern Africa’s herbivore faunas came to resemble those of the present, here we analyze functional trait changes in a comprehensive dataset of 305 modern and fossil herbivore communities spanning the last ∼7 Myr. We show that nearly all communities prior to ∼700 ka were functionally non-analog, largely due to a greater richness of non-ruminants and megaherbivores (species >1,000 kg). The emergence of functionally modern communities precedes that of taxonomically modern communities by 100,000s of years, and can be attributed to the combined influence of Plio-Pleistocene C4 grassland expansion and pulses of aridity after ∼1 Ma. Given the disproportionate ecological impacts of large-bodied herbivores on factors such as vegetation structure, hydrology, and fire regimes, it follows that the vast majority of early hominin evolution transpired in the context of ecosystems that functioned unlike any today. Identifying how past ecosystems differed compositionally and functionally from those today is key to conceptualizing ancient African environments and testing ecological hypotheses of hominin evolution.

Fakhraee, M., Katsev, S., 2019. Organic sulfur was integral to the Archean sulfur cycle. Nature Communications 10, 4556.

https://doi.org/10.1038/s41467-019-12396-y

The chemistry of the Early Earth is widely inferred from the elemental and isotopic compositions of sulfidic sedimentary rocks, which are presumed to have formed globally through the reduction of seawater sulfate or locally from hydrothermally supplied sulfide. Here we argue that, in the anoxic Archean oceans, pyrite could form in the absence of ambient sulfate from organic sulfur contained within living cells. Sulfides could be produced through mineralization of reduced sulfur compounds or reduction of organic-sourced sulfite. Reactive transport modeling suggests that, for sulfate concentrations up to tens of micromolar, organic sulfur would have supported 20 to 100% of sedimentary pyrite precipitation and up to 75% of microbial sulfur reduction. The results offer an alternative explanation for the low range of δ34S in Archean sulfides, and raise a possibility that sulfate scarcity delayed the evolution of dissimilatory sulfate reduction until the initial ocean oxygenation around 2.7 Ga.



Low salinity waterflooding (LSW) is an effective method for enhancing the oil recovery from many reservoirs, and its success has been traced to a host of low salinity effects. In this work, we perform molecular dynamics simulations to study the feasibility of recovering oil trapped by nanopores by lowering the reservoir salinity. The oil is initially trapped by a slit nanopore, with a portion of the oil protruding from the pore entrance. After the reservoir salinity is lowered, the thin brine films that separate the oil and pore walls become thicker to drive some of the trapped oil out of the pore. We quantify the free energy profile of this process and clarify the underlying molecular mechanisms. Interestingly, the brine film growth is dominated by the water transport from the brine reservoir into the pore rather than by the depletion of ions from the brine film. These results provide molecular evidence that low salinity brines benefit the recovery of the oil trapped by nanopores. They highlight that when ion depletion from thin brine films is suppressed, the osmosis of water can play a fundamental role in the expansion of the brine films; thus, the enhanced oil recovery. The slow osmosis of water through thin brine films and thus the slow displacement of oil from the pore may help explain the anomalously slow oil recovery reported in micro-modeling experiments of LSW.



A total of 30 core samples of organic matter-rich Lower Toarcian shale (Posidonia Shale) were geochemically analyzed to study systematic changes in the quantitative and qualitative composition of specific biomarkers at different thermal maturities ranging from 0.48 to 1.45% vitrinite reflectance (VRr). The samples are derived from 5 wells (Hils Syncline, NW Germany) each representing a different level of maturation (0.48, 0.68, 0.73, 0.88, 1.45 %VRr). In NW Germany, Posidonia Shale was deposited under marine, oxygen-deficient bottom water containing initially high amounts of TOC (above 10%) and marine type I-II kerogen. Upon maturation, organic carbon has been lost and hydrogen index values have decreased. Biomarker ratios reflecting this maturation very well include ratios of short over long-chain n-alkanes, ratios of pristane and phytane over nC17 and nC18, Ts/(Ts + Tm), C29Ts/(C29Ts + C29H), ratios based on DMDBTs, and TA(I)/TA(I + II) ratios (triaromatic steroids). The evolution of different steroid-, hopane-, naphthalene-, phenanthrene- and dibenzothiophene-related parameters is documented and compared to literature.

Concentrations of individual hydrocarbons were measured in order to obtain quantitative data on biomarker abundance and their evolution upon maturation. Whereas there is a general trend of increasing biomarker content from immature (0.48 %VRr) to early mature (0.68 %VRr) conditions and of decreasing biomarker content with maturation from 0.68 to 0.88 %VRr, there are some exceptions from this trend, especially at low levels of maturity. Almost no polycyclic biomarkers were detected at the highest maturity level of 1.45 %VRr in well Haddessen, where n-alkanes and aromatic hydrocarbons are predominant. The overall pattern of polycyclic biomarker abundance is not only determined by isomerization and aromatization processes, but mainly by preferential

degradation of thermally less stable biomarkers leading to the observed modifications of biomarker maturity parameters.

Furthermore, outer and inner sections from the 10 cm wide cores were compared in order to find out, whether 40 years of dry storage in a core repository affected the biomarker parameters. No significant and systematic differences have been observed, with exception of the most mature Haddessen well, where low molecular weight n-alkanes (<nC21) are more abundant in the outer part.

Fang, Y., Yang, E., Cui, X., 2019. Study on distribution characteristics and displacement mechanism of microscopic residual oil in heterogeneous low permeability reservoirs. Geofluids 2019, 9752623.

https://doi.org/10.1155/2019/9752623

In order to explore the development methods suitable for heterogeneous low permeability reservoirs and study the distribution characteristics of residual oil, photoetched glass and artificial core models with three permeability ratios of 1, 6, and 9 were prepared in this research. Three displacement schemes including polymeric surfactant flooding, polymeric surfactant with binary flooding, and binary flooding were designed at the same expenses to obtain the displacement mechanism of various residual oil saturations. The results show that the best displacement efficiency can be achieved by polymeric surfactant flooding, followed by polymeric surfactant with binary flooding, and binary flooding for the models with the same permeability ratio. Binary flooding mainly activates cluster and oil drop residual oils, polymeric surfactant with binary flooding mainly activates cluster, oil film, and column residual oils, whereas polymeric surfactant flooding mainly activates cluster, oil drop, and column residual oils. In addition, with the increase of the model permeability ratio, the recovery ratio of water flooding decreases, whereas the enhanced oil recovery and the variations in residual oil saturation gradually increase after carrying out different displacement measures. The viscoelastic and shearing effects of the polymeric surfactant flooding system can better displace the residual oil, assisting in the further development of heterogeneous low permeability reservoirs.


https://doi.org/10.1186/s40168-019-0741-3

Natural gas seeps contribute to global climate change by releasing substantial amounts of the potent greenhouse gas methane and other climate-active gases including ethane and propane to the atmosphere. However, methanotrophs, bacteria capable of utilising methane as the sole source of carbon and energy, play a significant role in reducing the emissions of methane from many environments. Methylocella-like facultative methanotrophs are a unique group of bacteria that grow on other components of natural gas (i.e. ethane and propane) in addition to methane but a little is known about the distribution and activity of Methylocella in the environment. The purposes of this study were to identify bacteria involved in cycling methane emitted from natural gas seeps and, most importantly, to investigate if Methylocella-like facultative methanotrophs were active utilisers of natural gas at seep sites.

Filatova, N.I., 2019. A Jurassic anoxic event in the Pacific based on data from the West Kamchatka–Asian region. Doklady Earth Sciences 487, 894-897.

https://doi.org/10.1134/S1028334X1908018X

Based on allochthonous complexes of the Asian–West Kamchatka region, an Early Jurassic (Sinemurian–Toarcian) oceanic anoxic event (J-OAE) in the Nothern Pacific has been revealed for the first time. This event is indicated by sulfide-containing bituminous black cherts that accumulated under euxinic conditions of deep oceanic basins. The anoxia gradually weakened to end completely by the beginning of the Late Jurassic, when hematite jaspers began to accumulate in the aerated water mass. The J-OAE in the Pacific was synchronous to the global warming stage caused by worldwide magmatism; gas-hydrothermal contribution induced a euxinic regime of oceanic water, a change in the carbon cycle, and the change in the taxonomy of radiolarians revealed by Hori [3]. The J-OAE of the Pacific expands the time interval of the known T-OAE and is also supported by the data from other oceanic basins of the world.

Fogel, M.L., 2019. My stable isotope journey in biogeochemistry, geoecology, and astrobiology. Geochemical Perspectives 8, 105-281.

http://www.geochemicalperspectives.org/online/v8n2

Stable isotope biogeochemistry started in earnest in the 1960s with isotope ratio mass spectrometers hand made in physicists’ laboratories. I began my career at the time when people were realising that the biosphere was important in shaping the geosphere. Bringing sophisticated chemical instrumentation to study the relationships between living organisms and their environment, in particular in fossils over geological time, was exploding in the 1970s and 1980s. Follow along on insights gained over a nearly 50 year career.



Editorial: Microbialites represent one of the oldest known ecosystems on Earth, with a fossil record dating back over 3.5 billion years. These long-lived communities form sedimentary structures as a result of the synergy between microbial metabolisms and the environment. Although once global on the ancient Earth, modern microbialites are found mainly in restricted habitats with sparse eukaryotic populations. Living microbialites offer an opportunity to examine how these ancient ecosystems interface and respond to changes in their environment. Even today, microbialites are bellwethers for an ever-changing Earth and are becoming increasingly exposed to effects of global climate change, such as rising sea levels, ocean acidification, and warmer temperatures. Investigations into extant microbialites represent a unique opportunity to understand the feedbacks that occur between microbialite communities and their environment.

In this collection of research articles, experts investigate and discuss the formation of modern microbialites and the interactions between microbes and the environment. These research contributions target communities from a diverse range of freshwater, marine, and hypersaline environments. Key questions addressed by the papers include (Q1) what are the taxa and metabolic processes that influence microbialite formation? (Q2) How do microbes network and coordinate their activities to form lithified structures? (Q3) How do environmental conditions influence microbialite ecosystems both in the past and present? And (Q4) how are modern microbialite systems likely to respond to ongoing climate change?

Questions 1 and 2 are highly integrative and most papers in the collection touched upon these key areas of research. For example, Wilmeth et al. use novel tracer experiments to quantify mat biomass addition as well as assess the deposition of calcium carbonate within hot spring microbial mats. Their analysis of the rates of carbon fixation and biogenic carbonate precipitation suggests that metabolic processes other than autotrophy may play critical roles in the preservation of mats as microbialites. Additionally, Kraus et al. looked at the formation of minerals in microbialites to help improve our understanding of biosignature in hot springs. Their results reveal that abiotic mineralization of calcite can be subsequently modified by microbial activities, suggesting that biosignature formation is a complex, multi-stage process.

Also addressing Q1 and Q2, the role of certain phototrophic taxa in the formation of mineral precipitates was examined in diverse hypersaline environments including Laguna Negra in Argentina (Mlewski et al.) and Lake Dziani Dzaha on Mayotee Island (Gérard et al.), revealing a multifaceted role of phototrophs in microbialite precipitation. Additionally, several of the articles begin to characterize and close the genomes of some of the more abundant taxa within freshwater microbialites derived from Pavilion Lake in British Columbia (White et al.; White et al.), including novel species of the Exiguobacterium and Agrococcus genera. These efforts have helped expand the genome databases of taxa associated with the formation and growth of modern microbialites.

Although most studies on microbialites typically focus role of bacteria and archaea in the molecular and biochemical processes associated with element cycling and carbonate precipitation in microbialites, such as the study of Valdespino-Castillo et al., two studies within this collection also addressed Question 1 by targeting organisms that are typically overlooked—algae and viruses. In Frommlet et al., in vitro experiments using the alga Symbiodinium and its naturally associated microbial consortia revealed that bacterial-algal associations can affect the physicochemical macroenvironment in culture and that the structural integrity of the bacterial-algal biofilms in the microenvironment influences and can facilitate calcification. Alternatively, the role of viruses within microbialite-forming communities was explored by White et al. Their analysis revealed a diverse assemblage of single-stranded DNA viruses within the microbialites, which may be important in element cycling and perhaps modulating microbial diversity of microbialite communities.

In addition to examining microbialite formation, other authors explored Question 3 regarding the impact of the environment on microbialite-forming communities. In the paper by De Anda et al., the authors used metagenomic techniques to examine the specific interactions between taxa in response to environmental perturbations in the freshwater microbialites of Cuatros Ciénegas in Mexico. Their results show that water availability impacts the balance between competition and cooperation interactions. Similarly in the hypersaline system of Hamelin Pool in Western Australia, Babilonia et al. used comparative metagenomics to reveal different metabolic strategies for microbialite formation that was highly dependent on environment, in particular water depth.

Together, this collection of articles has provided new insight into the processes by which microbialites form and how these dynamic ecosystems potentially adapt to and alter their surrounding environment. These articles also reveal several universal processes associated with mineral precipitation across different habitats and help elucidate dynamic feedbacks that occur between microbialites and their environment. Although several of the manuscripts in this collection touch upon how modern microbialite systems are affected by ongoing changes in the climate, this last key question (Q4) represents an important frontier for microbialite research. As microbialites have persisted on Earth for most of evolutionary history, the mechanisms and pathways in which they have caused, responded and adapted to climate change represent a valuable resource to more fully explore the feedbacks and constraints underlying the continued habitability of our planet.



The hydrogen isotope values of plant waxes (δ2Hwax) primarily reflect plant source water. δ2Hwax preserved in lake sediments has therefore been widely used to investigate past hydroclimate. The processes by which plant waxes are integrated at regional and catchment scales are poorly understood and may affect the δ2Hwax values recorded in sediments. Here, we assess the variability of sedimentary δ2Hwax for two plant wax compound classes (n-alkanes and n-alkanoic acids) across 12 lakes in the Adirondack Mountains that receive similar regional precipitation δ2H but vary at the catchment-scale in terms of vegetation structure and basin morphology. Total long-chain (n-C27 to n-C35) alkane concentrations were similar across all sites (191 ± 53 µg/g TOC) while total long-chain (n-C28 and n-C30) alkanoic acid concentrations were more variable (117 ± 116 µg/g TOC) and may reflect shoreline vegetation composition. Lakes with shorelines dominated by evergreen gymnosperm plants had significantly higher concentrations of long-chain n-alkanoic acids relative to n-alkanes, consistent with our observations that deciduous angiosperms produced more long-chain n-alkanes than evergreen gymnosperms (471 and 33 µg/g TOC, respectively). In sediments, the most abundant chain lengths in each compound class were n-C29 alkane and n-C28 alkanoic acid, which had mean δ2H values of −188 ± 6‰ and −164 ± 9‰, respectively. Across sites, the range in sedimentary n-C29 alkane (22‰) and n-C28 alkanoic acid δ2H (35‰) was larger than expected based on the total range in modeled mean annual precipitation δ2H (4‰). We observed larger mean εapp (based on absolute values) for n-alkanes (−123‰) than for n-alkanoic acids (−97‰). Across sites, the δ2H offset between n-C29 alkane and the biosynthetic precursor n-C30 alkanoic acid (εC29-C30) ranged from −8 to −58‰, which was more variable than expected based on observations in temperate trees (−20 to −30‰). Sediments with greater aquatic organic matter contributions (lower C/N ratios) had significantly larger (absolute) εC29-C30 values, which may reflect long-chain n-alkanoic acids from aquatic sources. Concentration and δ2Hwax data in Adirondack lakes suggest that long-chain n-alkanes are more sensitive to regional-scale precipitation signals, while n-alkanoic acids are more sensitive to basin-scale differences in catchment vegetation and wax sourcing.

Frey, L., Coates, M., Ginter, M., Hairapetian, V., Rücklin, M., Jerjen, I., Klug, C., 2019. The early elasmobranch Phoebodus: phylogenetic relationships, ecomorphology and a new time-scale for shark evolution. Proceedings of the Royal Society B: Biological Sciences 286, 20191336.

https://doi.org/10.1098/rspb.2019.1336

Anatomical knowledge of early chondrichthyans and estimates of their phylogeny are improving, but many taxa are still known only from microremains. The nearly cosmopolitan and regionally abundant Devonian genus Phoebodus has long been known solely from isolated teeth and fin spines. Here, we report the first skeletal remains of Phoebodus from the Famennian (Late Devonian) of the Maïder region of Morocco, revealing an anguilliform body, specialized braincase, hyoid arch, elongate jaws and rostrum, complementing its characteristic dentition and ctenacanth fin spines preceding both dorsal fins. Several of these features corroborate a likely close relationship with the Carboniferous species Thrinacodus gracia, and phylogenetic analysis places both taxa securely as members of the elasmobranch stem lineage. Identified as such, phoebodont teeth provide a plausible marker for range extension of the elasmobranchs into the Middle Devonian, thus providing a new minimum date for the origin of the chondrichthyan crown-group. Among pre-Carboniferous jawed vertebrates, the anguilliform body shape of Phoebodus is unprecedented, and its specialized anatomy is, in several

respects, most easily compared with the modern frilled shark Chlamydoselachus. These results add greatly to the morphological, and by implication ecological, disparity of the earliest elasmobranchs.

Fröbisch, N.B., Witzmann, F., 2019. Early tetrapods had an eye on the land. Nature 574, 494-495.


Fossil finds that can provide clues about how aquatic vertebrates evolved into land dwellers are elusive. But the ancient bones of a newly discovered species of tetrapod now provide some crucial missing evidence.

Following the scientific investigations into how vertebrates transitioned from water to land is like reading a good crime novel. We have a range of suspects, patchy evidence and a lot of unanswered questions. And to complicate matters, this transition from finned fish to four-limbed creatures (tetrapods) is a ‘cold case’ from nearly 400 million years ago. In a paper in Nature, Beznosov et al.1 present some compelling detective work that sheds light on this.

The earliest-known tetrapod specimens are 380-million-year-old bone fragments that, although identifiable as belonging to a tetrapod, do not provide many details about what these animals looked like or how they lived2. There are also fossilized tetrapod footprints that pre-date these fossil finds by more than 14 million years3, indicating the presence of a four-limbed, still fully aquatic track maker — but they do not reveal what the track maker looked like above the soles of its feet.

More-detailed insights into the body shape, life and growth of our early vertebrate ancestors are provided by more-complete fossil finds, including the iconic tetrapods Acanthostega and Ichthyostega2,4. However, these lived 365 million years ago, when tetrapods had already achieved an impressive geographical distribution and a diverse variety of body shapes and ways of life2.

By contrast, the earliest phase of tetrapod evolution and diversification has long been mysterious. However, Beznosov and colleagues now describe skeletal fossils of a species they call Parmastega aelidae, which is the most ancestral (basal-most) tetrapod reported so far.

Like its known younger relatives, P. aelidae was a gill-breathing water dweller, and the authors estimate that this animal reached a size of more than one metre long. It lived about 372 million years ago during the Devonian period, and inhabited a shallow lagoon in a landmass that is now part of northwestern Russia. These excellently preserved fossils provide crucial data about how the major changes in breathing, sensory perception, locomotion and feeding might have taken place as tetrapods transitioned to life on land. The discovery also raises many exciting questions.

The earliest-known tetrapod specimens are 380-million-year-old bone fragments that, although identifiable as belonging to a tetrapod, do not provide many details about what these animals looked like or how they lived2. There are also fossilized tetrapod footprints that pre-date these fossil finds by more than 14 million years3, indicating the presence of a four-limbed, still fully aquatic track maker — but they do not reveal what the track maker looked like above the soles of its feet.

More-detailed insights into the body shape, life and growth of our early vertebrate ancestors are provided by more-complete fossil finds, including the iconic tetrapods Acanthostega and Ichthyostega2,4. However, these lived 365 million years ago, when tetrapods had already achieved an impressive geographical distribution and a diverse variety of body shapes and ways of life2.

By contrast, the earliest phase of tetrapod evolution and diversification has long been mysterious. However, Beznosov and colleagues now describe skeletal fossils of a species they call Parmastega aelidae, which is the most ancestral (basal-most) tetrapod reported so far.

Like its known younger relatives, P. aelidae was a gill-breathing water dweller, and the authors estimate that this animal reached a size of more than one metre long. It lived about 372 million years ago during the Devonian period, and inhabited a shallow lagoon in a landmass that is now part of northwestern Russia. These excellently preserved fossils provide crucial data about how the major changes in breathing, sensory perception, locomotion and feeding might have taken place as tetrapods transitioned to life on land. The discovery also raises many exciting questions.

Mudskippers (species from the family Oxudercidae) are modern amphibious fish that inhabit marine mud flats, and they are useful living creatures with which to compare P. aelidae because their eyes have a similar shape and position. Mudskippers peek above the water surface to look out for prey and potential danger5. But what was P. aelidae looking for? The need to detect enemies on land or in the air can be ruled out, because during the late Devonian period, such animals were not yet present there.

One possibility is that P. aelidae was looking for prey on the shore. If so, what kind of terrestrial or semi-terrestrial prey was it watching? Some have suggested that early water-dwelling tetrapods and their closest fish-like relatives might have preyed on terrestrial invertebrates of the phylum Arthropoda, which includes insects6. However, the large arthropods that could have provided sufficient food to sustain an animal the size of P. aelidae were still rare in the Devonian period7. Moreover, P. aelidae had large fangs, which suggests that it preyed mainly on vertebrates. Perhaps it searched for fish carcasses stranded on the shore. Or, to make an even more speculative suggestion, maybe it scavenged early amphibious tetrapods that rested near the water. However, evidence for such creatures has not yet been found among the fossils of the Sosnogorsk Formation (the rock layers that contained the P. aelidae fossil).

Another notable feature of P. aelidae is the extremely low position, close to its jaws, of the external openings of its nose (the nares), which would have been under water (Fig. 1). This is in striking contrast to the high position of its eyes and is quite different from the configuration of nares in modern-day aquatic tetrapod animals, such as crocodiles, hippopotamuses or frogs. The eyes of those animals sit on top of their head, and their nares are likewise positioned high on the snout, which enables them to breathe air while looking above water. Judging from their submerged position, P. aelidae nares acted as openings through which an inflow of water was directed towards the gills during breathing. P. aelidae also had the option of breathing air through a large opening in its skull called a spiracle (Fig. 1), and such a breathing process would probably have been similar to that used by modern air-breathing fish8.

This low position of the nares is found in most known early tetrapods (called stem tetrapods) of the Devonian period (approximately 419.2 million to 358.9 million years ago) and Carboniferous period (358.9 million to 298.9 million years ago). In all of these animals, the passage from the nares to the mouth cavity might still have served to transport water rather than air. Some fossils of stem tetrapods, such as those of a grouping called colosteids (Fig. 1), had lost their spiracle opening — they must therefore have relied on gill breathing. In some other early tetrapods that arose later than P. aelidae and were more evolved than their ancestors (a state described as being more derived), the spiracle is absent, and its place is taken by an ear2. These tetrapods’ nares are larger and higher on the snout (Fig. 1) compared with the ancestral form, suggesting that they used their nares to transport air towards the lungs while peeking out of the water when on the lookout for prey.

The P. aelidae fossils offer a treasure trove of information that could help to disentangle some of the complex evolutionary changes that took place when vertebrates made the transition from aquatic to

terrestrial life. This discovery also reminds us that much still remains to be learnt in the next gripping chapter of this detective story.

References1. Beznosov, P. A., Clack, J. A., Lukševičs, E., Ruta, M. & Ahlberg, P. E. Nature 574, 527–531

(2019).2. Clack, J. A. Gaining Ground: The Origin and Evolution of Tetrapods 2nd edn (Indiana Univ.

Press, 2012).3. Niedźwiedzki, G., Szrek, P., Narkiewicz, K., Narkiewicz, M. & Ahlberg, P. E. Nature 463, 43–48

(2010).4. Sanchez, S., Tafforeau, P., Clack, J. A. & Ahlberg, P. E. Nature 537, 408–411 (2016).5. Schultze, H.-P. Sber Ges. Naturf. Freunde Berl. 36, 59–77 (1997).6. MacIver, M. A., Schmitz, L., Mugan, U., Murphey, T. D. & Mobley, C. D. Proc. Natl Acad. Sci.

USA 114, E2375–E2384 (2017).7. Shear, W. A. & Kukalová-Peck, J. Can. J. Zool. 68, 1807–1834 (1990).8. Graham, J. B. et al. Nature Commun. 5, 3022 (2014).


https://doi.org/10.1038/s41396-019-0452-6

Up to half of marine N losses occur in oxygen-deficient zones (ODZs). Organic matter flux from productive surface waters is considered a primary control on N2 production. Here we investigate the offshore Eastern Tropical North Pacific (ETNP) where a secondary chlorophyll a maximum resides within the ODZ. Rates of primary production and carbon export from the mixed layer and productivity in the primary chlorophyll a maximum were consistent with oligotrophic waters. However, sediment trap carbon and nitrogen fluxes increased between 105 and 150 m, indicating organic matter production within the ODZ. Metagenomic and metaproteomic characterization indicated that the secondary chlorophyll a maximum was attributable to the cyanobacterium Prochlorococcus, and numerous photosynthesis and carbon fixation proteins were detected. The presence of chemoautotrophic ammonia-oxidizing archaea and the nitrite oxidizer Nitrospina and detection of nitrate oxidoreductase was consistent with cyanobacterial oxygen production within the ODZ. Cyanobacteria and cyanophage were also present on large (>30 μm) particles and in sediment trap material. Particle cyanophage-to-host ratio exceeded 50, suggesting that viruses help convert cyanobacteria into sinking organic matter. Nitrate reduction and anammox proteins were detected, congruent with previously reported N2 production. We suggest that autochthonous organic matter production within the ODZ contributes to N2 production in the offshore ETNP.

Fujii, H., Mazzitelli, J.-B., Adilbekov, D., Olmer, F., Mathe, C., Vieillescazes, C., 2019. FT-IR and GC–MS analyses of Dressel IA amphorae from the Grand Congloué 2 wreck. Journal of Archaeological Science: Reports 28, 102007.


This research work is focused on the chemical characterization of the substance present in the internal surfaces of Roman amphorae that made them waterproof and on the identification of their content. The samples come from the wreck of the Grand Congloué 2 that was studied in the Bay of Marseille

by Commander Cousteau in 1952. The twenty studied amphorae are of type Dressel 1A and were provided by Cosa in Etruria (Tuscany, Italy). The FT-IR analysis indicated different bands concerning organic matter, as the chemical link O–H from carboxylic acid, C–H of the methylene group and C–O of the methyl ester. The study carried out by GC–MS showed nineteen diterpenoids, such as dehydroabietic acid and retene, which are chemical markers of Pinaceae family. Methyl ester by-products were also characterized and they revealed a pitch pyrogenically prepared from resinous wood (Pinus sp.). Principal Component Analysis allowed to group all of the twenty studied amphorae in two lots indicating two types of pitch. Concerning the content of these amphorae, the results from pitch as well as shards allowed to detect the presence of tartaric and syringic acids which are the main markers of the red wine. The comparison study between pitch and shard samples of same amphorae indicates that pitch analyses has permitted to obtain a high qualitative and quantitative proportion of wine markers.

Fursenko, E.A., Kim, N.S., 2019. Geochemistry of condensates of Maloyamal’skoe Field (Yamal Peninsula, Western Siberia). Petroleum Chemistry 59, 1138-1146.

https://doi.org/10.1134/S0965544119100049

Analysis of distribution of saturated and aromatic hydrocarbon markers identified in five condensates of Maloyamal’skoe field (beds Yu2–3, Yu4 and Yu6, Middle Jurassic) leads to the conclusion that their generation is due to lipid components of predominantly terrigenous organic matter (OM) which accumulated under weakly reducing conditions. Values of the isomeric ratios of steranes and homohopanes, Ts/Tm, maturity indicators based on the arene composition suggest the formation of condensates under conditions of the main phase of oil generation. Comparison of compositions of condensates and extractable bitumens of dispersed organic matter (DOM) of rocks showed genetic relation of condensates with the organic matter of Middle Jurassic deposits.


http://www.syxb-cps.com.cn/EN/abstract/abstract5747.shtml

Organic pores in the continental shale show a relatively strong heterogeneity. Taking the Shahezi Formation shale in the Changling fault depression of Songliao Basin as an example, and based on observation using the field emission scanning electron microscopy and optical microscopy, this paper explores the heterogeneity characteristics and genetic mechanism of organic pores in the continental shale. The results show that there are four main factors controlling the heterogeneity of organic matters in the continental shale, i.e., remnants of primary organic pores, differences in hydrocarbon generation potential, differences in the solid bitumen reflectance and catalyses of clay minerals. Due to the fact that the cell lumens were not filled or subjected to external force, the components with higher plant fiber structure, such as telinite, fusinite, semi-fusinite and sclerotinite, formed the fold superimposed with residual pores. Pores are best developed in solid bitumen, followed by vitrinite and intertinite; the weight percentage of carbon in the three components increases successively, indicating that the difference in pore development among the three organic matters is essentially controlled by the difference in the hydrocarbon generation potential. Not all of the organic pores are developed in solid bitumen. Statistics show that the porous solid bitumen mostly has the reflectivity of 1.60% -2.00%, in the stage of petroleum cracking and gas generation; the non-porous solid bitumen mostly has the reflectance of 1.20% -1.60%, in the stage of kerogen cracking and

hydrocarbon generation. Under the catalyses of clay minerals, almost all solid bitumens in the organoclay complex are developed with rich honeycomb pores. The specific catalytic activity can be enhanced by illite, thus facilitating the formation of gaseous hydrocarbon and the generation of pores.



We present a study of vanadium (V) isotope compositions for 17 crude oils spanning a wide range of concentrations and formation ages. Bulk organic geochemical and biomarker compositions are investigated for 11 co-genetic crude oils from the Barbados oil field. About 2‰ V isotope fractionation was observed and they are primarily correlated with V/Ni ratios and most likely reflect the depositional environment of the petroleum source rocks. Factors such as the lithology of the source rocks, Eh and pH of the depositional environment, and possibly the V isotope composition of seawater could all play a role in the V isotope composition. The Eh and pH conditions determine the speciation and coordination of V ions in fluids, whereas the lithology of the source rock defines the competing phases for available V ions in solution. The V isotopes are significantly modified by maturation and biodegradation. The V isotope fractionation during biodegradation has most probably resulted from the microbial activity-induced changes in the species and coordination geometries of V ions in fluids. The progressive decrease of δ51V with the increase of maturation might suggest a preferential loss of 51V during de-metalation and/or a preferential incorporation of 50V in the newly formed V-organometallic compounds.

Garschagen, L.S., Mancinelli, R.L., Moeller, R., 2019. Introducing Vibrio natriegens as a microbial model organism for microgravity research. Astrobiology 19, 1211-1220.

https://doi.org/10.1089/ast.2018.2010

Microbial contamination of human-tended spacecraft is unavoidable, making the study of microbial growth under space conditions essential for the preservation of astronauts' health and equipment integrity. Previous studies suggested that spaceflight conditions, such as microgravity, cause a range of physiological microbial alterations including increased growth yields and decreased antibiotic susceptibility. Because of its fast generation time, Vibrio natriegens could be used as a model organism for a variety of studies where generation time is a critical factor. In this study, V. natriegens was used as a tool to study growth characteristics by determining the viable cell number and antibiotic susceptibility under simulated microgravity using a 2-D clinostat (60 rpm) to establish a test system that resolves changes in microbial growth on a solid surface (agar) under microgravity. The data show that V. natriegens biomass increases significantly after 24 h at 37°C under simulated microgravity. The final cell population after cultivation under simulated microgravity was 60-fold greater than when cultivated under normal terrestrial gravity (1 × g). No change in susceptibility to the antibiotic rifampicin after cultivation under simulated microgravity or normal gravity was detected. These data show that V. natriegens is a new and innovative model organism for microbial microgravity research.

Geiger, R.A., Junghare, M., Mergelsberg, M., Ebenau-Jehle, C., Jesenofsky, V.J., Jehmlich, N., von Bergen, M., Schink, B., Boll, M., 2019. Enzymes involved in phthalate degradation in sulphate-reducing bacteria. Environmental Microbiology 21, 3601-3612.

https://doi.org/10.1111/1462-2920.14681

The complete degradation of the xenobiotic and environmentally harmful phthalate esters is initiated by hydrolysis to alcohols and o‐phthalate (phthalate) by esterases. While further catabolism of phthalate has been studied in aerobic and denitrifying microorganisms, the degradation in obligately anaerobic bacteria has remained obscure. Here, we demonstrate a previously overseen growth of the δ‐proteobacterium Desulfosarcina cetonica with phthalate/sulphate as only carbon and energy sources. Differential proteome and CoA ester pool analyses together with in vitro enzyme assays identified the genes, enzymes and metabolites involved in phthalate uptake and degradation in D. cetonica. Phthalate is initially activated to the short‐lived phthaloyl‐CoA by an ATP‐dependent phthalate CoA ligase (PCL) followed by decarboxylation to the central intermediate benzoyl‐CoA by an UbiD‐like phthaloyl‐CoA decarboxylase (PCD) containing a prenylated flavin cofactor. Genome/metagenome analyses predicted phthalate degradation capacity also in the sulphate‐reducing Desulfobacula toluolica, strain NaphS2, and other δ‐proteobacteria. Our results suggest that phthalate degradation proceeds in all anaerobic bacteria via the labile phthaloyl‐CoA that is captured and decarboxylated by highly abundant PCDs. In contrast, two alternative strategies have been established for the formation of phthaloyl‐CoA, the possibly most unstable CoA ester in biology.

Ghadimi, M., Ghaedi, M., Malayeri, M.R., Amani, M.J., 2020. A new approach to model asphaltene induced permeability damage with emphasis on pore blocking mechanism. Journal of Petroleum Science and Engineering 184, 106512.


Asphaltene deposition in porous media could reduce permeability up to 90%. Nonetheless, this would occur often for a slight reduction in porosity. This, in turn, indicates that while the volume of deposition is not noticeable it can block pore throats and consequently, it affects conductivity of porous media. This phenomenon is strongly dependent on the pore structure, initial porosity and permeability and also precipitated asphaltene particle size which is a function of oil composition and the condition of asphaltene precipitation. Often, regardless of these facts, permeability reduction is simulated by a power law porosity-permeability relationship. This study highlights the necessity of a new permeability model based on previous studies and experiments. A new permeability reduction model based on Gruesbeck and Collins' parallel plugging/non-plugging pathways model is proposed. The model considers two different mechanisms including surface deposition and throat plugging based on pore size distribution, and is implemented into an IMPEC (Implicit Pressure and Explicit Composition) compositional cylindrical simulator. Precipitated asphaltenes, considered as moving phase during simulation, are characterized by LLE (Liquid/Liquid equilibrium) calculations using PR-EoS. It is observed that permeability damage due to throat blocking is severe and abrupt while surface deposition is a gradual mechanism. Furthermore, convexity and concavity of permeability reduction curves are obtained for plugging and non-plugging pathways, respectively.

Gigler, G.M., Sośnicka, M., Erasmus, R., Schapira, J., Kinnaird, J.A., 2020. Microfossils or pseudofossils? Cu-Co sulphide microfeatures in the Neoproterozoic Katangan Supergroup, Democratic Republic of Congo. Precambrian Research 336, 105481.


In this paper we investigate a group of microfeatures discovered in the mineralised, Neoproterozoic Mines Subgroup of the Katangan Copperbelt, Democratic Republic of Congo (DRC), at the Mashitu South Cu-Co deposit. The features are bacillus-shaped, composed of Cu-Co sulphides and occur within syn-diagenetic apatite veins in a low-grade metasedimentary shale. They exhibit a range of evidence for biogenicity, including indicators of cellular complexity, and were therefore investigated as candidate microfossils of chasmoendolithic prokaryotes. However, our study found that the features are likely to be pseudofossils, formed from abiogenic rutile crystals which have been replaced by sulphides in such a way as to mimic biogenicity indicators. This method of sulphide-replacement adds to the list of possible ‘false-positives’ in the search for early life, and emphasises the importance for micropalaeontological studies to consider such features with a sceptical, holistic approach and rigorous scientific method.

Ginot, S., Goudemand, N., 2019. Conodont size, trophic level, and the evolution of platform elements. Paleobiology 45, 458-468.

https://doi.org/10.1017/pab.2019.19

Conodonts are among the first vertebrates to have evolved mineralized tooth-like structures. Among these, the so-called P1 elements are known to have been used to break down food and display a wide variety of morphologies. In particular, the repeated independent evolution of platform-like P1 elements have been suggested to correspond to similar functional constraints linked to diet. To test this hypothesis of convergence, we measured size (as element length) for various conodont taxa and used it as a proxy for trophic level. We then tested the correlation between size and platform presence/absence, both on raw data and in a phylogenetic context. Retaining or excluding the platform traits from the character matrix has limited impact on the resulting phylogeny. Contrary to platform presence/absence, size shows no phylogenetic signal. Using the raw data, size and platform presence appear positively correlated. That correlation, however, is no longer significant if one corrects for the phylogeny. We conclude that platform presence cannot be explained by an enlargement of the conodont element, be it via a trophic-level change or developmental constraints. This suggests that conodonts as a whole, and in particular platform-bearing conodonts, were an ecologically diverse group and that the various known platform types are likely to reflect different, rather than convergent, ecological niches.


https://doi.org/10.1029/2019JG005149

The hydrogen (δDwax) and carbon (δ13Cwax) isotope compositions of long‐chain alkanes derived from plant waxes record hydrological and environmental conditions. However, the integration of plant n‐alkanes into the sedimentary cycle, the variability of δDwax and δ13Cwax in soils, and the paleoclimate applicability in paleosols and archaeological sediments are poorly constrained. We sampled plants and soils across a steep climate transect in Israel to understand how plant type and environmental parameters shape δ13Cwax and δDwax. This transect has three advantages: existence of long‐term precipitation isotopic composition (δDr) records, a single wet season potentially reduces variability due to seasonality, and abandoned Byzantine period (~300–600 AD) agricultural terraces that reduce modern and ancient soil mixing and provide age constraints. We find that soil δ13Cwax is constant (0.4‰, 1σ) across a 500‐ to 1,300‐mm/year rainfall gradient and appears insensitive to rainfall amount, unlike bulk plant δ13C. The absence of a rainfall effect suggests that δ13Cwax may be better

suited to reconstructing C3/C4 plant ratios than bulk δ13C. Homologue average soil δDwax significantly correlate with δDr, and the offset between δDr and soil δDwax (εapp) correlates with growing season relative humidity. The seasonality of leaf production accounted for at most ~10% of total plant δDwax variability. Lastly, soil δDwax and δ13Cwax variability is reduced by ~80% relative to plant δDwax and δ13Cwax variability. Our results show that soil δDwax and δ13Cwax faithfully record δDr and landscape C3‐C4 plant contributions and thus support the utility of these proxy data in paleosols and archaeological sites.



Unconventional reservoirs (e.g., shales) remain poorly understood, compared to conventional reservoirs, due to their complex compositional and structural anisotropy. These heterogeneities profoundly influence petrophysical and geomechanical properties of shales. Current advances in correlative multi-scale and multi-modal 2D/3D imaging provide a tremendous opportunity to image and characterize shales across multiple length scales – from core-to pore-scale. In this study, a Mancos Shale rock sample was characterized across multiple length scales – from a few centimeters to a few nanometers via digital rock analysis using correlative micro 3D X-ray computed tomography (micro-CT), micro 3D X-ray microscopy (micro-XRM), light microscopy (LM), scanning electron microscopy (SEM), and focused ion beam (FIB) – SEM (FIB-SEM) image datasets. These multi-scale/-modal 2D/3D image datasets were then correlated with each other and used to reconstruct digital rock 2D/3D models from which petrophysical properties (porosity and mineralogy) were quantified. Additionally, the SEM/FIB-SEM imaged porosity was compared with bulk porosity measured with the traditional laboratory technique of helium porosimetry. The micro-CT, LM, and (low-resolution) SEM indicated that the investigated Mancos Shale rock sample consisted of interlaminated silt- and mud-rich laminae. The silt-rich laminae were characterized further using micro-XRM, whereas mud-rich laminae were characterized in great detail using high-resolution SEM and FIB-SEM. The SEM and FIB-SEM showed the presence of various fine-grained minerals (clay) and micrometer- and nanometer-sized pores within the mud-rich laminae, whereas micro-XRM showed coarse-grained minerals (quartz) cemented with the mud-rich nanoporous matrix within the silt-rich laminae. Furthermore, the results indicated that micro-fractures significantly contributed to the porosity of the investigated core-plug rock sample.

Goulden, S.K.E., Ohkouchi, N., Freeman, K.H., Chikaraishi, Y., Ogawa, N.O., Suga, H., Chadwick, O., Houlton, B.Z., 2019. Strong correspondence between nitrogen isotope composition of foliage and chlorin across a rainfall gradient: implications for paleo-reconstruction of the nitrogen cycle. Biogeosciences 16, 3869-3882.

https://www.biogeosciences.net/16/3869/2019/

Nitrogen (N) availability influences patterns of terrestrial productivity and global carbon cycling, imparting strong but poorly resolved feedbacks on Earth's climate system. Central questions concern the timescale of N cycle response to elevated CO2 concentration in the atmosphere and whether availability of this limiting nutrient increases or decreases with climate change. Nitrogen isotopic composition of bulk plant leaves provides information on large-scale patterns of N availability in the modern environment. Here we examine the utility of chlorins, degradation products of chlorophyll, hypothesized to persist in soil subsequent to plant decay, as proxies for reconstructing past plant δ15N. Specifically, we test the hypothesis that δ15N of plant leaves (δ15Nleaf) is recorded in δ15N of

pheophytin a (δ15Npheo) along the leaf–litter–soil continuum across an array of ecosystem climate conditions and plant functional types (C3, C4, legumes, and woody plants). The δ15N of live foliage and bulk soil display marked declines with increasing rainfall, consistent with past studies in Hawaii and patterns worldwide. We find measurable chlorin concentrations along soil–depth profiles at all sites, with pheophytin a present in amounts required for isotopic analysis (>10 nmol). δ15Npheo in leaves, litter, and soil track δ15Nleaf of plant leaves. We find potential for δ15Npheo records from soil to provide proxy information on δ15Nleaf.

Gözen, İ., 2019. A hypothesis for protocell division on the early Earth. ACS Nano 13, 10869-10871.

https://doi.org/10.1021/acsnano.9b06584

I hypothesize that the division of the first protocell might have occurred before genetic polymers were synthesized and redistributed. In the light of recent findings, it is conceivable that the first division event of a primitive protocell might have occurred at the same time as its surface-assisted formation.

Grant, G.R., Naish, T.R., Dunbar, G.B., Stocchi, P., Kominz, M.A., Kamp, P.J.J., Tapia, C.A., McKay, R.M., Levy, R.H., Patterson, M.O., 2019. The amplitude and origin of sea-level variability during the Pliocene epoch. Nature 574, 237-241.

https://doi.org/10.1038/s41586-019-1619-z

Earth is heading towards a climate that last existed more than three million years ago (Ma) during the ‘mid-Pliocene warm period’, when atmospheric carbon dioxide concentrations were about 400 parts per million, global sea level oscillated in response to orbital forcing and peak global-mean sea level (GMSL) may have reached about 20 metres above the present-day value. For sea-level rise of this magnitude, extensive retreat or collapse of the Greenland, West Antarctic and marine-based sectors of the East Antarctic ice sheets is required. Yet the relative amplitude of sea-level variations within glacial–interglacial cycles remains poorly constrained. To address this, we calibrate a theoretical relationship between modern sediment transport by waves and water depth, and then apply the technique to grain size in a continuous 800-metre-thick Pliocene sequence of shallow-marine sediments from Whanganui Basin, New Zealand. Water-depth variations obtained in this way, after corrections for tectonic subsidence, yield cyclic relative sea-level (RSL) variations. Here we show that sea level varied on average by 13 ± 5 metres over glacial–interglacial cycles during the middle-to-late Pliocene (about 3.3–2.5 Ma). The resulting record is independent of the global ice volume proxy3 (as derived from the deep-ocean oxygen isotope record) and sea-level cycles are in phase with 20-thousand-year (kyr) periodic changes in insolation over Antarctica, paced by eccentricity-modulated orbital precession between 3.3 and 2.7 Ma. Thereafter, sea-level fluctuations are paced by the 41-kyr period of cycles in Earth’s axial tilt as ice sheets stabilize on Antarctica and intensify in the Northern Hemisphere. Strictly, we provide the amplitude of RSL change, rather than absolute GMSL change. However, simulations of RSL change based on glacio-isostatic adjustment show that our record approximates eustatic sea level, defined here as GMSL unregistered to the centre of the Earth. Nonetheless, under conservative assumptions, our estimates limit maximum Pliocene sea-level rise to less than 25 metres and provide new constraints on polar ice-volume variability under the climate conditions predicted for this century.



Twenty-three gas oil samples from different origins were analyzed in positive and negative ion modes by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI(±)-FT-ICR MS). Sample ionization and ion transfer conditions were first optimized using Design of Experiment approach. Advanced characterization of basic and neutral nitrogen compounds in these samples was then performed through ESI(±)-FT-ICR MS analysis. A good repeatability was observed from the analysis of six replicates for each gas oil sample. Significant differences in molecular composition were spotted between the gas oils, either considering identified heteroatomic classes or within nitrogen families and were later correlated to samples macroscopic properties. The evolution of nitrogen relative intensities for one feed and two corresponding effluents has also been studied to monitor hydrotreatment reaction pathways toward aromaticity and alkylation levels evolutions.

Guo, W., 2020. Kinetic clumped isotope fractionation in the DIC-H2O-CO2 system: Patterns, controls, and implications. Geochimica et Cosmochimica Acta 268, 230-257.


The carbonate clumped isotope thermometer is a powerful tool in paleoclimate research, because it constrains carbonate formation temperature based on the extent of 13C and 18O clumping within the carbonate lattice (Δ47) and thus does not require knowledge of the isotopic composition of the water from which carbonates precipitate. However, there is growing evidence that kinetic processes in the precipitating solution, particularly the slow inter-conversion between CO2 and HCO3

−, can cause deviations of the clumped isotope composition of dissolved inorganic carbon (DIC) from their expected equilibrium values, leading to disequilibrium clumped isotope composition in the carbonate precipitates. Such disequilibrium effects impede the application of the carbonate clumped isotope thermometer to important climate archives (e.g., speleothems and corals), and hinder the realization of the full potential of this novel thermometer. Here, I systematically examine the patterns and controls of kinetic clumped isotope fractionations (i.e., Δ47, Δ48 and Δ49) in the DIC-H2O-CO2 system through first-principles theoretical calculations and numerical modeling (IsoDIC), and explore their implications for the carbonate clumped isotope thermometry.

I show that, in contrast to the large carbon and oxygen isotope effects, intrinsic clumped isotope fractionations associated with CO2 hydration and hydroxylation and their reverse reactions (i.e., HCO3

− dehydration and dehydroxylation) will lead to only relatively small disequilibrium Δ47 effects in the HCO3

− that are directly produced or consumed by these reactions. Instead, the disequilibrium Δ47 effects observed in most natural and laboratory-synthesized carbonates arise in large part from the mixing or removal of DIC pools with similar Δ47 compositions but distinct bulk carbon and oxygen isotope compositions. Further, my model simulations show characteristic evolutions of the clumped isotope composition of DIC during three common isotope fractionation processes, i.e., DIC-H2O isotope exchange, CO2 degassing, and CO2 absorption, and predict correlated enrichments in δ13C, δ18O and Δ48 but depletions in Δ47 and Δ49 of DIC during the early stage of CO2 degassing and vice versa during CO2 absorption, yielding typical disequilibrium Δ47/δ18O, Δ48/δ18O and Δ47/Δ48 slopes of about −0.03, 0.03, and −1.0 for CO2 degassing and about −0.02, 0.04, and −0.6 for CO2 absorption. While both the physicochemical condition (e.g., T, pH, [DIC], pCO2) and the isotopic composition (e.g., δ13C, δ18O, Δ47, Δ48, Δ49) of the aqueous solution and air CO2 can affect the magnitudes of these disequilibrium isotope effects, the correlations among these disequilibrium effects are relatively insensitive to changes in most environmental parameters except the isotopic composition of the aqueous solution and air CO2. The quantitative agreements between my model results and the existing observations from laboratory experiments and natural carbonates suggest that the model captures the key processes governing clumped isotope fractionations in the DIC-H2O-CO2-CaCO3 system, and

support the development of novel approaches, e.g., coupled Δ47-Δ48 measurements, to discern the kinetic processes involved in carbonate formation and to correct for disequilibrium clumped isotope effects in carbonate archives and derive accurate estimates of their formation temperatures.

Gure, A.J., Sorenson, T., Dewey, J.C., Kraus, T., Eggleston, C.M., Parkinson, B.A., 2019. Photostationary state in photoelectrochemical generation of perchlorate: Relevance to Mars. ACS Earth and Space Chemistry 3, 2171-2174.


The discovery of abundant perchlorate (ClO4–) on Mars has prompted renewed interest in the

production, accumulation, and transport of ClO4– and other oxychlorine species in natural systems.

Here, we focus on the role of semiconducting minerals in the photochemical generation and destruction of ClO4

– and chlorate (ClO3–). Illumination of single-crystal or nanocrystalline films of

titanium dioxide polymorphs, rutile and anatase, in chloride (Cl–) solutions can both generate and destroy ClO4

– depending upon starting ClO4– and Cl– concentrations. For single-crystal anatase, we

observe an apparent photostationary state, in which ClO4– production and destruction reach a near-

steady state. We observe more ClO3– production and less ClO4

– at higher Cl– concentrations. An inventory of measured dissolved chlorine (Cl) species indicates that some Cl was lost to a volatile form or dissolved form not measured. Our experiments were performed in an aqueous medium under Earth atmosphere and temperature conditions; further experiments under Mars-like conditions are in progress. Photochemical processes as described here, in which activation energy is provided by photons, are particularly important under cold conditions with limited thermal activation.



Remnants of paleoflora were discovered in impact melt rocks from the El'gygytgyn crater, Chukotka, Russia. El'gygytgyn is a 3.58 Ma, 18 km diameter impact structure in Chukotka, northeastern Russia. A circular crater basin is surrounded by an uplifted rim. The crater floor is occupied by the El'gygytgyn Lake, 12 km in diameter, surrounded by lacustrine terraces up to 80 m in height. Impactites found at the El'gygytgyn crater include impact melt rocks, glass bombs, and shock metamorphosed volcanic rocks. Most impact melt rocks occur only in redeposited state in the terrace lake deposits. Floral remnants were discovered in impact melt rocks from various locations in the terrace deposits. The floral remnants include fragments of leaves, cell tissue, and undetermined organic matter that occur in vesicles within glassy melt rocks and impact melt breccias. After the discovery of floral remnants in impact melt breccias from upper Miocene strata in Argentina, and the description of floral imprints in the Dakhleh Glass of proposed impact origin in Egypt, the detection of paleoflora remnants in impact melt rocks of the El'gygytgyn structure is the first such occurrence in a confirmed impact crater on Earth.


https://doi.org/10.1111/1462-2920.14743

We present the first geomicrobiological characterization of the meromictic water column of Powell Lake (British Columbia, Canada), a former fjord, which has been stably stratified since the last glacial period. Its deepest layers (300?350?m) retain isolated, relict seawater from that period. Fine-scale vertical profiling of the water chemistry and microbial communities allowed subdivision of the water column into distinct geomicrobiological zones. These zones were further characterized by phylogenetic and functional marker genes from amplicon and shotgun metagenome sequencing. Binning of metagenomic reads allowed the linkage of function to specific taxonomic groups. Statistical analyses (analysis of similarities, Bray?Curtis similarity) confirmed that the microbial community structure followed closely the geochemical zonation. Yet, our characterization of the genetic potential relevant to carbon, nitrogen and sulphur cycling of each zone revealed unexpected features, including potential for facultative anaerobic methylotrophy, nitrogen fixation despite high ammonium concentrations and potential micro-aerobic nitrifiers within the chemocline. At the oxic?suboxic interface, facultative anaerobic potential was found in the widespread freshwater lineage acI (Actinobacteria), suggesting intriguing ecophysiological similarities to the marine SAR11. Evolutionary divergent lineages among diverse phyla were identified in the ancient seawater zone and may indicate novel adaptations to this unusual environment.



Cholesterol is related to many health diseases and is considered as a metabolic disorder biomarker. This compound, present in all food products of animal origin, can also be used as food authentication biomarker. In this work and for the first time, positional 13C isotope contents were determined for such a high molecular weight compound. This was possible by means of NMR using adiabatic refocused INEPT. In order to test the potential of this approach for discrimination, hen eggs from different origins were collected. Quantitative extraction of egg yolk cholesterol was optimized, and partial reduced molar fractions of its different 13C isotopomers were used as predictors in discriminant analysis. Compared with the global 13C isotopic composition determined using isotope ratio monitoring by Mass Spectrometry, the relative content of cholesterol 13C isotopomers added valuable power to sample classifications according to their origins. This study paves the way to isotopomics of other steroids and similar molecular weight compounds.

Hakkila, J., Nemiroff, R., 2019. Time-reversed gamma-ray burst light-curve characteristics as transitions between subluminal and superluminal motion. The Astrophysical Journal 883, 70.

http://dx.doi.org/10.3847/1538-4357/ab3bdf

We introduce a simple model to explain the time-reversed and stretched residuals in gamma-ray burst (GRB) pulse light curves. In this model an impactor wave in an expanding GRB jet accelerates from subluminal to superluminal velocities, or decelerates from superluminal to subluminal velocities. The impactor wave interacts with the surrounding medium to produce Cerenkov and/or other collisional radiation when traveling faster than the speed of light in this medium, and other mechanisms (such as thermalized Compton or synchrotron shock radiation) when traveling slower than the speed of light. These transitions create both a time-forward and a time-reversed set of light-curve features through the process of relativistic image doubling. The model can account for a variety of unexplained yet observed GRB pulse behaviors, including the amount of stretching observed in time-reversed GRB pulse residuals and the relationship between stretching factor and pulse asymmetry. The model is applicable to all GRB classes since similar pulse behaviors are observed in long/intermediate GRBs,

short GRBs, and X-ray flares. The free model parameters are the impactor’s Lorentz factor when moving subluminally, its Lorentz factor when moving superluminally, and the speed of light in the impacted medium.

Hao, L., Zhu, Y., Wei, P., Johnson, J., Buchberger, A., Frost, D., Kao, W.J., Li, L., 2019. Metandem: An online software tool for mass spectrometry-based isobaric labeling metabolomics. Analytica Chimica Acta 1088, 99-106.


Mass spectrometry-based stable isotope labeling provides the advantages of multiplexing capability and accurate quantification but requires tailored bioinformatics tools for data analysis. Despite the rapid advancements in analytical methodology, it is often challenging to analyze stable isotope labeling-based metabolomics data, particularly for isobaric labeling using MS/MS reporter ions for quantification. We report Metandem, a novel online software tool for isobaric labeling-based metabolomics, freely available at http://metandem.com/web/. Metandem provides a comprehensive data analysis pipeline integrating feature extraction, metabolite quantification, metabolite identification, batch processing of multiple data files, online parameter optimization for custom datasets, data normalization, and statistical analysis. Systematic evaluation of the Metandem tool was demonstrated on UPLC-MS/MS, nanoLC-MS/MS, CE-MS/MS and MALDI-MS platforms, via duplex, 4-plex, 10-plex, and 12-plex isobaric labeling experiments and the application to various biological samples.


https://doi.org/10.1089/ast.2018.1946

This article presents the proportional evolutionary time (PET) hypothesis, which posits that the mean time required for the evolution of complex life is a function of stellar mass. The “biological available window” is defined as the region of a stellar spectrum between 200 and 1200 nm that generates free energy for life. Over the ∼4 Gyr history of Earth, the total energy incident at the top of the atmosphere and within the biological available window is ∼1034 J. The hypothesis assumes that the rate of evolution from the origin of life to complex life is proportional to this total energy, which would suggest that planets orbiting other stars should not show signs of complex life if the total energy incident on the planet is below this energy threshold. The PET hypothesis predicts that late K- and M-dwarf stars (M < 0.7 ) are too young to host any complex life at the present age of the Universe. F-, G-, and early K-dwarf stars (M > 0.7 ) represent the best targets for the next generation of space telescopes to search for spectroscopic biosignatures indicative of complex life.

Hashizume, H., Theng, B.K.G., van der Gaast, S., Fujii, K., 2019. Formation of adenosine from adenine and ribose under conditions of repeated wetting and drying in the presence of clay minerals. Geochimica et Cosmochimica Acta 265, 495-504.


Ribonucleic acid (RNA) was possibly the most important biopolymer in Earth’s early existence. However, the prebiotic synthesis of the nucleoside component of RNA is problematic. Here we report the formation of adenosine by subjecting a mixture of adenine and ribose to repeated wetting and drying from 40 to 80 °C in air, with or without the addition of clay minerals. Using liquid

chromatography-mass spectrometry (LCMS) and 1H NMR spectroscopy, we were able to detect the formation of adenosine in the presence of kaolinite and Mg2+-exchanged montmorillonite at 70 °C. At this temperature adenosine was also formed in the absence of these minerals but none was detected in the presence of the raw (sodium-rich) montmorillonite. In all instances, only small amounts of adenosine were formed. On the other hand, a 12–13% yield of adenosine was measured in the presence of kaolinite at 60–80 °C, using the highly sensitive method of liquid chromatography coupled with tandem mass spectrometry (LCMS/MS). Kaolinite can apparently act as both a concentrating surface and a catalyst in the formation of adenosine from adenine and ribose although the underlying mechanism has yet to be established. The mild experimental conditions used here for nucleoside formation could plausibly obtain in some parts of the prebiotic Earth.



The ~2490 Ma DS4 impact layer in the Dales Gorge Member is the only bed in the Brockman Iron Formation (Hamersley Group, Western Australia) known to contain “splash form” impact spherules. At a newly discovered site in Munjina Gorge (MG), the internal stratigraphy of the DS4 impact layer differs from previously known occurrences; it ranges from 36 to 57 cm in total thickness and consists of two distinct subunits. The lower subunit contains abundant cobble‐ to boulder‐scale intraclasts and spherules supported by a finer matrix. We interpret this subunit as the product of poorly cohesive debris flows. The upper subunit is 11–15 cm of low‐density turbidites. The DS4 layer also consists of two newly recognized subunits at Yampire Gorge (YG). The lower subunit is rich in well‐sorted spherules, 0–22 cm thick, and comprises an unstratified bedform with an irregular or swaley upper surface. This is overlain by 2 dm‐scale, fine‐grained, irregularly laminated beds that we interpret as low density turbidites laterally equivalent to the upper subunit at MG. The bedform at YG could be the lateral equivalent of the debrite at MG, genetically related to the overlying turbidites, or a product of impact tsunami‐induced bottom return flow. Other DS4 layer sites that have debrites similar to the one at MG are geographically separated from one another by sites that both lack debrite facies and feature well‐sorted spherules like YG. These characteristics suggest the DS4 layer had a complex depositional history that generated multiple debrites.

Hauser, N., Reimold, W.U., Cavosie, A.J., Crósta, A.P., Schwarz, W.H., Trieloff, M., Da Silva Maia de Souza, C., Pereira, L.A., Rodrigues, E.N., Brown, M., 2019. Linking shock textures revealed by BSE, CL, and EBSD with U-Pb data (LA-ICP-MS and SIMS) from zircon from the Araguainha impact structure, Brazil. Meteoritics & Planetary Science 54, 2286-2311.


A silicious impact melt rock from polymict impact breccia of the northern part of the alkali granite core of the Araguainha impact structure, central Brazil, has been investigated. The melt rock is thought to represent a large mass of impact‐generated melt in suevite. In particular, a diverse population of zircon grains, with different impact‐induced microstructures, has been analyzed for U‐Pb isotopic systematics. Backscattered electron and cathodoluminescence images reveal heterogeneous intragrain domains with vesicular, granular, vesicular plus granular, and vesicular plus (presumably) baddeleyite textures, among others. The small likely baddeleyite inclusions are not only preferentially located along grain margins but also occur locally within grain interiors. LA‐ICP‐MS U‐Pb data from different domains yield lower intercept ages of 220, 240, and 260 Ma, a result

difficult to reconcile with the previous “best age” estimate for the impact event at 254.7 ± 2.7 Ma. SIMS U‐Pb data, too, show a relatively large range of ages from 245 to 262 Ma. A subset of granular grains that yielded concordant SIMS ages were analyzed for crystallographic orientation by EBSD. Orientation mapping shows that this population consists of approximately micrometer‐sized neoblasts that preserve systematic orientation evidence for the former presence of the high‐pressure polymorph reidite. In one partially granular grain (#36), the neoblasts occur in linear arrays that likely represent former reidite lamellae. Such grains are referred to as FRIGN zircon. The best estimate for the age of the Araguainha impact event from our data set from a previously not analyzed type of impact melt rock is based on concordant SIMS data from FRIGN zircon grains. This age is 251.5 ± 2.9 Ma (2σ, MSWD = 0.45, p = 0.50, n = 4 analyses on three grains), indistinguishable from previous estimates based on zircon and monazite from other impact melt lithologies at Araguainha. Our work provides a new example of how FRIGN zircon can be combined with in situ U‐Pb geochronology to extract an accurate age for an impact event.

Hawbaker, N.A., Blackmond, D.G., 2019. Energy threshold for chiral symmetry breaking in molecular self-replication. Nature Chemistry 11, 957-962.

https://doi.org/10.1038/s41557-019-0321-y

The homochirality of biological molecules (right-handed sugars and left-handed amino acids) is a signature of life. Extensive research has been devoted to understanding how enrichment of one enantiomer over the other might have emerged from a prebiotic world. Here, we use experimental data from the model Soai autocatalytic reaction system to evaluate the energy required for symmetry breaking and chiral amplification in molecular self-replication. One postulate for the source of the original imbalance is the tiny difference in energy between enantiomers due to parity violation in the weak force. We discuss the plausibility of parity violation energy difference coupled with asymmetric autocatalysis as a rationalization for absolute asymmetric synthesis and the origin of the homochirality of biological molecules. Our results allow us to identify the magnitude of the energy imbalance that gives rise to directed symmetry breaking and asymmetric amplification in this autocatalytic system.

He, H., Guo, Z., Wen, Y., Xu, S., Liu, Z., 2019. Recent advances in nanostructure/nanomaterial-assisted laser desorption/ionization mass spectrometry of low molecular mass compounds. Analytica Chimica Acta 1090, 1-22.


Laser desorption ionization mass spectrometry (LDI-MS) has been developed to be an essential tool for the analysis and identification of a large variety of species, ranging from small metabolites, drugs and pollutants to peptides and proteins and even to bacteria. Matrix assisted LDI-MS has shown a great power for macromolecules, but its analytical capability to low mass compounds is limited due to inherent drawbacks, including abundant interference in low mass range (<800 Da) caused by matrix self-dissociation and poor reproducibility due to inhomogeneous crystallization. Several matrix-free methods have been developed to solve these issues, mainly through altering organic matrix with inorganic nanostructured surfaces or nanomaterials as LDI medium. In the past five years, improvements on conventional silicon-based, metal-based, metal oxide-based and carbon-based LDI media as well as emerging novel materials such as 2D nanomaterials and organic frameworks have gained important progresses. Meanwhile, with the deep research in light-matter interaction, LDI mechanism studies begin to grow and become to attach great importance. Advances in both medium and mechanism promote to expand the applicable potential of nanostructure/nanomaterial-assisted

LDI-MS in many aspects, including trace analysis, structural analysis and MS imaging. In this review, we survey the major progresses in this area in recent years. We also sketch remaining challenges and directions for future development.

Hecht, E.E., Smaers, J.B., Dunn, W.D., Kent, M., Preuss, T.M., Gutman, D.A., 2019. Significant neuroanatomical variation among domestic dog breeds. The Journal of Neuroscience 39, 7748-7758.

http://www.jneurosci.org/content/39/39/7748.abstract

Abstract: Humans have bred different lineages of domestic dogs for different tasks such as hunting, herding, guarding, or companionship. These behavioral differences must be the result of underlying neural differences, but surprisingly, this topic has gone largely unexplored. The current study examined whether and how selective breeding by humans has altered the gross organization of the brain in dogs. We assessed regional volumetric variation in MRI studies of 62 male and female dogs of 33 breeds. Neuroanatomical variation is plainly visible across breeds. This variation is distributed nonrandomly across the brain. A whole-brain, data-driven independent components analysis established that specific regional subnetworks covary significantly with each other. Variation in these networks is not simply the result of variation in total brain size, total body size, or skull shape. Furthermore, the anatomy of these networks correlates significantly with different behavioral specialization(s) such as sight hunting, scent hunting, guarding, and companionship. Importantly, a phylogenetic analysis revealed that most change has occurred in the terminal branches of the dog phylogenetic tree, indicating strong, recent selection in individual breeds. Together, these results establish that brain anatomy varies significantly in dogs, likely due to human-applied selection for behavior.

Significance statement: Dog breeds are known to vary in cognition, temperament, and behavior, but the neural origins of this variation are unknown. In an MRI-based analysis, we found that brain anatomy covaries significantly with behavioral specializations such as sight hunting, scent hunting, guarding, and companionship. Neuroanatomical variation is not simply driven by brain size, body size, or skull shape, and is focused in specific networks of regions. Nearly all of the identified variation occurs in the terminal branches of the dog phylogenetic tree, indicating strong, recent selection in individual breeds. These results indicate that through selective breeding, humans have significantly altered the brains of different lineages of domestic dogs in different ways.



Wax precipitation is a significant problem in the oil and gas industry as it may cause plugging of the process equipment and transportation pipelines during oil transportation, production, and refining. Therefore, an accurate thermodynamic model for prediction of the wax appearance temperature (WAT) at especially high pressures can be helpful to deal with this problem. In this work, first, the WAT values for nine types of Iranian live crude oils were measured using a PVT cell equipped with a solids detection system (SDS). Then, an improved thermodynamic model based on the multi-solid (MS) model of wax precipitation, which was coupled with the chain form of the statistical associating fluid theory (PC-SAFT) equation of state (EOS), was developed to correlate the measured experimental data. Also, the MS model of wax precipitation was coupled with the Peng–Robinson (PR) EOS to be compared with the proposed model. Solid–liquid equilibria (SLE) were employed for

the pressures above the bubble curve, and vapor–liquid–solid equilibria (VLSE) were utilized below the bubble curve in the P-T diagram. In the proposed model, the crude oil was considered as a mixture of the paraffinic, naphthenic, and aromatic fractions, and the plus fraction has been characterized using the three-parameter gamma probability function theory, to improve the characterization of the previous models based on two-parameter gamma probability function theory. The results of the experiments indicated that the WAT values decreased by increasing the pressure at the lower range of pressures. Also, the correlated values show that the proposed model based on PC-SAFT EOS with the correlated parameters can predict the WAT values better than the MS model with PR EOS with the %AAD below %1 at a wide range of pressures.


https://doi.org/10.1089/ast.2019.2069

Extraterrestrial environments encompass physicochemical conditions and habitats that are unknown on Earth, such as perchlorate-rich brines that can be at least temporarily stable on the martian surface. To better understand the potential for life in these cold briny environments, we determined the maximum salt concentrations suitable for growth (MSCg) of six different chloride and perchlorate salts at 25°C and 4°C for the extremotolerant cold- and salt-adapted bacterial strain Planococcus halocryophilus. Growth was measured through colony-forming unit (CFU) counts, while cellular and colonial phenotypic stress responses were observed through visible light, fluorescence, and scanning electron microscopy. Our data show the following: (1) The tolerance to high salt concentrations can be increased through a stepwise inoculation toward higher concentrations. (2) Ion-specific factors are more relevant for the growth limitation of P. halocryophilus in saline solutions than single physicochemical parameters like ionic strength or water activity. (3) P. halocryophilus shows the highest microbial sodium perchlorate tolerance described so far. However, (4) MSCg values are higher for all chlorides compared to perchlorates. (5) The MSCg for calcium chloride was increased by lowering the temperature from 25°C to 4°C, while sodium- and magnesium-containing salts can be tolerated at 25°C to higher concentrations than at 4°C. (6) Depending on salt type and concentration, P. halocryophilus cells show distinct phenotypic stress responses such as novel types of colony morphology on agar plates and biofilm-like cell clustering, encrustation, and development of intercellular nanofilaments. This study, taken in context with previous work on the survival of extremophiles in Mars-like environments, suggests that high-concentrated perchlorate brines on Mars might not be habitable to any present organism on Earth, but extremophilic microorganisms might be able to evolve thriving in such environments.

Hendry, J.I., Bandyopadhyay, A., Srinivasan, S., Pakrasi, H.B., Maranas, C.D., 2020. Metabolic model guided strain design of cyanobacteria. Current Opinion in Biotechnology 64, 17-23.


Cyanobacteria are oxygenic photoautotrophs that serve as potential platforms for the production of biochemicals from cheap and renewable raw materials – sunlight, water, and carbon dioxide. Systems level analysis of the metabolic network of these organisms could enable the successful engineering of these organisms for the enhanced production of target chemicals. Metabolic modeling techniques including both stoichiometric and kinetic modeling with a genome-wide coverage enable a global assessment of metabolic capabilities. Recent studies guided by such modeling techniques have

engineered strains for the enhanced production of valuable chemicals such as ethanol, n-butanol, 1,3-propanediol, glycerol, limonene, and isoprene from CO2.


https://doi.org/10.1038/s41467-019-12574-y

Several recent studies have shown the presence of genes for the key enzyme associated with archaeal methane/alkane metabolism, methyl-coenzyme M reductase (Mcr), in metagenome-assembled genomes (MAGs) divergent to existing archaeal lineages. Here, we study the mcr-containing archaeal MAGs from several hot springs, which reveal further expansion in the diversity of archaeal organisms performing methane/alkane metabolism. Significantly, an MAG basal to organisms from the phylum Thaumarchaeota that contains mcr genes, but not those for ammonia oxidation or aerobic metabolism, is identified. Together, our phylogenetic analyses and ancestral state reconstructions suggest a mostly vertical evolution of mcrABG genes among methanogens and methanotrophs, along with frequent horizontal gene transfer of mcr genes between alkanotrophs. Analysis of all mcr-containing archaeal MAGs/genomes suggests a hydrothermal origin for these microorganisms based on optimal growth temperature predictions. These results also suggest methane/alkane oxidation or methanogenesis at high temperature likely existed in a common archaeal ancestor.



Samples from a single outcrop of the Graenseso spherule layer, Midternaes, South Greenland, consist of a spherule‐bearing dolomixtite with matrix‐supported intraclasts up to 1 m in size. In addition to field observations, we performed mineralogical and whole rock geochemical analysis, including electron microprobe, neutron activation analysis, X‐ray fluorescence, and mass spectrometry of the horizon and the overlying and underlying strata. We show that the spherules are petrographically similar to those in the Zaonega spherule layer, Karelia, Russia. Our petrographic and chemical results are consistent with the previous suggestion that the Grænsesø layer correlates with the Zaonega layer, and it is possible that both layers are related to the Vredefort impact event. The samples containing spherules, as well as the overlying rocks, have elevated REEs compared to the underlying pre‐impact layer, suggestive of a new continental source of sediment that may be coincident with the impact event. Zircons separated from the lower part of the Grænsesø spherule layer display complex age patterns suggesting that they have genetically different origins based on distinctly different Th/U ratios. Crystallization ages of all groups are ≥ 2.8 Ga, with ~2.8 Ga representing a time of major crustal growth globally. Therefore, we cannot conclusively determine in this study if the zircons are locally derived or if they are transported with the ejecta. The spherule layer was deposited by a high‐energy, subaqueous debris flow, an origin that is consistent with the hypothesis that the layer was deposited by impact‐induced waves and/or currents.

Hud, N.V., Fialho, D.M., 2019. RNA nucleosides built in one prebiotic pot. Science 366, 32-33.


For decades, the RNA world has been one of the most influential hypotheses regarding the origins of life on Earth. In this hypothetical era before the emergence of DNA and proteins, “life” on primordial Earth consisted of RNA molecules that both store genetic information and catalyze self-replication reactions (1). Despite its popularity with researchers, the RNA world hypothesis has suffered from its own origins conundrum: A mechanism for the simultaneous prebiotic synthesis of RNA nucleosides from both the purine and pyrimidine families has long eluded scientists (2). Although disparate prebiotic syntheses have been demonstrated for the two classes of RNA nucleosides (3, 4), no single geochemical scenario has generated both. Now, on page 76 of this issue, Becker et al. (5) report on chemistry that accomplishes this long-awaited goal.

“Prebiotic” processes are those that could conceivably have contributed to the origin of life on the primitive Earth. A fundamental difficulty with the prebiotic formation of RNA is that the RNA nucleobases (the purines, adenine and guanine; and the pyrimidines, cytosine and uracil) are reluctant to spontaneously form a bond with the sugar ribose; this glycosidic bond holds the nucleobases to the phosphate-ribose backbone of RNA. Within the past decade, a focus on the pyrimidine nucleosides yielded two completely different, experimentally supported approaches for prebiotic nucleoside synthesis. In one, the pyrimidine base is built along with ribose in a concerted fashion (3). In the other, pyrimidines slightly different from those found in modern RNA formed alternative nucleosides that might have served as subunits of an ancestral form of RNA (6). Unfortunately, neither approach suggested a corresponding prebiotic synthetic mechanism for purine nucleosides that is likely to succeed to a similar degree.

Stepping up to this challenge, Becker et al. (4) demonstrated, in 2016, a plausible prebiotic synthesis of purine nucleosides from formamidopyrimidines (FaPys), a sort of “unraveled” form of a purine that readily reacts with ribose in water to form nucleosides (4). Once the FaPy nucleoside is formed, raising the solution's pH induces a ring-closure reaction that produces the intact purine nucleoside. Although this approach was considered an important advance in the field of prebiotic chemistry, there was no obvious way to reconcile this synthesis with the previously demonstrated disparate prebiotic syntheses of pyrimidine nucleosides by a dissimilar chemical pathway (3). How could two totally different synthesis routes to the purine and pyrimidine nucleosides occur in unison to produce the necessary subunits of RNA, presumably in the same prebiotic milieu?

In the new study, Becker et al. present an alternative prebiotic synthesis of pyrimidine nucleosides under geochemical conditions designed to be compatible with their previously published synthesis of the purine nucleosides (5). Using a similar strategy for the pyrimidine nucleosides, the authors formed a heterocyclic precursor (which can be viewed as a “scrambled” pyrimidine nucleobase) in a model prebiotic reaction mixture, which then reacted with ribose to form a non-natural ribonucleoside not found in modern RNA. The subsequent addition of specific prebiotic reagents—an iron catalyst and hydrogen sulfide—induced a rearrangement in the heterocyclic moiety to yield a cytosine nucleoside. This product can then be converted, under prebiotic reaction conditions, to a uracil nucleoside (7).

The non-natural nucleoside precursors used by Becker et al. for both the RNA purine and pyrimidine nucleosides are formed by wet-dry cycling—a method used for inducing chemical reactions by evaporating an aqueous solution of the reactants at increased temperatures. The dried reactants coalesce into a highly concentrated, low–water activity state, where their condensation (that is, the joining through covalent bond formation with the release of water molecules) becomes thermodynamically favorable. This wet-dry method for driving model prebiotic reactions spans the history of prebiotic chemistry research and has proven its utility for producing other chemical bonds necessary for formation of RNA (2, 8), lipid precursors (9), and peptides (10, 11). Unlike volcanic eruptions and meteorite impacts—events that often are proposed as drivers of prebiotic reactions—

wet-dry cycles would have been regular events on all exposed land of the prebiotic Earth, as they are driven by reliable fluctuations in temperature (e.g., daynight or seasonal cycles) and water activity (e.g., rainfall, tides, or geothermal activity in hydrothermal fields). With the simultaneous formation of purine and pyrimidine nucleosides, Becker et al. provide further evidence for the relevance of prebiotic wet-dry cycles (see the figure).

In 2004, Orgel, a pioneer in the field of prebiotic chemistry, reviewed the previous four decades of efforts to uncover plausible prebiotic reactions that would support the existence of an RNA world (2). At that time, Orgel argued that the synthesis of nucleosides was “the weakest link” in the proposed chain of prebiotic reactions that lead to RNA products. As mentioned above, in the ensuing years, model prebiotic reactions were developed in which extant pyrimidine nucleosides are prepared by building the nucleobases along with the sugar in a concerted reaction (rather than joining preformed bases and a sugar) (3). Furthermore, organic chemists discovered heterocycles that react with ribose in wet-dry cycles to provide possible ancestral RNA nucleosides (6). Now, Becker et al. present what is arguably the most direct prebiotic route to the RNA nucleosides.

Given this progress, do origins-of-life researchers consider the problem of prebiotic nucleoside formation to be solved by a variety of approaches? Alas, like many seminal scientific problems, crucial advances often yield more questions than answers. It is now fair to ask which experimentally demonstrated route reflects the true historical origin of RNA in the primordial soup. Also, did the various proposed synthesis methods contribute to the emergence of life simultaneously or at different times during the hypothetical RNA world era? Grappling with such issues is far more gratifying than wallowing in the despair that overshadowed the field two decades ago, when many prebiotic chemists believed that a plausible, prebiotic solution to the synthesis of nucleosides was impossible. Not anymore.

References1. G. F. Joyce, L. E. Orgel, in The RNA World, R. F. Gesteland, J. F. Atkins, Eds. (Cold Spring

Harbor Laboratory Press, Cold Spring Harbor, NY, ed. 2, 1999), pp. 49–77.2. L. E. Orgel, Crit. Rev. Biochem. Mol. Biol. 39, 99 (2004).3. M. W. Powner, B. Gerland, J. D. Sutherland, Nature 459, 239 (2009).r4. S. Becker et al., Science 352, 833 (2016).5. S. Becker et al., Science 366, 76 (2019).6. M. C. Chen et al., J. Am. Chem. Soc. 136, 5640 (2014).7. R. Shapiro, Proc. Natl. Acad. Sci. U.S.A. 96, 4396 (1999).8. W. D. Fuller, R. A. Sanchez, L. E. Orgel, J. Mol. Evol. 1, 249 (1972).9. C. L. Apel, D. W. Deamer, Orig. Life Evol. Biosph. 35, 323 (2005).10. J. G. Forsythe et al., Angew. Chem. Int. Ed. 54, 9871 (2015).11. M. Rodriguez-Garcia et al., Nat. Commun. 6, 8385 (2015).

Hwang, J., Pini, R., 2019. Supercritical CO2 and CH4 uptake by illite-smectite clay minerals. Environmental Science & Technology 53, 11588-11596.


Clay minerals abound in sedimentary formations and the interaction of reservoir gases with their submicron features have direct relevance to many geoenergy applications. The quantification of gas uptake over a broad range of pressures is key toward assessing the significance of these physical interactions on enhancing storage capacity and gas recovery. We report a systematic investigation of the sorption properties of three source clay minerals—Na-rich montmorillonite (SWy-2), illite-smectite mixed layer (ISCz-1), and illite (IMt-2)—using CO2 and CH4 up to 30 MPa at 25–115 °C.

The textural characterization of the clays by gas physisorption indicates that micropores are only partly accessible to N2 (77 K) and Ar (87 K), while larger uptakes are measured with CO2 (273 K) in the presence of illite. The supercritical excess sorption experiments confirm these findings while revealing differences in uptake capacities that originate from the clay-specific pore size distribution. The lattice density functional theory model describes accurately the measured sorption isotherms by using a distribution of properly weighted slit pores and clay-specific solid–fluid interaction energies, which agree with isosteric heats of adsorption obtained experimentally. The model indicates that the maximum degree of pore occupancy is universal to the three clays and the two gases, and it depends solely on temperature, reaching values near unity at the critical temperature. These observations greatly support the model’s predictive capability for estimating gas adsorption on clay-bearing rocks and sediments.

Ilgrande, C., Defoirdt, T., Vlaeminck, S.E., Boon, N., Clauwaert, P., 2019. Media optimization, strain compatibility, and low-shear modeled microgravity exposure of synthetic microbial communities for urine nitrification in regenerative life-support systems. Astrobiology 19, 1353-1362.

https://doi.org/10.1089/ast.2018.1981

Urine is a major waste product of human metabolism and contains essential macro- and micronutrients to produce edible microorganisms and crops. Its biological conversion into a stable form can be obtained through urea hydrolysis, subsequent nitrification, and organics removal, to recover a nitrate-enriched stream, free of oxygen demand. In this study, the utilization of a microbial community for urine nitrification was optimized with the focus for space application.

To assess the role of selected parameters that can impact ureolysis in urine, the activity of six ureolytic heterotrophs (Acidovorax delafieldii, Comamonas testosteroni, Cupriavidus necator, Delftia acidovorans, Pseudomonas fluorescens, and Vibrio campbellii) was tested at different salinities, urea, and amino acid concentrations. The interaction of the ureolytic heterotrophs with a nitrifying consortium (Nitrosomonas europaea ATCC 19718 and Nitrobacter winogradskyi ATCC 25931) was also tested. Lastly, microgravity was simulated in a clinostat utilizing hardware for in-flight experiments with active microbial cultures. The results indicate salt inhibition of the ureolysis at 30 mS cm−1, while amino acid nitrogen inhibits ureolysis in a strain-dependent manner. The combination of the nitrifiers with C. necator and V. campbellii resulted in a complete halt of the urea hydrolysis process, while in the case of A. delafieldii incomplete nitrification was observed, and nitrite was not oxidized further to nitrate. Nitrate production was confirmed in all the other communities; however, the other heterotrophic strains most likely induced oxygen competition in the test setup, and nitrite accumulation was observed. Samples exposed to low-shear modeled microgravity through clinorotation behaved similarly to the static controls. Overall, nitrate production from urea was successfully demonstrated with synthetic microbial communities under terrestrial and simulated space gravity conditions, corroborating the application of this process in space.

Inaba, Y., Xu, S., Vardner, J.T., West, A.C., Banta, S., 2019. Microbially influenced corrosion of stainless steel by Acidithiobacillus ferrooxidans supplemented with pyrite: importance of thiosulfate. Applied and Environmental Microbiology 85, e01381-19.


Abstract: Microbially influenced corrosion (MIC) results in significant damage to metallic materials in many industries. Anaerobic sulfate-reducing bacteria (SRB) have been well studied for their involvement in these processes. Highly corrosive environments are also found in pulp and paper

processing, where chloride and thiosulfate lead to the corrosion of stainless steels. Acidithiobacillus ferrooxidans is a critically important chemolithotrophic acidophile exploited in metal biomining operations, and there is interest in using A. ferrooxidans cells for emerging processes such as electronic waste recycling. We explored conditions under which A. ferrooxidans could enable the corrosion of stainless steel. Acidic medium with iron, chloride, low sulfate, and pyrite supplementation created an environment where unstable thiosulfate was continuously generated. When combined with the chloride, acid, and iron, the thiosulfate enabled substantial corrosion of stainless steel (SS304) coupons (mass loss, 5.4 ± 1.1 mg/cm2 over 13 days), which is an order of magnitude higher than what has been reported for SRB. There results were verified in an abiotic flow reactor, and the importance of mixing was also demonstrated. Overall, these results indicate that A. ferrooxidans and related pyrite-oxidizing bacteria could produce aggressive MIC conditions in certain environmental milieus.

Importance: MIC of industrial equipment, gas pipelines, and military material leads to billions of dollars in damage annually. Thus, there is a clear need to better understand MIC processes and chemistries as efforts are made to ameliorate these effects. Additionally, A. ferrooxidans is a valuable acidophile with high metal tolerance which can continuously generate ferric iron, making it critical to copper and other biomining operations as well as a potential biocatalyst for electronic waste recycling. New MIC mechanisms may expand the utility of these cells in future metal resource recovery operations.

Jahnke, L.L., Des Marais, D.J., 2019. Carbon isotopic composition of lipid biomarkers from an endoevaporitic gypsum crust microbial mat reveals cycling of mineralized organic carbon. Geobiology 17, 643-659.


Microbial mats that inhabit gypsum deposits in ponds at Guerrero Negro, Baja California Sur, Mexico, developed distinct pigmented horizons that provided an opportunity to examine the fixation and flow of carbon through a trophic structure and, in conjunction with previous phylogenetic analyses, to assess the diagenetic fates of molecular δ13C biosignatures. The δ13C values of individual biomarker lipids, total carbon, and total organic carbon (TOC) were determined for each of the following horizons: tan‐orange (TO) at the surface, green (G), purple (P), and olive‐black (OB) at the bottom. δ13C of individual fatty acids from intact polar lipids (IPFA) in TO were similar to δ13C of dissolved inorganic carbon (DIC) in the overlying water column, indicating limited discrimination by cyanobacteria during CO2 fixation. δ13CTOC of the underlying G was 3‰ greater than that of TO. The most δ13C‐depleted acetogenic lipids in the upper horizons were the cyanobacterial biomarkers C17 n‐alkanes and polyunsaturated fatty acids. Bishomohopanol was 4 to 7‰ enriched, relative to alkanes and intact polar fatty acids (IPFA), respectively. Acyclic C20 isoprenoids were depleted by 14‰ relative to bishomohopanol. Significantly, ∆[δ13CTOC − δ13C∑IPFA] increased from 6.9‰ in TO to 14.7‰ in OB. This major trend might indicate that 13C‐enriched residual organic matter accumulated at depth. The permanently anoxic P horizon was dominated by anoxygenic phototrophs and sulfate‐reducing bacteria. P hosted an active sulfur‐dependent microbial community. IPFA and bishomohopanol were 13C‐depleted relative to upper crust by 7 and 4‰, respectively, and C20 isoprenoids were somewhat 13C‐enriched. Synthesis of alkanes in P was evidenced only by 13C‐depleted n‐octadecane and 8‐methylhexadecane. In OB, the marked increase of total inorganic carbon δ13C (δ13CTIC) of >6‰ perhaps indicated terminal mineralization. This δ13CTIC increase is consistent with degradation of the osmolyte glycine betaine by methylotrophic methanogens and loss of 13C‐depleted methane from the mat.

Jang, S., Kim, M., Hwang, J., Jung, G.Y., 2019. Tools and systems for evolutionary engineering of biomolecules and microorganisms. Journal of Industrial Microbiology & Biotechnology 46, 1313-1326.

https://doi.org/10.1007/s10295-019-02191-5

Evolutionary approaches have been providing solutions to various bioengineering challenges in an efficient manner. In addition to traditional adaptive laboratory evolution and directed evolution, recent advances in synthetic biology and fluidic systems have opened a new era of evolutionary engineering. Synthetic genetic circuits have been created to control mutagenesis and enable screening of various phenotypes, particularly metabolite production. Fluidic systems can be used for high-throughput screening and multiplexed continuous cultivation of microorganisms. Moreover, continuous directed evolution has been achieved by combining all the steps of evolutionary engineering. Overall, modern tools and systems for evolutionary engineering can be used to establish the artificial equivalent to natural evolution for various research applications.

Janjic, A., 2019. Assisted evolution in astrobiology—Convergence of ecology and evolutionary biology within the context of planetary colonization. Astrobiology 19, 1410-1417.

https://doi.org/10.1089/ast.2019.2061

In ecology and conservation biology, the concept of assisted evolution aims at the optimization of the resilience of organisms and populations to changing environmental conditions. What has hardly been considered so far is that this concept is also relevant for future astrobiological research, since in artificial extraterrestrial habitats (e.g., plants and insects in martian greenhouses) novel environmental conditions will also affect the survival and performance of organisms. The question therefore arises whether and how space-relevant organisms can be artificially adapted to the desired circumstances in advance. Based on several adaptation and acclimatization strategies in wild ecosystems of Earth, I discuss which methods can be considered for assisted evolution in the context of astrobiological research. This includes enhanced selective breeding, induction of epigenetic inheritance, and genetic engineering, as well as possible problems of these applications. This short overview article aims to stimulate an emerging discussion as to whether humans, which are already prominent drivers of Earth's evolution, should consider such interventions for future planetary colonization as well.

Jarzyna, J.A., Krakowska, P.I., Puskarczyk, E., Wawrzyniak-Guz, K., Zych, M., 2019. Total organic carbon from well logging - statistical approach, Polish shale gas formation case study. International Journal of Oil, Gas and Coal Technology 22, 140-162.

https://dx.doi.org/10.1504/IJOGCT.2019.102784

Advanced statistical methods - artificial neural networks (ANN) and support vector machines (SVM) were used to calculate total organic carbon (TOC) on the basis of well logging. Data from three wells from the Silurian and Ordovician formations in the Baltic Basin from the north Poland were used. In learning procedures TOC data as Rock-Eval pyrolysis results were applied. Research was undertaken in four steps aiming to determine the best ANN in aspect of number and type of input variables. Regarding increase of cases number used in learning process data from two wells were combined and next, determined ANN and SVR were used to predict TOC. There were also made tests of number of input variables (results of standard and sophisticated well logs and laboratory data). Results obtained using standard logs when number of available cases for learning was big enough did not gave way to results based on very many input variables.

Jiang, J.-Y., Zhu, S., Zhang, Y., Sun, X., Hu, X., Huang, H., Ren, L.-J., 2019. Integration of lipidomic and transcriptomic profiles reveals novel genes and regulatory mechanisms of Schizochytrium sp. in response to salt stress. Bioresource Technology 294, 122231.


In this study, the effects of salt stress on the physiological, lipidomic and transcriptomic profiles of halophilic microalga Schizochytrium sp. were investigated. In general, Schizochytrium sp. could survive under high osmotic fermentation medium containing 30 g/L NaCl, and showed a significant increase in C14:0 percentage in total fatty acids. In lipidomic analysis, C14:0 was specifically enriched in phosphatidylcholine (PC), and membrane phospholipids participated in the salt stress response mostly. Specially, one novel signal lipid N-acylphosphatidylethanolamine (NAPE) (18:0/20:3/14:0) was upregulated significantly. Transcriptomic analysis revealed glycerol-3-phosphate acyltransferase (GPAT) and phospholipase ABHD3 (PLABDH3) were involved in C14:0 metabolism and NAPE biosynthesis. Signalling pathways they mediated were activated as evident by high expression level of Myristoyl-CoA: protein N-myristoyltransferase (NMT) and NAPE-hydrolyzing PLD (NAPE-PLD). This study gives us an insight in specific responses to salt stress in Schizochytrium sp. and provides a considerable proportion of novel genes that could commendably be used for engineering modification.

Jiang, Y., Fu, Y., Xie, J., Dong, D., Zhou, K., Cheng, X., Qi, L., Zhang, H., Chen, C., Ma, T., Gu, Y., 2019. Development trend of marine shale gas reservoir evaluation and a suitable comprehensive evaluation system Natural Gas Industry 39, 1-9.


At present, shale gas exploration and development in China is faced with some problems, such as the imperfect evaluation system of reservoir effectiveness and the limitations of reservoir evaluation system on efficient development of shale gas. In order to improve the content and the standard of reservoir evaluation, this paper analyzed the shortcomings and challenges in the static evaluation of shale gas reservoirs on the basis of existing reservoir evaluation, and established a method for evaluating shale gas reservoir effectiveness and a scheme for classifying pore systems. Then, the dynamic evaluation parameters after shale fracturing and their effects on drainage and production measures were discussed. In addition, the potential evaluation parameters of "automatic mitigating water blocking" were studied, and a comprehensive reservoir evaluation system of "static–dynamic" combination was established. And the following research results were obtained. First, new challenges to the shale gas reservoir evaluation are emerged as the lack of in-depth study on "reservoir effectiveness, dynamic evaluation parameter system after fracturing and drainage and production measures after fracturing", which leads to the serious lag of existing shale gas reservoir evaluation system behind production. Second, The evaluation of reservoir effectiveness is mainly presented as the evaluation on the lower limit of effective porosity, and is embodied in the influence of clay bound water and unconnected pores on the development of shale gas. Third, the development of shale gas reservoir evaluation follows the trend of refining the static reservoir evaluation parameters, defining the potential evaluation indexes of "automatic mitigating water blocking" and establishing the reservoir comprehensive evaluation system of "static–dynamic" combination. Fourth, a postfrac dynamic evaluation system is determined for the potential evaluation indexes of "automatic mitigating water blocking" (e.g. wettability, water imbibition retention capacity, water imbibition expansion mode, expansion rate, and water imbibition cracking capacity). Fifth, a reservoir evaluation idea is put forward that "static evaluation of shale gas reservoir is the foundation and postfrac

dynamic evaluation is the complement", and a comprehensive reservoir evaluation system is established of "static–dynamic" combination suitable for the evaluation of marine shale gas reservoirs in China.

Jiang, Y., Zhao, K., Imber, J., Chen, L., Hu, H., 2020. Recognizing the internal structure of normal faults in clastic rocks and its impact on hydrocarbon migration: A case study from Nanpu Depression in the Bohai Bay Basin, China. Journal of Petroleum Science and Engineering 184, 106492.


The fault and its internal structure have great influence on hydrocarbon migration and accumulation in faulted basins, and the mechanism of hydrocarbon migration in fault zones remains to be a difficult point in petroleum geology. The fault core and damage zone are two potential components of the fault internal structure. They are obviously different in the structure, filling material, porosity and permeability, which leads to the differences in logging response. Our study shows that the fault core has the characteristics of low AC (Sonic Logging value), low CNL (Compensated Neutron Loggingvalue) and high DEN (Density Logging value), while the damage zone has the characteristics of high AC, high CNL and low DEN. On this basis, an identification method consisting of four steps, namely vertical comparison of single well, lateral comparison of adjacent wells, quantitative identification by instruction curves, and result verification by cross-plots, is proposed. On the basis of the logging curve analysis of more than 50 study wells in the Nanpu Depression by this identification method, the fault zones can be divided into six types, and each of them plays a different role in the process of hydrocarbon migration. This research provides significant insights into the characteristics of the fault internal structure and guidance for exploration in faulted basins.

Jiao, F., 2019. Re-recognition of “unconventional” in unconventional oil and gas. Petroleum Exploration and Development 46, 847-855.


Taking the Wufeng–Longmaxi shale gas in the Sichuan Basin as a typical example, based on the new progress in exploration and development, this study re-examines the “unconventional” of unconventional oil and gas from two aspects: oil and gas formation and accumulation mechanisms, and main features of oil and gas layers. The oil and gas of continuous accumulation and distribution from integrated source and reservoir is unconventional oil and gas, and the study focusing on shale oil and gas in comparison with conventional oil and gas has made progress in five aspects: (1) Unconventional oil and gas have source-reservoir-in-one and in-situ accumulation; according to the theory of continuous oil and gas accumulation, the accumulation power of oil and gas is overpressure and diffusion; for conventional oil and gas, the source and reservoir are different formations, the trapping accumulation is its theoretical foundation, and the accumulation power is characterized by buoyancy and capillary force. (2) The unconventional oil and gas reservoirs are mainly formed in the low-energy oxygen-anaerobic environment, dominantly semi-deep to deep shelf facies and the semi-deep to deep lake facies, simple in lithology, rich in organic matter and clay minerals; conventional oil and gas mainly occur in coarse-grained sedimentary rocks formed in high-energy waters with complex lithology. (3) The unconventional oil and gas reservoirs have mainly nano-scale pores, of which organic matter pores take a considerable proportion; conventional oil and gas reservoirs mainly have micron-millimeter pores and no organic matter pores. (4) Unconventional shale oil and gas reservoirs have oil and gas in uniform distribution, high oil and gas saturation, low or no water content, and no obvious oil and gas water boundary; conventional oil and gas reservoirs have oil and gas of complex properties, moderate oil and gas saturation, slightly higher water content, and obvious

oil, gas and water boundaries. (5) Organic-rich shale is the main target of unconventional oil and gas exploration; the sedimentary environment controls high organic matter abundance zone and organic matter content controls oil and gas abundance; positive structure and high porosity control the yields of shale wells; bedding and fracture development are important factors deciding high yield.

Jin, G., Liu, Y., Xue, S., Meng, Y., Yan, J., Yang, F., Guo, Z., Zhu, J., Liang, X., 2019. Determination of three carotenoids in microalgae by matrix solid-phase dispersion extraction and high-performance liquid chromatography. Chromatographia 82, 1593-1601.

https://doi.org/10.1007/s10337-019-03795-w

A HPLC method based on matrix solid-phase dispersion (MSPD) was developed for simultaneous determination of fucoxanthin, lutein and astaxanthin in different microalgae. First, the powder of microalgae was blended with C8 adsorbent. Then the SPE column made from the microalgal matrix/sorbent (1:2) was eluted with 4 mL methanol (containing 0.1% BHT). The eluent was analyzed by HPLC. A C8 column and acetonitrile (ACN)/H2O as the mobile phase were used. The coefficient (R2) of each calibration curve was higher than 0.998. Limits of detection (LODs) and limits of quantification (LOQs) for each carotenoid were 0.30 µg g−1 and 1.00 µg g−1, respectively. The recovery at three concentration levels ranged from 69.1 to 106.5%, and the RSDs were lower than 5%. As a new sample preparation method for microalgal analysis, the MSPD procedure was optimized, validated and compared with conventional methods including ultrasonic and ice-bath extraction. The MSPD–HPLC method was accurate and reproducible. It was suitable for the quantitative determination of carotenoids in microalgae.



Owing to the depletion of light sweet crude, high-temperature corrosion by sulfidation and naphthenic acids in the oil phase has become one of major challenges for crude oil refineries. The corrosion by model sulfur compounds and naphthenic acids has been extensively studied in laboratories, but the effect of thiophenes, which are widely present in crude oil, is often ignored due to their noncorrosiveness. In the current study, sulfidation and naphthenic acid corrosion are studied in the presence/absence of two model thiophenes, dibenzothiophene and benzothiophene. It is found that thiophenes show an inhibitory effect on naphthenic acid corrosion while not deterring sulfidation significantly. It was proposed that naphthenic acid may corrode the steel, generating iron naphthenates underneath an adsorption layer of thiophenes and producing magnetite.

Jourdan, F., Nomade, S., Wingate, M.T.D., Eroglu, E., Deino, A., 2019. Ultraprecise age and formation temperature of the Australasian tektites constrained by 40Ar/39Ar analyses. Meteoritics & Planetary Science 54, 2573-2591.


The Australasian tektites are quench melt glass ejecta particles distributed over the Asian, Australian, and Antarctic regions, the source crater of which is currently elusive. New 40Ar/39Ar age data from four tektites: one each from Thailand, China, Vietnam, and Australia measured using three different instruments from two different laboratories and combined with published 40Ar/39Ar data yield a weighted mean age of 788.1 ± 2.8 ka (±3.0 ka, including all sources of uncertainties) (P = 0.54). This

age is five times more precise compared to previous results thanks, in part, to the multicollection capabilities of the ARGUS VI noble gas mass spectrometer, which allows an improvement of almost fourfold on a single plateau age measurement. Diffusion experiments on tektites combined with synthetic age spectra and Monte Carlo diffusion models suggest that the minimum temperature of formation of the Thai tektite is between 2350 °C and 3950 °C, hence a strict minimum value of 2350 °C.



Fractionation of petroleum during migration through sedimentary rock matrices has been observed across lengths of meters to kilometers. Selective adsorption of specific chemical moieties at mineral surfaces and/or the phase behavior of petroleum during pressure changes typically are invoked to explain this behavior. Such phenomena are of interest as they impact both the quality and recoverability of petroleum resources. Given the current emphasis on unconventional (continuous) resources, there is a need to understand petroleum fractionation occurring during expulsion and migration at the nanometer to micrometer scale, due to the fine-grained nature of petroliferous mudrocks. Here, we explore organic matter compositional differences observed within kukersites (petroleum source beds containing acritarch Gloeocapsomorpha prisca) and the overlying carbonate reservoir layer from the Ordovician Stonewall Formation using a suite of spectroscopic methods, primarily through atomic force microscopy-based infrared spectroscopy (AFM-IR). AFM-IR is capable of providing spatial resolution approaching 50 nm and allows for assessment of the molecular fingerprint of kukersite organic matter across transition zones from organic-rich “source” layers into neighboring carbonate “reservoir” layers ∼150 μm away. Results indicate that organic matter composition begins to vary immediately following expulsion from source layers, with loss of carbonyl groups and a concomitant decrease in alkyl chain-length, as migration distance increases. These chemical transitions correlate with a decrease in fluorescence intensity, increase in solid bitumen reflectance, and increase in Raman aromaticity proxies (D-G band separation) in the organic matter. Our findings are consistent with the retention of polar compounds onto mineral grains during expulsion and migration, following primary cracking and bituminization of the Gloeocapsomorpha prisca kerogen.

Kahana, A., Schmitt-Kopplin, P., Lancet, D., 2019. Enceladus: First observed primordial soup could arbitrate origin-of-life debate. Astrobiology 19, 1263-1278.

https://doi.org/10.1089/ast.2019.2029

A recent breakthrough publication has reported complex organic molecules in the plumes emanating from the subglacial water ocean of Saturn's moon Enceladus (Postberg et al.,2018, Nature 558:564–568). Based on detailed chemical scrutiny, the authors invoke primordial or endogenously synthesized carbon-rich monomers (<200 u) and polymers (up to 8000 u). This appears to represent the first reported extraterrestrial organics-rich water body, a conceivable milieu for early steps in life's origin (“prebiotic soup”). One may ask which origin-of-life scenario appears more consistent with the reported molecular configurations on Enceladus. The observed monomeric organics are carbon-rich unsaturated molecules, vastly different from present-day metabolites, amino acids, and nucleotide bases, but quite chemically akin to simple lipids. The organic polymers are proposed to resemble terrestrial insoluble kerogens and humic substances, as well as refractory organic macromolecules

found in carbonaceous chondritic meteorites. The authors posit that such polymers, upon long-term hydrous interactions, might break down to micelle-forming amphiphiles. In support of this, published detailed analyses of the Murchison chondrite are dominated by an immense diversity of likely amphiphilic monomers. Our specific quantitative model for compositionally reproducing lipid micelles is amphiphile-based and benefits from a pronounced organic diversity. It thus contrasts with other origin models, which require the presence of very specific building blocks and are expected to be hindered by excess of irrelevant compounds. Thus, the Enceladus finds support the possibility of a pre-RNA Lipid World scenario for life's origin.



Human society's rapid release of vast quantities of CO2 into the atmosphere is a significant planetary experiment. An obvious natural process capable of similar emissions over geologically short time spans are very large bolide impacts. When striking a carbon-rich target, bolides significantly, and potentially catastrophically, disrupt the global biogeochemical carbon cycle. Independent factors, such as sulfur-rich targets, redox state of the oceans or encountering ecosystems already close to a tipping point, dictated the magnitude of further consequences and determined which large bolide strikes shaped Earth's evolution. On the early Earth, where carbon-rich sedimentary targets were rare, impacts may not have been purely destructive. Instead, enclosed subaqueous impact structures may have contributed to initiating Earth's unique carbon cycle.

Kang, Y., Rao, Q., Zhao, Q., Wang, H., 2019. Exploration and development potential of the low-maturity continental shale gas in the Fuxin Basin. Natural Gas Industry B 6, 435-443.


In order to promote the exploration and development of continental shale gas reservoirs in China further, we systematically summarized the geological features of typical continental shale, such as the Ordos Basin. Then, the shale gas reservoir characteristics, geochemical characteristics and fracturing performance of the Lower Cretaceous Shahai Fm in the Fuxin Basin were analyzed by using the data of TOC contents, rock specific surface, pore size distribution and X-ray diffraction analysis of the whole rock. Based on this, it was compared with the marine/continental shale gas reservoirs from the aspect of geological feature. Finally, the shale gas reservoir and resource potential of the Shahai Fm were evaluated. And the following research results were obtained. First, the formation age of China's continental shale is later, its TOC contents vary in a large range, and its organic matters are mainly of a mixed-humic type. And it is characterized by low thermal evolution degree, low quartz content, high feldspar content, high carbonate content, and comparability of total brittle mineral content to marine shale. Second, shale in the Shahai Fm has shallow burial depth and its mineral composition is dominated by quartz, feldspar and carbonate minerals. Its pores are mainly mesopores with an average porosity of 3.47%. There are diverse reservoir spaces, which is favorable for the accumulation of shale gas. Third, the TOC content of the Shahai Fm shale is mainly above 2%, with a moderate thermal evolution degree of organic matter and high gas content. Fourth, the total brittle mineral content of Shahai Fm shale is up to 60%, indicating a good fracturing performance. Fifth, shale reservoirs in the Shahai Fm can be classified into three categories. Type I is target reservoirs of exploration and development, and Type II is favorable reservoirs. It is estimated that the amount of shale gas resources are in the range of 232.2–286.2 billion m3. It is concluded that the Shahai Fm shale in the Fuxin Basin has both resource potential in geology and fracturing performance in

engineering, and its exploration and development prospect is broad. What's more, the potential of commercial shale gas development is great in the sweet-point areas.



The Upper Carboniferous (Westphalian A) Kozlu Formation consisting chiefly of sandstone, thick coal layers, shale, and conglomerate levels crops out in the Zonguldak-Amasra Basin, NW Anatolia. The Kozlu Formation contains a total of 20 mineable coal layers with the thickness varying from 0.5 to 6 m. The lower level of formation is represented by lacustrine deposits, whereas the upper part is made up of thick flood plain sediments and meandering river deposits bearing laterally continuous coal levels. In this study, coal samples taken from coal layers within the Kozlu Formation at the Kozlu Underground Coal Mining site were evaluated using the data obtained from pyrolysis/total organic matter (TOC), gas chromatography, and gas chromatography–mass spectrometry. The average total organic matter (TOC) value of Kozlu coals is 40.28%. The coals are characterized by relatively high hydrogen index (HI) value (average 262 mg HC/gTOC) and very low oxygen index value (2 mg CO2/gTOC). Pyrolysis data indicate that coals contain dominantly type II and less amount of type III kerogen, and Tmax values range from 454 to 468 °C. In gas chromatographs, the recorded distribution consists predominantly of low-carbon-numbered n-alkanes and subordinately of high-carbon-numbered n-alkanes and the terrigenous/aquatic ratio value is very low (0.05–0.09). Pristane abundance is greater than that of phytane, and Pr/Ph ratios are in the range of 1.11–1.60. The sterane abundances in the Kozlu coals are in the following order: C29 > C28 > C27. Coals have high C19 and C20 tricyclic terpane concentrations and high (C19 + C20)/C30 ratio, high C30* (diahopane) and C29Ts concentrations, and high C30*/C29Ts ratio and low C31R/C30 and C29/C30 hopane ratios. The dibenzothiophene-to-phenanthrene ratio of Kozlu coals is found to be very low (0.04–0.14). Based on the pyrolysis and biomarker data, the Kozlu coals are interpreted as being deposited in a suboxic–oxic continental environment in which there is effective input of clay and dominantly terrestrial (with significant lipid-rich components) and bacterial organic matter. High Tmax values, CPI values close to 1, low moretane/hopane (0.23–0.12), equilibrated 22S/(22S + 22R) homopane (for C32), 20S/(20S + 20R) C29 sterane (0.52–0.54) and TA(I)/TA(I + II) steroid ratios, high ββ/(ββ + αα) sterane (0.51–0.55), C30*/C29Ts, C30*/(C30* + C30H), MPI-3(α/β) (1.24–1.41), and MDR and MA(I)/MA(I + II) steroid are indicative of mature–late mature organic matter. Ro values between 0.9 and 1.25% determined from Tmax (454–468 °C) values indicate “high-volatile bituminous B–medium-volatile bituminous” rank for Kozlu coals. Kozlu coals having HI values (up to 331 mg HC/gTOC) extremely higher than those of classical coals indicates that these coals have significant oil and gas generation potential, and high S1 (average 6.04 mg HC/g rock) and S2 (110.08 mg HC/g rock) values imply that they generate notably high amount of liquid hydrocarbons and still have generation potential.

Karthikeyan, R., Singh, R., Bose, A., 2019. Microbial electron uptake in microbial electrosynthesis: a mini-review. Journal of Industrial Microbiology & Biotechnology 46, 1419-1426.

https://doi.org/10.1007/s10295-019-02166-6

Microbial electron uptake (EU) is the biological capacity of microbes to accept electrons from electroconductive solid materials. EU has been leveraged for sustainable bioproduction strategies via

microbial electrosynthesis (MES). MES often involves the reduction of carbon dioxide to multi-carbon molecules, with electrons derived from electrodes in a bioelectrochemical system. EU can be indirect or direct. Indirect EU-based MES uses electron mediators to transfer electrons to microbes. Although an excellent initial strategy, indirect EU requires higher electrical energy. In contrast, the direct supply of cathodic electrons to microbes (direct EU) is more sustainable and energy efficient. Nonetheless, low product formation due to low electron transfer rates during direct EU remains a major challenge. Compared to indirect EU, direct EU is less well-studied perhaps due to the more recent discovery of this microbial capability. This mini-review focuses on the recent advances and challenges of direct EU in relation to MES.

Kayukova, G.P., Mikhailova, A.N., Morozov, V.P., Musin, R.Z., Vandyukova, I.I., Sotnikov, O.S., Remeev, M.M., 2019. Comparative study of changes in the composition of organic matter of rocks from different sampling-depth intervals of domanik and domankoid deposits of the Romashkino oilfield. Petroleum Chemistry 59, 1124-1137.

https://doi.org/10.1134/S0965544119100050

This paper presents the results of a comparative study of rock samples from depth intervals of 1705–1728 m of Semilukian–Mendymian (domanik) deposits of the Berezovskaya area and 1379–1394 m of carbonate (domanikoid) deposits of the Dankovian–Lebedyanian horizon of the Zelenogorskaya area of the Romashkino oilfield. It has been shown that rocks with different mineral compositions differ in the content and composition of organic matter (OM), including kerogen, and its resistance to thermal impacts. The yield of extracts from the rocks and the differences in their group, structural-group, and hydrocarbon-group compositions have been determined. According to the molecular-mass distribution of normal and isoprenoid alkanes, the extracts from the rocks are oils of types A1 and A2. Peculiarities in the distribution of higher biomarkers have been revealed, indicating that the hydrocarbons of the examined samples of domanik and domanikoid rocks are genetically uniform in nature, but differ in the geochemical environment of the transformation of the original OM and, possibly, in the effect of migration processes.

Khawaja, N., Postberg, F., Hillier, J., Klenner, F., Kempf, S., Nölle, L., Reviol, R., Zou, Z., Srama, R., 2019. Low-mass nitrogen-, oxygen-bearing, and aromatic compounds in Enceladean ice grains. Monthly Notices of the Royal Astronomical Society 489, 5231-5243.

https://doi.org/10.1093/mnras/stz2280

Saturn’s moon Enceladus is erupting a plume of gas and ice grains from its south pole. Linked directly to the moon’s subsurface global ocean, plume material travels through cracks in the icy crust and is ejected into space. The subsurface ocean is believed to be in contact with the rocky core, with ongoing hydrothermal activity present. The Cassini spacecraft’s Ion and Neutral Mass Spectrometer (INMS) detected volatile, gas phase, organic species in the plume and the Cosmic Dust Analyser (CDA) discovered high-mass, complex organic material in a small fraction of ice grains. Here, we present a broader compositional analysis of CDA mass spectra from organic-bearing ice grains. Through analogue experiments, we find spectral characteristics attributable to low-mass organic compounds in the Enceladean ice grains: nitrogen-bearing, oxygen-bearing, and aromatic. By comparison with INMS results, we identify low-mass amines [particularly (di)methylamine and/or ethylamine] and carbonyls (with acetic acid and/or acetaldehyde most suitable) as the best candidates for the N- and O-bearing compounds, respectively. Inferred organic concentrations in individual ice particles vary but may reach tens of mmol levels. The low-mass nitrogen- and oxygen-bearing compounds are dissolved in the ocean, evaporating efficiently at its surface and entering the ice grains

via vapour adsorption. The potentially partially water soluble, low-mass aromatic compounds may alternatively enter ice grains via aerosolization. These amines, carbonyls, and aromatic compounds could be ideal precursors for mineral-catalysed Friedel–Crafts hydrothermal synthesis of biologically relevant organic compounds in the warm depths of Enceladus’ ocean.

Khot, M., Raut, G., Ghosh, D., Alarcón-Vivero, M., Contreras, D., Ravikumar, A., 2020. Lipid recovery from oleaginous yeasts: Perspectives and challenges for industrial applications. Fuel 259, 116292.


Oleaginous yeasts are promising candidates for generating renewable fatty acid-based fuels and oleochemicals. The quantitative recovery of the total intracellular lipid from the yeast cell is a critical step to their subsequent analysis and development of a bioprocess. However, the scalable process for lipid recovery from either wet or dry yeast biomass is far from commercialization. The major drawback for this is its rigid cell wall with high chitin and mannan content, which makes the oleaginous yeast cell resistant to lysis. Multiple procedures have been developed for the extraction of yeast lipids each with its limitations. Hence, a better understanding of the cell wall composition and knowledge of cell wall chemistry would provide information to aid in the design of better protocols for oil extraction. This review attempts to integrate both conventional and newly published oleaginous yeast biomass conditioning methods from extraction protocols into a unified body of knowledge. Existing lab-scale physical, chemical, and mechanical pretreatment methods for cell-mass were described and compared. A road-map based on cell wall modification approach is proposed for enhanced cell harvesting and lipid extraction from an oleaginous yeast species.


https://doi.org/10.1007/s13762-018-2087-y

Oil pollution is a major global environmental concern. Bioremediation is considered as a suitable approach for remediation of oil-contaminated environments. In this study, two crude oil-contaminated soils were collected to isolate and identify some native and active oil-degrading bacteria to be used in remediation of contaminated sites. Five isolates were selected according to “hole-plate diffusion method” and were grown in crude oil. They were cultured in a mineral salt medium in which crude oil was employed as the sole carbon source. Biochemical, morphological and genomic identifications demonstrated the bacteria species as Pseudomonas resinovorans, Plantibacter auratus, Bacillus subtilis, Staphylococcus pasteuri and Bacillus atrophaeus. These bacteria were able to degrade 86.0%, 61.3%, 81.1%, 55.0% and 76.2% of aliphatic compounds and 58.6%, 39.4%, 55.5%, 39.0% and 49.9% of aromatic hydrocarbons in a medium containing crude oil (1% v/v) over 21 days, respectively. The degradation rates of aromatic compounds from 14 to 21 days were higher than of aliphatic hydrocarbons. This rate was 28.4% by Bacillus subtilis, 30.9% by Bacillus atrophaeus, 27.2% by Staphylococcus pasteuri and 21.3% by Pseudomonas resinovorans. In Plantibacter auratus, this rate was 16.19% which is less than aliphatic hydrocarbons. To our knowledge, it seems this is the first time to report Pseudomonas resinovorans and Plantibacter auratus as crude oil degraders. Results of this study indicated that the isolated bacteria could have a high potential to be used in bioremediation of oil-contaminated environments.

Kim, G.B., Kim, W.J., Kim, H.U., Lee, S.Y., 2020. Machine learning applications in systems metabolic engineering. Current Opinion in Biotechnology 64, 1-9.


Systems metabolic engineering allows efficient development of high performing microbial strains for the sustainable production of chemicals and materials. In recent years, increasing availability of bio big data, for example, omics data, has led to active application of machine learning techniques across various stages of systems metabolic engineering, including host strain selection, metabolic pathway reconstruction, metabolic flux optimization, and fermentation. In this paper, recent contributions of machine learning approaches to each major step of systems metabolic engineering are discussed. As the use of machine learning in systems metabolic engineering will become more widespread in accordance with the ever-increasing volume of bio big data, future prospects are also provided for the successful applications of machine learning.

King, A.C.F., Thomas, E.R., Pedro, J.B., Markle, B., Potocki, M., Jackson, S.L., Wolff, E., Kalberer, M., 2019. Organic compounds in a Sub-Antarctic ice core: A potential suite of sea ice markers. Geophysical Research Letters 46, 9930-9939.

https://doi.org/10.1029/2019GL084249

Abstract: Investigation of organic compounds in ice cores can potentially unlock a wealth of new information in these climate archives. We present results from the first ever ice core drilled on sub‐Antarctic island Bouvet, representing a climatologically important but understudied region. We analyze a suite of novel and more familiar organic compounds in the ice core, alongside commonly measured ions. Methanesulfonic acid shows a significant, positive correlation to winter sea ice concentration, as does a fatty acid compound, oleic acid. Both may be sourced from spring phytoplankton blooms, which are larger following greater sea ice extent in the preceding winter. Oxalate, formate, and acetate are positively correlated to sea ice concentration in summer, but sources of these require further investigation. This study demonstrates the potential application of organic compounds from the marine biosphere in generating multiproxy sea ice records, which is critical in improving our understanding of past sea ice changes.

Plain Language Summary: Ice cores are vertical cylinders of ice drilled from an ice sheet, younger at the top and older at the bottom. Particles emitted from plants and animals on land and in the ocean, containing organic chemical compounds, are carried by atmospheric circulation, deposited on the ice surface, and become trapped inside ice layers. They are a record of environmental conditions at the location and time the particles originally formed. Here, we look for a number of these organic compounds in an ice core from Bouvet Island in the sub‐Antarctic. We find the amounts of some are related to amounts of sea ice around the island in the spring. This is because the particles are originally emitted by phytoplankton, for which the amount of sea ice that year controls the amount of phytoplankton (more sea ice in the winter = greater area of sea ice break up in spring = more phytoplankton in spring). We find other organic compounds are related to amounts of sea ice in summer, but their sources are less well known. Combining these records with their relationships to sea ice will be useful in helping us to better understand sea ice changes in the past.

Kitadai, N., Nishiuchi, K., 2019. Thermodynamic impact of mineral surfaces on amino acid polymerization: Aspartate dimerization on goethite. Astrobiology 19, 1363-1376.

https://doi.org/10.1089/ast.2018.1967

This article presents a thermodynamic predictive scheme for amino acid polymerization in the presence of minerals as a function of various environmental parameters (pH, ionic strength, amino acid concentration, and the solid/water ratio) using l-aspartate (Asp) and goethite as a model combination. This prediction is enabled by the combination of the surface adsorption constants of amino acid and its polymer, determined from the extended triple layer model characterization of the corresponding experimental results, with the thermodynamic data of these organic compounds in water reported in the literature. Calculations for the Asp–goethite system showed that the goethite surface drastically shifts the Asp monomer–dipeptide equilibrium toward the dipeptide side; when the dimerization of 0.1 mM Asp was considered in the presence of 10 m2 L−1 of goethite, an Asp dipeptide concentration around 105 times larger was computed to be thermodynamically attainable compared with that in the absence of goethite at acidic pH (4–5) and low ionic strength (0.1 mM NaCl). Under this condition, the dipeptide-to-monomer molecular ratio in the adsorbed state reached 20%. In contrast, no significant enhancement by goethite was predicted at alkaline pH (>8), where the electrostatic interactions of the goethite surface with Asp and Asp dipeptide are weak. Thus, mineral surfaces should have had a significant impact on the thermodynamics of prebiotic peptide bond formation on the early Earth, although the influences likely depended largely on the environmental conditions. Future experimental studies for various amino acid–mineral interactions using our proposed methodology will provide a quantitative constraint on favorable geochemical settings for the chemical evolution on Earth. This approach can also offer important clues for future exploration of extraterrestrial life.

Kittilä, A., Jalali, M.R., Evans, K.F., Willmann, M., Saar, M.O., Kong, X.Z., 2019. Field comparison of DNA-labeled nanoparticle and solute tracer transport in a fractured crystalline rock. Water Resources Research 55, 6577-6595.

https://doi.org/10.1029/2019WR025021

Field tracer experiments were conducted to examine tracer transport properties in a fracture-dominated crystalline rock mass at the Grimsel Test Site, Switzerland. In the experiments reported here, both the DNA nanotracers and solute dye tracers were simultaneously injected. We compare the transport of DNA nanotracers to solute dye tracers by performing temporal moment analysis on the recorded tracer breakthrough curves and estimate the swept volumes and flow geometries. The DNA nanotracers, approximately 166 nm in diameter, are observed to travel at a higher average velocity than the solutes but with lower mass recoveries, lower swept volumes, and less dispersion. Moreover, size exclusion and potentially, particle density effects are observed during the transport of the DNA nanotracers. Compared to solute tracers, the greatest strength of DNA nanotracers is the demonstrated zero signal interference of background noise during repeat or multitracer tests. This work provides encouraging results in advancing the use of DNA nanotracers in hydrogeological applications, for example, during contaminant transport investigations or geothermal reservoir characterization.

Klintzsch, T., Langer, G., Nehrke, G., Wieland, A., Lenhart, K., Keppler, F., 2019. Methane production by three widespread marine phytoplankton species: release rates, precursor compounds, and potential relevance for the environment. Biogeosciences 16, 4129-4144.


Methane (CH4) production within the oceanic mixed layer is a widespread phenomenon, but the underlying mechanisms are still under debate. Marine algae might contribute to the observed CH4 oversaturation in oxic waters, but so far direct evidence for CH4 production by marine algae has only been provided for the coccolithophore Emiliania huxleyi.

In the present study we investigated, next to E. huxleyi, other widespread haptophytes, i.e., Phaeocystis globosa and Chrysochromulina sp. We performed CH4 production and stable carbon isotope measurements and provide unambiguous evidence that all three investigated marine algae are involved in the production of CH4 under oxic conditions. Rates ranged from 1.9±0.6 to 3.1±0.4 µg of CH4 per gram of POC (particulate organic carbon) per day, with Chrysochromulina sp. and E. huxleyi showing the lowest and highest rates, respectively. Cellular CH4 production rates ranged from 16.8±6.5 (P. globosa) to 62.3±6.4 ag CH4 cell−1 d−1 (E. huxleyi; ag = 10−18 g). In cultures that were treated with 13C-labeled hydrogen carbonate, δ13CH4 values increased with incubation time, resulting from the conversion of 13C–hydrogen carbonate to 13CH4. The addition of 13C-labeled dimethyl sulfide, dimethyl sulfoxide, and methionine sulfoxide – known algal metabolites that are ubiquitous in marine surface layers – resulted in the occurrence of 13C-enriched CH4 in cultures of E. huxleyi, clearly indicating that methylated sulfur compounds are also precursors of CH4. By comparing the algal CH4 production rates from our laboratory experiments with results previously reported in two field studies of the Pacific Ocean and the Baltic Sea, we might conclude that algae-mediated CH4 release is contributing to CH4 oversaturation in oxic waters. Therefore, we propose that haptophyte mediated CH4 production could be a common and important process in marine surface waters.

Koeberl, C., Ferrière, L., 2019. Libyan Desert Glass area in western Egypt: Shocked quartz in bedrock points to a possible deeply eroded impact structure in the region. Meteoritics & Planetary Science 54, 2398-2408.


Libyan Desert Glass (LDG) is an enigmatic natural glass, about 28.5 million years old, which occurs on the floor of corridors between sand dunes of the southwestern corner of the Great Sand Sea in western Egypt, near the Libyan border. The glass occurs as centimeter‐ to decimeter‐sized, irregularly shaped, and strongly wind‐eroded pieces. The origin of the LDG has been the subject of much debate since its discovery, and a variety of exotic processes were suggested, including a hydrothermal sol‐gel process or a lunar volcanic source. However, evidence of an impact origin of these glasses included the presence of schlieren and partly or completely digested minerals, such as lechatelierite, baddeleyite (a high‐T breakdown product of zircon), and the presence of a meteoritic component in some of the glass samples. The source material of the glass remains an open question. Geochemical data indicate that neither the local sands nor sandstones from various sources in the region are good candidates to be the sole precursors of the LDG. No detailed studies of all local rocks exist, though. There are some chemical and isotopic similarity to rocks from the BP and Oasis impact structures in Libya, but no further evidence for a link between these structures and LDG was found so far. These complications and the lack of a crater structure in the area of the LDG strewn field have rendered an origin by airburst‐induced melting of surface rocks as a much‐discussed alternative. About 20 years ago, a few shocked quartz‐bearing breccias (float samples) were found in the LDG strewn field. To study this question further, several basement rock outcrops in the LDG area were sampled during three expeditions in the area. Here we report on the discovery of shock‐produced planar microdeformation features, namely planar fractures (PFs), planar deformation features (PDFs), and feather features (FFs), in quartz grains from bedrock samples. Our observations show that the investigated samples were shocked to moderate pressure, of at least 16 GPa. We interpret these observations to indicate that there was a physical impact event, not just an airburst, and that the crater has been almost completely eroded since its formation.



Several Snowball Earth periods, in which the Earth has been (almost) totally glaciated, are known from Earth history. Neither the trigger for the initiation, nor the reason for the ending of such phases, are well understood. Here we discuss some mechanical effects of the impact of asteroids 5-10 km in diameter on the Snowball Earth environment. An impact of this scale is the largest impact that is statistically predictable for 10-60 Myr time periods. The impact cratering itself (shock waves, impact crater formation) is not powerful enough to change the natural climate evolution path on Earth. However, the products of impact (mainly?water vapor) can be quickly distributed over a substantial part of the globe, influencing the global circulation (e.g., facilitating cloud formation). It is a question for future studies to confirm if such an event (which is possible statistically during this interval) may or may not have influenced the global climate of the Snowball Earth, and/or contributed to deglaciation.

Krings, M., 2019. Palaeolyngbya kerpii sp. nov., a large filamentous cyanobacterium with affinities to Oscillatoriaceae from the Lower Devonian Rhynie chert. PalZ 93, 377-386.

https://doi.org/10.1007/s12542-019-00475-w

The Lower Devonian Rhynie chert contains abundant fossil evidence of cyanobacteria. However, only a few of these fossils have been described. A newly discovered type of cyanobacterial filament is 22 to > 30 µm wide, and thus substantially larger than all filamentous cyanobacteria previously known from the Rhynie chert. Trichomes are uniseriate, composed of short, discoid cells not constricted at the cross walls, and enveloped in a distinct sheath. Because the filaments correspond in morphology to Palaeolyngbya barghoorniana, a fossil cyanobacterium described from the Precambrian, they are assigned to the fossil genus Palaeolyngbya and formally proposed as a new species, P. kerpii. Palaeolyngbya is attributed to the Oscillatoriaceae (Oscillatoriales) and compared to the modern genus Lyngbya sensu lato. All specimens of P. kerpii occur in a small area of clear chert intercalated between substrate layers, and thus support the hypothesis that substrate served as a conservation trap for delicate microbial life in the Rhynie setting.

Kuang, W., Lu, M., Yeboah, I., Qian, G., Duan, X., Yang, J., Chen, D., Zhou, X., 2019. A comprehensive kinetics study on non-isothermal pyrolysis of kerogen from Green River oil shale. Chemical Engineering Journal 377, 120275.


Fundamentally understanding the pyrolysis kinetics of kerogen is of prime scientific and industrial importance. Herein, bitumen- and carbonates-free kerogen sample is prepared through Soxhlet extraction followed by decarbonation of Green River oil shale, and its pyrolysis is studied by non-isothermal thermogravimetric analysis. The systematic analyses show that both the Popescu and master plots methods are not applicable to describe the kerogen pyrolysis process due to the changed reaction model and the varied activation energy over certain conversion range, respectively, while the piecewise non-linear least squares analysis is identified as an effective method to discriminate the most probable kinetic model from commonly used 15 reaction models based on four solid-state pyrolysis mechanisms. Two-stage reaction model, i.e., F1 at the early stage and F2 at the later one, is proposed to well describe the kerogen pyrolysis process, which demonstrates a wide applicability owing to their insensitivities on the heating rate and estimation methods of the activation energies. The methodology revealed here could be applicable to determine other solid-state pyrolysis kinetics and reaction mechanism.



Kendrick mass defect (KMD) analysis is widely used for helping the detection and identification of chemically related compounds based on exact mass measurements. We report here the use of KMD as a criterion for filtering complex mass spectrometry data set. The method allow automated, easy and efficient data processing, enabling the reconstruction of 2D distributions of families of homologous compounds from MSI images. We show that KMD filtering, based on in-house software, is suitable and robust for high resolution (full width at half-maximum, fwhm, at m/z 410 of 20 000) and very high-resolution (fwhm, at m/z 410 of 160 000) MSI data. This method has been successfully applied to two different types of samples, bacteria cocultures, and brain tissue sections.

Łącka, M., Cao, M., Rosell-Melé, A., Pawłowska, J., Kucharska, M., Forwick, M., Zajączkowski, M., 2019. Postglacial paleoceanography of the western Barents Sea: Implications for alkenone-based sea surface temperatures and primary productivity. Quaternary Science Reviews 224, 105973.


The increasing influence of Atlantic Water (AW) in the Barents Sea, a process known as “Atlantification”, is gradually decreasing sea ice cover in the region. Ongoing global climate warming is likely to be one of its drivers, but to further understand the role of natural variability and the biogeochemical impacts of the inflow of AW into the western Barents Sea, we reconstructed sea surface temperatures (SSTs) and primary productivity in Storfjordrenna, a climatically sensitive area south of Spitsbergen, between approximately 13,950 cal yr BP and 1300 cal yr BP. The alkenone U37K* proxy has been applied to reconstruct SSTs, and the alkenone accumulation rate in marine sediments has been used to infer changes in primary productivity. Our data show that the SST increase was concomitant with the progressive loss of sea ice cover and an increase in primary productivity in the western Barents Sea. We interpret these changes as reflecting the increasing influence of AW in the area as the ice sheets retreated in Svalbard. The transition from the Arctic to the Atlantic domain first occurred after 11,500 cal yr BP, as the Arctic Front moved eastward of the study site but with considerable variability in surface ocean conditions. High SSTs at approximately 6400 cal yr BP may have led to limited winter surface cooling, likely inhibiting convective mixing and the return of nutrients to the euphotic zone and/or enhanced organic matter consumption by zooplankton due to an earlier light signal in the ice-free Storfjordrenna. During the late Holocene (3600-1300 cal yr BP), low insolation facilitated sea ice formation and thus brine production. The former may have launched convective water mixing and increased nutrient resupply to the sea surface, consequently enhancing primary productivity in Storfjordrenna. We propose that, on the basis of the paleoceanographic evidence, the modern increasing inflow of warm AW and the disappearance of pack ice on the Eurasian continental shelf are likely to weaken convective water mixing and decrease primary production in the region.

Lajoinie, M.F., Sial, A., Ballivián Justiniano, C.A., Cingolani, C.A., Recio, C., Etcheverry, R.O., Basei, M., Lanfranchini, M.E., 2019. First geochronological constraint for the Palaeoproterozoic

Lomagundi-Jatuli δ13C anomaly in the Tandilia Belt basement (Argentina), Río de la Plata Craton. Precambrian Research 334, 105477.


Geochronological data of Palaeoproterozoic carbonates with δ13C values between +5‰ and +16‰ suggest that the positive carbon isotope excursion of the global Lomagundi-Jatuli event (LJE) occurred mostly between 2220 and 2060 Ma.

In the southern portion of the Río de la Plata Craton, the LJE was recorded in calcite-diopside marble of the Tandilia Belt basement. The marble was found at the San Miguel area as part of a metamorphic rock assemblage, mainly composed of gneisses and migmatites, formed during the Transamazonian Orogeny. The latter represents the maximum magmatic and metamorphic activity in the Tandilia Belt basement. The marble, derived from a calcareous-siliciclastic sedimentary marine sequence, was intruded by leucogranites that provoked the San Miguel skarn formation.

First U-Pb LA-ICP-MS age of 2206 ± 14 Ma, obtained from titanites of the skarn, also placed the metasomatic processes into the Transamazonian Orogeny. In addition, this age corresponds to the minimum age for the marble’s protolith deposition which matches with the beginning of the LJE worldwide. These new data would favor the correlation between the San Miguel marble and the Montevideo Formation marble of the Tandilia Terrane (Uruguay), within the Río de la Plata Craton, and not with the Paso Severino Formation of the Piedra Alta Terrane, which is at least 60 Ma younger.

New δ13C determinations in calcite crystals from the marble allowed the lowest and the highest carbon values (+3.19‰ and +6.90‰, respectively) to be obtained. The lowest values are within the range of normal marine carbonates (between −5‰ and +5‰), despite having been altered by contact metamorphism, while the highest values are typical of the LJE carbonates. In this sense, the early deposition of the carbonate protolith within the LJE, together with the effect of post-depositional metamorphic processes would justify the wide range of values shown by the isotopic ratios of C.

Lammel, D.R., Arlt, T., Manke, I., Rillig, M.C., 2019. Testing contrast agents to improve micro computerized tomography (μCT) for spatial location of organic matter and biological material in soil. Frontiers in Environmental Science 7, 153. doi: 10.3389/fenvs.2019.00153.

https://www.frontiersin.org/article/10.3389/fenvs.2019.00153

Soil carbon is essential for soil and ecosystem functioning. Its turnover and storage in soil are multifaceted processes that involve microbial activity in complex physical matrices. Biological litter, which include plants, animals, and microorganisms, is decomposed in soil stimulating soil biota (archaea, bacteria, fungi, protists, and animals) activity and yielding soil organic matter (SOM). Such decomposition processes are influenced by local physico-chemical characteristics including the spatial distribution of aggregates and pores. More refined analytical tools are needed to better understand these processes, especially considering the spatial 3D structure of soil matrices. Using synchrotron radiation (X-ray) micro computerized tomography (SR-μCT), we tested different contrast agents (staining methods) based on silver (Ag), eosin (Br based), and liquid and gaseous iodine (I) in order to spatially image biological material and SOM in soil samples. We also performed K-edge SR-μCT for the Ag and I2 treatments and conventional μCT for additional soil samples applying the I2 treatment. Our results indicated that I2 was the most efficient contrast method for SR-μCT imaging of soil samples. I2 qualitatively improved the images, but mainly, by using the K-edge SR-μCT, this method provided a powerful tool to determine the spatial location of SOM. We acknowledge that the

use of SR-μCT is an expensive technique to study soil samples, which comes with bottlenecks in terms of access to facilities and measurement time. Nevertheless, we show that the I2 treatment improved soil images also using standard μCT. In conventional μCT the I2 treatment improved the visualization of biological material and consequently improved the qualitative analysis of fine plants roots and micro-fauna (Collembola). This improvement may have a positive implication in soil biology, by improving a non-destructive method to detect fungi (SR-μCT), soil fauna (conventional μCT) and roots in undisturbed soil samples. An unexpected finding was that the I2 treatment also stained the plastic sample containers (nylon and polyimide), indicating the potential for the I2 staining procedure to be applied for the detection of plastic pollution in soil samples.

Lan, W., Luterbacher, J.S., 2019. A road to profitability from lignin via the production of bioactive molecules. ACS Central Science 5, 1642-1644.

https://doi.org/10.1021/acscentsci.9b00954

A new study opens a route to convert lignin, the world largest natural source of aromatics, into valuable bioactive compounds.

Lignin, one of the three major components in lignocellulosic biomass, is by far the largest natural source of aromatic functionalities and as such is an obvious feedstock for the production of renewable chemicals or fuels. Industrial development of lignin depolymerization has long been contemplated but has remained limited to a few niche applications. A team lead by Katalin Barta has developed a novel route to convert lignin into tetrahydro-2-benzazepines, a class of compound with promising pharmacological activities, and high potential value, which could help add value to this feedstock that is notoriously difficult to valorize.(1)

A longstanding roadblock to lignin deconstruction and use has been the quality of the lignin available industrially, which has largely been produced by the pulp and paper industry and, to a lesser extent, by biorefineries. In traditional pulp and paper plant, lignin is a highly modified side product and burned directly to generate energy for the plant.(2) In most of the biorefinery strategies, polysaccharides are separated, deconstructed, and converted to fuels, chemicals, or materials, leaving behind a lignin with a completely altered structure as a byproduct. These technical lignins are almost impossible to valorize because any condition that is harsh enough to isolate them generally leads to condensation and the associated formation of interunit C–C linkages, which cannot be cleaved selectively with current chemical techniques. As a result, these lignins can barely be depolymerized into low molecular weight monomers and thus are a poor feedstock for producing platform molecules that could be upgraded to other products.(3)

Increasingly, there has been a realization that integrated utilization of biomass and associated lignin valorization is necessary for the development of a profitable biorefinery. Therefore, several researchers have been developing methods for depolymerizing lignin to a select group of molecules at high yields and selectivity as part of the integrated conversion of all fractions of biomass.(4−7) Reductive catalytic fractionation (RCF) is one of these methods and has been developed among others by Barta and her co-workers.(4,7) This method mixes untreated biomass and a catalyst to directly cleave the ethers of native lignin and rapidly hydrogenate its fragments in the presence of a hydrogen donor at high temperature (180–250 °C).(5) Because lignin is directly converted as it is being extracted, this process avoids the aforementioned condensation issues and allows the recovery of a select number of products at high yield and selectivity. The major products of RCF (and other isolation methods) are propylphenols and phenylpropanols, which do not have a market application as of yet. They can be deoxygenated and converted to phenol, benzene, or alkane derivatives, but the low market value of these bulk chemicals makes it very challenging to build a profitable process,

especially for an emerging technology. For this reason, targeting higher value compounds such as pharmaceuticals could be interesting.

Barta’s group has developed a copper-doped porous metal oxide (Cu20-PMO) for the RCF process and achieved interesting aromatic monomer yields (10 wt % of lignin) with 86% selectivity toward phenylpropanol from pine (Figure 1, route B).(7) On the basis of this work, they further developed the transformation of phenylpropanol to pharmaceutical platform chemicals, 2-benzazepine derivatives, and the result is published in this issue of ACS Central Science.(1) The idea to produce benzazepines from lignin-based phenylpropanols is clever because the seven-membered N-heterocyclic benzazepine is synthetically challenging to produce from petroleum-based chemistry. The fossil-based route to benzazepines consists of multiple steps that produce stoichiometric quantities of waste and use toxic organic solvents. In contrast, the lignocellulosic-based scheme is environmentally friendly because it features a waste-free process and uses a bioderived green solvent. Furthermore, this biomass-derived route is able to integrate the entire structure of phenylpropanol, which leads to high atom economy.

The novel synthetic route included three steps (Figure 1): (1) reductive catalytic fractionation of biomass using Cu20-PMO to generate phenylpropanol, (2) Ru-catalyzed amination of dihydroconiferyl (G) and/or dihydrosinapyl alcohol (S) in the depolymerized mixture, and (3) cyclization of the secondary amine to generate the seven-membered N-heterocyclic ring. After hydrogenolysis of the biomass (step 1), G and S along with other aromatic monomers, dimers, oligomers, and carbohydrates (mainly from hemicellulose) were dissolved in the liquor. A direct amination of this raw mixture was possible but required much more reagent (4 equiv) and catalyst (10 mol %) and resulted in a lower yield (64% of theoretical yield) of the desired product, because the other OH-containing products in the RCF mixture also consumed the reagent and catalyst. A simple ethyl acetate extraction of the RCF mixture can remove the high molecular weight fractions and some of the carbohydrates to improve the amination process (84% yield of aminated dihydroconiferyl alcohol using 2 equiv of amines and 5 mol % catalyst). However, the consumption of reagents illustrates the challenges ahead for developing any transformation that starts with biomass-derived liquor. The last cyclization step was performed in deep eutectic solvent under mild conditions with up to 95% yield of tetrahydro-2-benzazepines depending on different types of amines used.

Tetrahydro-2-benzazepines are high value molecules due to their remarkable pharmacological properties. Compounds containing 2-benzazepines show strong neuroleptic and neurotropic activities.(8) Moreover, they are extractable from Galanthus nivalis and clinically used for the treatment of Alzheimer’s disease.(9) The lignin-derived tetrahydro-2-benzazepines synthesized in this study also exhibited interesting biological activities. They were notably active against Staphylococcus aureus and inhibited the viability of HepG2 cells by >85%, indicating their promising anti-infective and anticancer activities.

Various biorefinery schemes have long suffered from limited profitability and the difficulty of competing against the petrochemical industry, which has had over a century to develop and optimize its technology. Valorization of lignin is regarded as a possible route to palliate this problem. However, as these new technologies emerge they will inherently cost more than mature and highly optimized petrochemical processes. Targeting a highly valuable pharmaceutical precursor such as the lignin-derived bioactive tetrahydro-2-benzazepines discussed here could add significant profitability to biomass deconstruction. The demand volume for such chemicals is likely to be small, which will limit large-scale implementation. However, a profitable small-scale demonstration plant could derisk lignin conversion technology and lower costs for a much larger scale production of lignin-derived bulk aromatic chemicals—paving the way for renewable chemical production.

References

1. Elangovan, S.; Afanasenko, A.; Haupenthal, J.; Sun, Z.; Liu, Y.; Hirsch, A. K. H.; Barta, K. From wood to tetrahydro-2-benzazepines in three waste-free steps: modular synthesis of biologically active lignin-derived scaffolds ACS Central Sci. 2019.DOI: 10.1021/acscentsci.9b00781

2. Rinaldi, R.; Jastrzebski, R.; Clough, M. T.; Ralph, J.; Kennema, M.; Bruijnincx, P. C. A.; Weckhuysen, B. M. Paving the Way for Lignin Valorisation: Recent Advances in Bioengineering, Biorefining and Catalysis. Angew. Chem., Int. Ed. 2016, 55 (29), 8164– 8215, DOI: 10.1002/anie.201510351

3. Shuai, L.; Talebi Amiri, M.; Luterbacher, J. S. The Influence of Interunit Carbon–Carbon Linkages during Lignin Upgrading. Current Opinion in Green and Sustainable Chemistry 2016, 2, 59– 63, DOI: 10.1016/j.cogsc.2016.10.001

4. Van den Bosch, S.; Schutyser, W.; Koelewijn, S.-F.; Renders, T.; Courtin, C. M.; Sels, B. F. Tuning the Lignin Oil OH-Content with Ru and Pd Catalysts during Lignin Hydrogenolysis on Birch Wood. Chem. Commun. 2015, 51 (67), 13158– 13161, DOI: 10.1039/C5CC04025F

5. Lan, W.; Luterbacher, J. S. Preventing Lignin Condensation to Facilitate Aromatic Monomer Production. Chimia 2019, 73 (7–8), 591– 598, DOI: 10.2533/chimia.2019.591

6. Lan, W.; Amiri, M. T.; Hunston, C. M.; Luterbacher, J. S. Protection Group Effects During α,γ-Diol Lignin Stabilization Promote High-Selectivity Monomer Production. Angew. Chem., Int. Ed. 2018, 57 (5), 1356– 1360, DOI: 10.1002/anie.201710838

7. Sun, Z.; Bottari, G.; Afanasenko, A.; Stuart, M. C. A.; Deuss, P. J.; Fridrich, B.; Barta, K. Complete Lignocellulose Conversion with Integrated Catalyst Recycling Yielding Valuable Aromatics and Fuels. Nature Catalysis 2018, 1 (1), 82– 92, DOI: 10.1038/s41929-017-0007-z

8. Dumoulin, D.; Lebrun, S.; Couture, A.; Deniau, E.; Grandclaudon, P. Asymmetric Synthesis of Trans-3, 4-Disubstituted Tetrahydro-2-Benzazepines. General Papers ARKIVOC 2010, 2010, 195– 204

9. Quick, M. P.; Fröhlich, R.; Schepmann, D.; Wünsch, B. Asymmetric Synthesis of 3-Substituted Tetrahydro-2-Benzazepines. Org. Biomol. Chem. 2015, 13 (26), 7265– 7281, DOI: 10.1039/C5OB00731C



Computer simulation studies aimed at elucidating the phase behavior of crude oils inevitably require atomistically detailed models of representative molecules. For the lighter fractions of crudes, such molecules are readily available, as the chemical composition can be resolved experimentally. Heavier fractions pose a challenge, on the one hand because of their polydispersity and on the other because of the poor description of the morphology of the molecules involved. The quantitative molecular representation approach is used here to generate a catalogue of 100 plausible asphaltene and resin structures based on elemental analysis and 1H–13C NMR spectroscopy experimental data. The computer-generated models are compared in the context of a review of previously proposed literature structures and categorized by employing their molecular weights, double-bond equivalents, and hydrogen to carbon ratios. Sample atomistic molecular dynamics simulations were carried out for two

of the proposed asphaltene structures with contrasting morphologies, one island-type and one archipelago-type, at 7 wt % in either toluene or heptane. Both asphaltene models, which shared many characteristics in terms of average molecular weight, chemical composition, and solubility parameters, showed marked differences in their aggregation behavior. The example showcases the importance of including diversity and polydispersity when considering molecular models of heavy fractions.



This paper provides an overview of the role that geochemistry plays in petroleum systems analysis, and how this can be used to derive constraints on the key elements and processes that give rise to a successful petroleum system. We discuss the history of petroleum geochemistry before reflecting on the next frontier in geochemical applications in hydrocarbon systems. We then review the individual contributions to this Special Publication. These papers present new geochemical techniques that allow us to develop a more systematic understanding of critical petroleum system elements; including the temperature and timing of source-rock deposition and maturation, the mechanisms and timescales associated with hydrocarbon migration, trapping, storage and alteration, and the impact of fluid flow on reservoir properties. Finally, we provide a practical example of how these different geochemical techniques can be integrated to constrain and generate a robust understanding of the prolific Paleozoic petroleum system of the Bighorn Basin.

Le Moigne, F.A.C., 2019. Pathways of organic carbon downward transport by the oceanic biological carbon pump. Frontiers in Marine Science 6, 634. doi: 10.3389/fmars.2019.00634.

https://www.frontiersin.org/article/10.3389/fmars.2019.00634

The oceanic biological carbon pump (BCP) regulates the Earth carbon cycle by transporting part of the photosynthetically fixed CO<sub>2</sub> into the deep ocean. Suppressing this mechanism would result in an important increase of atmospheric CO<sub>2</sub> level. The BCP occurs mainly in the form of (1) organic carbon (OC) particles sinking out the surface ocean, of (2) neutrally buoyant OC (dissolved or particulate) entrained by downward water masses movements and/or mixing, and of (3) active transport of OC by migrating animals such as zooplankton and fishes. These various pools of OC differ in size since their sinking, production and decomposition rates vary spatially and temporally. Moreover, the OC transported to depths via these various export pathways as well as their decomposition pathways all have different ecological origins and therefore may response differently to climate changes. Currently, most ocean biogeochemical models do not resolve these various of OC pathways explicitly; rather, they imply that OC is therein created and destroyed equally. In addition, the organic composition of these various pools is largely unknown, especially at depths below 500 m. Here, known processes of OC export from the surface ocean to the mesopelagic zone (100–1000 m) are briefly reviewed. Three OC export pathways and some of their sub-categories are considered. I refer to published studies of OC fluxes associated with the specific downward export pathways and identify gaps that need to be addressed to better understand the OC fluxes associated with the BCP.

Lee, B.J., Kim, J., Hur, J., Choi, I.H., Toorman, E.A., Fettweis, M., Choi, J.W., 2019. Seasonal dynamics of organic matter composition and its effects on suspended sediment flocculation in river water. Water Resources Research 55, 6968-6985.

https://doi.org/10.1029/2018WR024486

Organic matter (OM) and suspended sediment are abundant, and interact with each other, in rivers and lakes. OM is usually adsorbed by suspended sediment and causes either particle stabilization or flocculation. In this study, the OM composition and suspended sediment flocculation potential of river water were regularly measured throughout the year 2016. The OM composition of the river water samples was measured with a liquid chromatography-organic carbon detection system and fluorescence excitation-emission matrix spectroscopy, and the flocculation potential was measured in a standard jar test experiment. Results from the OM analyses and flocculation potential tests, in association with a multivariate data analysis, demonstrated that the OM composition and flocculation potential of the river water were dynamic under different meteorological, hydrological, ecological, and anthropogenic conditions and closely correlated with each other. Dry seasons with low rainfall and water discharge induced a lacustrine condition and led to the OM composition being more aquagenic and flocculation-favorable. The most favorable condition for the enhancement of flocculation was during algae bloom and associated with the production of biopolymers from algae. In contrast, rainy seasons were advantageous for stabilization of suspended sediment because of excessive transport of terrigenous humic substances from catchment areas into the river. Such terrigenous humic substances enhanced stabilization by creating enhanced electrostatic repulsion via adsorption onto the sediment surface. Findings from this research provide a better insight into the highly complex behaviors of and interactions between OM and suspended sediment in natural water environments.

Lee, J.-C., Lee, B., Heo, J., Kim, H.-W., Lim, H., 2019. Techno-economic assessment of conventional and direct-transesterification processes for microalgal biomass to biodiesel conversion. Bioresource Technology 294, 122173.


The simplified direct-transesterification (DT) process was compared to the conventional biodiesel production process based on a reported previous experimental work with economic standpoint. Based on the process flow diagram, capital and operating costs were itemized properly and then unit biodiesel production cost was calculated. The results show the biodiesel production costs were 18.2 $ kg−1 (conventional process) and 12.5 $ kg−1 (DT process), respectively. Sensitivity analysis shows the source of biomass and chemical consumption are the major factors to determine total biodiesel production cost. The affecting factors were a solvent recycling, yield of biodiesel, and plant capacity and these values were varied to evaluate the variation of unit biodiesel production cost. As a result, the maximized biodiesel production cost went down to 3.5 $ kg−1, which is cost-competitive with other reported values of production cost.

Leglise, J., Müller, M., Piel, F., Otto, T., Wisthaler, A., 2019. Bulk organic aerosol analysis by proton-transfer-reaction mass spectrometry: An improved methodology for the determination of total organic mass, O:C and H:C elemental ratios, and the average molecular formula. Analytical Chemistry 91, 12619-12624.


We have recently shown in this journal (Müller et al. Anal. Chem. 2017, 89, 10889–10897) how a proton-transfer-reaction mass spectrometry (PTR-MS) analyzer measured particulate organic matter in urban atmospheres using the “Chemical Analysis of Aerosol Online” (CHARON) inlet. Our initial CHARON studies did not take into account fragmentation of protonated analyte molecules, which introduced a small but significant negative bias in the determination of bulk organic aerosol parameters. Herein, we studied the ionic fragmentation of 26 oxidized organic compounds typically found in atmospheric particles. This allowed us to derive a correction algorithm for the determination of the bulk organic mass concentration, mOA, the bulk-average hydrogen-to-carbon ratio, (H:C)bulk, the bulk-average oxygen-to-carbon ratio, (O:C)bulk, and the bulk-average molecular formula, MFbulk. The correction algorithm was validated against AMS data using two sets of published data. Finally, we determined MFbulk of particles generated from the reaction of α-pinene and ozone and compared and discussed the results in relation to the literature.

Leifer, I., 2019. A synthesis review of emissions and fates for the Coal Oil Point marine hydrocarbon seep field and California marine seepage. Geofluids 2019, 4724587.

https://doi.org/10.1155/2019/4724587

Anthropogenic oil in the ocean is of great concern due to its potential immediate and long-term impacts on the ecosystem, economy, and society, leading to intense societal efforts to mitigate and reduce inputs. Sources of oil in the ocean (in the order of importance) are natural marine seepage, run-off from anthropogenic sources, and oil spills, yet uncertainty and variability in these budgets are large, particularly for natural seepage, which exhibits large spatial and temporal heterogeneity on local to regional scales. When source inputs are comparable, discriminating impacts is complicated, because petroleum is both a bioavailable, chemosynthetic energy source to the marine ecosystem and a potential toxic stressor depending on concentration, composition, and period of time. This synthesis review investigates the phenomena underlying this complexity and identifies knowledge gaps. Its focus is on the Coal Oil Point (COP) seep field, arguably the best-studied example, of strong natural marine hydrocarbon seepage, located in the nearshore, shallow waters of the Northern Santa Barbara Channel, Southern California, where coastal processes complicate oceanography and meteorology. Many of our understandings of seep processes globally are based on insights learned from studies of the oil and gas emissions from the COP seep field. As one of the largest seep fields in the world, its impacts spread far as oil drifts on the sea surface and subsurface, yet much remains unknown of its impacts.

Lenardic, A., Seales, J., 2019. Different is more: The value of finding an inhabited planet that is far from Earth2.0. Astrobiology 19, 1398-1409.

https://doi.org/10.1089/ast.2018.1833

The search for an inhabited planet, beyond our own, is a driver of planetary exploration in our solar system and beyond. Using information from our own planet to inform search strategies allows for a targeted search. It is, however, worth considering some span in the strategy and in a priori expectation. An inhabited, Earth-like planet is one that would be similar to Earth in ways that extend beyond having biota. To facilitate a comparative cost/risk/benefit analysis of different potential search strategies, we use a metric akin to the Earth-similarity index. The metric extends from zero, for an inhabited planet that is like Earth in all other regards (i.e., zero differences), toward end-member

values for planets that differ from Earth but maintain life potential. The analysis shows how finding inhabited planets that do not share other Earth characteristics could improve our ability to assess galactic life potential without a large increase in time-commitment costs. Search strategies that acknowledge the possibility of such planets can minimize the potential of exploration losses (e.g., searching for long durations to reach conclusions that are biased). Discovering such planets could additionally provide a test of the Gaia hypothesis—a test that has proven difficult when using only Earth as a laboratory. Finally, we discuss how an Earth2.0 narrative that has been presented to the public as a search strategy comes with nostalgia-laden baggage that does not best serve exploration.



The gas-in-place content in coal and shale reservoirs is one of the key parameters, which impacts the exploitation potential of natural gas resources. Though its estimation has been paid close attention in the last decades, there is not an effective method that can be utilized to obtain reliable gas content data (including total, adsorbed, and free gas contents) in coal and shale reservoirs. In this paper, a process analysis method is proposed, which suggests dividing the coring and on-site desorption processes into five stages and comprehensively considers the gas release behaviors of only free gas and both adsorbed and free gas during different stages. Significantly, the two key parameters of time zero and lost gas time were precisely determined. The release of free gas can be described by the equation of gas state. The release of both adsorbed and free gas can be described by the Langmuir isothermal adsorption equation, the equation of gas state, and Fick’s first law. As a case study, the gas-in-place contents of two cores obtained from coal and shale reservoirs, respectively, were estimated. Prior to the application of the method, a series of operations involving the coring, on-site canister desorption, and reservoir characterization should be performed. Then, the total gas and the adsorbed and free gas contents can be obtained using this method combined with the on-site desorption data. The method proposed in this paper has a wide application potential in the estimation of coalbed methane and shale gas resources.

Li, S., Sang, Q., Dong, M., Luo, P., 2019. Determination of inorganic and organic permeabilities of shale. International Journal of Coal Geology 215, 103296.


Shale oil resources have become important energy supplies worldwide, but their storage features and flow mechanisms remain unclear. It is now well-accepted that shale formations are complex systems with both inorganic and organic contents. This study aims to characterize the permeabilities for inorganic and organic pore systems separately in shale samples using an innovative modeling approach validated with experimental data. Oil and water vacuum–imbibition tests were first conducted along with helium porosity measurements for four shale rock samples. A mathematical model considering imbibition and diffusion was then proposed and used to match the lab-measured oil and water imbibition curves. The critical parameters for these shale samples, including inorganic/organic porosities, fluid saturations, and permeabilities were successfully determined using this approach. Among all the samples in the study, the results showed that 33.93 to 40.54% of total oil in place was stored inside kerogen as either the free oil within the organic pores or the dissolved oil. Moreover, the flow of this part of the oil was controlled by the organic permeability as well as by the diffusion coefficient, which was different than the flow character of oil in the inorganic pore system.

The organic permeabilities of the samples used in this study were between 2.24 × 10−6 and 1.59 × 10−5 md, which were 243 to 2741 times less than each sample's corresponding inorganic permeability. The sensitivity analysis indicated that organic permeability significantly affected the oil imbibition rate. The proposed methodology should be adopted in future reservoir characterizations, and the determined permeabilities for both inorganic and organic pore material should accordingly be considered in future reservoir simulations in order to accurately describe fluid flow in shale reservoirs.



Polycyclic aromatic hydrocarbons (PAHs), some of the most widespread organic contaminants, are highly toxic to soil microorganisms. Whether long-term polluted soils can still respond to the fresh input of pollutants is unknown. In this study, the soil enzyme activity, soil microbial community structure and function and microbial metabolism pathways were examined to systematically investigate the responses of soil microorganisms to fresh PAH stress. Microbial activity as determined by soil dehydrogenase and urease activity was inhibited upon microbe exposure to PAH stress. In addition, the soil microbial community and function were obviously shifted under PAH stress. Both microbial diversity and richness were decreased by PAH stress. Rhizobacter, Sphingobium, Mycobacterium, Massilia, Bacillus and Pseudarthrobacter were significantly affected by PAH stress and can be considered important indicators of PAH contamination in agricultural soils. Moreover, the majority of microbial metabolic function predicted to respond to PAH stress were affected adversely. Finally, soil metabolomics further revealed specific inhibition of soil metabolism pathways associated with fatty acids, carbohydrates and amino acids. Therefore, the soil metabolic composition distinctively changed, reflecting a change in the soil metabolism. In summary, fresh contaminant introduction into long-term polluted soils inhibited microbial activity and metabolism, which might profoundly affect the whole soil quality.

Li, Y., Chang, X., Zhang, J., Xu, Y., Gao, D., 2019. Genetic mechanism of heavy oil in the Carboniferous volcanic reservoirs of the eastern Chepaizi Uplift, Junggar Basin. Arabian Journal of Geosciences 12, 648.

https://doi.org/10.1007/s12517-019-4849-3

A suite of crude oils from the Carboniferous volcanic reservoirs in the eastern Chepaizi Uplift, Junggar Basin, was analyzed to study the alteration of molecular compositions by severe biodegradation and the accumulation mechanisms of the crude oils. The investigation indicates that most of the crude oils of the Carboniferous reservoirs in the eastern Chepaizi Uplift are typical heavy oil with low wax and sulfur contents. The density of crude oils in the study area increases gradually from east to west, and as the burial depth increases, the density of crude oil decreases. All selected oil samples were severely degraded, with a degree of biodegradation (DOB) ranging from PM 7 to PM 9. The C21–22 steranes and diasteranes remain stable when the level of biodegradation is lower than PM 8, and they can be used as conserved “internal standards” to evaluate the biodegradation of hopanes, regular steranes, and tricyclic terpanes. However, the C21–22 steranes and diasteranes are degraded when the DOB is over PM 9. The biodegradation of tricyclic terpanes begins when the level of biodegradation reaches PM 8. Among the tricyclic terpane family, the C21 and C23 tricyclic terpanes are the most readily degraded members, while the C24-26 tricyclic terpanes seem more resistant to

biodegradation. Most of the heavy oil accumulations are formed by the adjustment and remigration of paleoaccumulations due to the activity of the Hongche Fault and tectonic movement. During the remigration of hydrocarbons, biodegradation and water washing occurred in the pathways, controlling the formation of heavy oil.



Scanning Electron Microscopy (SEM) and Atomic Force Microscope (AFM), two easily acquired and widely applied image acquisition and analysis methods, have rarely been combined to study the pore structure for unconventional natural gas reservoir rocks. In this work, we present an investigation of nanoscale detection of the pore distribution and mechanical properties of coals using SEM and AFM observations, and conduct quantitative analyses on pore structure distribution, surface roughness and mechanical properties. The morphological characteristics of the coal surface can be revealed by both SEM and AFM methods, and the mechanical parameters of the selected position were obtained under the peakforce quantitative nano-mechanics (PF-QNM) AFM mode, including the Young's modulus, peak force error, deformation, and adhesion forces. By fusing 800 high resolution SEM images into one single image (named as MAPS), the pores morphology and distribution of different scales were acquired. And the studied coal shows different types of cellular pores and gas pores with multiresolution. The mechanical property difference between the matrix and minerals of coal are clearly observed, with the Young’s modulus of organic component around 2 GPa, and that of the minerals generally higher than 10 GPa. The maximum adhesion force values range between 20 and 50 nN. The high values occurred where pores are developed. This work demonstrated that the combination of two dimensional (2D) SEM and three dimensional (3D) AFM results is effective in detection of surface properties, and is of significance in revealing the pore structure and mechanical properties at nanoscale.



Microbial communities within anaerobic ecosystems have evolved to degrade and recycle carbon throughout the earth. A number of strains have been isolated from anaerobic microbial communities, which are rich in carbohydrate active enzymes (CAZymes) to liberate fermentable sugars from crude plant biomass (lignocellulose). However, natural anaerobic communities host a wealth of microbial diversity that has yet to be harnessed for biotechnological applications to hydrolyze crude biomass into sugars and value-added products. This review highlights recent advances in ‘omics’ techniques to sequence anaerobic microbial genomes, decipher microbial membership, and characterize CAZyme diversity in anaerobic microbiomes. With a focus on the herbivore rumen, we further discuss methods to discover new CAZymes, including those found within multi-enzyme fungal cellulosomes. Emerging techniques to characterize the interwoven metabolism and spatial interactions between anaerobes are also reviewed, which will prove critical to developing a predictive understanding of anaerobic communities to guide in microbiome engineering.


https://doi.org/10.1007/s00253-019-10115-7

Bacteria from the genus Geobacillus are generally obligately thermophilic, with a unique bioenergy production capacity and unique enzymes. Geobacillus species were isolated primarily from hot springs, oilfields, and associated soils. They often exhibit unique survival patterns in these extreme oligotrophic environments. With the development of the microbial resources found in oilfields, Geobacillus spp. have been proven as valuable bacteria in many reports related to oilfields. After the isolation of Geobacillus by culture methods, more evidence was found that they possess the abilities of hydrocarbon utilization and bioemulsifier production. This paper mainly summarizes some characteristics of the Geobacillus species found in the oilfield environment, focusing on the inference and analysis of hydrocarbon degradation and bioemulsifier synthesis based on existing research, which may reveal their potential value in microbial enhanced oil recovery. It also provides references for understanding microbes in extreme environments.

Lindsay, M.R., Colman, D.R., Amenabar, M.J., Fristad, K.E., Fecteau, K.M., Debes II, R.V., Spear, J.R., Shock, E.L., Hoehler, T.M., Boyd, E.S., 2019. Probing the geological source and biological fate of hydrogen in Yellowstone hot springs. Environmental Microbiology 21, 3816-3830.

https://doi.org/10.1111/1462-2920.14730

Hydrogen (H2) is enriched in hot springs and can support microbial primary production. Using a series of geochemical proxies, a model to describe variable H2 concentrations in Yellowstone National Park (YNP) hot springs is presented. Interaction between water and crustal iron minerals yields H2 that partition into the vapour phase during decompressional boiling of ascending hydrothermal fluids. Variable vapour input leads to differences in H2 concentration among springs. Analysis of 50 metagenomes from a variety of YNP springs reveals that genes encoding oxidative hydrogenases are enriched in communities inhabiting springs sourced with vapour‐phase gas. Three springs in the Smokejumper (SJ) area of YNP that are sourced with vapour‐phase gas and with the most H2 in YNP were examined to determine the fate of H2. SJ3 had the most H2, the most 16S rRNA gene templates and the greatest abundance of culturable hydrogenotrophic and autotrophic cells of the three springs. Metagenomics and transcriptomics of SJ3 reveal a diverse community comprised of abundant populations expressing genes involved in H2 oxidation and carbon dioxide fixation. These observations suggest a link between geologic processes that generate and source H2 to hot springs and the distribution of organisms that use H2 to generate energy.

Liu, J., Liu, Q., Zhu, D., Meng, Q., Huang, X., 2019. The function and impact of deep fluid on the organic matter during the hydrogeneration and evolution process. Journal of Natural Gas Geoscience 4, 231-244.


As the formation and development of organic-inorganic interaction continues, people have came to realize the importance of organic matter during the process of organic matter maturing and generating hydrocarbon. Deep fluids act as the carrier of inner earth substances as it previously carried massive inorganic matter from deep earth. The injection of deep fluids provide sedimentary basin with hydrogen sources and catalyst, which promotes the maturation and evolution of organic matters within basins. By providing essential carbon sources for inorganic reaction, deep fluids also took

apart in inorganic hydrocarbon generation reaction. This paper collected recent achievements in regards to organic matter hydrogenation reaction and inorganic hydrocarbon generation reaction such as F-T synthesis. By giving a detailed analysis of the effect of extraneous hydrogen sources and catalyst on organic maturation and hydrocarbon-producing process, this paper confirms the “increasing hydrocarbon yield” effect of deep fluid.

Liu, K., Ostadhassan, M., Hackley, P.C., Gentzis, T., Zou, J., Yuan, Y., Carvajal-Ortiz, H., Rezaee, R., Bubach, B., 2019. Experimental study on the impact of thermal maturity on shale microstructures using hydrous pyrolysis. Energy & Fuels 33, 9702-9719.


Hydrous pyrolysis was applied to four low-maturity aliquots from the Utica, Excello, Monterey, and Niobrara Shale Formations in North America to create artificial maturation sequences, which could be used to study the impact of maturation on geochemical and microstructural properties. Modified Rock-Eval pyrolysis, reflectance, organic petrology, and Fourier transform infrared spectroscopy (FTIR) were employed to analyze their geochemical properties, while gas adsorption (CO2 and N2) was used to characterize their pore structures (pores < 200 nm). Organic petrography using white and blue light (fluorescence) before and after hydrous pyrolysis showed that amorphous organic matter cracked into solid bitumen, oil, and gas during hydrous pyrolysis. A reduction of the CH2/CH3 ratio in hydrous pyrolysis residues was observed from FTIR analysis. Rock-Eval pyrolysis showed that kerogens in the four samples were dissimilar, and hydrous pyrolysis residues showed smaller hydrogen index and Sh2 values than starting materials. Results from CO2 and N2 gas adsorption analysis showed that pore structures (micropore volume, micropore surface area, meso-macropore volume, and meso-macropore surface area) changed significantly during hydrous pyrolysis. However, changes in pore structure were dissimilar among the four samples, which was attributed to different activation energies of organic matter. A thermodynamic fractal model showed a decrease in fractal dimensions of Utica, Monterey, and Excello after hydrous pyrolysis, indicating a decrease in surface roughness. The pore size heterogeneity in the Utica sample increased as hydrous pyrolysis temperature increased, whereas the pore size heterogeneity distributions in the Monterey and Excello decreased based on the N2 adsorption data.



Along with the breakup of the supercontinent Nuna and Rodinia during the Mesoproterozoic and Neoproterozoic, a series of sedimentary basins formed within or at the periphery of the ancient cratons. Under the regime of breakup of the supercontinent, these basins underwent different evolutionary history hence formed different geological elements constituting the petroleum systems. In this contribution, the distribution and the stratigraphic successions of the Meso-Neoproterozoic basins in the North China Craton (NCC) were examined, as well as the retrospective review for the mechanisms of the basin formation. The synthesized geological and geochronological data support a long-term extensional environment for the basins in the northern NCC. The Mesoproterozoic basins in the Yanshan, western Liaoning (Yan-Liao) and the Zhaertai areas formed at the intracratonic position later than that in the Bayan Obo, which possibly deposited in the continental margin. The further efforts still need to be devoted to decipher the huge controversial around the tectonic nature of the basins in the southern NCC, as well as their stratigraphic correlations with the basins in the north and central. The distribution and organic geochemical characteristics of the Mesoproterozoic source

rock were also summarized. Three sets of source rock in the central NCC, namely the Chuanlinggou, Hongshuizhuang and Xiamaling Formations developed favorable geological and geochemical conditions for the generation of the hydrocarbon. While in the south, the Cuizhuang Formation was the only interval feasible for potential source rock. The progress in seismic geophysics and borehole drilling suggested the existence of the Mesoproterozoic beneath deep Ordos Basin. This open a new window for the reconstruction of the Mesoproterozoic paleogeography as well as the evaluation of the source potential of the Mesoproterozoic basins in the North China Craton.

Liu, X., Zhou, L., Shi, X., Xu, G., 2019. New advances in analytical methods for mass spectrometry-based large-scale metabolomics study. TrAC Trends in Analytical Chemistry 121, 115665.


Large-scale metabolomics study based on large population cohorts is increasingly applied to identify important metabolites or critical metabolic alterations related to the metabolite perturbation in disease states or under interventions and to investigate metabolic difference and stimuli response in genetically different individuals. Mass spectrometry (MS) coupled with different chromatographic methods, is suitable for large-scale metabolomics study due to its high sensitivity and selectivity, wide dynamic range, and rich information. However, there are still a series of challenges for really realizing large-scale metabolomics applications. Hence, in this review, we mainly focused on new advances in sample pretreatment methods, nontargeted, targeted and pseudotargeted metabolic data collection techniques, and data correction methods used for MS-based large-scale metabolomics study. Typical applications of MS-based large-scale metabolomics methods in molecular epidemiology, precision medicine, and genome-wide association studies with metabolomics (mGWAS) are also given.

Liu, Y., Wu, Y., Xia, Y., Xing, L., Tian, C., Lei, T., 2019. The methylation of aromatic nuclei — I: Implications for the geochemical evolution of gas. International Journal of Coal Geology 215, 103302.


Aromatic hydrocarbons are an important component in crude oil and sediments. Furthermore, the structure of macromolecular organic matter (such as kerogen) is also based on aromatic nuclei. The earlier methylation and later demethylation of various aromatic nuclei would affect the chemical components and carbon isotopes of aromatics as well as saturated hydrocarbons and gaseous hydrocarbons. The scope of the present study was to investigate the role of aromatic nuclei in the formation and geochemical evolution of natural gas in complex geological systems. The use of model compounds could simplify the complex system, and n-tricosane (n-C23), n-tetracosane (n-C24), and naphthalene (N) were selected as model compounds for paraffins and aromatic hydrocarbons and subjected to pyrolysis experiments. The results showed that aromatic nuclei had a slight influence on the gas generation without using a catalyst. However, the gaseous components were substantially affected by aromatic nuclei under the catalysis of clay, when the temperature was lower than 400 °C. The ratios of isoparaffin to n-alkane of gaseous hydrocarbons were reduced by the aromatic nuclei. As carbon isotopically lighter methyls preferred to combine with the aromatic nuclei, the gas productions were reduced, and there was a 13C depletion of methane with increasing temperature, which is contrary to the case of paraffin cracking alone. This trend can also be observed in the pyrolysis gases formed from the type II and III kerogens. The macromolecular aromatic nuclei played a similar role with the small aromatic hydrocarbons. These effects would mainly occur in the mature to highly mature stage of the organic matter (the paleo-geothermal temperature is ≤ 150 °C). The

above explorative experiments suggested that a large number of aromatic nuclei and their methylation reactions could exert a significant influence on the distributions and the carbon isotopic compositions of gaseous hydrocarbons in the evolution of sedimentary organic matter. This research also provided a new explanation for the carbon isotopic abnormality (the 13C-depleted methane and the increasing δ13C2-δ13C1 values) of deep natural gas of the Tarim Basin, in northwest China.

Liu, Z., Callies, U., 2020. A probabilistic model of decision making regarding the use of chemical dispersants to combat oil spills in the German Bight. Water Research 169, 115196.


Oil spills are one of the major threats to the marine environment in the German Bight (North Sea). In case of an accident, application of chemical dispersants would be one response option among others. Dispersion breaks oil slicks into small droplets which get then mixed into the water column. Removal of the oil from the water surface may reduce contamination of the coast. However, the window of opportunity for effective dispersant application is short and there are concerns about potential effects to the marine life. We propose a Bayesian network (BN) as an interactive and intuitive tool for responders to justify decisions on using chemical dispersants and possibly the provision of appropriate assets. The BN combines detailed sub-BNs for different criteria that govern the decision process. Expected drift trajectories are estimated based on comprehensive numerical ensemble simulations of hypothetical oil spills. Ecological impacts are represented prototypically, focusing on vulnerability of seabird concentrations to pollution in coastal areas. Dispersant effectiveness is estimated considering oil properties and weather conditions. Decision making is supposed to be based on expected satisfaction. The definition of what is considered satisfactory is of central importance for the whole analysis.

López-Sepulcre, A., Balucani, N., Ceccarelli, C., Codella, C., Dulieu, F., Theulé, P., 2019. Interstellar formamide (NH2CHO), a key prebiotic precursor. ACS Earth and Space Chemistry 3, 2122-2137.


Formamide (NH2CHO) has been identified as a potential precursor of a wide variety of organic compounds essential to life, and many biochemical studies propose it likely played a crucial role in the context of the origin of life on our planet. The detection of formamide in comets, which are believed to have—at least partially— inherited their current chemical composition during the birth of the Solar System, raises the question whether a non-negligible amount of formamide may have been exogenously delivered onto a very young Earth about four billion years ago. A crucial part of the effort to answer this question involves searching for formamide in regions where stars and planets are forming today in our Galaxy, as this can shed light on its formation, survival, and chemical reprocessing along the different evolutionary phases leading to a star and planetary system such as our own. The present review primarily addresses the chemistry of formamide in the interstellar medium, from the point of view of (i) astronomical observations, (ii) experiments, and (iii) theoretical calculations. While focusing on just one molecule, this review also more generally reflects the importance of joining efforts across multiple scientific disciplines in order to make progress in the highly interdisciplinary science of astrochemistry.

Louca, S., Astor, Y.M., Doebeli, M., Taylor, G.T., Scranton, M.I., 2019. Microbial metabolite fluxes in a model marine anoxic ecosystem. Geobiology 17, 628-642.


Permanently anoxic regions in the ocean are widespread and exhibit unique microbial metabolic activity exerting substantial influence on global elemental cycles and climate. Reconstructing microbial metabolic activity rates in these regions has been challenging, due to the technical difficulty of direct rate measurements. In Cariaco Basin, which is the largest permanently anoxic marine basin and an important model system for geobiology, long-term monitoring has yielded time series for the concentrations of biologically important compounds; however, the underlying metabolite fluxes remain poorly quantified. Here, we present a computational approach for reconstructing vertical fluxes and in situ net production/consumption rates from chemical concentration data, based on a 1-dimensional time-dependent diffusive transport model that includes adaptive penalization of overfitting. We use this approach to estimate spatiotemporally resolved fluxes of oxygen, nitrate, hydrogen sulfide, ammonium, methane, and phosphate within the sub-euphotic Cariaco Basin water column (depths 150-900 m, years 2001-2014) and to identify hotspots of microbial chemolithotrophic activity. Predictions of the fitted models are in excellent agreement with the data and substantially expand our knowledge of the geobiology in Cariaco Basin. In particular, we find that the diffusivity, and consequently fluxes of major reductants such as hydrogen sulfide, and methane, is about two orders of magnitude greater than previously estimated, thus resolving a long-standing apparent conundrum between electron donor fluxes and measured dark carbon assimilation rates.



As coalbed methane (CBM) becomes an increasingly important resource in the global natural gas market, gas transport in CBM reservoirs remains a crucial research topic that has not been fully understood. Gas migration in coal matrix is identified as a diffusion process which is quantified by effective diffusivity. This paper aims to explore the diffusion process in coal and measure the effective diffusivity using X-ray microcomputed tomography (micro-CT) imaging. By visualising the krypton gas migration process using micro-CT imaging, we are able to simulate the gas transport and better understand the diffusion mechanism of adsorptive gas in coal. The effective diffusivity of krypton that we obtain in the coal matrix is estimated to be 3.4 × 10−11 m2/s which falls in the mid-range of reported value in the literature. In this paper, we develop a method based on using micro-CT imaging and high X-ray attenuated gas to visualise gas transport and quantitatively analyse diffusion process in porous media. The experiment can be conducted at in situ pressure conditions to mimic CBM storage and production process. This method is ought to provide more insights into the gas diffusion mechanism in coal while preserving the original rock structure.

Lü, X., He, Q., Wang, Z., Cao, M., Zhao, J., Jiang, J., Zhao, R., Zhang, H., 2019. Calcium carbonate precipitation mediated by bacterial carbonic anhydrase in a karst cave: Crystal morphology and stable isotopic fractionation. Chemical Geology 530, 119331.


Stable oxygen (δ18O) and carbon (δ13C) isotopes of speleothems are widely used as important proxies for paleoclimatic and paleoenvironment reconstructions. However, the influence of microbial activity on carbon and oxygen isotope fractionation during speleothem precipitation remains unclear. Bacterial carbonic anhydrase (CA) can promote calcium carbonate precipitation to catalyze the mutual transformation between CO2 and HCO3-. CA-producing bacteria (Lysinibacillus sp. strain

LHXY2) were separated in the Xueyu Cave, Chongqing, SW China, and used in laboratory and cave in situ models to investigate their influence on the precipitation amount, mineral components, crystal morphology and carbon and oxygen isotope fractionation of CaCO3. A CA activity gradient was applied in the laboratory model by considering various CA inhibitor acetazolamide (AZ) concentrations, which showed that the CA activity could substantially enhance precipitation, alter the mineral components and morphology, and reduce the δ13C and δ18O values of the CaCO3 formed. Most importantly, the laboratory and in situ model results revealed approximately -7‰ and -1.4‰ δ13C shifts, respectively, compared to the bacteria-free model results, which indicated that microbial-driven carbon isotopic fractionation can cause great uncertainties in paleoclimate and paleoenvironment reconstructions.



The lower assemblage under the Cretaceous in the southern margin of Junggar Basin has large exploration potential, but low exploration discovery rate at present. Qigu oilfield, located in the piedmont fault-fold belt of the southern margin of Junggar Basin, was discovered in 1957. In 2011, that the industrial gas flow yielded in Well Qigu-1 drilled in the west of the Qigu anticline brought a new life to Qigu oilfield, and strengthened confidence in exploring the lower assemblage in the southern margin of Junggar. Reconsidering the complex oil and gas accumulation process of Qigu oilfield helps to clarify the reservoir forming conditions and favorable exploration direction of lower assemblage in the southern margin of Junggar Basin. By analyzing the structural model, tectonic evolution, hydrocarbon distribution and geochemical characteristics of Qigu anticline, and comprehensively utilizing the techniques and methods such as oil-gas source correlation, fluid inclusion observation and temperature measurement, basin modeling, effectiveness evaluation of mudstone caprock, this paper analyzes the multi-layer and multi-stage hydrocarbon accumulation process and pattern of Qigu oilfield in detail. The results show that the northern Qigu fault, a long-term inherited active fault from Late Jurassic to Neogene, plays an important role in the formation of Qigu structure and the migration and accumulation of oil and gas. At the end of the Late Jurassic period, paleostructure was developed in the Qigu area. Since the Late Cenozoic, the thrust folds have been developed into the current Qigu anticline, while the paleostructure development area became the north limb of the present anticline under the action of tectonic tilt. The evaporation/migration fractionation caused by the "early oil and late gas" accumulation process led to the high density of residual crude oil and high wax content. Influenced by the strong thrust in the late Himalayas, the high-mature coal-derived gases generated by the Jurassic source rocks deeply buried in the footwall passed through the northern Qigu fault to accumulate in the Qigu anticline. However, in various parts, due to the different destruction to the caprock preservation conditions caused by the multi-phase oil and gas charging and the Late Cenozoic tectonic uplift, the Qigu area generally presents an abnormal oil and gas distribution pattern of "oil in the upper and gas in the lower". Reconsidering the reservoir-forming process of Qigu oilfield has important implications for exploration, which the paleostructure of the north limb of Qigu anticline is the favorable area for the early residual oil exploration, the lower part of the northwest-plunging end is the area for gas exploration, and the Jurassic in-situ thrust structure in the footwall of the northern Qigu fault and the thrust structure of the Paleogene Ziniquanzi Formation are the potential areas for oil and gas exploration. The discovery of high-mature coal-derived gas in Qigu oilfield confirmed that the Jurassic source rocks in the southern margin of Junggar Basin effectively generated gases in a large scale, indicating that in the middle

section of Wukui anticline near the Qigu oilfield, the exploration potential of natural gas in the lower assemblage is quite large.

Lu, Y., Xia, X., Cheung, S., Jing, H., Liu, H., 2019. Differential distribution and determinants of ammonia oxidizing archaea sublineages in the oxygen minimum zone off costa Rica. Microorganisms 7, 453.

https://doi.org/10.3390/microorganisms7100453

Ammonia oxidizing archaea (AOA) are microbes that are widely distributed in the ocean that convert ammonia to nitrite for energy acquisition in the presence of oxygen. Recent study has unraveled highly diverse sublineages within the previously defined AOA ecotypes (i.e., water column A (WCA) and water column B (WCB)), although the eco-physiology and environmental determinants of WCB subclades remain largely unclear. In this study, we examined the AOA communities along the water columns (40–3000 m depth) in the Costa Rica Dome (CRD) upwelling region in the eastern tropical North Pacific Ocean. Highly diverse AOA communities that were significantly different from those in oxygenated water layers were observed in the core layer of the oxygen minimum zone (OMZ), where the dissolved oxygen (DO) concentration was < 2μM. Moreover, a number of AOA phylotypes were found to be enriched in the OMZ core. Most of them were negatively correlated with DO and were also detected in other OMZs in the Arabian Sea and Gulf of California, which suggests low oxygen adaptation. This study provided the first insight into the differential niche partitioning and environmental determinants of various subclades within the ecotype WCB. Our results indicated that the ecotype WCB did indeed consist of various sublineages with different eco-physiologies, which should be further explored. /2076-2607/7/10/453/htm

Lukhele, T., Selvarajan, R., Nyoni, H., Mamba, B.B., Msagati, T.A.M., 2019. Diversity and functional profile of bacterial communities at Lancaster acid mine drainage dam, South Africa as revealed by 16S rRNA gene high-throughput sequencing analysis. Extremophiles 23, 719-734.

https://doi.org/10.1007/s00792-019-01130-7

This study surveyed physicochemical properties and bacterial community structure of water and sediments from an acid mine drainage (AMD) dam in South Africa. High-throughput sequence analysis revealed low diversity bacterial communities affiliated within 8 dominant phyla; Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, Nitrospirae, Proteobacteria, Saccharibacteria, and ca. TM6_(Dependentiae). Acidiphilium spp. which are common AMD inhabitants but rarely occur as dominant taxa, were the most abundant in both AMD water and sediments. Other groups making up the community are less common AMD inhabitants; Acidibacillus, Acidibacter, Acidobacterium, Acidothermus, Legionella, Metallibacterium, Mycobacterium, as well as elusive taxa (Saccharibacteria, ca. TM6_(Dependentiae) and ca. JG37-AG-4). Although most of the taxa are shared between sediment and water communities, alpha diversity indices indicate a higher species richness in the sediments. From canonical correspondence analysis, DOC, Mn, Cu, Cr, Al, Fe, Ca were identified as important determinants of community structure in water, compared to DOC, Ca, Cu, Fe, Zn, Mg, K, Mn, Al, sulfates, and nitrates in sediments. Predictive functional profiling recovered genes associated with bacterial growth and those related to survival and adaptation to the harsh environmental conditions. Overall, the study reports on a distinct AMD bacterial community and highlights sediments as microhabitats with higher species richness than water.

Lusinier, N., Seyssiecq, I., Sambusiti, C., Jacob, M., Lesage, N., Roche, N., 2019. Biological treatments of oilfield produced water: A comprehensive review. SPE Journal 24, 2135-2147.

https://doi.org/10.2118/195677-PA

Crude-oil extraction leads to the production of water, called produced water (PW). PW-flow rate increases along with the time of operation, up to more than 20 times the flow rate of crude oil. PW is often considered toxic because of its complex composition. At the moment, only dispersed hydrocarbons are targeted by water regulation. However, as regulations are becoming more stringent, they are also targeting dissolved compounds and/or the whole effluent toxicity. Consequently, PW treatments have to be more efficient, also allowing for high reliability of installations and high compactness (offshore processes). Biological treatments are often considered to offer the best compromise between removal performances and operating costs. However, their lack of compactness is unsuitable for offshore implementation. Hybrid processes, defined here as the combination of two or more processes, show promising performance and should be further studied to overcome the drawbacks noted in the case of other technologies.

Ma, S., Zheng, J.-n., Tian, M., Tang, D., Yang, M., 2020. NMR quantitative investigation on methane hydrate formation characteristics under different driving forces. Fuel 261, 116364.


Methane hydrate is an important energy source and a good form of methane storage and transportation. The limit of gas storage capacity in hydrates is still not clear. In this study, we employed a low-field nuclear magnetic resonance to study the gas-water consumption characteristics quantitatively at various formation conditions. Nine methane hydrate formation experiments of different temperatures pressures were conducted in porous media. The consumption of gas and water for hydrate formation displayed as asynchronous trend, due to the change in hydrate cage occupancy. The results indicated that higher pressures or lower temperatures improved both the amount of hydrate formation and the cage occupancy of hydrate. In addition, the driving forces affected the formation of methane hydrate more obviously under a lower temperature. Ultimately, the hydration number of methane hydrate under different driving forces were determined. This study is of great significance to the estimation of hydrate and gas capacity in the hydrate based technology application in methane storage and transportation.

Ma, W., Han, W., Hou, L., Tao, S., Tao, X., Chang, X., 2019. Geochemical characteristics, genetic types and sources of natural gas in the Yingjisu Depression, Tarim Basin, China. International Journal of Coal Geology 215, 103300.


The Yingjisu Depression in the Tarim Basin produces gas with high wetness, nitrogen content, and ethane carbon isotope is abnormally depleted. The hydrocarbon generation capability of the Jurassic coal strata in this area has been controversial. Anomalies in the geochemical characteristics and the actual geological conditions have resulted in challenges in identifying the source and genetic type of natural gas in the Yingjisu Depression. In the present study, the composition and carbon isotope of natural gas are investigated. In addition, the controversial Jurassic coal strata are comprehensively evaluated, and the biomarkers are analyzed. The actual geological conditions of the Yingjisu Depression are studied combined with geochemical analysis. The components and carbon isotope suggest that the natural gas in the Yingjisu Depression is oil-associated gas generated from marine

source rocks in the late mature stage. The formation temperature of the natural gas was higher than 185 °C, which represents secondary cracking oil at high thermal maturity. The Jurassic coal strata has low Tmax (lower than 435 °C) and %Ro = 0.3–0.7. These strata cannot be the source rocks of natural gas in the Yingjisu Depression with high content of N2, typical of marine sediment. However, the biomarkers confirmed that the oil and gas in the Yingjisu Depression were derived from the Cambrian–Ordovician source rocks rather than the Jurassic. Therefore, the natural gas in the Yingjisu Depression is the secondary cracking of oil from the Cambrian–Ordovician paleo-reservoir. According to the actual geological conditions, the cracked gas migrated upward along deep faults to accumulate in the Silurian and Jurassic reservoirs, eventually forming the Yingjisu Depression gas field.

Ma, Z.-H., Wei, X.-Y., Liu, G.-H., Liu, Z.-Q., Liu, F.-J., Zong, Z.-M., 2019. Insight into the compositions of the soluble/insolube portions from the acid/base extraction of five fractions distilled from a high temperature coal tar. Energy & Fuels 33, 10099-10107.


Light oil, phenol oil, naphthalene oil, washing oil, and anthracene oil separated from a high-temperature coal tar (HTCT) were extracted via a modified HCl/NaOH extraction method to obtain acid-soluble portions (ASPs), base-soluble portions (BSPs), and acid/base-insoluble portions (ISPs), which were further analyzed with a gas chromatograph/mass spectrometer (GC/MS) to understand the composition of the HTCT. The results show that the recoveries of the 3 portions separated from each fraction decrease in the order of ISPs ≫ BSPs > ASPs. According to the analysis with a GC/MS, a total of 403 compounds were detected from the 5 fractions and their separated portions. Noteworthily, nitrogen-containing organic compounds, oxygen-containing organic compounds, and arenes dominate BSPs, ASPs, and ISPs, respectively. Combined with the distribution of fragmental ions in the mass spectra, detailed pathways for fragmentating the major compounds in different fragmentation modes were proposed, which facilitates the identification of different compounds. Moreover, possible compound separation pathways were investigated.


https://doi.org/10.1029/2019GC008314

The Mg isotopic composition in biogenic CaCO3 is expected to reflect oceanic Mg cycles, yet its practical application for paleoenvironmental reconstruction is complicated by the influences of seawater temperature and biologically mediated isotope fractionation. In this study, we investigated the relationship between water temperature, growth rate, and the Mg isotope ratio (δ26Mg) of the biogenic high‐Mg calcite that forms the tests of large benthic foraminifers. We cultured asexually reproduced large benthic foraminifers (Amphisorus kudakajimensis and Calcarina gaudichaudii) at 21–30 °C. We measured Mg/Ca ratios, chemical Mg speciation, and δ26Mg for both species. Mg/Ca ratios showed significant temperature dependence for both species, while the δ26Mg values for different populations of C. gaudichaudii exhibited increasing discrimination of heavy isotope with increasing temperature. X‐ray absorption of near‐edge structure spectra of the foraminiferal tests showed Mg speciation to be consistent with that of inorganic calcite, indicating ideal substitution of Mg for Ca in the crystal lattice. The δ26Mg values for both species were close to those of inorganic calcite and other marine organisms that precipitate high‐Mg calcite. These results suggest that precipitation of high‐Mg calcite tests for both species is similar to that of inorganic calcite and that

Mg isotope fractionation for both species is only slightly influenced by individual physiological processes related to growth temperature. The ∆26Mgcarb‐sol values of multiple field samples fell within the ∆26Mgcarb‐sol range for inorganic calcite, providing preliminary evidence that the effects of intraspecific differences in δ26Mg values can be averaged out by careful choice of samples for analysis.

Maggiano, C.M., White, C.D., Stern, R.A., Peralta, J.S., Longstaffe, F.J., 2019. Focus: Oxygen isotope microanalysis across incremental layers of human bone: Exploring archaeological reconstruction of short term mobility and seasonal climate change. Journal of Archaeological Science 111, 105028.


In archaeological populations the oxygen isotope composition (δ18O) of human bones and teeth can be used to reconstruct climatic conditions and landscape mobility by serving as a proxy for changes in δ18O of consumed water. Until now, providing this information at the seasonal scale, across broad periods of an individual's life, has been considered impossible because bone remodeling was thought to completely disrupt meaningful patterns preserved in bone microstructure. Recent studies, however, have described large (often > 1 mm) deposits of incremental primary bone persisting well into adulthood, and new technology permits finer scale analysis than ever before. Our objective was to determine the δ18O variation across human primary bone layers using high spatial resolution Secondary Ion Mass Spectrometry (SIMS). Results show patterned sinusoidal periodicity, similar to expectations for weather-induced fluctuations in seasonal drinking water. The bone formation rate suggested by the isotopic variation in our study is consistent with other histological assessments of primary lamellar bone formation. The technique thus enables sampling of δ18O at approximately monthly intervals over more than a decade of bone deposition. Because bone is the most commonly recovered archaeological tissue, applications of this method, even using fragmentary remains, have the potential to enable more detailed reconstructions of political, economic, health, and sociocultural change at life history levels. Future applications may also include identification of remains in historic and forensic contexts and determination of developmental or pathogenic rates in ancient or modern health investigations.

Mahajan, D., Sengupta, S., Sen, S., 2019. Strategies to enhance of microbial lipid production using metabolic engineering approach. Biocatalysis and Agricultural Biotechnology 22, 101321.


The exponentially depleting fossil fuel reserves has led to the growth of lipids being used as an alternate potential feedstock, derived from varied sources including plants, animals and microbes. In comparison to plant and animal sources, microbial sources can generate higher fractions of polyunsaturated fatty acids but their extraction is not industrially feasible or economical. Although statistical optimization techniques have enhanced lipid accumulation, these aren't sufficient to compete on a commercial scale. Advances in genetic engineering and systems biology tools have helped us get a better insight of the complex pathways involved, hence has a more directed and definite approach. This review discusses about the recent advances in microbial lipid accumulation, predominantly focusing on the metabolic engineering strategies.

Maierhofer, K., Koeberl, C., Brigham-Grette, J., 2019. Petrography and geochemistry of the impact to postimpact transition layer at the El'gygytgyn impact structure in Chukotka, Arctic Russia. Meteoritics & Planetary Science 54, 2510-2531.


The 3.6 Ma El'gygytgyn impact structure, located in northeast Chukotka in Arctic Russia, was largely formed in acidic volcanic rocks. The 18 km diameter circular depression is today filled with Lake El'gygytgyn (diameter of 12 km) that contains a continuous record of lacustrine sediments of the Arctic from the past 3.6 Myr. In 2009, El'gygytgyn became the focus of the International Continental Scientific Drilling Program (ICDP) in which a total of 642.4 m of drill core was recovered. Lithostratigraphically, the drill cores comprise lacustrine sediment sequences, impact breccias, and deformed target rocks. The impactite core was recovered from 316.08 to 517.30 meters below lake floor (mblf). Because of the rare, outstanding recovery, the transition zone, ranging from 311.47 to 317.38 m, between the postimpact lacustrine sediments and the impactite sequences, was studied petrographically and geochemically. The transition layer comprises a mixture of about 6 m of loose sedimentary and volcanic material containing isolated clasts of minerals and melt. Shock metamorphic effects, such as planar fractures (PFs) and planar deformation features (PDFs), were observed in a few quartz grains. The discoveries of silica diaplectic glass hosting coesite, kinked micas and amphibole, lechatelierite, numerous impact melt shards and clasts, and spherules are associated with the impact event. The occurrence of spherules, impact melt clasts, silica diaplectic glass, and lechatelierite, about 1 m below the onset of the transition, marks the beginning of the more coherent impact ejecta layer. The results of siderophile interelement ratios of the transition layer spherules give indications of the relative contribution of the meteoritical component.


https://doi.org/10.1038/s41598-019-50179-z

The biorecovery of europium (Eu) from primary (mineral deposits) and secondary (mining wastes) resources is of interest due to its remarkable luminescence properties, important for modern technological applications. In this study, we explored the tolerance levels, reduction and intracellular bioaccumulation of Eu by a site-specific bacterium, Clostridium sp. 2611 isolated from Phalaborwa carbonatite complex. Clostridium sp. 2611 was able to grow in minimal medium containing 0.5 mM Eu3+. SEM-EDX analysis confirmed an association between Eu precipitates and the bacterium, while TEM-EDX analysis indicated intracellular accumulation of Eu. According to the HR-XPS analysis, the bacterium was able to reduce Eu3+ to Eu2+ under growth and non-growth conditions. Preliminary protein characterization seems to indicate that a cytoplasmic pyruvate oxidoreductase is responsible for Eu bioreduction. These findings suggest the bioreduction of Eu3+ by Clostridium sp. as a resistance mechanism, can be exploited for the biorecovery of this metal.

Malkin, A.Y., 2019. Oil as an object of rheology (review). Petroleum Chemistry 59, 1092-1107.

https://doi.org/10.1134/S0965544119100062

A review of the current state of research in the field of oil rheology is presented as the basis for quantitative characterization of oil flow in the pipeline system. Based on recent publications, a picture is presented of the dependence of the rheological properties of oils of various types on their composition. The features of the flow of waxy oils, including the problem of correct assessment and depression of the pour point, have been analyzed. The flow of crystallizing oil has been considered proceeding from the concept of oil as a viscoplastic thixotropic medium. It has been shown how the results of rheological studies can be used to solve technological problems, including the restart

problem. The rheology of heavy oil has been considered on the basis of the strategic objective of reducing viscosity to a level that meets the requirements of its transport in existing pipeline systems. Various existing and promising ways to solve this problem are discussed. Particular attention is paid to the role of asphaltenes and the formation of emulsions and their importance in oil rheology.

Malta, J.Á.M.S.C., Calabrese, C., Nguyen, T.-B., Trusler, J.P.M., Vesovic, V., 2020. Measurements and modelling of the viscosity of six synthetic crude oil mixtures. Fluid Phase Equilibria 505, 112343.


The viscosity and density are reported for six synthetic mixtures, composed of up to 13 components, designed to match a light, dead crude oil of API 32° and molar mass of approximately 184 g mol−1. The measurements were made in the liquid region at temperatures between (323 and 398) K and in the pressure range from 1 MPa to 70 MPa. The viscosity was measured with a vibrating-wire viscometer, while the density was measured by means of a vibrating U-tube densimeter. The density and viscosity data have expanded relative uncertainties of 0.12% and 1.2%, respectively with a coverage factor of 2.

We have used the measured viscosity data to test the predictive power of the four viscosity models, the extended hard sphere (EHS), one-component EHS (1-cEHS), three-component EHS (3-cEHS) and Vesovic-Wakeham (VW), that have their basis in kinetic theory and the molecular description of the fluid. Two of the models (EHS and VW) require full compositional description of the mixture, while the other two belong to a new family of models which dispense with full compositional characterization, but retain molecular description. On average the EHS and VW models predict the viscosity data with lower deviations than 1-cEHS and 3-cEHS models, but all four models represent the data with uncertainty of 5–10%.

Martin-Cuadrado, A.-B., Senel, E., Martínez-García, M., Cifuentes, A., Santos, F., Almansa, C., Moreno-Paz, M., Blanco, Y., García-Villadangos, M., del Cura, M.Á.G., Sanz-Montero, M.E., Rodríguez-Aranda, J.P., Rosselló-Móra, R., Antón, J., Parro, V., 2019. Prokaryotic and viral community of the sulfate-rich crust from Peñahueca ephemeral lake, an astrobiology analogue. Environmental Microbiology 21, 3577-3600.

https://doi.org/10.1111/1462-2920.14680

Peñahueca is an athalassohaline hypersaline inland ephemeral lake originated under semiarid conditions in the central Iberian Peninsula (Spain). Its chemical composition makes it extreme for microbial life as well as a terrestrial analogue of other planetary environments. To investigate the persistence of microbial life associated with sulfate‐rich crusts, we applied cultivation‐independent methods (optical and electron microscopy, 16S rRNA gene profiling and metagenomics) to describe the prokaryotic community and its associated viruses. The diversity for Bacteria was very low and was vastly dominated by endospore formers related to Pontibacillus marinus of the Firmicutes phylum. The archaeal assemblage was more diverse and included taxa related to those normally found in hypersaline environments. Several ‘metagenome assembled genomes’ were recovered, corresponding to new species of Pontibacillus, several species from the Halobacteria and one new member of the Nanohaloarchaeota. The viral assemblage, although composed of the morphotypes typical of high salt systems, showed little similarity to previously isolated/reconstructed halophages. Several putative prophages of Pontibacillus and haloarchaeal hosts were identified. Remarkably, the Peñahueca sulfate‐rich metagenome contained CRISPR‐associated proteins and repetitions which were over 10‐fold higher than in most hypersaline systems analysed so far.


https://doi.org/10.1038/s41598-019-51784-8

The molecular form of nitrogen, N2, is universally available but is biochemically inaccessible for life due to the strength of its triple bond. Prior to the emergence of life, there must have been an abiotic process that could fix nitrogen in a biochemically usable form. The UV photo-catalytic effects of minerals such as pyrite on nitrogen fixation have to date been overlooked. Here we show experimentally, using X-ray photoemission and infrared spectroscopies that, under a standard earth atmosphere containing nitrogen and water vapour at Earth or Martian pressures, nitrogen is fixed to pyrite as ammonium iron sulfate after merely two hours of exposure to 2,3 W/m 2 of ultraviolet irradiance in the 200–400 nm range. Our experiments show that this process exists also in the absence of UV, although about 50 times slower. The experiments also show that carbonates species are fixed on pyrite surface.

Matiasek, S.J., Hernes, P.J., 2019. The chemical fingerprint of solubilized organic matter from eroded soils and sediments. Geochimica et Cosmochimica Acta 267, 92-112.


Organic matter (OM) transfers between solid and water phases are critical components of OM cycling in surface waters as they contribute to compositional differences between dissolved OM (DOM) and particulate OM (POM). However, fractionation effects during such phase changes are not well-characterized, especially during the release of soluble OM from sediments and eroded soils. Agricultural practices alter the magnitude and timing of OM export and constitute a major source of sediment through soil erosion. This study assessed the elemental, biomolecular, and optical characteristics of DOM solubilized from sediments and soils in an agricultural watershed of northern California to trace compositional changes during OM flow from mobilized soils in streams. Relative to mineral-bound OM, solubilized DOM was nitrogen-poor (more than doubled C:N ratios) and depleted in amino acids and lignin (three- to six-fold decrease in carbon-normalized yields). Distinct fractionation patterns of individual amino acids and lignin phenols led to a more acidic pool of solubilized DOM that appeared substantially more degraded than its source POM, with decreased degradation index (DI) values and more than doubled molar contributions of non-protein amino acids and processing ratio (PR) values. Lignin composition also greatly differed in solubilized DOM compared to mineral-bound OM, with cinnamyl:vanillyl phenol ratios up to six-fold lower in solubilized lignin than in particulate lignin. Solubilized DOM generally resembled stream DOM more than its source POM and was chemically distinguishable from DOM leached from plants. Absorption coefficients and fluorescence peak intensities were strongly correlated with solubilized DOM concentrations and composition, while optical parameters established to characterize DOM origin and reactivity such as spectral slope, fluorescence index, and carbon-specific fluorescence intensities suggested unique compositional traits for solubilized DOM compared to stream DOM. This study therefore documented strong fractionation patterns during solubilization, linking eroded soil OM and stream DOM and highlighting a pathway that can account for compositional differences between DOM and POM in surface waters. A new amino acid parameter, the Solubilization Index (SI), was defined to capture the effects of solubilization processes on OM composition. SI values in solubilized DOM were up to an order of magnitude higher than in its source POM and were similar to SI values in stream DOM. Because the SI is based on empirical behaviors of individual amino acids, each tied

to mechanistic interpretations, the SI is demonstrating a strong potential for mechanistic-driven research on the extent of phase changes in streamwater DOM.

Mazzini, A., Lupi, M., Sciarra, A., Hammed, M., Schmidt, S.T., Suessenberger, A., 2019. Concentric structures and hydrothermal venting in the Western Desert, Egypt. Frontiers in Earth Science 7, 266. doi: 10.3389/feart.2019.00266.

https://www.frontiersin.org/article/10.3389/feart.2019.00266

Large-scale concentric structures are enigmatic geological features observed on the Earth surface and on other planetary bodies. Their formation has been attributed to several processes. Here we describe for the first time the results of mapping and characterization of ∼100 large concentric circular structures found in Early Cenomanian argillaceous strata of the Bahariya depression (Egyptian Western Desert). The geological processes that lead to the formation of these features have remained so far elusive. We investigate the concentric structures with a multidisciplinary approach combining field observations, statistical analysis, soil-flux gas measurements and laboratory analyses of rock samples. The whole depression is dissected by the ∼90 km long N60°E-striking dextral strike-slip Bahariya fault. Effusive lavas and shallow intrusions crop out in the down faulted blocks. The mapped circular structures increase in number approaching the fault zone. These features are up to 10 m high and 625 m wide, have a morphology similar in shape to impact craters with steeper external flanks and a gently dipping internal subsided zone. Halite-cemented brecciated sediments from different geological units have been sampled in the central part of the concentric circular structures implying a subsurface mechanism involved in their formation. Petrography analyses revealed also the presence of high- and low-temperature minerals (e.g., Ba-K-feldspars and ferroaluminoceladonite) suggesting former phases of hydrothermal circulation. Soil-gas flux profiles (CO2 and CH4) reveal a modest CO2 increase when crossing the central part of the circular structures inferring enhanced permeability. Field and laboratory data are consistent with a scenario envisaging a diffused and vigorous hydrothermal venting. The proposed scenario includes multiple phases where several geological elements and processes interact. The Bahariya fault, which activity initiated during the Late Cretaceous, provided pathways for Miocene magma ascent toward the surface and for the development of a network of subsurface intrusions in the organic-rich sedimentary rocks of the Bahariya Formation. The interaction of the igneous intrusions with carbon-rich sedimentary deposits produced overpressured fluids, causing the formation of sparse hydrothermal vents at the surface. The elongation of the main axis of the vents and the deformed structures located within the strike-slip zone suggest that faulting controlled the emplacement and the final shape of some of the hydrothermal vents. We speculate that this system may represent a palaeo sediment-hosted hydrothermal system and could be related to the opening of the Red Sea.

McAdams, B.C., Carter, K.E., Blotevogel, J., Borch, T., Hakala, J.A., 2019. In situ transformation of hydraulic fracturing surfactants from well injection to produced water. Environmental Science: Processes & Impacts 21, 1777-1786.

http://dx.doi.org/10.1039/C9EM00153K

Chemical changes to hydraulic fracturing fluids (HFFs) within fractured unconventional reservoirs may affect hydrocarbon recovery and, in turn, the environmental impact of unconventional oil and gas development. Ethoxylated alcohol surfactants, which include alkyl ethoxylates (AEOs) and polyethylene glycols (PEGs), are often present in HFF as solvents, non-emulsifiers, and corrosion inhibitors. We present detailed analysis of polyethoxylates in HFF at the time of injection into three hydraulically fractured Marcellus Shale wells and in the produced water returning to the surface.

Despite the addition of AEOs to the injection fluid during almost all stages, they were rarely detected in the produced water. Conversely, while PEGs were nearly absent in the injection fluid, they were the dominant constituents in the produced water. Similar numbers of ethoxylate units support downhole transformation of AEOs to PEGs through central cleavage of the ethoxylate chain from the alkyl group. We also observed a decrease in the average ethoxylate (EO) number of the PEG–EOs in the produced water over time, consistent with biodegradation during production. Our results elucidate an overlooked surfactant transformation pathway that may affect the efficacy of HFF to maximize oil and gas recovery from unconventional shale reservoirs.

McFarlin, J.M., Axford, Y., Masterson, A.L., Osburn, M.R., 2019. Calibration of modern sedimentary δ2H plant wax-water relationships in Greenland lakes. Quaternary Science Reviews 225, 105978.


Sedimentary plant wax distributions and isotopic compositions are powerful, widely applied paleoenvironmental proxies. However, there is conflicting evidence on the behavior of these proxies at high-latitude sites, where extreme climate and light conditions may uniquely influence plant physiology and growth. Here, we present modern sedimentary n-alkane and n-alkanoic acid abundances and compound-specific (δ2H and δ13C) isotope values from a 22-lake transect extending from northwest to southernmost Greenland, covering a large latitudinal and climatic gradient. Sedimentary plant waxes are similar in abundance and carbon isotopic composition across the transect, suggesting no major differences in biologic sources. There are strong correlations (r = 0.8–0.9) between δ2H values of many long-chain sedimentary waxes and those of modelled precipitation, with n-alkanes more tightly correlated to precipitation than n-alkanoic acids. Data presented here also demonstrate that δ2H values of mid-chain sedimentary waxes do not strongly correlate to the δ2H values of lake water when it decouples isotopically from precipitation (i.e. in glacier-fed and evaporatively-enriched lakes). This calls into question the common interpretation that mid-chain sedimentary waxes can be ascribed to aquatic plants. We contextualize our Greenland data with an updated global dataset of δ2H values of modern sedimentary waxes and precipitation. This update adds 100 + lakes from recently published literature to the seminal review presented by Sachse et al. (2012). This large new compilation suggests a global average apparent fractionation including Arctic data between n-C28 alkanoic acids and annual precipitation (εC28/ANN) of −99‰, and between n-C29 alkanes and annual precipitation (εC29/ANN) of −121‰. The latter value is remarkably consistent with the value first reported by Sachse et al. (2012).



On multimillion-year timescales, outgassing from the Earth's interior provides the principal source of CO2 to the ocean–atmosphere system, which plays a fundamental role in shaping the Earth's baseline climate. Fluctuations in global outgassing have been linked to icehouse–greenhouse transitions, although uncertainties surround paleo-outgassing fluxes. Here, we discuss how volcanic outgassing and the carbon cycle have evolved in concert with changes in plate tectonics and biotic evolution. We describe hypotheses of driving mechanisms for the Paleozoic icehouse–greenhouse climates and explore how climatic transitions may have influenced past biotic crises and, in particular, how variable outgassing rates established the backdrop for carbon cycle perturbations to instigate prominent mass extinction events.

McLoughlin, N., Grosch, E.G., Vullum, P.E., Guagliardo, P., Saunders, M., Wacey, D., 2019. Critically testing olivine-hosted putative martian biosignatures in the Yamato 000593 meteorite—Geobiological implications. Geobiology 17, 691-707.


On rocky planets such as Earth and Mars the serpentinization of olivine in ultramafic crust produces hydrogen that can act as a potential energy source for life. Direct evidence of fluid–rock interaction on Mars comes from iddingsite alteration veins found in martian meteorites. In the Yamato 000593 meteorite, putative biosignatures have been reported from altered olivines in the form of microtextures and associated organic material that have been compared to tubular bioalteration textures found in terrestrial sub‐seafloor volcanic rocks. Here, we use a suite of correlative, high‐sensitivity, in situ chemical, and morphological analyses to characterize and re‐evaluate these microalteration textures in Yamato 000593, a clinopyroxenite from the shallow subsurface of Mars. We show that the altered olivine crystals have angular and micro‐brecciated margins and are also highly strained due to impact‐induced fracturing. The shape of the olivine microalteration textures is in no way comparable to microtunnels of inferred biological origin found in terrestrial volcanic glasses and dunites, and rather we argue that the Yamato 000593 microtextures are abiotic in origin. Vein filling iddingsite extends into the olivine microalteration textures and contains amorphous organic carbon occurring as bands and sub‐spherical concentrations <300 nm across. We propose that a martian impact event produced the micro‐brecciated olivine crystal margins that reacted with subsurface hydrothermal fluids to form iddingsite containing organic carbon derived from abiotic sources. These new data have implications for how we might seek potential biosignatures in ultramafic rocks and impact craters on both Mars and Earth.

Meador, J.P., Nahrgang, J., 2019. Characterizing crude oil toxicity to early-life stage fish based on a complex mixture: Are we making unsupported assumptions? Environmental Science & Technology 53, 11080-11092.


Numerous studies of the water-soluble fraction (WSF) from crude oil have concluded that polycyclic aromatic hydrocarbons (PAHs) are the primary causative agents for early life stage (ELS) fish toxicity. Noteworthy is the lack of studies demonstrating that the sum of PAHs are capable of causing toxic effects in ELS fish at the low levels claimed (0.1–5 μg/L) without being part of a complex crude oil mixture. Crude oil and the WSF are composed of thousands of other compounds that co-occur and likely contribute to crude oil toxicity. Based on the available data, it appears that the syndrome of effects (lower heart rate, edemas, and morphological abnormalities) for ELS fish exposed to the aqueous fraction of a crude oil mixture is commonly observed in studies exposing fish embryos to high concentrations of a variety of compounds and may be a nonspecific response. We conclude that the available data support the hypothesis that this syndrome of effects is likely the result of baseline toxicity (not receptor based) due to membrane disruption and resulting alteration in ion (e.g., calcium and potassium) homeostasis. We acknowledge the possibility of some compounds in the WSF capable of causing a specific receptor based toxicity response to ELS fish; however, such compounds have not been identified nor their receptor characterized. Concluding that PAHs are the main toxic compounds for crude oil exposure is misleading and does not result in guideline values that can be useful for environmental protection. Water quality guidelines for any single chemical or suite of chemicals must be based on a complete understanding of exposure concentrations, mechanism of action, potency, and resulting response. This review focuses on the toxic effects reported for fish embryos and the purported toxic concentrations observed in the aqueous phase of an oil/water mixture, the known levels of toxicity for individual PAHs, a toxic unit approach for characterizing

mixtures, and the potential molecular initiating event for ELS toxicity in fish. This review also has implications for a large number of studies exposing ELS fish to a variety of compounds at high concentrations that result in a common baseline toxic response.

Mehta, N., Kocar, B.D., 2019. Geochemical conditions conducive for retention of trace elements and radionuclides during shale–fluid interactions. Environmental Science: Processes & Impacts 21, 1764-1776.

http://dx.doi.org/10.1039/C9EM00244H

Produced water generated during unconventional oil and gas extractions contains a complex milieu of natural and anthropogenic potentially toxic chemical constituents including arsenic (As), chromium (Cr), and cadmium (Cd), naturally occurring radioactive materials (NORMs) including U and Ra, and a myriad of organic compounds. The human-ecological health risks and challenges associated with the disposal of produced water may be alleviated by understanding geochemical controls on processes responsible for the solubilization of potentially hazardous natural shale constituents to produced water. Here, we investigated, through a series of batch treatments, the leaching behavior of As, Se, Cu, Fe, Ba, Cr, Cd, and radioactive nuclides U, Ra from shale to produced water. Specifically, the effect of four major controls on element mobility was studied: (1) solution pH, (2) ionic strength of the solution, (3) oxic–anoxic conditions, and (4) an additive used in fracking fluid. The mobilization of metals and metalloids from shale was greatest in treatments containing sodium persulfate, an oxidant and a commonly used additive in fracture fluid. In the high ionic strength treatments, dissolved Ba concentrations increased 5-fold compared to low ionic strength treatments. Overall, anoxic conditions superimposed with low pH resulted in the largest increase of dissolved metals and radionuclides such as Ra. Overall, our results suggest that (1) limiting pore water acidification by injection of alkaline fluid in carbonate-low shale and (2) minimizing strong oxidizing conditions in shale formations may result in cost-effective in situ retention of produced water contaminants.



There is increasing evidence that aqueous-phase atmospheric chemistry is an important source of secondary organic aerosols (SOA), but this chemistry is currently not adequately represented in atmospheric models due to the missing information on most products. The main focus of this study is to provide molecular-level insight into the photosensitized reaction mechanism of pyruvic acid (PA) alone in the atmospheric aqueous phase, and of mixtures of PA with glyoxal (GL), a typical and widely occurring carbonyl compound. With two ultrahigh resolution mass spectrometers, ORBITRAP and FT-ICR-MS, a broad and complex spectrum of organic products were unambiguously identified. The detected formation of organic compounds illustrates the progression from C3 to C20 molecules through direct PA photolysis and irradiation of PA + GL. The performed ab-initio calculations indicate that cross-reactions (i.e., PA + GL) are more likely than self-reactions (i.e., PA alone) in clouds and aerosol deliquescent particles. Hence, this result implies that photosensitizers like PA can initiate the transformation of common organic cloud constituents like GL into highly oxygenated multifunctional compounds. These high-molecular- weight compounds that are formed in significant amount could potentially impact optical and cloud-forming properties of aerosols, especially if they partition to the aerosol surface.

Mikhail, S., Füri, E., 2019. On the origin(s) and evolution of Earth's carbon. Elements 15, 307-312.


The isotopic “flavor” of Earth's major volatiles, including carbon, can be compared to the known reservoirs of volatiles in the solar system and so determine the source of Earth's carbon. This requires knowing Earth's bulk carbon isotope value, which is not straightforward to determine. During Earth's differentiation, carbon was partitioned into the core, mantle, crust, and atmosphere. Therefore, although carbon is omnipresent within the Earth system, scientists have yet to determine its distribution and relative abundances. This article addresses what we know of the processes involved in the formation of Earth's carbon reservoirs, and, by deduction, what we know about the possible origins of Earth's carbon.

Minto, J.M., Lunn, R.J., El Mountassir, G., 2019. Development of a reactive transport model for field-scale simulation of microbially induced carbonate precipitation. Water Resources Research 55, 7229-7245.

https://doi.org/10.1029/2019WR025153

Microbially induced carbonate precipitation (MICP) is a promising technique that could be used for soil stabilization, for permeability control in porous and fractured media, for sealing leaky hydrocarbon wells, and for immobilizing contaminants. Many further field trials are required before optimum treatment strategies can be established. These field trials will be costly and time consuming to \carry out and are currently a barrier to transitioning MICP from a lab-scale process to a practical field-scale deployable technology. To narrow down the range of potential treatment options into a manageable number, we present a field-scale reactive transport model of MICP that captures the key processes of bacteria transport and attachment, urea hydrolysis, tractable CaCO3 precipitation, and modification to the porous media in terms of porosity and permeability. The model, named biogroutFoam, is implemented in OpenFOAM, and results are presented for MICP treatment in a planar fracture, three-dimensional sand media at pore scale, and at continuum scale for an array of nine injection/abstraction wells. Results indicate that it is necessary to model bacterial attachment, that bacterial attachment should be a function of fluid velocity, and that phased injection strategies may lead to the most uniform precipitation in a porous media.


https://doi.org/10.1134/S0965544119100074

The presented review considers the currently relevant methods for studying petroleum porphyrins. For this purpose, the experimental approaches used during the investigation of the structure, concentration, and properties of metal complexes of petroleum porphyrins and their free bases are systematized, and the capabilities and limitations of the used methods (mass spectrometric, spectroscopic (electron paramagnetic resonance, UV–visible electronic absorption spectroscopy, and X-ray techniques) as well as high-performance and gel penetration liquid chromatography) are discussed. Published approaches to the concentration, fractionation, and purification of petroleum porphyrins based on the extraction and chromatographic methods of recovery of chemical compounds from complex multicomponent mixtures are also analyzed.



Viscosity model is important for the simulation of flow and recovery behaviour of different hydrocarbon systems. Various semi-theoretical models such as Friction-Theory and cubic Equation of State-based models have been found satisfactory for lighter crudes. However, for heavier hydrocarbon systems e.g. heavy oils, bitumens, these models are not reliable; one possible reason is that they are not reliable for heavier components. The objective of this research is to develop a viscosity model sensitive to molar mass and density of components and a mixture of hydrocarbons.

In this work, a Cubic Equation of Viscosity model where P-ρ-T form of cubic equation (Abbott, 1973) is converted into P-μ-T form of cubic equation, is developed with desired sensitivity to density and molar mass. The model requires three parameters, which are optimized by viscosity data matching. Separate sets of parameters are developed for hydrocarbon groups such as paraffins, naphthenes, and aromatics. Viscosity estimation for mixture requires mixing of the parameters and not the viscosity values of individual components.

The carbon number of heaviest component used in the model is 64. The P-μ-T viscosity model has AARD of 2.91%, 3.06% and 5.68% for paraffins, naphthenes, and aromatics respectively in comparison of 33.95%, 19.6%, and 48.9% from T-μ-P (Guo et al., 2001) model. Friction Theory (Quinones-Cisneros et al., 2000) based model results in 26.38% AARD for paraffins. For 19 paraffinic mixtures, AARD from P-μ-T is 5.56% in comparison to 29% from T-μ-P (Guo et al., 2001) model and 316% from Friction Theory (Quinones-cisneros et al., 2000) model.

Mißbach, H., Steininger, H., Thiel, V., Goetz, W., 2019. Investigating the effect of perchlorate on flight-like gas chromatography–mass spectrometry as performed by MOMA on board the ExoMars 2020 rover. Astrobiology 19, 1339-1352.

https://doi.org/10.1089/ast.2018.1997

The Mars Organic Molecule Analyzer (MOMA) instrument on board ESA's ExoMars 2020 rover will be essential in the search for organic matter. MOMA applies gas chromatography–mass spectrometry (GC-MS) techniques that rely on thermal volatilization. Problematically, perchlorates and chlorates in martian soils and rocks become highly reactive during heating (>200°C) and can lead to oxidation and chlorination of organic compounds, potentially rendering them unidentifiable. Here, we analyzed a synthetic sample (alkanols and alkanoic acids on silica gel) and a Silurian chert with and without Mg-perchlorate to evaluate the applicability of MOMA-like GC-MS techniques to different sample types and assess the impact of perchlorate. We used a MOMA flight analog system coupled to a commercial GC-MS to perform MOMA-like pyrolysis, in situ derivatization, and in situ thermochemolysis. We show that pyrolysis can provide a sufficient overview of the organic inventory but is strongly affected by the presence of perchlorates. In situ derivatization facilitates the identification of functionalized organics but showed low efficiency for n-alkanoic acids. Thermochemolysis is shown to be an effective technique for the identification of both refractory and functional compounds. Most importantly, this technique was barely affected by perchlorates. Therefore, MOMA GC-MS analyses of martian surface/subsurface material may be less affected by perchlorates than commonly thought, in particular when applying the full range of available MOMA GC-MS techniques.

Mitzscherling, J., Horn, F., Winterfeld, M., Mahler, L., Kallmeyer, J., Overduin, P.P., Schirrmeister, L., Winkel, M., Grigoriev, M.N., Wagner, D., Liebner, S., 2019. Microbial community composition and abundance after millennia of submarine permafrost warming. Biogeosciences 16, 3941-3958.


Warming of the Arctic led to an increase in permafrost temperatures by about 0.3 ∘C during the last decade. Permafrost warming is associated with increasing sediment water content, permeability, and diffusivity and could in the long term alter microbial community composition and abundance even before permafrost thaws. We studied the long-term effect (up to 2500 years) of submarine permafrost warming on microbial communities along an onshore–offshore transect on the Siberian Arctic Shelf displaying a natural temperature gradient of more than 10 ∘C. We analysed the in situ development of bacterial abundance and community composition through total cell counts (TCCs), quantitative PCR of bacterial gene abundance, and amplicon sequencing and correlated the microbial community data with temperature, pore water chemistry, and sediment physicochemical parameters. On timescales of centuries, permafrost warming coincided with an overall decreasing microbial abundance, whereas millennia after warming microbial abundance was similar to cold onshore permafrost. In addition, the dissolved organic carbon content of all cores was lowest in submarine permafrost after millennial-scale warming. Based on correlation analysis, TCC, unlike bacterial gene abundance, showed a significant rank-based negative correlation with increasing temperature, while bacterial gene copy numbers showed a strong negative correlation with salinity. Bacterial community composition correlated only weakly with temperature but strongly with the pore water stable isotopes δ18O and δD, as well as with depth. The bacterial community showed substantial spatial variation and an overall dominance of Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadetes, and Proteobacteria, which are amongst the microbial taxa that were also found to be active in other frozen permafrost environments. We suggest that, millennia after permafrost warming by over 10 ∘C, microbial community composition and abundance show some indications for proliferation but mainly reflect the sedimentation history and paleoenvironment and not a direct effect through warming.



Gas chromatography-mass spectrometry (GC-MS) and comprehensive two-dimensional gas chromatography-mass spectrometry (GC×GC-MS) are powerful techniques for measurement of all metabolites in complex metabolic samples. However, analyzing GC-MS and especially GC×GC-MS metabolomic data is a major challenge to the researchers in the field of metabolomics mainly due to the complexity and large data size. In this regard, an automated R based software entitled RMet has been developed to overcome the challenges in the metabolomic analysis workflow of GC-MS and GC×GC-MS data sets. Additionally, it is able to facilitate the complex process of extracting reliable and useful biological information from these data sets. Moreover, RMet can greatly accelerate the time-consuming data analysis process of large GC-MS and GC×GC-MS datasets by the means of modern chemometric methods. In fact, RMet transforms raw GC-MS and GC×GC-MS data files into the elution profiles and mass spectra of important (significantly affected metabolites) which can be imported into NIST MS search software for the final identification of these metabolites. To show the performance of the developed software, large GC×GC-MS data sets of a previously reported environmental metabolomics study on lettuce samples exposed to contaminants of emerging concerns (CECs) were analyzed by RMet. The procedure for analyzing GC-MS metabolic data with RMet is as same as GC×GC-MS data sets but some steps can be skipped due to the lower size of GC-MS data

sets. The software, its manual, sample data sets and source code are freely available on https://github.com/SUTChemometricsGroup/RMet.

Moeller, F.U., Webster, N.S., Herbold, C.W., Behnam, F., Domman, D., Albertsen, M., Mooshammer, M., Markert, S., Turaev, D., Becher, D., Rattei, T., Schweder, T., Richter, A., Watzka, M., Nielsen, P.H., Wagner, M., 2019. Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta. Environmental Microbiology 21, 3831-3854.

https://doi.org/10.1111/1462-2920.14732

Marine sponges represent one of the few eukaryotic groups that frequently harbour symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia‐oxidizers in many environments. However, in most studies, direct demonstration of ammonia‐oxidation by these archaea within sponges is lacking, and little is known about sponge‐specific adaptations of ammonia‐oxidizing archaea (AOA). Here, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and isotope‐based functional assays. ‘Candidatus Nitrosospongia ianthellae’ is only distantly related to cultured AOA. It is an abundant symbiont that is solely responsible for nitrite formation from ammonia in I. basta that surprisingly does not harbour nitrite‐oxidizing microbes. Furthermore, this AOA is equipped with an expanded set of extracellular subtilisin‐like proteases, a metalloprotease unique among archaea, as well as a putative branched‐chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge‐associated, but not in free‐living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic‐like proteins, and a DNA‐phosporothioation system, represent important adaptations of AOA to life within these ancient filter‐feeding animals.

Mohammadi, M., Mahani, H., 2020. Direct insights into the pore-scale mechanism of low-salinity waterflooding in carbonates using a novel calcite microfluidic chip. Fuel 260, 116374.


One of the key open questions in the area of low or controlled salinity water flooding (LSWF or CSWF) is how the observed oil recovery at macro-scale (e.g. Darcy or core-scale) can the explained and what underlying microscopic mechanisms drive it. Thus far, the micromodel investigation of LSWF has been limited to sandstones, remaining challenging to apply to carbonates. In this paper we aim to i) extend the capability to fabricate a novel calcite micromodel using Iceland spar calcite crystal, ii) investigate the pore-scale mechanisms leading to oil recovery from carbonates.

A target crude oil-brine-rock (COBR) system was first selected. To screen potential brines which can produce low-salinity-effect (LSE) and to guide the design of the micromodel experiments, contact angle measurements were carried out using two methods: i) contact angle under fixed, and ii) under dynamic salinity condition. The micromodel displacement experiments were then performed by flooding an oil saturated model with high salinity water followed by low salinity water injection to displace the high salinity water and observe any potential changes to the configuration and saturation of the residual oil. Additionally, the effect of connate water presence on the efficiency of LSE was investigated. To account for the time effects of the low salinity process, the experiments were monitored for an extended time period in order of several days to a month.

For the COBR system studied in the micromodel, the results clearly show that when brine salinity is lowered the microscopic sweep efficiency is improved; providing a direct in-situ evidence for wettability alteration to a more water-wetting state. The presence of connate water enhanced the efficiency of LSWF both in terms of speed (time-scale) and quantity of oil recovery. It is postulated that in the presence of connate water an initial water-film around the calcite surface is present which facilitates the diffusive transport of brine ions when low salinity is injected. Thus it is favorable to have an initial water film present; a case for mixed-wettability. We observed that the oil production was non-instantaneous characterized by a prolonged induction time and a slow “layer-by-layer” recovery either from the pore body or throat wall; a process we refer to as “peel-off”. Before the oil can be removed from the calcite surface, de-wetting (or de-pinning) patterns were formed which grew and coalesced toward formation of a clearly visible larger pattern. Ultimately, the remaining oil under low salinity was comparatively much less compared to the end of high salinity step.

The observed mechanism of the oil recovery and the slow associated time have direct implications for the pore-scale simulation of the process and upscaling to Darcy-scale, and the design of laboratory experiments to avoid false negative results. They would also likely imply lack of a clear oil-bank observation at core scale.

Mohr, C., Thornton, J.A., Heitto, A., Lopez-Hilfiker, F.D., Lutz, A., Riipinen, I., Hong, J., Donahue, N.M., Hallquist, M., Petäjä, T., Kulmala, M., Yli-Juuti, T., 2019. Molecular identification of organic vapors driving atmospheric nanoparticle growth. Nature Communications 10, 4442.

https://doi.org/10.1038/s41467-019-12473-2

Particles formed in the atmosphere via nucleation provide about half the number of atmospheric cloud condensation nuclei, but in many locations, this process is limited by the growth of the newly formed particles. That growth is often via condensation of organic vapors. Identification of these vapors and their sources is thus fundamental for simulating changes to aerosol-cloud interactions, which are one of the most uncertain aspects of anthropogenic climate forcing. Here we present direct molecular-level observations of a distribution of organic vapors in a forested environment that can explain simultaneously observed atmospheric nanoparticle growth from 3 to 50 nm. Furthermore, the volatility distribution of these vapors is sufficient to explain nanoparticle growth without invoking particle-phase processes. The agreement between observed mass growth, and the growth predicted from the observed mass of condensing vapors in a forested environment thus represents an important step forward in the characterization of atmospheric particle growth.

Moore, C.R., Brooks, M.J., Goodyear, A.C., Ferguson, T.A., Perrotti, A.G., Mitra, S., Listecki, A.M., King, B.C., Mallinson, D.J., Lane, C.S., Kapp, J.D., West, A., Carlson, D.L., Wolbach, W.S., Them, T.R., Harris, M.S., Pyne-O’Donnell, S., 2019. Sediment cores from White Pond, South Carolina, contain a platinum anomaly, pyrogenic carbon peak, and coprophilous spore decline at 12.8 ka. Scientific Reports 9, 15121.

https://doi.org/10.1038/s41598-019-51552-8

A widespread platinum (Pt) anomaly was recently documented in Greenland ice and 11 North American sedimentary sequences at the onset of the Younger Dryas (YD) event (~12,800 cal yr BP), consistent with the YD Impact Hypothesis. We report high-resolution analyses of a 1-meter section of a lake core from White Pond, South Carolina, USA. After developing a Bayesian age-depth model that brackets the late Pleistocene through early Holocene, we analyzed and quantified the following: (1) Pt and palladium (Pd) abundance, (2) geochemistry of 58 elements, (3) coprophilous spores, (4)

sedimentary organic matter (OC and sedaDNA), (5) stable isotopes of C (δ13C) and N (δ15N), (6) soot, (7) aciniform carbon, (8) cryptotephra, (9) mercury (Hg), and (10) magnetic susceptibility. We identified large Pt and Pt/Pd anomalies within a 2-cm section dated to the YD onset (12,785 ± 58 cal yr BP). These anomalies precede a decline in coprophilous spores and correlate with an abrupt peak in soot and C/OC ratios, indicative of large-scale regional biomass burning. We also observed a relatively large excursion in δ15N values, indicating rapid climatic and environmental/hydrological changes at the YD onset. Our results are consistent with the YD Impact Hypothesis and impact-related environmental and ecological changes.



While coalbed methane (CBM) is a significant source of natural gas production globally, uncertainties regarding the proportions of biogenic and thermogenic natural gas in CBM reservoirs still remain. We integrate major gases, hydrocarbon composition, hydrocarbon stable isotopes and noble gases in fluids from 20 producing CBM wells to more accurately constrain the genetic source of natural gases in the eastern Illinois Basin, USA. Previous studies have indicated primarily biogenic production of methane (>99.6%) with negligible contributions from thermogenic natural gases. However, by integrating noble gases, we identify quantifiable (up to 19.2%) contributions of exogenous thermogenic gas in produced gases from the Seelyville and Springfield coal seams. Thermogenic gases are distinguished by a positive relationship between methane, ethane and helium-4, lower C1/C2+, heavier δ13C-CH4, more radiogenic noble gases (4He, 21Ne*, 40Ar*), and lower abundances of atmospherically derived gases (20Ne, 36Ar). Biogenic gases displayed lighter δ13C-CH4, higher C1/C2+, higher levels of atmospheric gases and lower abundances of radiogenic noble gases. Our data suggest that natural gases from a deeper, exogenous thermogenic source likely migrated to the Pennsylvanian-aged coals at an unknown time and later mixed with biogenic methane diluting the geochemical signature of the thermogenic methane within the Springfield and Seelyville coal seams.

Moores, J.E., King, P.L., Smith, C.L., Martinez, G.M., Newman, C.E., Guzewich, S.D., Meslin, P.-Y., Webster, C.R., Mahaffy, P.R., Atreya, S.K., Schuerger, A.C., 2019. The methane diurnal variation and microseepage flux at Gale Crater, Mars as constrained by the ExoMars Trace Gas Orbiter and Curiosity observations. Geophysical Research Letters 46, 9430-9438.

https://doi.org/10.1029/2019GL083800

Abstract: The upper bound of 50 parts per trillion by volume for Mars methane above 5 km established by the ExoMars Trace Gas Orbiter, substantially lower than the 410 parts per trillion by volume average measured overnight by the Curiosity Rover, places a strong constraint on the daytime methane flux at the Gale crater. We propose that these measurements may be largely reconciled by the inhibition of mixing near the surface overnight, whereby methane emitted from the subsurface accumulates within meters of the surface before being mixed below detection limits at dawn. A model of this scenario allows the first precise calculation of microseepage fluxes at Gale to be derived, consistent with a constant 1.5 × 10−10 kg·m−2·sol−1 (5.4 × 10−5 tonnes·km−2·year−1) source at depth. Under this scenario, only 2.7 × 104 km2 of Mars's surface may be emitting methane, unless a fast destruction mechanism exists.

Plain Language Summary: The ExoMars Trace Gas Orbiter and the Curiosity Rover have recorded different amounts of methane in the atmosphere on Mars. The Trace Gas Orbiter measured very little methane (<50 parts per trillion by volume) above 5 km in the sunlit atmosphere, while Curiosity measured substantially more (410 parts per trillion by volume) near the surface at night. In this paper we describe a framework which explains both measurements by suggesting that a small amount of methane seeps out of the ground constantly. During the day, this small amount of methane is rapidly mixed and diluted by vigorous convection, leading to low overall levels within the atmosphere. During the night, convection lessens, allowing methane to build up near the surface. At dawn, convection intensifies and the near‐surface methane is mixed and diluted with much more atmosphere. Using this model and methane concentrations from both approaches, we are able—for the first time—to place a single number on the rate of seepage of methane at Gale crater which we find equivalent to 2.8 kg per Martian day. Future spacecraft measuring methane near the surface of Mars could determine how much methane seeps out of the ground in different locations, providing insight into what processes create that methane in the subsurface.



Anthropogenically-impacted environments offer the opportunity to discover novel microbial species and metabolisms, which may be undetectable in natural systems. Here, a combined metagenomic and geochemical study in Base Mine Lake, Alberta, Canada, which is the only oil sands end pit lake to date, revealed that nitrification was performed by members from Nitrosomonadaceae, Chloroflexi and unclassified Gammaproteobacteria “MBAE14.” While Nitrosomonadaceae and Chloroflexi groups were relatively abundant in the upper oxygenated zones, MBAE14 dominated the hypoxic hypolimnetic zones (approximately 30% of total microbial communities); MBAE14 was not detected in the underlying anoxic tailings. Replication rate analyses indicate that MBAE14 grew in metalimnetic and hypolimnetic water cap regions, most actively at the metalimnetic, ammonia/oxygen transition zone consistent with it putatively conducting nitrification. Detailed genomic analyses of MBAE14 evidenced both ammonia oxidation and denitrification into dinitrogen capabilities. However, the absence of known CO2-fixation genes suggests a heterotrophic denitrifying metabolism. Functional marker genes of ammonia oxidation (amo and hao) in the MBAE14 genome are homologous with those conserved in autotrophic nitrifiers, but not with those of known heterotrophic nitrifiers. We propose that this novel MBAE14 inhabits the specific ammonia-rich, oxygen and labile organic matter-limited conditions occurring in Base Mine Lake which selectively favors mixotrophic coupled nitrifier denitrification metabolism. Our results highlight the opportunities to better constrain biogeochemical cycles from the application of metagenomics to engineered systems associated with extractive resource sectors.

Morozova, A.V., Volkova, G.I., 2019. Effect of the petroleum resin structure on the properties of a petroleum-like system. Petroleum Chemistry 59, 1153-1160.

https://doi.org/10.1134/S0965544119100086

The structural group composition of benzene and alcohol–benzene petroleum resins used as modifying agents has been studied. Benzene resins are characterized by a higher content of naphthenic and aromatic structures and a smaller content of aliphatic moieties. The introduction of resins into a petroleum wax solution in n-decane leads to the suppression of the crystallization of

hydrocarbons (HCs) and contributes to a decrease in the structural, mechanical, and energy parameters of the system. The addition of benzene resins more effectively decreases the viscosity–temperature characteristics, i.e., leads to a substantial decrease in the viscosity, the activation energy for viscous flow, the specific energy of degradation of the disperse system, and the pour point.



A suite of biomarkers, including amino acids, pigments, and lignin phenols coupled with high resolution mass spectrometry were used to evaluate differences in the sources and fate of organic matter (OM) in Everglades treatment wetlands as a model for OM cycling in shallow water wetlands. Five components of the system (water column particulate matter, vertical traps, flocculent material, periphyton, and surface soil) were assessed for OM transformations down-profile (i.e. water column to soil) and between treatment cells dominated by emergent aquatic vegetation (EAV) and submerged aquatic vegetation (SAV), with comparisons to reference sites within the remnant Everglades. We found that OM cycling is fundamentally different between EAV and SAV wetlands, and that SAV wetlands have some shared characteristics with similar habitats in the remnant Everglades. Other than locations densely populated by Typha spp., water column particulate organic C was predominantly derived from microbial/cryptomonad sources, rather than macroscopic sources (vascular plants and algal mats). Bacterial amino acid biomarkers were positively correlated with amino acid degradation indices and organic P (Po), respectively suggesting that microbial abundance is associated with less degraded OM, and that further investigation into relationships between microbial biomass and Po is warranted. Overall, this multi-biomarker approach can elucidate the relative degradation of OM pools, identify sources of OM, and highlight the importance of water column processes in shallow water wetlands.

Mougel, B., Moynier, F., Koeberl, C., Wielandt, D., Bizzarro, M., 2019. Identification of a meteoritic component using chromium isotopic composition of impact rocks from the Lonar impact structure, India. Meteoritics & Planetary Science 54, 2592-2599.


The existence of mass‐independent chromium isotope variability of nucleosynthetic origin in meteorites and their components provides a means to investigate potential genetic relationship between meteorites and planetary bodies. Moreover, chromium abundances are depleted in most surficial terrestrial rocks relative to chondrites such that Cr isotopes are a powerful tool to detect the contribution of various types of extra‐terrestrial material in terrestrial impactites. This approach can thus be used to constrain the nature of the bolide resulting in breccia and melt rocks in terrestrial impact structures. Here, we report the Cr isotope composition of impact rocks from the ~0.57 Ma Lonar crater (India), which is the best‐preserved impact structure excavated in basaltic target rocks. Results confirm the presence of a chondritic component in several bulk rock samples of up to 3%. The impactor that created the Lonar crater had a composition that was most likely similar to that of carbonaceous chondrites, possibly a CM‐type chondrite.

Mukumoto, K., Tsuji, T., Hendriyana, A., 2019. Large gas reservoir along the rift axis of a continental back-arc basin revealed by automated seismic velocity analysis in the Okinawa Trough. Geophysical Research Letters 46, 9583-9590.

https://doi.org/10.1029/2019GL083065

Abstract: In the Okinawa Trough off southwestern Japan, hydrothermal circulation due to back‐arc rifting is active. Biogenic CH4 in discharging hydrothermal fluids at the Iheya North Knoll is derived from outside the knoll; however, the location of the gas reservoir has not been identified. Here, we applied automated velocity analysis to seismic reflection data to obtain a P wave velocity structure in high spatial resolution. The resulting profiles reveal large gas reservoirs as low‐velocity zones along the rifting axis (>5 km for axis direction) around the Iheya North Knoll. The main gaseous components in the reservoir could be CO2 and CH4. The heat flow inferred from seismic profiles (i.e., depth of reflector) indicates that CH4 hydrate could be trapping the gas. Furthermore, the heat flow is higher at the rifting axis and close to the knoll, reflecting the large gas reservoir feeding the hydrothermal fluids in the discharging area at the knoll.

Plain Language Summary: Magmatic activity in the middle Okinawa Trough region southwest of Japan gives rise to intense hydrothermal activity. Gases in the hot fluids discharging from the hydrothermal field at Iheya North Knoll consist mainly of biogenic CH4 originating from microbial activity and CO2. By applying high‐resolution automated velocity analysis to seismic reflection data, this study revealed widely distributed gas reservoirs as inferred from their low seismic velocities. Furthermore, our estimates of heat flow suggest that these gas reservoirs are capped by CH4 hydrate. If the main gas component is CH4, the gas reservoir may be a potential natural resource. If the gas includes CO2, the distribution of similar reservoirs is important because CO2 is the main contributor to global warming.

Muñoz Caro, G.M., Ciaravella, A., Jiménez-Escobar, A., Cecchi-Pestellini, C., González-Díaz, C., Chen, Y.-J., 2019. X-ray versus ultraviolet irradiation of astrophysical ice analogs leading to formation of complex organic molecules. ACS Earth and Space Chemistry 3, 2138-2157.


In astrochemistry, complex organic molecules (COMs) are defined as species with at least one C atom and six or more atoms in total. More than 70 COMs were detected toward various interstellar and circumstellar regions. With the exception of methanol, CH3OH, these COMs were only detected in the gas phase. But their sole existence challenges the scheme of gas-phase reactions and suggests a formation in ice covered dust grains or the ice–gas interface. Some COMs can be synthesized by surface reactions on dust, and other COMs seem to be indicative of energetic processing in the ice mediated by photons and cosmic rays. This work focuses on the formation of COMs in the ice driven by X-rays and ultraviolet photons. While the former should drive the chemistry in circumstellar environments of young stars, the latter start to dominate after about 100 Myr (million years) and are responsible for ice processing in interstellar dust. On the basis of our X-ray experiments of ice irradiation reported in the literature and new experiments on UV irradiation of ice samples of analog composition, a comparison of X-rays versus ultraviolet photon ice processing is presented here. Using infrared spectroscopy for the ice and mass spectrometry for the gas phase, pure/binary/ternary ice mixtures containing H2O, CO, or NH3 were studied. A wealth of COMs is made in the experimental simulations of ice analogs by both X-rays and UV photons. Among the COMs that result from ice photoprocessing are some of astrobiological interest that were confirmed in the UV irradiation of the H2O:CO:NH3 ice mixture, such as NH2CH2COOH (glycine), HCONH2 (formamide), or CH3CHO

(acetaldehyde), similar to those detected during the Rosetta mission in comet 67P/Churyumov–Gerasimenko.

Needham, D.M., Poirier, C., Hehenberger, E., Jiménez, V., Swalwell, J.E., Santoro, A.E., Worden, A.Z., 2019. Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes. Philosophical Transactions of the Royal Society B: Biological Sciences 374, 20190086.

https://doi.org/10.1098/rstb.2019.0086

Giant viruses have remarkable genomic repertoires—blurring the line with cellular life—and act as top–down controls of eukaryotic plankton. However, to date only six cultured giant virus genomes are available from the pelagic ocean. We used at-sea flow cytometry with staining and sorting designed to target wild predatory eukaryotes, followed by DNA sequencing and assembly, to recover novel giant viruses from the Pacific Ocean. We retrieved four ‘PacV’ partial genomes that range from 421 to 1605 Kb, with 13 contigs on average, including the largest marine viral genomic assembly reported to date. Phylogenetic analyses indicate that three of the new viruses span a clade with deep-branching members of giant Mimiviridae, incorporating the Cafeteria roenbergensis virus, the uncultivated terrestrial Faunusvirus, one PacV from a choanoflagellate and two PacV with unclear hosts. The fourth virus, oPacV-421, is phylogenetically related to viruses that infect haptophyte algae. About half the predicted proteins in each PacV have no matches in NCBI nr (e-value < 10−5), totalling 1735 previously unknown proteins; the closest affiliations of the other proteins were evenly distributed across eukaryotes, prokaryotes and viruses of eukaryotes. The PacVs encode many translational proteins and two encode eukaryotic-like proteins from the Rh family of the ammonium transporter superfamily, likely influencing the uptake of nitrogen during infection. cPacV-1605 encodes a microbial viral rhodopsin (VirR) and the biosynthesis pathway for the required chromophore, the second finding of a choanoflagellate-associated virus that encodes these genes. In co-collected metatranscriptomes, 85% of cPacV-1605 genes were expressed, with capsids, heat shock proteins and proteases among the most highly expressed. Based on orthologue presence–absence patterns across the PacVs and other eukaryotic viruses, we posit the observed viral groupings are connected to host lifestyles as heterotrophs or phototrophs.

Needham, D.M., Yoshizawa, S., Hosaka, T., Poirier, C., Choi, C.J., Hehenberger, E., Irwin, N.A.T., Wilken, S., Yung, C.-M., Bachy, C., Kurihara, R., Nakajima, Y., Kojima, K., Kimura-Someya, T., Leonard, G., Malmstrom, R.R., Mende, D.R., Olson, D.K., Sudo, Y., Sudek, S., Richards, T.A., DeLong, E.F., Keeling, P.J., Santoro, A.E., Shirouzu, M., Iwasaki, W., Worden, A.Z., 2019. A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators. Proceedings of the National Academy of Sciences 116, 20574-20583.


Significance: Although viruses are well-characterized regulators of eukaryotic algae, little is known about those infecting unicellular predators in oceans. We report the largest marine virus genome yet discovered, found in a wild predatory choanoflagellate sorted away from other Pacific microbes and pursued using integration of cultivation-independent and laboratory methods. The giant virus encodes nearly 900 proteins, many unlike known proteins, others related to cellular metabolism and organic matter degradation, and 3 type-1 rhodopsins. The viral rhodopsin that is most abundant in ocean metagenomes, and also present in an algal virus, pumps protons when illuminated, akin to cellular rhodopsins that generate a proton-motive force. Giant viruses likely provision multiple host species with photoheterotrophic capacities, including predatory unicellular relatives of animals.

Abstract: Giant viruses are remarkable for their large genomes, often rivaling those of small bacteria, and for having genes thought exclusive to cellular life. Most isolated to date infect nonmarine protists, leaving their strategies and prevalence in marine environments largely unknown. Using eukaryotic single-cell metagenomics in the Pacific, we discovered a Mimiviridae lineage of giant viruses, which infects choanoflagellates, widespread protistan predators related to metazoans. The ChoanoVirus genomes are the largest yet from pelagic ecosystems, with 442 of 862 predicted proteins lacking known homologs. They are enriched in enzymes for modifying organic compounds, including degradation of chitin, an abundant polysaccharide in oceans, and they encode 3 divergent type-1 rhodopsins (VirR) with distinct evolutionary histories from those that capture sunlight in cellular organisms. One (VirRDTS) is similar to the only other putative rhodopsin from a virus (PgV) with a known host (a marine alga). Unlike the algal virus, ChoanoViruses encode the entire pigment biosynthesis pathway and cleavage enzyme for producing the required chromophore, retinal. We demonstrate that the rhodopsin shared by ChoanoViruses and PgV binds retinal and pumps protons. Moreover, our 1.65-Å resolved VirRDTS crystal structure and mutational analyses exposed differences from previously characterized type-1 rhodopsins, all of which come from cellular organisms. Multiple VirR types are present in metagenomes from across surface oceans, where they are correlated with and nearly as abundant as a canonical marker gene from Mimiviridae. Our findings indicate that light-dependent energy transfer systems are likely common components of giant viruses of photosynthetic and phagotrophic unicellular marine eukaryotes.

Nekhaev, A.I., Maksimov, A.L., 2019. Diamondoids in oil and gas condensates (review). Petroleum Chemistry 59, 1108-1117.

https://doi.org/10.1134/S0965544119100098

Information is given on the presence of diamondoids, hydrocarbons with a diamond-like structure, in oils and gas condensates. Methods for their isolation and analysis are described.

Nelson, C.S., Campbell, K.A., Nyman, S.L., Greinert, J., Francis, D.A., Hood, S.D., 2019. Genetic link between Miocene seafloor methane seep limestones and underlying carbonate conduit concretions at Rocky Knob, Gisborne, New Zealand. New Zealand Journal of Geology and Geophysics 62, 318-340.

https://doi.org/10.1080/00288306.2018.1561474

Methane-derived authigenic carbonates (MDACs) in Miocene bathyal mudstones in North Island, New Zealand are typically expressed as either sub-seafloor conduit concretions or as seafloor seep limestones, but rarely are both types exposed in outcrop at one locality. Consequently, any potential genetic link between them is usually inferred. This also appears to be the case for global occurrences of MDAC. At the Rocky Knob seep complex near Gisborne both seep limestones and conduit concretions co-occur. The petrography and stable carbon (δ13C) and oxygen (δ18O) isotope compositions of their various authigenic carbonate components (automicrite, fibrous aragonite crystals, and granular, blocky and bladed calcite crystals) show that distinctive isotope and petrographic groupings for precipitates within the conduit concretions match or ?correlate? with several of those in the seep limestones. This corroborates their genetic tie and derivation from the same fluids, albeit in different parts (i.e. sub-seafloor vs. seafloor) of the seep complex.

Newell, A.J., Pourmalek, A., Butcher, A.S., Shariatipour, S.M., 2019. The importance of lithofacies control on fluid migration in heterogeneous aeolian formations for geological CO2 storage: Lessons

from observational evidence and modelling of bleached palaeoreservoirs at Salt Wash Graben, Utah. International Journal of Greenhouse Gas Control 91, 102841.


Exhumed bleached palaeoreservoirs provide a means of understanding fluid flow processes in geological media because the former movement of fluids is preserved as visible geochemical changes (grey bleaching of continental red-beds). The bleached palaeoreservoirs of the Jurassic Entrada Sandstone occur in a region (Utah) where there are high fluxes of naturally-occurring CO2 and form outcrop analogues for processes related to geological storage of CO2. In this paper a bleached palaeoreservoir now exposed at outcrop is used to test the importance of geological heterogeneity on fluid flow. The bleached palaeoreservoir is developed in ‘wet aeolian’ lithofacies composed of alternating layers of sandstone and cemented muddy sandstone that range across three or more orders of magnitude in permeability. Despite these permeability contrasts the bleaching shows a remarkably uniform distribution within the palaeoreservoir that crosses lithofacies boundaries. Evidence from bleaching therefore suggests that geological heterogeneity within the range 1–103 millidarcies should not greatly impede the relatively uniform distribution of low-viscosity CO2 charged fluids throughout a reservoir: a conclusion that has been substantiated here by flow modelling. Residence time is an important factor and where flows are transient the distribution of bleaching and modelling shows that flows are confined to high-permeability lithofacies.



Based on the analysis of the molecular composition as well as carbon and hydrogen isotopes of gases from the Upper Triassic Xujiahe and other formations in the Sichuan Basin in China, by combining previous research results and regional geological background, the gas origin, gas source, and significance of hydrogen isotopes are studied. The results show that gas from the Triassic Xujiahe Formation in the Sichuan Basin is mainly hydrocarbon gas. The methane content ranges 67.89%–98.05%, whereas the content of heavy hydrocarbon gas (C2+) ranges 0.42%–16.62%. Meanwhile, the non-hydrocarbon gas content (CO2, N2) is low. Except for the relatively high content of N2 and CO2 in Well Yue121, the average content of N2 and CO2 are 0.82% and 0.26%, respectively. The gas from the Xujiahe Formation in the Yuanba area has a high average dryness coefficient of 0.991, which indicates that it is dry gas. It is also worth noting that gases from other areas of central Sichuan have a dryness coefficient of less than 0.95, which is indicative of wet gas. The δ13C1 value varies from −43.8‰ to −29.2‰, the δ13C2 value ranges from −33.5‰ to −20.7‰, δ13C3 value ranges from −33.6‰ to −19.3‰, and the δ13C4 value ranges from −27.2‰ to −22.2‰. The δD1 value ranges from −191‰ to −148‰, δD2 value ranges from −165‰ to −115‰, and δD3 value ranges from −153‰ to −107‰. Methane and its homologues (C2-4) become more enriched in 13C and D as the carbon number increases (δ13C1 < δ13C2 < δ13C3 < δ13C4, δD1 < δD2 < δD3); the aforementioned is consistent with the carbon and hydrogen isotopic characteristics of thermogenic gases. The thermal maturity RO of the natural gas from the Xujiahe Formation in the Yuanba area ranges 1.09%–1.78%, whereas the RO value of the natural gas from the Xujiahe Formation in other areas of central Sichuan ranges 0.64%–0.92%. The natural gas from the Xujiahe Formation in central Sichuan is mainly from the coal measure source rocks of the Xujiahe Formation. The gas from the 2nd Member of the Xujiahe Formation (Xu-2 Member) in the Yuanba area is mixed gas; it is a mixture of the high-mature coal-derived gas from the coal measure source rock of the Xujiahe Formation and the oil-cracked gas from the Lower Cambrian (and Lower Silurian). The δD value of methane from the Xujiahe Formation in

the Sichuan Basin is relatively high as it is higher than −200‰. Compared to the coal-derived gas from the source rocks formed in limnetic facies with freshwater in the Taibei Sag, Turpan-Hami Basin, though at similar thermal evolution stage, the difference of the δD values of methane can be as high as 90‰, indicating that the source rock of the Xujiahe Formation is formed in an environment with water salinization.



Stable-isotope metabolic flux analysis is an important approach to unravel the metabolic network and its regulation in organisms. It has become a key analytical technology for biotechnological applications. During recent years non-model microorganisms have received increasing attention because they possess unique metabolic capabilities and can serve as a host for production of biofuels and biochemicals. Stable-isotope metabolic flux analysis has been widely used in these microorganisms for exploring novel pathways, elucidating the operation of central metabolic networks, and revealing the metabolic changes that result from genetic manipulations. Here, we review recent applications of stable-isotope metabolic flux analysis in characterizing non-model microbial hosts, guiding the development of rational engineering strategies for enhancement of biochemical production and extension of substrate range, and understanding of industrial production processes.

Nutman, A.P., Bennett, V.C., Friend, C.R.L., Kranendonk, M.V., 2019. The Eoarchean legacy of Isua (Greenland) worth preserving for future generations. Earth-Science Reviews 198, 102923.


The Eoarchean (>3600 Ma, or millions of years ago) folded and metamorphosed Isua supracrustal belt and the adjacent orthogneiss exposures of Greenland contain rare low deformation lenses that display some uniquely-preserved components of Earth's oldest rock record. These include world's oldest (but contested) stromatolites in dolomitic carbonates, conglomerates, pillow basalts demonstrating submarine eruption, slivers of upper mantle rocks, formation of earliest continental crust by multistage tonalite + diorite emplacement followed by intracrustal granite production. All these diverse occurrences are keys to establish early Earth's processes at the start of the geological record. Although some of these features are preserved at several localities, other critical ones are exposed on only a few m2 of rock at single localities or are of historical significance. None of these sites are currently protected, and there is a reliance on responsible sampling to keep them intact for future generations. Given the high interest in the Archean Eon, combined with the increased ease of fieldwork in remote localities, many significant ‘Deep Time’ localities in not only Greenland but worldwide are in danger of eradication. Here, five key Isua area geological sites are presented, with an explanation of their significance and worthiness for initially reliance on already-collected samples, but hopefully ultimately government protection. This highlights an increasing problem of destruction of in situ evidence of Earth's unique early geological heritage and the need for collaboration in protecting and archiving of these key scientific resources.


https://doi.org/10.1038/s41467-019-12404-1

The synthesis of nucleobases in natural environments, especially in interstellar molecular clouds, is the focus of a long-standing debate regarding prebiotic chemical evolution. Here we report the simultaneous detection of all three pyrimidine (cytosine, uracil and thymine) and three purine nucleobases (adenine, xanthine and hypoxanthine) in interstellar ice analogues composed of simple molecules including H2O, CO, NH3 and CH3OH after exposure to ultraviolet photons followed by thermal processes, that is, in conditions that simulate the chemical processes accompanying star formation from molecular clouds. Photolysis of primitive gas molecules at 10 K might be one of the key steps in the production of nucleobases. The present results strongly suggest that the evolution from molecular clouds to stars and planets provides a suitable environment for nucleobase synthesis in space.

Okushita, K., Hata, Y., Sugimoto, Y., Takahashi, T., Kanehashi, K., 2019. Protonated nitrogen structure in 15N-labeled model coal investigated by solid-state 1H–15N double-CP NMR experiments under ultrafast magic-angle spinning. Energy & Fuels 33, 9419-9428.


The nitrogen structure in coals has been focused on as a key factor for reducing NOx. Solid-state nuclear magnetic resonance (NMR) with high spectral resolution can be an effective tool for analyzing the nitrogen structure of coals once higher sensitivity is achieved in the future. To investigate the nitrogen structure in coals and coal-related molecules, we acquired quantitative 15N magic-angle spinning (MAS) NMR spectra of 15N-labeled synthesized coals produced from three different types of 15N-reagents. There were some variations in the relative peak intensity ratios of 15N MAS NMR spectra of the three model coals; in particular, the 15N-uracil-origin model coal showed a remarkable difference. Then, we elucidated the chemical environment around the 15N nuclei in the synthesized 15N-labeled coals using 1H–15N double cross-polarization techniques under the ultrafast MAS condition. From the 2D NMR results, it was clarified that there exist not only pyrrolic nitrogen groups but also amide-type nitrogen functional groups in the 1H–15N bonded region of the model coal with a sub-bituminous-level degree of carbonization.

Omanović, D., Santinelli, C., Marcinek, S., Gonnelli, M., 2019. ASFit - An all-inclusive tool for analysis of UV–Vis spectra of colored dissolved organic matter (CDOM). Computers & Geosciences 133, 104334.


The study of dissolved organic matter (DOM) in natural waters is hindered by its complex structure and low concentration. Spectroscopic methods (e.g. UV–Vis spectrometry) can be used for the characterization of its chromophoric fraction (CDOM) due to their simplicity, rapid response, low price and high sensitivity. The absorption spectrum of CDOM is unstructured with an exponential decrease in absorbance at increasing wavelength. Absorbance intensity gives an indirect estimate of CDOM concentration, whereas the shape of the spectrum provides insights into its composition. Changes in absorbance spectra can therefore be useful indicators of sources, degree of degradation as well as interactions of DOM with metals. There are over 20 different parameters that can be derived from the UV–Vis spectra in order to gain information on CDOM in natural waters. Only few of these parameters are commonly used (e.g. S275-290, S350-400, SR, SUVA, a254), the others are proposed based on "well correlated" relationship with other DOM specific parameters. Analysis and interpretation of

UV–Vis spectra are challenging since there are numerous possibilities to treat the raw spectra and there is still no general agreement among scientists on the interpretation of all these parameters.

Here we present ASFit, a new, windows-based "all-inclusive" software tool, for the basic and advanced treatment of CDOM UV/Vis spectra. It computes the most used parameters in few seconds and presents data in interactive graphs. ASFit can also be used to study trace metals complexation with DOM based on differential spectra.


https://doi.org/10.1089/ast.2018.1960

Here we review published studies on the abundance and diversity of terrestrial rock-hosted life, the environments it inhabits, the evolution of its metabolisms, and its fossil biomarkers to provide guidance in the search for life on Mars. Key findings are (1) much terrestrial deep subsurface metabolic activity relies on abiotic energy-yielding fluxes and in situ abiotic and biotic recycling of metabolic waste products rather than on buried organic products of photosynthesis; (2) subsurface microbial cell concentrations are highest at interfaces with pronounced chemical redox gradients or permeability variations and do not correlate with bulk host rock organic carbon; (3) metabolic pathways for chemolithoautotrophic microorganisms evolved earlier in Earth's history than those of surface-dwelling phototrophic microorganisms; (4) the emergence of the former occurred at a time when Mars was habitable, whereas the emergence of the latter occurred at a time when the martian surface was not continually habitable; (5) the terrestrial rock record has biomarkers of subsurface life at least back hundreds of millions of years and likely to 3.45 Ga with several examples of excellent preservation in rock types that are quite different from those preserving the photosphere-supported biosphere. These findings suggest that rock-hosted life would have been more likely to emerge and be preserved in a martian context. Consequently, we outline a Mars exploration strategy that targets subsurface life and scales spatially, focusing initially on identifying rocks with evidence for groundwater flow and low-temperature mineralization, then identifying redox and permeability interfaces preserved within rock outcrops, and finally focusing on finding minerals associated with redox reactions and associated traces of carbon and diagnostic chemical and isotopic biosignatures. Using this strategy on Earth yields ancient rock-hosted life, preserved in the fossil record and confirmable via a suite of morphologic, organic, mineralogical, and isotopic fingerprints at micrometer scale. We expect an emphasis on rock-hosted life and this scale-dependent strategy to be crucial in the search for life on Mars.

Osterhout, J.T., Czaja, A.D., Bartley, J.K., Fralick, P.W., 2019. Preservation of carbon isotopes in kerogen from thermally altered Mesoproterozoic lacustrine microbialites. Canadian Journal of Earth Sciences 56, 1017-1026.

https://doi.org/10.1139/cjes-2018-0309

Stable carbon isotope geochemistry is a well-established and reliable tool for studying metabolisms of microbial communities in the Precambrian record; however, the isotopic effects of high-temperature alteration from igneous intrusions (i.e., contact metamorphism) have not been thoroughly explored. The Mesoproterozoic (∼1.4 Ga) Middlebrun Bay Member of the Rossport Formation, Sibley Group, in Ontario, Canada, is composed of carbonaceous stromatolites and microbial laminites preserved in an evaporitic, lacustrine chert–carbonate deposit and is cross-cut by an intrusive mafic sill at the

studied locality. Sedimentary organic matter (kerogen) was investigated along two vertical stratigraphic transects to determine the spatial variability of its geochemical preservation. Thermal alteration of the preserved kerogen (as measured by Raman spectroscopy) increased toward the mafic sill, but the alteration was greater for kerogen preserved in carbonate mineralogies compared to that preserved in quartz (chert). Bulk δ13Corg values fluctuate throughout each vertical section, with a total average of −28.2‰ ± 0.8‰; however, values are unexpectedly lower for samples near the mafic sill, approaching −30‰, inconsistent with previously reported patterns. These measurements indicate that thermal alteration of sedimentary rocks does not universally result in 13C enrichment and increased δ13Corg values and suggests that ancient kerogen may be preferentially shielded from postdepositional heating effects due to micrometre-scale differences in mineralogy.



Archean spherule layers represent the only currently known remnants of the early impact record on Earth. Based on the lunar cratering record, the small number of spherule layers identified so far contrasts to the high impact flux that can be expected for the Earth at that time. The recent discovery of several Paleoarchean spherule layers in the BARB5 and CT3 drill cores from the Barberton area, South Africa, drastically increases the number of known Archean impact spherule layers and may provide a unique opportunity to improve our knowledge of the impact record on the early Earth. This study is focused on the spherule layers in the CT3 drill core from the northeastern Barberton Greenstone Belt. We present highly siderophile element (HSE: Re, Os, Ir, Pt, Ru, and Pd) concentrations and Re‐Os isotope signatures for spherule layer samples and their host rocks in order to unravel the potential presence of extraterrestrial fingerprints within them. Most spherule layer samples exhibit extreme enrichments in HSE concentrations of up to superchondritic abundances in conjunction with, in some cases, subchondritic present‐day 187Os/188Os isotope ratios. This indicates a significant meteoritic contribution to the spherule layers. In contrast to some of the data reported earlier for other Archean spherule layers from the Barberton area, the CT3 core is significantly overprinted by secondary events. However, HSE and Re‐Os isotope signatures presented in this study indicate chondritic admixtures of up to (and even above) 100% chondrite component in some of the analyzed spherule layers. There is no significant correlation between HSE abundances and respective spherule contents. Although strongly supporting the impact origin of these layers and the presence of significant meteoritic admixtures, peak HSE concentrations are difficult to explain without postdepositional enrichment processes.

Pacheco-Ruiz, R., Adams, J., Pedrotti, F., Grant, M., Holmlund, J., Bailey, C., 2019. Deep sea archaeological survey in the Black Sea – Robotic documentation of 2,500 years of human seafaring. Deep Sea Research Part I: Oceanographic Research Papers 152, 103087.


Between 2015 and 2017 the Black Sea Maritime Archaeology Project (Black Sea MAP) discovered and recorded 65 shipwreck sites dating from the 4th Century BC to the 19th Century AD in the Bulgarian Exclusive Economical Zone (EEZ). Using state-of-the-art remotely operated vehicles to survey the seabed, the team captured more than 250,000 high-definition (HD) photographs; hundreds of hours of ultra high-definition (UHD) video together with acoustic bathymetric, laser, side-scan sonar and seismic data. The wrecks were located in depths from 40 to 2200 m – those shipwrecks in

the deeper range presented extraordinary archaeological preservation due to the Black Sea's anoxic conditions. This paper will introduce the range of deep-sea optic and acoustic survey techniques to accurately record and create 3D and pseudo 4D models of the shipwrecks. It will focus on a Early 4th Century BC shipwreck demonstrating the project's survey strategy as well as adaptations developed in response to operational conditions; the implementation of deep sea robotics to generate georeferenced high-resolution photogrammetric models and the benefits this has as an on-site, as well as a post-cruise, interpretative tool. It demonstrates that in-theatre acquisition and processing of high-quality datasets is a working reality and has fundamental implications for management as well as the advantages that this brings to the archaeological research process: Firstly, in the creation of spatio-temporal models, i.e., 4D representations of a site pre and post archaeological excavation and secondly, in monitoring such wreck sites, and provides a viable non-intervention tool for the assessment of sites as part of a long-term management strategy. It also shows the value of well-funded collaboration between academia and industry and that deep water archaeology can and must be totally in accordance to the 2011 United Nations Educational, Scientific and Cultural Organization (UNESCO) convention.



The aim of this research was to compare the structure, sorption properties and the kinetics of sorption to CO2 and CH4 in nanomaterials with a very orderly structure and in structurally heterogeneous coal. The authors tested synthetic materials such as multiwall carbon nanotubes (MWCNT) and reduced graphene oxide (rGO) as well as natural materials such as coals of various ranks. The value of the surface area of Langmuir and Brunauer, Emmett and Teller, in MWCNTs and rGO was much higher than in the coal. The course of CH4 and CO2 sorption of the materials was investigated and the parameters of sorption isotherms in the pressure of 0–2.0 MPa were determined. The nanomaterials reached the sorption equilibria much faster than the coal. The highest total CH4 sorption capacity was found in low-rank coal. The highest CO2 total sorption capacity was found in MWCNTs and low-rank coal. The highest relative mean drop in CH4 and CO2 sorption capacity resulting from the increasing measurement temperature was found in the MWCNTs and the low-rank coal. The authors analysed the courses of CH4 and CO2 sorption kinetics in the materials of highly different structures. The kinetics of CH4 and CO2 accumulation in MWCNT and rGO nanomaterials progressed almost instantaneously, and their rate was many times higher than in the case of kinetics on hard coals.



In this work, a detailed analysis of a bio-oil obtained by pyrolysis of softwoods and its esterified product is described. Information of the type of chemical function groups were obtained by 13C and 1H nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy (FT-IR) and compositional analysis was obtained by Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS). The results obtained indicate that aliphatic hydrogen and carbon atoms are found in higher abundance, compared with aromatic hydrogen-carbon frameworks. Furthermore, a decrease in

oxygen functional groups was observed after esterification. According to the FTICR MS results, the samples contain highly oxygenated species corresponding to compound classes Ox, NOx and BOx, with a high predominance of Ox species. After esterification, the compositions shifted towards lower oxygen-content, lower number of rings and double bonds, and longer alkyl chains as a consequence of the water removal via the condensation reaction.

Pati, J.K., Poelchau, M.H., Reimold, W.U., Nakamura, N., Kuriyama, Y., Singh, A.K., 2019. Documentation of shock features in impactites from the Dhala impact structure, India. Meteoritics & Planetary Science 54, 2312-2333.


The fundamental approach for the confirmation of any terrestrial meteorite impact structure is the identification of diagnostic shock metamorphic features, together with the physical and chemical characterization of impactites and target lithologies. However, for many of the approximately 200 confirmed impact structures known on Earth to date, multiple scale‐independent tell‐tale impact signatures have not been recorded. Especially some of the pre‐Paleozoic impact structures reported so far have yielded limited shock diagnostic evidence. The rocks of the Dhala structure in India, a deeply eroded Paleoproterozoic impact structure, exhibit a range of diagnostic shock features, and there is even evidence for traces of the impactor. This study provides a detailed look at shocked samples from the Dhala structure, and the shock metamorphic evidence recorded within them. It also includes a first report of shatter cones that form in the shock pressure range from ~2 to 30 GPa, data on feather features (FFs), crystallographic indexing of planar deformation features, first‐ever electron backscatter diffraction data for ballen quartz, and further analysis of shocked zircon. The discovery of FFs in quartz from a sample of the MCB‐10 drill core (497.50 m depth) provides a comparatively lower estimate of shock pressure (~7–10 GPa), whereas melting of a basement granitoid infers at least 50–60 GPa shock pressure. Thus, the Dhala impactites register a strongly heterogeneous shock pressure distribution between <2 and >60 GPa. The present comprehensive review of impact effects should lay to rest the nonimpact genesis of the Dhala structure proposed by some earlier workers from India.

Patty, C.H.L., ten Kate, I.L., Buma, W.J., van Spanning, R.J.M., Steinbach, G., Ariese, F., Snik, F., 2019. Circular spectropolarimetric sensing of vegetation in the field: Possibilities for the remote detection of extraterrestrial life. Astrobiology 19, 1221-1229.

https://doi.org/10.1089/ast.2019.2050

Homochirality is a generic and unique property of all biochemical life, and the fractional circular polarization of light it induces therefore constitutes a potentially unambiguous biosignature. However, while high-quality circular polarimetric spectra can be easily and quickly obtained in the laboratory, accurate measurements in the field are much more challenging due to large changes in illumination and target movement. In this study, we measured various targets in the field, up to distances of a few kilometers, using the dedicated circular spectropolarimeter TreePol. We show how photosynthetic life can readily be distinguished from abiotic matter. We underline the potential of circular polarization signals as a remotely accessible means to characterize and monitor terrestrial vegetation, for example, for agriculture and forestry. In addition, we discuss the potential of circular polarization for the remote detection of extraterrestrial life.

Pearson, C.A., Philp, R.P., 2019. Geochemical characterization of the Upper Mississippian Goddard Formation, Noble Ranch Group, and related oils in the Anadarko Basin of Oklahoma. American Association of Petroleum Geologists Bulletin 103, 2545-2571.

http://archives.datapages.com/data/bulletns/2019/11nov/BLTN16504/bltn16504.html

The Woodford Shale is anecdotally assumed to be the major source of oil for plays in the Anadarko Basin, including the stacked oil and condensate play in the southcentral Oklahoma oil province (SCOOP). However, there is little published geochemical work to confirm this assumption. This study set out to identify a characteristic geochemical fingerprint for the Goddard Formation, another potential source rock in the SCOOP, to determine if the Goddard is contributing to oil accumulations within the SCOOP. The Upper Mississippian Goddard Formation has been a target for unconventional production in SCOOP since 2012. Published geochemical interpretations for the Goddard Formation are still limited, and this study represents the first detailed oil–source rock correlation for the Goddard in the SCOOP area.

The most characteristic geochemical signature of the Goddard extracts is a predominance of tricyclic terpanes relative to the hopanes in the mass-to-charge ratio 191 chromatogram, possibly related to enrichment via thermal stress or a unique source signature. Additional distinctive signatures were also identified for the triaromatic steroid hydrocarbons, sesquiterpenoids, and steranes. The biomarker fingerprints of SCOOP oils are nearly identical with those of the Goddard extracts in this study. Oils in the SCOOP, therefore, appear to originate from a Mississippian source, such as the Goddard rather than the Woodford. This observation demonstrates the value of oil–source rock correlation studies and suggests that there may be effective source rocks in the Anadarko Basin that have been overlooked in the past and should be re-evaluated in detail.



Compound-specific isotope analysis (CSIA) of individual organic compounds is a powerful but underutilized tool in petroleum exploration. When integrated with other organic geochemical methodologies it can provide evidence of fluid histories including source, maturity, charge history and reservoir processes that can support field development planning and exploration efforts. The purpose of this chapter is to provide a review of the methodologies used for generating carbon and hydrogen isotope data for mid- and high-molecular-weight n-alkanes.

We discuss the factors that control stable carbon and hydrogen isotope compositions of n-alkanes and related compounds in sedimentary and petroleum systems and review current and future applications of this methodology for petroleum exploration. We discuss basin-specific case studies that demonstrate the usefulness of CSIA either when addressing particular aspects of petroleum exploration (e.g. charge evaluation, source rock–oil correlation, and investigation of maturity and in-reservoir processes) or when this technique is used to corroborate interpretations from integrated petroleum systems analysis, providing unique insights which may not be revealed when using other methods. CSIA of n-alkanes and related n-alkyl structures can provide independent data to strengthen petroleum systems concepts from generation and expulsion of fluids from source rock, to charge history, connectivity, and in-reservoir processes.

Pedrosa-Pàmies, R., Conte, M.H., Weber, J.C., Johnson, R., 2019. Hurricanes enhance labile carbon export to the deep ocean. Geophysical Research Letters 46, 10484-10494.

https://doi.org/10.1029/2019GL083719

Abstract Tropical cyclones (hurricanes) generate intense surface ocean cooling and vertical mixing resulting in nutrient upwelling into the photic zone and episodic phytoplankton blooms. However, their influence on the deep ocean remains unknown. Here we present evidence that hurricanes also impact the ocean's biological pump by enhancing export of labile organic material to the deep ocean. In October 2016, Category 3 Hurricane Nicole passed over the Bermuda Time Series site in the oligotrophic NW Atlantic Ocean. Following Nicole's passage, particulate fluxes of lipids diagnostic of fresh phytodetritus, zooplankton, and microbial biomass increased by 30?300% at 1,500 m depth and 30?800% at 3,200 m depth. Mesopelagic suspended particles following Nicole were also enriched in phytodetrital material and in zooplankton and bacteria lipids, indicating particle disaggregation and a deepwater ecosystem response. Predicted climate-induced increases in hurricane frequency and/or intensity may significantly alter ocean biogeochemical cycles by increasing the strength of the biological pump.

Pennisi, E., 2019. How life blossomed after the dinosaurs died. Science 366, 409.


In 2014, when Ian Miller and Tyler Lyson first visited Corral Bluffs, a fossil site 100 kilometers south of the Denver Museum of Nature & Science where they work, Lyson was not impressed by the few vertebrate fossils he saw. But on a return trip later that year, he split open small boulders called concretions—and found dozens of skulls. Now, he, Miller, and their colleagues have combined the site's trove of plant and animal fossils with a detailed chronology of the rock layers to tell a momentous story: how life recovered from the asteroid impact that killed off the dinosaurs 66 million years ago.

Plants and animals came back much faster than thought, with plants spurring mammals to diversify, the team reports online in Science this week. “They get almost the whole picture, which is quite exciting,” says functional anatomist Amy Chew of Brown University. “This high-resolution integrated record really tells us what's going on.”

When the asteroid slammed into Earth, it wiped out 75% of living species, including any mammal much larger than a rat. Half the plant species died out. With the great dinosaurs gone, mammals expanded, and the new study traces that process in exquisite detail.

Most fossil sites from after the impact have gaps, but sediment accumulated nearly continuously for 1 million years on the flood plain that is now the Corral Bluffs site. So the site preserves a full record of ancient life and the environment.

Such sites can be hard to date. But Miller, a paleobotanist, and his colleagues collected 37,000 grains of pollen and spores, which revealed a clear marker of the asteroid impact: a surge in the growth of ferns, which thrive in disturbed environments. The site also includes two layers of ash from nearby volcanoes. Volcanic ash includes radioactive minerals whose decay can be used as a precise geochronological clock, providing two time markers. The known flips in Earth's magnetic poles, which some minerals in the layers had recorded, add detail to the chronology. “They have a very strong geochronological framework,” says David Fastovsky, a paleontologist at the University of Rhode Island in Kingston.

The record confirms the devastation wrought by the impact. Racoon-size mammal species had swarmed the site before the catastrophe, but for 1000 years afterward just a few furry creatures no bigger than 600-gram rats roamed a ferny world where flowering plants, with their nutritious seeds and fruits, were scarce.

By 100,000 years later, twice as many mammal species roamed, and they were back to raccoon size. These critters foraged in the palm forests that replaced the ferns. “It's a world that's coming back from complete and utter devastation,” Miller says.

Over the next 200,000 years, what he calls the “palm period” gave way to the “pecan pie” period, when walnutlike plants arose. New mammals evolved to take advantage of the nutritious seeds. Mammal diversity increased threefold, and the biggest of the new species reached 25 kilograms—beaver size.

After about 700,000 years, legumes showed up; their fossil pea pods are North America's oldest discovered to date. Pea and bean species from the “protein bar period” provided protein-rich meals that further boosted mammalian size and diversity, Lyson says. Mammals topped 50 kilograms—a 100-fold increase over those that survived the asteroid. The forests, too, had recovered. “The biggest message is how fast the recovery was … and how closely the vegetation and fauna are tied together,” says Vivi Vajda, a paleobiologist at the Swedish Museum of Natural History in Stockholm.

The team also classified 6000 leaves, counting how many species at each time interval had smooth or toothed edges. Smooth-edged species are more common in hot climates. The team concluded that the site underwent three warming periods. They estimate that the first, just after the impact, saw temperatures rise about 5°C, agreeing with earlier work. This period coincides with the massive volcanic eruptions of India's Deccan Traps, which could have warmed Earth by belching carbon dioxide (Science, 22 February, p. 862 and p. 866).

“At each warming period you see a change in the plant community and subsequently, changes in the mammals,” says Lyson, who thinks temperature drove the stepwise recovery.

Vajda thinks no matter what happened to temperature and plant life, the loss of dinosaurs alone might have opened the door to bigger, more diverse mammals. But Jukka Jernvall, an evolutionary biologist at the University of Helsinki, says the team's analysis of ancient ecosystems shows just how the recovery unfolded. “We are starting to get the time and spatial resolution to reconstruct the environment and what happened in a way that can be linked to ecological processes.”

The record also holds a sobering message about the future, and how quickly ecosystems might recover from ongoing, human-driven extinctions. Even a recovery that geologists call “fast” took hundreds of thousands of years, and the world was never the same. “A very dramatic resetting of the ecosystem could be in our future,” Chew says.

The team also classified 6000 leaves, counting how many species at each time interval had smooth or toothed edges. Smooth-edged species are more common in hot climates. The team concluded that the site underwent three warming periods. They estimate that the first, just after the impact, saw temperatures rise about 5°C, agreeing with earlier work. This period coincides with the massive volcanic eruptions of India's Deccan Traps, which could have warmed Earth by belching carbon dioxide (Science, 22 February, p. 862 and p. 866).



An explosion of fossil finds reveals that ancient mammals evolved a wide variety of adaptations allowing them to exploit the skies, rivers and underground lairs.

Night is falling in the early Jurassic 185 million years ago, and the Kayentatherium is tending to her newly hatched brood. Heavy rains pummel the bank above her den as she looks over her dozens of tiny young. She is about the size of a large cat and could easily pass for a mammal, but her large jawbone, characteristic teeth and lack of external ears give her away: she is a cynodont, a member of the group from which mammals evolved. At some point without warning, the sodden bank collapses, entombing the hatchlings and their mother in mud.

There they remained until the summer of 2000, when a fossil-hunting crew led by Timothy Rowe at the University of Texas at Austin chanced upon their scattered bones among rocks of the Kayenta Formation in northern Arizona.

That initial encounter with the fossils did little to impress the palaeontologists. They dug up the block and shipped it back to the laboratory for safekeeping. It wasn’t until nine years later that a specialist preparing the fossil for study noticed something startling: embedded in the block were tiny teeth, and jawbones just 1 centimetre in length. “Immediately they stopped the preparation and thought about ways of non-destructively examining the babies,” says Eva Hoffman, at Texas with Rowe at the time and now a palaeontologist at the American Museum of Natural History in New York City. Instead of breaking into the rock, Hoffman and Rowe digitally extracted the bones with a microcomputed tomography (microCT) scanner, which uses X-rays to create fine-grained 3D images.

What they found inside the rock were the first known babies of mammals or their relatives from the Jurassic — and not just one, but 38 of them, placing this among the most significant discoveries related to mammal origins made in the past decade1. Kayentatherium is at the cusp of mammalhood — and researchers say that it provides crucial insights into which traits define mammals and which were present in their earlier relatives.

Kayentatherium’s skeleton is mammal-like in many ways, but the fossil suggested that it still reproduced very much like a reptile, giving birth to large litters of small-brained offspring. By contrast, “mammal moms invest a lot in a smaller number of babies, each of which has a better chance of surviving”, says Hoffman. Mammal babies spend longer under their parents’ care, developing relatively large brains, whereas these fossil hatchlings had well-developed bones and teeth, hinting that they could fend for themselves and were not nourished by milk, as all mammals are today.

The find is among a mass of discoveries in the past 10–20 years that are illuminating milestones in mammalian evolution. Although major finds are emerging all over the world, the largest number are coming out of China; together, they have overturned the now dated belief that dinosaur-era mammals were small, unremarkable insectivores, eking out a life in the shadows of the giant reptiles.

The fossils have revealed that early mammals were ecologically diverse and experimenting in gliding, swimming, burrowing and climbing. The discoveries are also starting to reveal the evolutionary origins of many of the key traits of mammals — such as lactation, large brains and superbly keen senses.

“The explosion of early-mammal discoveries, particularly from China, over the last two decades has been eye-opening, mind-numbing and absolutely dazzling,” says David Krause, a vertebrate palaeontologist at the Denver Museum of Nature and Science in Colorado.

This avalanche of discovery is also stirring up debate: some researchers disagree over which fossil groups are true mammals and the shape of the mammal family tree. “We want to understand our early

history in the language of evolutionary biology, and that’s what fires me up,” says Zhe-Xi Luo, a palaeontologist at the University of Chicago in Illinois. “That’s why this entire field is so interesting, because the fossil record is getting better and better, and we are starting to really tackle some of these questions.”

Out of the shadows

In 1824, at the Geological Society of London, naturalist William Buckland presented bones from one of the first known dinosaurs, Megalosaurus. At the same talk, he revealed tiny mammalian jaws that had been found in the same fossil deposit. Their presence suggested that mammals had a very deep history, but as would happen repeatedly, the dinosaur discoveries completely overshadowed the mammal ones.

The slow trickle of mammal finds from around the world continued for 150 years. Then in 1997, researchers described the first ancient mammal from the fossil-rich rocks of Liaoning in northeastern China2, and the floodgates opened. Since then, 50 or more near-complete and “beautiful specimens” have been found there, according to Jin Meng, a palaeontologist at the American Museum of Natural History. Like the dinosaur fossils, they are dug up by local farmers and sold on to museums.

But the dinosaurs continued to get the vast majority of the attention, says palaeontologist Steve Brusatte at the University of Edinburgh, UK. “It’s only that very recently, through the work of Luo, Meng and others, that the mammals are getting their due.”

Most of China’s mammal fossils were formed when volcanoes buried the animals in ash — and they are exquisitely detailed. Typical mammal fossils from the Mesozoic era (252 million to 66 million years ago) are little more than teeth and jaw fragments, but Chinese specimens often have entire skeletons, with fur, skin and internal organs. “We have a lot of detail to answer scientific questions,” says Meng, He is interested in understanding the evolution of the mammalian ear, for instance.

The finds overturned previous dogma. “We used to say that during the time of dinosaurs, mammals were totally unspectacular. That they were just these little mousey things scampering around in the shadows,” says Brusatte. But these animals “were undergoing their own evolutionary explosion”, he says.

Mammals first appeared at least 178 million years ago, and scampered amid the dinosaurs until the majority of those beasts, with the exception of the birds, were wiped out 66 million years ago. But mammals didn’t have to wait for that extinction to diversify into many forms and species. “These new discoveries document a huge, hitherto-undreamed-of ecological diversity,” says Richard Cifelli, a palaeontologist at the University of Oklahoma in Norman.

Among the first innovations that researchers began to find in fossil form were those to do with locomotion. In 2006, Meng’s team reported the first gliding mammal3, 164-million-year-old Volaticotherium, which had wing membranes made of furry skin, like today’s flying squirrels. In 2017, Luo’s team added Vilevolodon and Maiopatagaium4,5, which lived at around the same time and belonged to a group called the haramiyids. These animals swooped between the trees alongside some of the first flying dinosaurs, taking advantage of previously unexploitable food resources.

Researchers found other specializations that they assumed had evolved only later: Agilodocodon could climb trees and gnawed into bark to feast on sap6; the platypus-sized river-dweller Castorocauda had webbed feet and a beaver-like tail for swimming7; and Docofossor had paws and claws for digging, and looked like a modern mole8.

These mammals had also adapted to a multitude of diets, much more diverse than previously assumed. In 2014, Krause described the groundhog-like Vintana from Madagascar9, a herbivore that perhaps fed on roots and seeds. And the wolverine-sized carnivore Repenomamus, which Meng’s team reported in 2005, had baby dinosaur bones in its stomach10. Many of these new-found fossil mammals belong to long-extinct subgroups, says Meng. In contrast to the panoply that existed in the Mesozoic, mammals today come in just three varieties: placentals, which make up the majority of species and include humans; marsupials, such as kangaroos and koalas, in which gestation in the womb is brief and development continues in a pouch; and the egg-laying monotremes, represented only by the platypus and several echidnas. “But in geological history, there were many other groups such as multituberculates, triconodonts and haramiyids,” says Meng. “Mammals were actually very diverse in the Jurassic.”

Some, such as the shrew-like Juramaia — described by Luo’s team in 2011 and dated to 160 million years ago — are among the earliest placental mammals and therefore have the potential to be our ancestors11.

And a few dinosaur-era mammals were much bigger than suspected, too. Repenomamus was 12–14 kilograms, and the racoon-sized Vintana weighed in at 9 kg. “It’s exciting that we kind of busted the old myths that early mammals came from a very humble generalized ancestor,” says Luo.

The finds are not solely from China. Important fossils are also coming from the United States, Spain, Brazil, Argentina, Madagascar and Mongolia. Some of the most intriguing and oldest fossils — as well as the biggest gaps in our knowledge — relate to the southern continents, where only five genera of Mesozoic mammals and their relatives are known, compared with more than 70 genera from northern latitudes. In the past two decades, Brazil has yielded several Triassic fossils that are more than 200 million years old. Guillermo Rougier, a palaeontologist at the University of Louisville in Kentucky, describes them as “incredible discoveries” that are right on the cusp between mammals and their cynodont ancestors. “These forms really show a very transitional progression from things that are typically non-mammalian, to things that pretty much have all the features of early mammals.”

Mammal must-haves

The latest finds are also offering clues to the evolution of key mammal features. For instance, the keen hearing of mammals is partly down to tiny bones in the middle ear — the malleus, incus and ectotympanic. But in the reptilian ancestors of mammals, these bones were part of the jaw, and were used for chewing instead of hearing. Mammal forerunners, such as shrew-like Morganucodon from 205 million years ago, sported a prototype of the mammal arrangement that allowed for both functions12.

In 2011, Meng reported an intermediary13: a 120-million-year-old specimen from China belonging to a group of mammals called eutriconodonts and named Liaoconodon hui (see ‘Mammal hallmarks’). The rat-sized fossil revealed three middle-ear bones, but they were still attached to the jaw by cartilage. “The hearing function and the chewing function were still not completely separated,” he explains. This was hard evidence of the evolutionary transition from jaw to ear.

Another unique trait of mammals is the sophisticated way they chew and ingest food in small parcels, rather than swallowing things whole as snakes and alligators do. To make that possible, mammals evolved a wide variety of complex teeth for biting and grinding food.

But as babies, mammals are nourished another way — by suckling from their mother’s mammary glands. “Our whole group is named after this incredible biological innovation,” says Luo. Drinking

milk is made possible by the ability to suck and swallow, aided by the hyoid bones in the throat and muscles that support them. This apparatus also forms the voice box.

In July, Luo published a paper revealing a 165-million-year-old vole-sized docodont — a close relative of true mammals — that had the hyoid bones of its throat preserved14. Microdocodon gracilis is the earliest animal known to have been able to suckle like a modern mammal.

This level of detail is rare, and — similar to the study of the Kayentatherium hatchlings — the work on both the ear and throat bones has been made possible only through advances in microCT scanning techniques, says Krause. The technique has also revealed details about the olfactory abilities and brains of early mammals. These revelations are “breathing life into these early mammals in ways that were previously impossible and almost inconceivable”, he says.

Much of the constellation of features we think of as defining mammals — complex teeth, excellent senses, lactation, small litter size — might actually have evolved before true mammals, and quite quickly. “More and more it looks like it all came out in a very short burst of evolutionary experimentation,” Luo says. By the time mammal-like creatures were roaming around in the Mesozoic, he says, “the lineage has already acquired its modern look and modern biological adaptations”.

Family drama

Although the experts concur on many points, there is still much debate about how early mammal groups are related, and which groups are true mammals. That leads to uncertainty about how key traits evolved, says Hoffman.

One sticking point between Meng and Luo, who have each developed their own evolutionary trees, is the haramiyids. Meng thinks this early group belongs with true mammals, whereas Luo is convinced it’s a side branch. The oldest known haramiyids are from 208 million years ago in the Triassic. If they are true mammals, then mammal origins date back at least that far — if not, then the oldest known mammal is 178 million years old, well into the Jurassic.

More fossils will help to resolve such questions, and bring more surprises. Krause and Meng say they are both studying exciting fossils, but are yet to publish their findings on them, and tens of unstudied specimens lie piled in the offices of their Chinese colleagues.

Palaeontologists have many items on their wish lists. One characteristic that Luo wants to understand is growth rates. Reptiles grow slowly throughout their lives, whereas mammals grow in bursts in youth and then plateau. He’d love to find a series of fossils from babies to adults to watch this happening. “That is one of the most critical features in mammals that help to define our biology,” he says.

Both Hoffman and Meng agree that embryos and more babies would be significant finds — and, like the Kayentatherium discovery with its dozens of hatchlings, they would help us to pinpoint the date that mammal-style small litter sizes appeared. Meng’s dream is to find a pregnant mammal. “This is always in my mind that I will find a mammal that inside the skeleton you can see some very delicate skeleton, which is either an egg that hasn’t hatched, or it’s a more interesting fetus,” he says.

If the flurry of discoveries has taught researchers anything, it’s that every fossil find has the potential to add a chapter to evolutionary history or even flip the prevailing narrative on its head. “We’re really in this exciting, almost manic phase of lots of new evidence coming in, and it’s going to take time to synthesize,” says Brusatte.

References1. Hoffman, E. A. & Rowe, T. B. Nature 561, 104–108 (2018).2. Hu, Y., Wang, Y., Luo, Z. & Li, C. Nature 390, 137–142 (1997).3. Meng, J., Hu, Y., Wang, Y., Wang, X. & Li, C. Nature 444, 889–893 (2006).4. Luo, Z.-X. et al. Nature 548, 326–329 (2017).5. Meng, Q.-J. et al. Nature 548, 291–296 (2017).6. Meng, Q.-J. et al. Science 347, 764–768 (2015).7. Ji, Q., Luo, Z.-X., Yuan, C.-X. & Tabrum, A. R. Science 311, 1123–1127 (2006).8. Luo, Z.-X. et al. Science 347, 760–764 (2015).9. Krause, D. W. et al. Nature 515, 512–517 (2014).10. Hu, Y., Meng, J., Wang, J. & Li, C. Nature 433, 149–152 (2005).11. Luo, Z.-X., Yuan, C.-X., Meng, Q.-J. & Ji, Q. Nature 476, 442–445 (2011).12. Allin, E. F. & Hopson, J. A. in The Evolutionary Biology of Hearing (eds Webster, D. B. & Fay,

R. R.) 587–614 (Springer, 1992).13. Meng, J., Wang, Y. & Li, C. Nature 472, 181–185 (2011).14. Zhou, C.-F., Bhullar, B.-A. S., Neander, A. I., Martin, T. & Luo, Z.-X. Science 365, 276–279

(2019).

Plank, T., Manning, C.E., 2019. Subducting carbon. Nature 574, 343-352.

https://doi.org/10.1038/s41586-019-1643-z

A hidden carbon cycle exists inside Earth. Every year, megatons of carbon disappear into subduction zones, affecting atmospheric carbon dioxide and oxygen over Earth’s history. Here we discuss the processes that move carbon towards subduction zones and transform it into fluids, magmas, volcanic gases and diamonds. The carbon dioxide emitted from arc volcanoes is largely recycled from subducted microfossils, organic remains and carbonate precipitates. The type of carbon input and the efficiency with which carbon is remobilized in the subduction zone vary greatly around the globe, with every convergent margin providing a natural laboratory for tracing subducting carbon.

Planková, B., Lísal, M., 2020. Molecular dynamics of aqueous salt solutions in clay nanopores under the thermodynamic conditions of hydraulic fracturing: Interplay between solution structure and molecular diffusion. Fluid Phase Equilibria 505, 112355.


Shale gas has become an important unconventional energy resource and is extracted by hydraulic fracturing of shale rocks. In shale rocks, kerogen and clays are present, the former providing storage for hydrocarbons, the latter preventing hydrocarbon transport. Clays are hydrophilic and have a layered structure. They can adsorb aqueous salt solutions in the interlayer space, and the interlayer ions contribute to a very high salinity of the flow-back water. We used montmorillonite (MMT) as a proxy of clays and study the interplay between the interlayer structure and the molecular diffusion of the aqueous salt solutions confined in the clay nanopores. We considered water with monovalent Na and divalent Ca ions in the MMT slit pores under a typical shale gas reservoir condition of a temperature of 365 K and a pressure of 275 bar. The confined systems were electrostatically balanced by Cl ions. We varied the amount of water to cover one-, two-, three-, and four-layer hydrate states. We quantified the solution structure in terms of the interlayer atomic density profiles, complemented by the charge density and water orientation profiles. We further evaluated the in-plane self-diffusivity of water and ions to provide insight into the diffusion behaviour of the concentrated water-NaCl and water-CaCl2 solutions in the interlayer galleries of the Na- and Ca-MMT pores. We found that the

interlayer water structure displays an attraction of water hydrogens to the clay surfaces as a result of the strong H-bond interactions of water molecules with the surface oxygens and formation of a diffusive layer inside wide clay pores. The presence of divalent Ca ions has more pronounced effects on the interlayer water structures than the monovalent Na ions. Divalent Ca ions exhibit a preference for inner-sphere complexes over outer-sphere complexes due to the strong adsorption on the clay surfaces while Na ions show the opposite trend. The diffusion of water and ions in the clay pores is reduced in comparison with the diffusion in the bulk, especially for the one-layer hydrate states. The presence of the salts in the clay pores further decreases the water diffusion, with a stronger decrease for the divalent CaCl2 than the monovalent NaCl. The diffusion of small Na+ and Ca2+ is lower than large Cl− due to the low mobility of the adsorbed cations and the distribution of Cl ions inside the pores where they can diffuse faster.

Pletnev, S.P., Romanova, A.V., Wu, Y., Annin, V.K., Utkin, I.V., Vereshchagina, O.F., 2019. Holocene methane emissions in the southwestern Sea of Okhotsk: Evidence from carbon isotopes in benthic foraminifera shells. Doklady Earth Sciences 488, 1081-1083.

https://doi.org/10.1134/S1028334X19090058

Several negative stable carbon isotope excursions are revealed in benthic foraminifera from the LV50-05 gas-bearing core collected from an area of active methane venting on the eastern slope of Sakhalin Island, Sea of Okhotsk. Within the study area, four methane events (ME) were established to have taken place during the Holocene, short-term ones—ME-1 (700–900 yrs BP) and ME-2 (1200–1400 yrs BP)—and long-term ones—ME-3 (2500–5400 yrs BP) and ME-4 (7400–10 000 yrs BP).

Podosokorskaya, O.A., Teplyuk, A.V., Zayulina, K.S., Kopitsyn, D.S., Dominova, I.N., Elcheninov, A.G., Toshchakov, S.V., Kublanov, I.V., 2019. The metabolism of thermophilic hydrolytic bacterium Thauera hydrothermalis strain Par-f-2 isolated from the West Siberian subsurface biosphere. Microbiology 88, 556-562.

https://doi.org/10.1134/S0026261719050126

A novel moderately thermophilic, organotrophic bacterium, strain Par-f-2, was isolated from a sample of hot water emerging from a 2775 m-deep well in Western Siberia, Russia. Cells of the novel isolate were non-sporulating Gram-negative motile rods, often forming groups and aggregates. Strain Par-f-2 grew at 25–60°C, pH 6.0–9.5, and at NaCl concentration from 5 to 7 g L–1. The isolate is an aerobe capable of utilizing mono- and polysaccharides, yeast extract, and some organic acids and aminoacids as the carbon and energy sources. Microaerobic growth was observed. Elemental sulfur, sulfate, nitrate, fumarate, and arsenate were not reduced. The major fatty acids were C16:0 (69.7%) and C16:1ω7 (19.3%). The G+C content of the DNA was 63.5 mol%. 16S rRNA gene sequence-based phylogenetic analysis showed Thauera hydrothermalis (Betaproteobacteria) being its closest relative with 99.8% of 16S rRNA gene sequences identity. Strain Par-f-2 was deposited in the DSMZ and VKM (=DSM 26751=VKM V-2822).

Prado, R.L., Espin Fenoll, I.C., Ullah, I., Miura, G.C.M., Crósta, A.P., Zanon dos Santos, R.P., Reimold, W.U., Elis, V.R., Imbernon, E., Riccomini, C., Diogo, L.A., 2019. Geophysical investigation of the Colônia structure, Brazil. Meteoritics & Planetary Science 54, 2357-2372.


The origin of the nearly circular Colônia structure, located at the southwestern edge of the city of São Paulo, Brazil, has been the subject of a long‐standing debate, ever since the 1960s when the structure was first investigated by geophysical methods. The structure still raises interest for geological research, as its sedimentary infill holds important paleoclimatic information about the evolution of the tropical rainforest, as well as the interplay between the South American summer monsoon, the Intertropical Convergence Zone, and the southern Westerly wind belt—for possibly as long as several million years. In addition, the search for evidence to conclusively establish the origin of this structure continues, and the answer most likely lies in the lower portions of the basin's sedimentary infill, which also holds a significant potential for underground water resources. Here, we present the results from recent seismic (reflection and HVSR), gravimetric, and geoelectrical surveys. They have provided a reliable image of the sedimentary infill, and the maximum depth to basement within the structure has been constrained consistently by the different methods to approximately −400 m. The geophysical data have also allowed to map the lateral contact between the crystalline basement rocks and the sedimentary infill, which indicates a diameter of approximately 2.8 km for the sedimentary basin, with 3.6 km being the diameter of the outermost limit of the structure. A total of six seismic stratigraphic boundaries were identified within the sedimentary infill, providing a framework for the planning of a deep drilling campaign and subsequent sampling program aimed at geological and paleoclimatology studies.


https://doi.org/10.1038/s41598-019-50740-w

The microbial colonization of plastic wastes has been extensively studied in marine environments, while studies on aged terrestrial wastes are scarce, and mostly limited to the isolation of plastic-degrading microorganisms. Here we have applied a multidisciplinary approach involving culturomics, next-generation sequencing analyses and fine-scale physico-chemical measurements to characterize plastic wastes retrieved in landfill abandoned for more than 35 years, and to assess the composition of bacterial communities thriving as biofilms on the films’ surfaces. All samples were characterized by different colors but were all of polyethylene; IR and DSC analyses identified different level of degradation, while FT-Raman spectroscopy and X-ray fluorescence further assessed the degradation level and the presence of pigments. Each plastic type harbored distinct bacterial communities from the others, in agreement with the differences highlighted by the physico-chemical analyses. Furthermore, the most degraded polyethylene films were found to host a bacterial community more similar to the surrounding soil as revealed by both α- and β-diversity NGS analyses. This work confirms the novel hypothesis that different polyethylene terrestrial waste samples select for different bacterial communities, and that structure of these communities can be correlated with physico-chemical properties of the plastics, including the degradation degree.



Waste leachate is a pool of complicated metabolites from waste treatment and disposal as a global environmental problem. The recognition of dissolved organic matter (DOM) in leachate is crucial to improve leachate treatment efficiency and comprehend waste stabilization process. The present study

acquired the molecular information for DOM in 22 waste leachate samples using ultra-performance liquid chromatography coupled with hybrid quadrupole Orbitrap mass spectrometry (UPLC Orbitrap MS/MS) based on two dimensions of retention time and mass-to-charge ratio. Unique mass peaks occupied more than 20% of the detected mass peaks in each leachate, implying that the molecular information for DOM could be the fingerprint of waste landfills and storage pits. Waste age and composition predominately accounted for this unique DOM. The double-bond equivalent increased and the H/C decreased with waste age. We further found that 57 precursor ion peaks and artificial matter (confirmed as N-butylbenzenesulfonamide) were significantly correlated with waste age by multiple test and non-target screening. These molecular characteristics of raw leachate were first determined to compensate for the evolution of leachate with waste age. The fingerprints of waste leachate can be further applied in environmental monitoring scenarios, e.g., tracing landfill leakage.

Qu, Z.G., Yin, Y., Wang, H., Zhang, J.F., 2020. Pore-scale investigation on coupled diffusion mechanisms of free and adsorbed gases in nanoporous organic matter. Fuel 260, 116423.


The long-term productivity of shale reservoirs is determined by shale gas diffusion properties in tight mudrocks, particularly in nanoporous organic matter (OM), within which the shale gas is mainly stored as free gas in the centers of pores and as adsorbed gas on pore surfaces. Although the multiple diffusion of free gas in porous media has been previously studied, the coupled diffusion mechanisms that involve both free and adsorbed gases as well as the contribution of surface diffusion induced by adsorbed gas, remain elusive. In this paper, a novel local coupled diffusivity lattice Boltzmann model (LCD-LBM), which considers both multiple diffusions of free gas and surface diffusion of adsorbed gas, is developed. The developed model allows prediction of the coupled diffusion mechanisms of free and adsorbed gases in the reconstructed nanoporous OM. The proposed model is validated by a molecular dynamic simulation result for shale gas diffusion in the nanoscale slit pore. The results show that OM diffusivity is in the magnitude order of 10−8 m2/s for an effective pore diameter of the OM ranging from 1 nm to 10 nm. The contribution of the adsorbed gas is prominent in the nanopores whose effective pore diameters are less than 2 nm. Furthermore, OM diffusivity is nearly independent of the gases diffusion direction and adsorbed gas molecules distribution pattern. The present work is conducted at the pore-scale, and thus it can be easily extended to evaluate the gas coupled diffusion mechanisms in other nanoporous materials.


https://doi.org/10.1007/s13762-018-2114-z

Comparative study on the petroleum crude oil degradation potential of microbes from petroleum-contaminated soil and non-contaminated soil was performed in the present paper. Three samples were employed to conduct the evaluation, of which two are from the petroleum-contaminated soil of Yanchang oil field, and one is from non-contaminated soil of Northwest University Campus, Xi’an. The bacterial plate counts in sample No. 1 of the petroleum-contaminated soil were 6.0 × 102 and the bacterial plate counts in sample No. 2 of the petroleum-contaminated soil were 4.0 × 103, while the bacterial plate counts in sample No. 3 of non-petroleum-contaminated were 6.0 × 104. Petroleum-degrading microbes were isolated from Bushnell Haas mineral salt medium and 16 bacterial strains and two fungal strains from PCS sample No. 1, five bacterial strains and one fungal strain from PCS sample No. 2, and 17 bacterial strains and one fungal strain from garden soil, respectively. For

primary screening of potential petroleum-degrading microbes, 2, 6-dichlorophenol indophenol test was carried out and nine bacterial strains from PCS No. 1 and four bacterial strains from garden soil showed the potential petroleum-degrading activity. The petroleum degradation percentage of mixture of 13 bacteria was 47.57%, and it was higher than that of four fungi and the combined mixture (13 bacteria and four fungi). Study showed that the microbes isolated from non-contaminated soil had the good petroleum degradation potential.

Rahayu, Y.P., Solihuddin, T., Kusumaningtyas, M.A., Afi Ati, R.N., Salim, H.L., Rixen, T., Hutahaean, A.A., 2019. The sources of organic matter in seagrass sediments and their contribution to carbon stocks in the Spermonde Islands, Indonesia. Aquatic Geochemistry 25, 161-178.

https://doi.org/10.1007/s10498-019-09358-7

Seagrass ecosystems have a potential role in climate change mitigation due to their ability to store high amount of carbon, particularly in the sediment. Studying the factors and mechanisms responsible for this storing capacity is essential to understand seagrass carbon sink function. Therefore, in this study, we identified the sources of organic carbon (Corg) in seagrass sediments and the implication to Corg stocks from four islands in the Spermonde Islands that located at different zones. We used the Bayesian stable isotope mixing model to estimate the proportional contribution of different sources to sediment carbon. Seagrass meadows that located in adjacent to high anthropogenic activities (deforestation and aquacultures) with direct exposure to wave actions, such as on the Bauluang Island, accumulated organic carbon that derived from multiple sources, where phytoplankton contributed the highest, while on the other three islands that are relatively protected from wave actions, the highest contribution (~ 75%) was from autochthonous production (seagrass-derived). Sediment Corg stocks vary spatially, ranging from 11.9 to 32.1 Mg C ha−1 (based on the obtained depth of 20–55 cm), or 40.5 to 83.5 Mg C ha−1 if extrapolated to 1 m depth. The variability of sediment properties and Corg stocks in this study is not solely determined by the geographical differences (inshore, nearshore and offshore islands), but also influenced by other local factors such as hydrodynamics that control the distribution of carbon sources, anthropogenic pressures and species composition. These factors should be taken into account when developing coastal management strategies, as efforts are being undertaken to include coastal ecosystems (including seagrass ecosystems) on the National Green House Gasses Reduction Strategy.

Rajak, P.K., Singh, V.K., Singh, P.K., Singh, M.P., Singh, A.K., 2019. Environment of paleomire of lignite seams of Bikaner-Nagaur basin, Rajasthan (W. India): petrological implications. International Journal of Oil, Gas and Coal Technology 22, 218-245.


Petrological and chemical investigations of lignites from the Bikaner-Nagaur Basin, Rajasthan (Western India) have been undertaken to understand their petrographic characteristics and the paleomire. The huminite reflectance (VRr) (0.21-0.26%) put these lignites as 'low rank C' coals. Huminite is the most abundant maceral group which is dominated by detrohuminite (densinite and attrinite). Telohuminite (chiefly ulminite-A and ulminite-B) occurs next in abundance. Liptinite and inertinite occur in subordinated amount. High GI and low TPI values indicate a continuous wet condition in the basin with a slow rate of subsidence. However, Gurha lignites, suffered few spell of relatively drier period as revealed by increased inertinite content in few bands. The study indicates a limno-telmatic swamp and a slow fall in ground water table. Petrography based models suggest a wet moor condition having a moderate flooding with increasing bacterial activity that prevailed under coastal-marshy setting during the transgressive phase.

Ranchou-Peyruse, M., Auguet, J.-C., Mazière, C., Restrepo-Ortiz, C.X., Guignard, M., Dequidt, D., Chiquet, P., Cézac, P., Ranchou-Peyruse, A., 2019. Geological gas-storage shapes deep life. Environmental Microbiology 21, 3953-3964.

https://doi.org/10.1111/1462-2920.14745

Around the world, several dozen deep sedimentary aquifers are being used for storage of natural gas. Ad hoc studies of the microbial ecology of some of them have suggested that sulfate reducing and methanogenic microorganisms play a key role in how these aquifers' communities function. Here, we investigate the influence of gas storage on these two metabolic groups by using high‐throughput sequencing and show the importance of sulfate‐reducing Desulfotomaculum and a new monophyletic methanogenic group. Aquifer microbial diversity was significantly related to the geological level. The distance to the stored natural gas affects the ratio of sulfate‐reducing Firmicutes to deltaproteobacteria. In only one aquifer, the methanogenic archaea dominate the sulfate‐reducers. This aquifer was used to store town gas (containing at least 50% H2) around 50 years ago. The observed decrease of sulfates in this aquifer could be related to stimulation of subsurface sulfate‐reducers. These results suggest that the composition of the microbial communities is impacted by decades old transient gas storage activity. The tremendous stability of these gas‐impacted deep subsurface microbial ecosystems suggests that in situ biotic methanation projects in geological reservoirs may be sustainable over time.

Reimold, W.U., Crósta, A.P., Hasch, M., Kowitz, A., Hauser, N., Sanchez, J.P., Simões, L.S.A., de Oliveira, G.J., Zaag, P.T., 2019. Shock deformation confirms the impact origin for the Cerro do Jarau, Rio Grande do Sul, Brazil, structure. Meteoritics & Planetary Science 54, 2384-2397.


Cerro do Jarau is a conspicuous, circular morpho‐structural feature in Rio Grande do Sul State (Brazil), with a central elevated core in the otherwise flat “Pampas” terrain typical for the border regions between Brazil and Uruguay. The structure has a diameter of approximately 13.5 km. It is centered at 30o12′S and 56o32′W and was formed on basaltic flows of the Cretaceous Serra Geral Formation, which is part of the Paraná‐Etendeka Large Igneous Province (LIP), and in sandstones of the Botucatu and Guará formations. The structure was first spotted on aerial photographs in the 1960s. Ever since, its origin has been debated, sometimes in terms of an endogenous (igneous) origin, sometimes as the result of an exogenous (meteorite impact) event. In recent years, a number of studies have been conducted in order to investigate its nature and origin. Although the results have indicated a possible impact origin, no conclusive evidence could be produced. The interpretation of an impact origin was mostly based on the morphological characteristics of the structure; geophysical data; as well as the occurrence of different breccia types; extensive deformation/silicification of the rocks within the structure, in particular the sandstones; and also on the widespread occurrence of low‐pressure deformation features, including some planar fractures (PFs). A detailed optical microscopic analysis of samples collected during a number of field campaigns since 2007 resulted in the disclosure of a large number of quartz grains from sandstone and monomict arenite breccia from the central part of the structure with PFs and feather features (FFs), as well as a number of quartz grains exhibiting planar deformation features (PDFs). While most of these latter grains only carry a single set of PDFs, we have observed several with two sets, and one grain with three sets of PDFs. Consequently, we here propose Cerro do Jarau as the seventh confirmed impact structure in Brazil. Cerro do Jarau, together with Vargeão Dome (Santa Catalina state) and Vista Alegre (Paraná State), is one of very few impact structures on Earth formed in basaltic rocks.

Ren, C., He, F., Gao, X., Wu, D., Yao, W., Tian, J., Guo, H., Huang, Y., Wang, L., Feng, H., Li, J., 2019. Prediction of exploration targets based on integrated analyses of source rock and simulated hydrocarbon migration direction: a case study from the gentle slope of Shulu Sag, Bohai Bay Basin, northern China. Geosciences Journal 23, 977-989.

https://doi.org/10.1007/s12303-018-0078-0

The Shulu Sag which is a rifted sag with NNE trend is located in the south of Jizhong Depression, Bohai Bay Basin, northern China. The gentle slope and three troughs are situated in the west and east of the sag, respectively. Both of the lower part of Shasan Member (Es3x) and the lower part of Shayi Member (Es1x) act as source rocks in this sag. Researches on the type, quantity, quality and thermal maturity of the respective organic matter have been conducted using Rock-Eval pyrolysis data. Type II is the dominant kerogen in Es1x of all troughs. However, Type II1 and III is the dominant kerogen in Es3x of Middle-Southern and Northern trough, respectively. TOC (total organic carbon) and pyrolysis S2 (hydrocarbon) values suggest that the Es1x source rocks in Middle-Southern and Northern trough are fair to good and poor to fair generative potential of hydrocarbon, separately. The Es3x source rocks in Middle-Southern and Northern trough possess fair to excellent and poor to fair generative potential of hydrocarbon, individually. Tmax (pyrolysis temperature at maximum S2) values indicate that most of Es3x samples are thermally mature, but all Es1x samples are thermally immature. Under large scale condition, the hydrocarbon secondary migration in the upper part of Shasan Member (Es3s), Shaer Member (Es2) and the upper part of Shayi Member (Es1s) have been simulated using fluid potential model with Arcgis 9.3 software. The simulation results reveal the direction of hydrocarbon secondary migration and the distribution of hydrocarbon migration-accumulation units (HMAUS), and also suggest that the hydrocarbon migration direction is obviously controlled by nose-like structure belts where most of hydrocarbons accumulate. That shows high reliability because they are consistent with the hydrocarbon exploration result in this area. On the basis of integrated analyses of source rocks and hydrocarbon migration direction, the following five areas in the gentle slope are identified to be the preferred hydrocarbon accumulation area: Taijiazhuang area, northern and southern Xicaogu area, as well as northern and southern Leijiazhuang area. It is considerably helpful to reduce the risk in hydrocarbon exploration of Shulu Sag.



With the rising plastic pollution in the oceans, research on the plastisphere—the microorganisms interacting with marine plastic debris—has emerged. Microbial communities colonizing plastic have been characterized from several ocean regions and they are distinct from the communities of the surrounding waters, and a few plastic-degrading microorganisms have been isolated from other environments. Therefore, we propose that marine microorganisms have adapted to plastic as a surface for colonization and potentially degradation. When comparing the taxonomic patterns of plastic-associated, marine bacteria, recurring groups and families such as the families Erythrobacteraceae and Rhodobacteraceae (Alphaproteobacteria), Flavobacteriaceae (Bacteriodetes), and the phylum of cyanobacteria (such as the Phormidium genus) can be identified. Thereby, we provide a perspective on which bacterial candidates could play a role in the colonization and possible degradation of plastic in the oceans due to their occurrence on marine plastic debris. We emphasize the need for extended and reproducible collection of data to assess the existence of a core microbiome or core functionalities of the plastisphere and confirm the capability of these bacterial candidates for

biodegradation of plastic. Furthermore, we suggest the next steps in research to elucidate the level of natural bioremediation and the exploitation of bacterial degradative mechanisms of plastic.

Rogel, E., Moir, M.E., Hurt, M., Miao, T., Lee, E., 2019. Asphaltene and maltene adsorption into graphene. Energy & Fuels 33, 9538-9545.


In this work, the mechanism by which insoluble asphaltenes represented by small graphene fragments interact with different components of crude oils is explored. Adsorption isotherms of maltenes and asphaltenes into graphene from toluene were determined by the depletion method. The results indicate that the adsorption of these heavy fractions occurs in two steps: after the initial adsorption, a plateau is reached that seems to follow a Langmuir type adsorption isotherm. In the second step, at higher concentrations, the adsorbed amount starts to increase sharply after an inflection point indicating strong interactions between the adsorbates. A multilayer adsorption model was successful in describing this adsorption behavior. Dispersion of graphene in the solution was observed for some of the samples in the concentration range studied. It was found that asphaltenes can disperse graphene at lower concentrations than maltenes. From the same crude oil, it was observed that heptane-extracted asphaltenes disperse graphene at lower concentrations than the pentane-extracted ones. Mass spectrometry analysis of the species of molecules left in the solution after adsorption shows the preferential adsorption of highly aromatic molecules, high molecular weight molecules, and molecules containing several heteroatoms. A reduction of 92% on the relative abundance of porphyrins points to a great affinity of these species to graphene. These results indicate that graphene-like molecules in hydrocarbons cannot remain in solution unless they are dispersed by other components. Therefore, the existence of a critical nanoaggregate concentration for these crude oil components is unlikely.



In this work, the compositional changes of asphaltene deposits as a function of time were analyzed. It has been demonstrated using ultrahigh-resolution magnetic resonance mass spectrometry that the precipitation of asphaltenes is a dynamic process where the composition of the deposit shows variations that are linked to the exchange of molecules between the deposit and fluid. The detailed analysis of the nature of the species that were exchanged during this process indicates that the species that are more aromatic and richer in heteroatom molecules are less soluble and become enriched in the deposit as it ages, as those that are less aromatic with fewer heteroatoms go back into the fluid. It was also found that the oxygen-containing species that precipitate are less aromatic and have smaller sizes than those that do not contain oxygen. This is an indication that for these molecules, hydrogen bond and dipole–dipole interactions might play a significant role in their solubility, while for the species that do not contain oxygen, the driving force for precipitation is aromaticity. These findings support a previously proposed model that suggests that during aging, the aggregates become more organized as the more soluble molecules are expelled, whereas others, the less soluble molecules, are incorporated into the precipitated material.

Romera-Castillo, C., Álvarez, M., Pelegrí, J.L., Hansell, D.A., Álvarez-Salgado, X.A., 2019. Net additions of recalcitrant dissolved organic carbon in the deep Atlantic Ocean. Global Biogeochemical Cycles 33, 1162-1173.

https://doi.org/10.1029/2018GB006162

Most dissolved organic carbon (DOC) sequestered in the deep ocean has residence times of decades to thousands of years, with clear implications for climate regulation, though some net removal is typically observed with increasing water mass age. Here, a high‐quality‐high‐resolution data set has allowed us to identify net additions of recalcitrant DOC in specific water masses of the deep South Atlantic. Overall, the South Atlantic is a net source of recalcitrant DOC, adding 0.027 ± 0.019 Pg C/year, while the North Atlantic is a net sink that removes 0.298 ± 0.141 Pg C/year. We find that the balance of addition/removal of recalcitrant DOC depends not only on the origin but also on the temperature, age, and depth of the water masses that circulate and mix in the Atlantic Ocean. Future changes in the water mass composition and circulation patterns due to climate change would eventually affect that balance, altering the carbon cycle.

Roostaie, M., Leonenko, Y., 2020. Analytical modeling of methane hydrate dissociation under thermal stimulation. Journal of Petroleum Science and Engineering 184, 106505.


In this study, a one-dimensional analytical model to describe heat and mass transfer during methane hydrate dissociation under thermal stimulation in porous media has been developed. The model is based on a similarity solution that considers a moving dissociation boundary which separates the dissociated zone containing produced gas and water from the un-dissociated zone containing only methane hydrate. The results of temperature distribution, pressure distribution, energy efficiency, and parametric study considering various initial and boundary conditions as well as various reservoir properties are presented and compared with previous studies. Sensitivity analysis of gas production on reservoir properties is also presented in this paper. The dissociation boundary moves faster by increasing the heat source temperature while decreasing the heat source pressure simultaneously, but the associated energy efficiency decreases. Increasing the well thickness has a negative effect on the energy efficiency of the process. Among the proposed thermal properties of the system, only the thermal diffusivities and conductivities of the reservoir as well as the porosity of the sediment affect the dissociation. The main contribution of this work is investigating analytically the hydrate dissociation using thermal stimulation by taking into account the effect of wellbore thickness and structure.

Rosset, T., Binet, S., Antoine, J.-M., Lerigoleur, E., Rigal, F., Gandois, L., 2019. Drivers of seasonal and event scale DOC dynamics at the outlet of mountainous peatlands revealed by high frequency monitoring. Biogeosciences Discussions 2019, 1-33.


Peatlands store about 20 % of the global soil organic carbon stock and are an important source of dissolved organic carbon (DOC) for inland waters. Recent improvements for in situ optical monitoring revealed that the DOC concentration in streams draining peatlands is highly variable, showing seasonal variation and short and intense DOC concentration peak periods. This study aimed to determine the variables driving stream DOC concentration variations at seasonal and event scales. Two mountainous peatlands (one fen and one bog) were monitored in the French Pyrenees to capture

their outlet DOC concentration variability at a high frequency rate (30 min). Abiotic variables including precipitation, stream temperature and water level, water table depth and peat water temperature were also monitored at high frequency and used as potential predictors to explain DOC concentration variability. Results show that at both sites, DOC concentration time series can be decomposed into a seasonal baseline interrupted by many short and intense peaks of higher concentrations. The DOC concentration baseline is driven, at the seasonal scale, by peat water temperature. At the event scale, DOC concentration increases are mostly driven by water table increases within the peat at both sites. Univariate linear models between DOC concentration and peat water temperature or water table increases show greater efficiency at the fen site. Water recession times were derived from water level time series using master recession curve coefficients. They vary greatly between bog and fen but also within one peatland site. They partly explain the differences between DOC dynamics in the studied peatlands, including porewater DOC concentrations and the links between stream DOC concentration and water table rise. This highlights that peatland complexes are composed of a mosaic of heterogeneous peat units distinctively producing or transferring DOC to streams.

Roux, S., Krupovic, M., Daly, R.A., Borges, A.L., Nayfach, S., Schulz, F., Sharrar, A., Matheus Carnevali, P.B., Cheng, J.-F., Ivanova, N.N., Bondy-Denomy, J., Wrighton, K.C., Woyke, T., Visel, A., Kyrpides, N.C., Eloe-Fadrosh, E.A., 2019. Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes. Nature Microbiology 4, 1895-1906.

https://doi.org/10.1038/s41564-019-0510-x

Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content and infection cycle. One of the most striking features of inoviruses is their ability to establish a chronic infection whereby the viral genome resides within the cell in either an exclusively episomal state or integrated into the host chromosome and virions are continuously released without killing the host. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications, such as phage display, or because of their effect on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis. Here, we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly diverse group of inoviruses. Using a machine learning approach leveraging a combination of marker gene and genome features, we identified 10,295 inovirus-like sequences from microbial genomes and metagenomes. Collectively, our results call for reclassification of the current Inoviridae family into a viral order including six distinct proposed families associated with nearly all bacterial phyla across virtually every ecosystem. Putative inoviruses were also detected in several archaeal genomes, suggesting that, collectively, members of this supergroup infect hosts across the domains Bacteria and Archaea. Finally, we identified an expansive diversity of inovirus-encoded toxin–antitoxin and gene expression modulation systems, alongside evidence of both synergistic (CRISPR evasion) and antagonistic (superinfection exclusion) interactions with co-infecting viruses, which we experimentally validated in a Pseudomonas model. Capturing this previously obscured component of the global virosphere may spark new avenues for microbial manipulation approaches and innovative biotechnological applications.

Saha, R., Sharma, A., Uppaluri, R.V.S., Tiwari, P., 2019. Interfacial interaction and emulsification of crude oil to enhance oil recovery. International Journal of Oil, Gas and Coal Technology 22, 1-15.

https://www.inderscience.com/info/inarticle.php?artid=102281

This work addresses the characterisation of crude oil to examine opportunities for chemical enhanced oil recovery. Interfacial tension (IFT) studies were conducted for alkalis (NaOH and Na2CO3), surfactants (cetyltrimethylammonium bromide and sodium dodecyl sulphate), and their combinations. IFT studies revealed that the optimum concentrations of individual alkalis, NaOH and Na2CO3 are 0.1 wt%, 0.25 wt% for which IFT values of 5.15 × 10−2 and 0.40 mN/m have been obtained respectively. For synergy of alkali-surfactant, the complex IFT behaviour indicated values in the range of 10−2 mN/m. Emulsification and sandpack flooding studies affirmed that alkali and alkali-surfactant flooding can provide 24.25% and 38.79% residual oil recovery, respectively.

Sakthivel, S., Adebayo, A., Kanj, M.Y., 2019. Experimental evaluation of carbon dots stabilized foam for enhanced oil recovery. Energy & Fuels 33, 9629-9643.


Foams are used as divergent fluids for conformance control in enhanced oil recovery (EOR) operations. It is created by mixing a surfactant and a gas in situ in high-permeability reservoirs (e.g., surfactant alternating gas or SAG). Foams exhibit instability issues at reservoir conditions with a highly complex pore network, high pressure, high temperature, and high salinity. Here, we examine the stability and efficacy of foams formed with and without the addition of carbon nanoparticles (or nanodots). Carbon particles have demonstrated stability, mobility, and scalability for harsh reservoir environment use and application as a tracer technology. In this study, we investigate the feasibility of using inexpensive carbon dots as “foam boosters.” The experiments involved using different levels of brine salinities (ranging from seawater to formation connate water), different concentrations of the nanodots (ranging from 5 to 500 ppm), different types of surfactants (anionic, cationic, and nonionic) and gases (CO2, N2, and air), and different levels of temperature (ranging from 27 to 100 °C) to target representative conditions of Saudi Arabian reservoirs. In addition, we examined both foam structure, such as the gas–liquid interface, and liquid film lamella to better understand the mechanisms contributing to foamability and foam stability. The study highlights and unravels the complex interrelationship of the different influencing components on the stability of foam with the addition of the carbon particles. The bulk and porous media stabilities of the foams are analyzed using a static foam analyzer and an HP/HT core-flood system, respectively. Foam stability is assessed in terms of type and amount of modified/functionalized carbon particles, surfactant, and gas. We observed that the bulk foam containing only trace amounts (5–10 ppm) of carbon nanodots shows improved stability in a high-salinity medium. The particles improved the foam stability maximum by 70% and more than doubled the foam half-life for some foams. Confocal microscopy images of the foam structure of systems containing an increased concentration of carbon particles reveal an increased thickness of the lamellae and a decreased average bubble size. This is a clear indication of the enhanced foam stability. Carbon dots decreased the drainage rate of the lamellae and delayed the bubble rupture point or coalescence. The particles improved the foam stability by preferentially positioning itself in the lamella and preventing liquid drainage and film thinning.

Salcher, M.M., Schaefle, D., Kaspar, M., Neuenschwander, S.M., Ghai, R., 2019. Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae. The ISME Journal 13, 2764-2777.

https://doi.org/10.1038/s41396-019-0471-3

The most abundant aquatic microbes are small in cell and genome size. Genome-streamlining theory predicts gene loss caused by evolutionary selection driven by environmental factors, favouring superior competitors for limiting resources. However, evolutionary histories of such abundant,

genome-streamlined microbes remain largely unknown. Here we reconstruct the series of steps in the evolution of some of the most abundant genome-streamlined microbes in freshwaters (“Ca. Methylopumilus”) and oceans (marine lineage OM43). A broad genomic spectrum is visible in the family Methylophilaceae (Betaproteobacteria), from sediment microbes with medium-sized genomes (2–3 Mbp genome size), an occasionally blooming pelagic intermediate (1.7 Mbp), and the most reduced pelagic forms (1.3 Mbp). We show that a habitat transition from freshwater sediment to the relatively oligotrophic pelagial was accompanied by progressive gene loss and adaptive gains. Gene loss has mainly affected functions not necessarily required or advantageous in the pelagial or is encoded by redundant pathways. Likewise, we identified genes providing adaptations to oligotrophic conditions that have been transmitted horizontally from pelagic freshwater microbes. Remarkably, the secondary transition from the pelagial of lakes to the oceans required only slight modifications, i.e., adaptations to higher salinity, gained via horizontal gene transfer from indigenous microbes. Our study provides first genomic evidence of genome reduction taking place during habitat transitions. In this regard, the family Methylophilaceae is an exceptional model for tracing the evolutionary history of genome streamlining as such a collection of evolutionarily related microbes from different habitats is rare in the microbial world.

Saleh, F., Antcliffe, J.B., Lefebvre, B., Pittet, B., Laibl, L., Perez Peris, F., Lustri, L., Gueriau, P., Daley, A.C., 2020. Taphonomic bias in exceptionally preserved biotas. Earth and Planetary Science Letters 529, 115873.


Exceptionally preserved fossil biotas provide crucial data on early animal evolution. Fossil anatomy allows for reconstruction of the animal stem lineages, informing the stepwise process of crown group character acquisition. However, a confounding factor to these evolutionary analyses is information loss during fossil formation. Here we identify that the Ordovician Fezouata Shale has a clear taphonomic difference when compared to the Cambrian Burgess Shale and Chengjiang Biota. In the Fezouata Shale, soft cellular structures are most commonly associated with partially mineralized and sclerotized tissues, which may be protecting the soft tissue. Also, entirely soft non-cuticularized organisms are absent from the Fezouata Shale. Conversely, the Cambrian sites commonly preserve entirely soft cellular bodies and a higher diversity of tissue types per genus. The Burgess and Chengjiang biotas are remarkably similar, preserving near identical proportions of average tissue types per genus. However, the Burgess shale has almost double the proportion of genera that are entirely soft as compared to the Chengjiang Biota, indicating that the classic Burgess Shale was the acme for soft tissue preservation. Constraining these biases aids the differentiation of evolutionary and taphonomic absences, which is vital to incorporating anatomical data into a coherent framework of character acquisition during the earliest evolution of animals.



Drill core UNAM‐7, obtained 126 km from the center of the Chicxulub impact structure, outside the crater rim, contains a sequence of 126.2 m suevitic, silicate melt‐rich breccia on top of a silicate melt‐poor breccia with anhydrite megablocks. Total reflection X‐ray fluorescence analysis of altered silicate melt particles of the suevitic breccia shows high concentrations of Br, Sr, Cl, and Cu, which may indicate hydrothermal reaction with sea water. Scanning electron microscopy and energy‐

dispersive spectrometry reveal recrystallization of silicate components during annealing by superheated impact melt. At anhydrite clasts, recrystallization is represented by a sequence of comparatively large columnar, euhedral to subhedral anhydrite grains and smaller, polygonal to interlobate grains that progressively annealed deformation features. The presence of voids in anhydrite grains indicates SOx gas release during anhydrite decomposition. The silicate melt‐poor breccia contains carbonate and sulfate particles cemented in a microcrystalline matrix. The matrix is dominated by anhydrite, dolomite, and calcite, with minor celestine and feldspars. Calcite‐dominated inclusions in silicate melt with flow textures between recrystallized anhydrite and silicate melt suggest a former liquid state of these components. Vesicular and spherulitic calcite particles may indicate quenching of carbonate melts in the atmosphere at high cooling rates, and partial decomposition during decompression at postshock conditions. Dolomite particles with a recrystallization sequence of interlobate, polygonal, subhedral to euhedral microstructures may have been formed at a low cooling rate. We conclude that UNAM‐7 provides evidence for solid‐state recrystallization or melting and dissociation of sulfates during the Chicxulub impact event. The lack of anhydrite in the K‐Pg ejecta deposits and rare presence of anhydrite in crater suevites may indicate that sulfates were completely dissociated at high temperature (T > 1465 °C)—whereas ejecta deposited near the outer crater rim experienced postshock conditions that were less effective at dissociation.

Salim, F., Górecki, T., 2019. Theory and modelling approaches to passive sampling. Environmental Science: Processes & Impacts 21, 1618-1641.

http://dx.doi.org/10.1039/C9EM00215D

Designs and applications of passive samplers for various environmental compartments have been broadened significantly since their introduction. Understanding the theory behind passive sampling is essential for proper development of sampling methods and for accurate interpretation of the results. Theoretical underpinnings of passive sampling have been explored using different approaches. The aim of this review is to describe passive sampling theory and modelling approaches presented in the literature in a manner that allows researchers to obtain comprehensive understanding of them and to recognize the assumptions behind each approach together with their applicability to a given passive sampling technique. A common approach originates from Whitman's two-film theory and produces an exponential model that describes the entire passive sampling process. This approach, however, is based on several assumptions including linear exchange kinetics between the sampled medium and the passive sampler. Two-phase air passive samplers with a well-defined barrier are commonly modeled based on the zero-sink assumption, which assumes efficient trapping of analytes in the receiving phase. This assumption may become invalid under various scenarios; consequently, other approaches to modelling have been introduced including simulation of the sampling process by approximate temporal-steady states in hypothetical segments in the adsorption phase. Another approach uses dynamic models to determine accumulation of analytes in passive samplers. Dynamic models are capable of describing mass accumulation in the passive sampler, its transient response, and its response to fluctuations in environmental concentrations. Finally, empirically calibrated models, attempting to simplify the process of passive sampling rate determination, are also presented. In general, dynamic models are used to establish a profound understanding of the sampling process and analyse the applicability of the simpler models and their assumptions, while the simplified models are desirable and practical for most users. Nonetheless, due to the advancement in the computational tools, application of the dynamic models could be made simple and user-friendly.

Sangok, F.E., Sugiura, Y., Maie, N., Melling, L., Nakamura, T., Ikeya, K., Watanabe, A., 2020. Variations in the rate of accumulation and chemical structure of soil organic matter in a coastal peatland in Sarawak, Malaysia. CATENA 184, 104244.


To determine the variation in the rate of accumulation and chemical structure of soil organic matter (SOM) in a tropical coastal peatland, series of soil cores samples were collected in the Maludam National Park, Sarawak, Malaysia and analyzed. Duplicate soil core samples were collected from three phasic communities in the peat swamp forests, Mixed Peat Swamp (MPS; depth of 50–450 cm), Alan Batu (ABt; depth of 200–700 cm), and Alan Bunga (ABg; depth of 200–800 cm), which were located at outer, middle, and inner sites on the peat dome. The 14C age of the SOM was determined at depths of every 50 or 100 cm and 4–6 samples from each profile were subjected to ramp cross polarization/magic angle spinning 13C nuclear magnetic resonance (NMR) analysis. The 14C age of SOM ranged from 1602 to 5162 years before the present (yBP), 1134–4043 yBP, and 928–3376 yBP in the cases of the MPS, ABt, and ABg forests, respectively. Those after calibration were in the ranges of 1482–5958 (MPS), 1322–4603 (ABt), and 837–3629 (ABg) yBP. The relationship between calibrated 14C age and soil depth, when regressed to a linear function with the constraint that the age of surface sediment is 0 year, showed that the rate of peat accumulation was 0.60 ± 0.01 (MPS), 1.5 ± 0.0 (ABt), and 1.9 ± 0.1 (ABg) mm y−1. However, in the case of the MPS forest, this rate was not constant but decreased toward the present. The 13C NMR results showed the decrease in the relative abundance of alkyl C and an increase in that of carbohydrate C with soil age/depth in the MPS forest soil profiles, suggesting an acceleration in the decomposition of SOM as the cause of the decrease in the rate of accumulation of the peat. Variations in the C composition of the other two forest soils with soil age were small. The relative content of aromatic C remained relatively constant, indicating that aromatic C is consistently a major component of the C pool throughout the peat soil layers.

Sannomiya, T., Arai, Y., Nagayama, K., Nagatani, Y., 2019. Transmission electron microscope using a linear accelerator. Physical Review Letters 123, 150801.

https://link.aps.org/doi/10.1103/PhysRevLett.123.150801

High-voltage transmission electron microscopes (HVTEMs), which can visualize internal structures of micron thick samples, intrinsically have large instrument sizes because of the static voltage isolation. In this Letter, we develop a compact HVTEM, employing a linear accelerator, a subpicosecond beam chopper, and a linear decelerator. 100 kV electrons initially accelerated by a static field are accelerated at radio frequency (rf) up to 500 kV, transmitting through the sample and finally rf decelerated down to 200 kV to be imaged through a 200 kV energy filter. 500 kV imaging, as well as subnanometer resolution at 200 kV, have been demonstrated.

Savenko, A.V., Pokrovsky, O.S., 2019. Distribution of dissolved matter in the Yenisei estuary and adjacent Kara Sea areas and its inter-annual variability. Geochemistry International 57, 1201-1212.

https://doi.org/10.1134/S0016702919110089

he distribution of dissolved matter (major ions, nutrients, and trace elements) in the estuary of the Yenisei River and nearby areas of the Kara Sea was studied based on natural observations data acquired in 2009–2016. These results were compared with literature hydrochemical data on the area. It was demonstrated that the transport of major ions (Na, K, Mg, Ca, and SO4) and some trace elements (Li, Rb, Cs, Sr, B, F, Cr, Ge, As, Mo, and U) is described by equations (which remain

unchanging during long periods of time) of conservative mixing between riverine and marine waters. Although alkalinity is a conservative component, its distribution exhibits a significant spatiotemporal variability, which is caused by the complex hydrological structure of the Yenisei Bay and adjoining part of the Kara Sea. Concentrations of Pmin, Si, and V in the desalinized waters of the photic layer decrease seaward during the vegetation period owing to uptake by phytoplankton. The losses of these elements reach 30–57, 30, and 9%, respectively, of their supply with riverine runoff. The contents of dissolved Pmin and V in the intermediate and bottom water layers of the Yenisei estuary strongly increase with increasing salinity due to the regeneration of the precipitated organic matter, whereas silica remineralization is much less intense. As much as 20–100% dissolved Ba in the riverine runoff is intensely desorbed from suspended matter, depending on seasonal variations in chemical composition of the runoff, throughout the whole estuary. The transport of dissolved forms of heavy metals (Mn, Fe, and Pb) and hydrolysate elements (Al, Ti, Y, La, Ce, and Pr) in the mixing zone of riverine and marine water masses is likely controlled by the coagulation and flocculation of organic and organomineral colloids, as follows from the decrease (by 20–61%) in the concentrations of these elements during initial salinization and subsequent approach to the characteristics of the seawater.

Scerri, E.M.L., Chikhi, L., Thomas, M.G., 2019. Beyond multiregional and simple out-of-Africa models of human evolution. Nature Ecology & Evolution 3, 1370-1372.

https://doi.org/10.1038/s41559-019-0992-1

The past half century has seen a move from a multiregionalist view of human origins to widespread acceptance that modern humans emerged in Africa. Here the authors argue that a simple out-of-Africa model is also outdated, and that the current state of the evidence favours a structured African metapopulation model of human origins.

Schmidt, R., Ulanova, D., Wick, L.Y., Bode, H.B., Garbeva, P., 2019. Microbe-driven chemical ecology: past, present and future. The ISME Journal 13, 2656-2663.

https://doi.org/10.1038/s41396-019-0469-x

In recent years, research in the field of Microbial Ecology has revealed the tremendous diversity and complexity of microbial communities across different ecosystems. Microbes play a major role in ecosystem functioning and contribute to the health and fitness of higher organisms. Scientists are now facing many technological and methodological challenges in analyzing these complex natural microbial communities. The advances in analytical and omics techniques have shown that microbial communities are largely shaped by chemical interaction networks mediated by specialized (water-soluble and volatile) metabolites. However, studies concerning microbial chemical interactions need to consider biotic and abiotic factors on multidimensional levels, which require the development of new tools and approaches mimicking natural microbial habitats. In this review, we describe environmental factors affecting the production and transport of specialized metabolites. We evaluate their ecological functions and discuss approaches to address future challenges in microbial chemical ecology (MCE). We aim to emphasize that future developments in the field of MCE will need to include holistic studies involving organisms at all levels and to consider mechanisms underlying the interactions between viruses, micro-, and macro-organisms in their natural environments.

Schneider, S.R., Collins, D.B., Lim, C.Y., Zhu, L., Abbatt, J.P.D., 2019. Formation of secondary organic aerosol from the heterogeneous oxidation by ozone of a phytoplankton culture. ACS Earth and Space Chemistry 3, 2298-2306.


The sea surface microlayer (SSML) is often present at the ocean interface and provides a unique environment for chemical reactions to occur. One such reaction is the heterogeneous oxidation of the SSML components with ozone, which is hypothesized to be an important source of volatile compounds that may participate in marine aerosol formation and growth. To better understand this source, a biologically relevant model SSML is constructed using axenic Thalassiosira pseudonana cultures. This model SSML is shown to be reasonably reproducible for repeated experiments with a biological system and offers considerably more chemical and morphological complexities than single-molecule SSML representations for trying to understand the impact of marine biological processes on the atmosphere. Using proton transfer reaction mass spectrometry, this study demonstrates that C7–C10 gas-phase carbonyls arise from the oxidation of the model SSML with ozone. The ability of gas-phase products of ozone oxidation at the SSML to form aerosol particles was investigated with a scanning mobility particle sizer analyzer to determine the particle size and concentration of newly formed ultrafine aerosol particles. These particles are confirmed to be secondary organic aerosol (SOA) by analyzing their composition with an aerosol mass spectrometer, indicating that the source of the aerosol precursors is the organic material generated by the T. pseudonana cultures. The rates of SOA and carbonyl production are larger for 21 day-old cultures than for 7 day-old cultures, likely due to the release of the organic material from cell lysis in the older cultures. By demonstrating that the heterogeneous oxidation of the SSML forms SOA precursors that contribute to aerosol growth, this study emphasizes the importance of biological processes on the chemical reactions that can occur within the SSML.

Schobben, M., van de Schootbrugge, B., Wignall, P.B., 2019. Interpreting the carbon isotope record of mass extinctions. Elements 15, 331-337.


Mass extinctions are global-scale environmental crises marked by the loss of numerous species from all habitats. They often coincide with rapid changes in the stable carbon isotope ratios (13C/12C) recorded in sedimentary carbonate and organic matter, ratios which can indicate substantial inputs to the surface carbon reservoirs and/or changes in the cycling of carbon. Models to explain these changes have provided much fuel for debate on the causes and consequences of mass extinctions. For example, the escape of methane from gas hydrate deposits or the emission of huge volumes of gaseous carbon from large-scale volcanic systems, known as large igneous provinces, may have been responsible for decreases of 13C/12C in sedimentary deposits. In this article, we discuss the challenges in distinguishing between these, and other, alternatives.

Schulz, T., Sackl, F., Fragner, E., Luguet, A., van Acken, D., Abate, B., Badjukov, D.D., Koeberl, C., 2020. The Zhamanshin impact structure, Kazakhstan: A comparative geochemical study of target rocks and impact glasses. Geochimica et Cosmochimica Acta 268, 209-229.


The Zhamanshin impact structure, which is about 1 Myr old, has a diameter of 14 km and is situated in the semi-arid region of Kazakhstan (48°24′N, 60°58′E). It has a heterogeneous suite of target rocks, including predominantly crustal lithologies (e.g., clays and siltstones) with minor ultramafics.

Zhamanshin is known for its unique association of impact glasses, including basic and acidic varieties of zhamanshinites and (tektite-like and a few aerodynamically-shaped) irghizites. The origin of both

of these impact glasses has long been debated, which is complicated by incomplete sampling of target lithologies at the Zhamanshin site and a limited number of isotopic analyses. However, such studies are a prerequisite for a comprehensive discussion of the mechanisms that formed the unique association of different impact glasses in one impact event.

We present major and trace element contents, as well as combined Sr-Nd isotope data for target rocks and impact glasses from the Zhamanshin impact structure. These data, for the first time, include Paleogene clays and siltstones from a core drilled in the vicinity of the crater and cutting through all major target lithologies. The core samples contain important source lithologies for the impactites from the Zhamanshin area.

Mixing calculations, based on geochemical data and Sr-Nd isotope signatures, indicate that irghizites and Si-rich zhamanshinites can be produced from variously homogenized mixtures of mainly clays and siltstones with minor additions of ultrabasic rocks. Based on highly siderophile element (HSE) and Os isotope data (including the first analyses of the clay and siltstone lithologies) we calculated a hypothetical Os composition of the irghizite precursor, allowing us to approximate a chondritic admixture to the irghizites of roughly 1% of a chondritic component. This confirms previous suggestions about the amount of extraterrestrial components. A new HSE and Os isotope dataset for five zhamanshinites reveals, on average, crust-like HSE concentrations and Os isotope compositions, confirming earlier suggestions of a lack of meteoritic admixtures to these impact glasses.

Seknazi, E., Kozachkevich, S., Polishchuk, I., Bianco Stein, N., Villanova, J., Suuronen, J.-P., Dejoie, C., Zaslansky, P., Katsman, A., Pokroy, B., 2019. From spinodal decomposition to alternating layered structure within single crystals of biogenic magnesium calcite. Nature Communications 10, 4559.

https://doi.org/10.1038/s41467-019-12168-8

As organisms can form crystals only under ambient conditions, they demonstrate fascinating strategies to overcome this limitation. Recently, we reported a previously unknown biostrategy for toughening brittle calcite crystals, using coherently incorporated Mg-rich nanoprecipitates arranged in a layered manner in the lenses of a brittle star, Ophiocoma wendtii. Here we propose the mechanisms of formation of this functional hierarchical structure under conditions of ambient temperature and limited solid diffusion. We propose that formation proceeds via a spinodal decomposition of a liquid or gel-like magnesium amorphous calcium carbonate (Mg-ACC) precursor into Mg-rich nanoparticles and a Mg-depleted amorphous matrix. In a second step, crystallization of the decomposed amorphous precursor leads to the formation of high-Mg particle-rich layers. The model is supported by our experimental results in synthetic systems. These insights have significant implications for fundamental understanding of the role of Mg-ACC material transformation during crystallization and its subsequent stability.

Semenova, E.M., Sokolova, D.S., Grouzdev, D.S., Poltaraus, A.B., Vinokurova, N.G., Tourova, T.P., Nazina, T.N., 2019. Geobacillus proteiniphilus sp. nov., a thermophilic bacterium isolated from a high-temperature heavy oil reservoir in China. International Journal of Systematic and Evolutionary Microbiology 69, 3001-3008.

https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.003486

A rod-shaped, spore-forming, thermophilic, chemoorganotrophic, aerobic or facultatively anaerobic bacterial strain, 1017T, was isolated from production water sampled at the Dagang oilfield (PR China), and was characterized by using a polyphasic approach. The strain is capable of anaerobic

glucose fermentation. Nitrate is reduced to nitrite. Optimal growth was observed at 60–65 °C, at pH between pH 7.0 and 7.5, and with 1–2 % (w/v) NaCl. The major cellular fatty acids were iso-C17 : 0, anteiso-C17 : 0, iso-C15 : 0, iso-C16 : 0 and C16 : 0. The predominant polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. Phylogenetic analysis based on the 16S rRNA, gyrB and parE gene sequences indicated that the isolate belonged to the genus Geobacillus and was most closely related to Geobacillus thermoleovorans KCTC 3570T (99.5, 96.1 and 97.9 % sequence similarity, respectively). Genome sequencing revealed a genome size of 3.57495 Mb and a DNA G+C content of 51.8 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between the genomes of strain 1017T and G. thermoleovorans KCTC 3570T were 95.9 and 64.9 %, respectively. Results of phylogenomic metrics analysis of the genome and 1172 core genes of strain 1017T and its physiological and biochemical characteristics confirmed that strain 1017T represented a novel species of the genus Geobacillus , for which the name Geobacillus proteiniphilus sp. nov. is proposed. The type strain is 1017T (=VKM B-3132T=KCTC 33986T).

Sengupta, A., Indivero, J., Gunn, C., Tfaily, M.M., Chu, R.K., Toyoda, J., Bailey, V.L., Ward, N.D., Stegen, J.C., 2019. Spatial gradients in the characteristics of soil-carbon fractions are associated with abiotic features but not microbial communities. Biogeosciences 16, 3911-3928.


Coastal terrestrial–aquatic interfaces (TAIs) are dynamic zones of biogeochemical cycling influenced by salinity gradients. However, there is significant heterogeneity in salinity influences on TAI soil biogeochemical function. This heterogeneity is perhaps related to unrecognized mechanisms associated with carbon (C) chemistry and microbial communities. To investigate this potential, we evaluated hypotheses associated with salinity-associated shifts in organic C thermodynamics; biochemical transformations; and nitrogen-, phosphorus-, and sulfur-containing heteroatom organic compounds in a first-order coastal watershed on the Olympic Peninsula of Washington, USA. In contrast to our hypotheses, thermodynamic favorability of water-soluble organic compounds in shallow soils decreased with increasing salinity (43–867 µS cm−1), as did the number of inferred biochemical transformations and total heteroatom content. These patterns indicate lower microbial activity at higher salinity that is potentially constrained by accumulation of less-favorable organic C. Furthermore, organic compounds appeared to be primarily marine- or algae-derived in forested floodplain soils with more lipid-like and protein-like compounds, relative to upland soils that had more lignin-, tannin-, and carbohydrate-like compounds. Based on a recent simulation-based study, we further hypothesized a relationship between C chemistry and the ecological assembly processes governing microbial community composition. Null modeling revealed that differences in microbial community composition – assayed using 16S rRNA gene sequencing – were primarily the result of limited exchange of organisms among communities (i.e., dispersal limitation). This results in unstructured demographic events that cause community composition to diverge stochastically, as opposed to divergence in community composition being due to deterministic selection-based processes associated with differences in environmental conditions. The strong influence of stochastic processes was further reflected in there being no statistical relationship between community assembly processes (e.g., the relative influence of stochastic assembly processes) and C chemistry (e.g., heteroatom content). This suggests that microbial community composition does not have a mechanistic or causal linkage to C chemistry. The salinity-associated gradient in C chemistry was, therefore, likely influenced by a combination of spatially structured inputs and salinity-associated metabolic responses of microbial communities that were independent of community composition. We propose that impacts of salinity on coastal soil biogeochemistry need to be understood in the context of C chemistry, hydrologic or depositional dynamics, and microbial physiology, while microbial composition may have less influence.

Seto, M., Noguchi, K., Cappellen, P.V., 2019. Potential for aerobic methanotrophic metabolism on Mars. Astrobiology 19, 1187-1195.

https://doi.org/10.1089/ast.2018.1943

Observational evidence supports the presence of methane (CH4) in the martian atmosphere on the order of parts per billion by volume (ppbv). Here, we assess whether aerobic methanotrophy is a potentially viable metabolism in the martian upper regolith, by calculating metabolic energy gain rates under assumed conditions of martian surface temperature, pressure, and atmospheric composition. Using kinetic parameters for 19 terrestrial aerobic methanotrophic strains, we show that even under the imposed low temperature and pressure extremes (180–280 K and 6–11 hPa), methane oxidation by oxygen (O2) should in principle be able to generate the minimum energy production rate required to support endogenous metabolism (i.e., cellular maintenance). Our results further indicate that the corresponding metabolic activity would be extremely low, with cell doubling times in excess of 4000 Earth years at the present-day ppbv-level CH4 mixing ratios in the atmosphere of Mars. Thus, while aerobic methanotrophic microorganisms similar to those found on Earth could theoretically maintain their vital functions, they are unlikely to constitute prolific members of hypothetical martian soil communities.

Sewiło, M., Charnley, S.B., Schilke, P., Taquet, V., Oliveira, J.M., Shimonishi, T., Wirström, E., Indebetouw, R., Ward, J.L., van Loon, J.T., Wiseman, J., Zahorecz, S., Onishi, T., Kawamura, A., Chen, C.H.R., Fukui, Y., Hamedani Golshan, R., 2019. Complex organic molecules in star-forming regions of the Magellanic Clouds. ACS Earth and Space Chemistry 3, 2088-2109.


The Large and Small Magellanic Clouds (LMC and SMC), gas-rich dwarf companions of the Milky Way, are the nearest laboratories for detailed studies on the formation and survival of complex organic molecules (COMs) under metal-poor conditions. To date, only methanol, methyl formate, and dimethyl ether have been detected in these galaxies—all three toward two hot cores in the N113 star-forming region in the LMC, the only extragalactic sources exhibiting complex hot-core chemistry. We describe a small and diverse sample of the LMC and SMC sources associated with COMs or hot-core chemistry, and compare the observations to theoretical model predictions. Theoretical models accounting for the physical conditions and metallicity of hot molecular cores in the Magellanic Clouds have been able to broadly account for the existing observations, but they fail to reproduce the dimethyl ether abundance by more than an order of magnitude. We discuss future prospects for research in the field of complex chemistry in the low-metallicity environment. The detection of COMs in the Magellanic Clouds has important implications for astrobiology. The metallicity of the Magellanic Clouds is similar to that of galaxies in the earlier epochs of the universe; thus, the presence of COMs in the LMC and SMC indicates that a similar prebiotic chemistry leading to the emergence of life, as it happened on Earth, is possible in low-metallicity systems in the earlier universe.

Shang, X., Bai, Y., Sun, J., Dong, C., 2019. Performance and displacement mechanism of a surfactant/compound alkaline flooding system for enhanced oil recovery. Colloids and Surfaces A: Physicochemical and Engineering Aspects 580, 123679.


Monoethanolamine and sodium carbonate were simultaneously applied with sulfonate surfactant to form a surfactant/compound alkaline flooding system, whose optimized composition is 0.20% SLPS, 0.15% Na2CO3, and 0.10% MEA. This system has better anti-salt performance. It can significantly decrease the oil/water interfacial tension (IFT) to ultra-low (＜10−3 mN/m) when NaCl concentration is lower than 40,000 mg/L, CaCl2 concentration is less than 400 mg/L, and the temperature is below 90 . Because of the synergistic effect among SLPS, MEA and Na℃ 2CO3, the flooding system shows obviously higher emulsion stability. Micro displacement experiments were performed to investigate the displacement mechanisms of the system. Results indicate that the oil/water IFT reduction and interfacial film softening are two fundamental micro mechanisms which can make crude oil easy to be emulsified by the flooding system. According to the flow velocity and the contact time between crude oil and the system, turbulent-emulsification and self-emulsification are main emulsification mechanisms. During the migration process of emulsion in porous media, the coalescence-entrainment and the coalescence-dispersion phenomena appear, which both can improve the displacement efficiency of remaining and irreducible oil and ultimately enhance the crude oil recovery.



The advent and advancement in hydraulic fracturing techniques have resulted in the rapid growth of unconventional shale oil and gas production over the last couple of decades. Unlike conventional hydrocarbon systems, these shale formations serve as both the source and reservoir and therefore are directly drilled into for hydrocarbon production. Studies in different shale basins have revealed that these reservoirs are geologically complex, heterogeneous, and every play is unique. Therefore, for efficient hydrocarbon recovery, physicochemical, and mechanical attributes of individual shale reservoir need to be taken into account. Even after significant technological advancements, we are still struggling to understand the spatiotemporal variations in type and amount of hydrocarbon produced within a single basin, rapid declines in hydrocarbon production, and the low fracturing fluid recovery rates. In this review article, we briefly summarize how biogeochemical tools can be used to 1) understand variations in the quantity of organic matter (OM) that ultimately controls production of hydrocarbon, 2) determine variations in the quality of OM that ultimately controls the quality and type of hydrocarbons generated, 3) predict the fracturing potential of rock, and 4) increase efficiency of hydrocarbon production by controlling the water-rock-microbe interactions that ensue after hydraulic fracturing fluids are injected into the shale reservoirs. A better understanding and utilization of these biogeochemical processes and tools will help identify sweet spots for shale gas drilling, increase hydrocarbon recovery and open up the possibility of engineering the hydraulic fracturing fluids to enhance recovery and life of these shale reservoirs.

Shotwell, R.F., Hays, L.E., Beaty, D.W., Goreva, Y., Kieft, T.L., Mellon, M.T., Moridis, G., Peterson, L.D., Spycher, N., 2019. Can an off-nominal landing by an MMRTG-powered spacecraft induce a special region on Mars when no ice is present? Astrobiology 19, 1315-1338.

https://doi.org/10.1089/ast.2017.1688

This work aims at addressing whether a catastrophic failure of an entry, descent, and landing event of a Multimission Radioisotope Thermoelectric Generator-based lander could embed the heat sources into the martian subsurface and create a local environment that (1) would temporarily satisfy the conditions for a martian Special Region and (2) could establish a transport mechanism through which introduced terrestrial organisms could be mobilized to naturally occurring Special Regions elsewhere

on Mars. Two models were run, a primary model by researchers at the Lawrence Berkeley National Laboratory and a secondary model by researchers at the Jet Propulsion Laboratory, both of which were based on selected starting conditions for various surface composition cases that establish the worst-case scenario, including geological data collected by the Mars Science Laboratory at Gale Crater. The summary outputs of both modeling efforts showed similar results: that the introduction of the modeled heat source could temporarily create the conditions established for a Special Region, but that there would be no transport mechanism by which an introduced terrestrial microbe, even if it was active during the temporarily induced Special Region conditions, could be transported to a naturally occurring Special Region of Mars.

Shu, Y., Lu, Y., Chen, L., Wang, C., Zhang, B., 2020. Factors influencing shale gas accumulation in the lower Silurian Longmaxi formation between the north and South Jiaoshiba area, Southeast Sichuan Basin, China. Marine and Petroleum Geology 111, 905-917.


Owing to successful shale gas exploration and development, wells were drilled into the Longmaxi shale formation in the Jiaoshiba area, Southeast Sichuan Basin, China. However, shale gas production in Longmaxi varies greatly between the North and South Jiaoshiba areas. To determine the factors controlling the shale gas accumulation mechanism, the total organic carbon (TOC) content, mineralogy, porosity, permeability, total gas content, gas preservation conditions, and tectonic activities of Longmaxi Shale in both the North and South Jiaoshiba areas were studied in detail. The results show that the concentration of organic matter and minerals in the Longmaxi shale differed slightly between the South and North Jiaoshiba areas, and the lower Longmaxi Shale (Long 1 Member), which is used in commercial shale gas production, is characterized by a high quartz content and low clay content. In addition, the Longmaxi shale in the North Jiaoshiba area is characterized by high porosity and low permeability, while that in the South Jiaoshiba area has low porosity and high permeability. Two different reservoir types were identified in the Jiaoshiba area. The major storage spaces are pores in the Longmaxi shale reservoirs located in the North Jiaoshiba area, while the storage capacity of shale reservoirs in the South Jiaoshiba area is predominantly provided by fractures. Shale gas mainly exists as free gas in the Northern Jiaoshiba area due to the good gas preservation conditions. However, owing to the development of abundant faults in the South Jiaoshiba area, a large amount of free gas was lost, causing absorbed gas to dominate the shale reservoir in this area.

Siegert, S., Hecht, L., 2019. Heterogeneity of melts in impact deposits and implications for their origin (Ries suevite, Germany). Meteoritics & Planetary Science 54, 2409-2447.


Impact melt‐bearing clastic deposits (suevites) are one of the most important records of the impact cratering process. A deeper understanding of their composition and formation is therefore essential. This study focuses on impact melt particles in suevite at Ries, Germany. Textures and chemical evidence indicate that the suevite contains three melt types that originate from different shock levels in the target. The most abundant melt type (“melt type 1”) represents well‐mixed whole‐rock melting of crystalline basement and includes incompletely mixed mafic melt schlieren (“melt type 1 mafic”). Polymineralic melt type 2 comprises mixes between monomineralic melt types 3 and melt type 1. Melt types 2 and 3 are located within melt type 1 as small patches or schlieren but also isolated within the suevite matrix. The main melt type 1 is heterogeneous with respect to trace elements, varying geographically around the crater: in the western sector, it has lower values in trace elements, e.g., Ba,

Zr, Th, and Ce, than in the eastern sector. The west–east zoning likely reflects the heterogeneous nature of crystalline basement target rocks with lower trace element contents, e.g., Ba, Zr, Th, and Ce, in the west compared to the east. The chemical zoning pattern of suevite melt type 1 indicates that mixing during ejection and emplacement occurred only on a local (hundreds of meters) scale. The incomplete larger scale mixing indicated by the preservation of these local chemical signatures, and schlieren corroborate the assumption that mixing, ejection, and quenching were very rapid, short‐lived processes.



The Monteville spherule layer (MSL) was deposited in the Griqualand West Basin (GWB) on the Kaapvaal Craton approximately 2.63 Ga. The spherules were generated by a large impact and reworked by impact‐generated waves and/or currents. The MSL has been intersected in three previously undescribed cores. Two of the cores, GKF‐1 and GKP‐1, were drilled ~30 km west of the southernmost outcrop of the MSL. The third core, BH‐47, was drilled ~250 km south and east of the GWB. The MSL contains medium to coarse sand‐size spherules like those described previously in all three cores but each one was emplaced in a different way. In GKF‐1, the MSL is 90 cm thick and contains large rip‐up clasts of basinal carbonate and early diagenetic pyrite. In GKP‐1, the MSL is only 1.5 cm thick and consists largely of fine carbonate sand, yet it contains pyrite intraclasts up to ~1 cm long. In BH‐47, the MSL consists of a lower coarse sandy zone ~37 cm thick rich in spherules, carbonate peloids/ooids, pyrite intraclasts, and quartzose sand and an upper, finer sandy zone ~46 cm thick; neither zone contains any large intraclasts. The new occurrences triple the known extent of the MSL from ~15,000 to ~46,000 km2, support the oceanic impact model for the formation of the MSL, demonstrate that it is a persistent regional time‐stratigraphic marker, place new constraints on the Kaapvaal paleoshoreline at the time of impact, and support the existence of Vaalbara.

Slobodkin, A.I., Slobodkina, G.B., 2019. Diversity of sulfur-disproportionating microorganisms. Microbiology 88, 509-522.

https://doi.org/10.1134/S0026261719050138

Microorganisms disproportionating inorganic sulfur compounds are involved in biogeochemical cycles of elements in the modern biosphere. Sulfur-disproportionating prokaryotes are represented by 30 species of the Bacteria domain and belong to the phyla Proteobacteria, Thermodesulfobacteria, and Firmicutes. Most of the sulfur-disproportionating bacteria belong to four orders of the class Deltaproteobacteria. The microorganisms responsible for dismutation of sulfur compounds inhabit freshwater and shallow marine sediments, hypersaline and soda lakes, anthropogenic environments, and various natural thermal ecosystems. Most sulfur-disproportionating organisms are able to use other processes for growth, primarily dissimilatory sulfate reduction. Ability to grow autotrophically was shown for 17 sulfur-disproportionating strains from different phylogenetic groups. The biochemical mechanisms involved in disproportionation of sulfur compounds remain uncertain, which hinders the application of the current omics techniques. Comparative analysis of available complete genomes of the microorganisms capable of elemental sulfur disproportionation is provided. The presence of the complete set of the dissimilatory sulfate reduction genes was found not to be necessary for S0 disproportionation. This process does not require dissimilatory sulfite reductase (Dsr) and adenylyl-sulfate reductase (Apr). Sulfur relay proteins and the elemental sulfur- and/or

polysulfides-reducing enzymes are important in sulfur disproportionation, but different microorganisms probably employ different sulfur transferases and polysulfide reductases in these processes.

Song, H., Bao, J., Wen, Z., Cheng, D., 2019. Comparative study of aromatic hydrocarbons in bitumens and expelled oils generated by hydrous pyrolysis of coal. International Journal of Coal Geology 215, 103303.


An immature humic coal sample from the Yaojie Formation of the Muli coal field is pyrolysed in a hydrous closed system. The differences in aromatic hydrocarbon compositon between bitumens and expelled oils are investigated with the simulation temperature ranging from 250 to 500 °C. The absolute concentrations of the main aromatic classes in bitumens and expelled oils initially increase and thereafter decrease with increasing maturity. The absolute concentrations of naphthalene are always higher in expelled oils than in the corresponding bitumens; however, the absolute concentrations of alkyl-naphthalenes, phenanthrene, and alkyl-phenanthrenes are higher in bitumens than in expelled oils at the lower-maturity stage, and reversals occur with continuous increase in RO. Most of the common parameters—MNR, MPI1, MPR, F1, and F2—exhibit regular differences in bitumen–expelled oil pairs. The ratios of different alkylation degrees of naphthalenes and phenanthrenes (such as N/C1–5-N, C1-N/C1–5-N, C1-N/C5-N, P/C1–3-P, and C1-P/C3-P) and the ratios of aromatic components (such as naphthalene/phenanthrene, phenanthrene/fluoranthene, and phenanthrene/pyrene) that have different numbers of aromatic rings exhibit regular differences in bitumen–expelled oil pairs. These ratios of expelled oils are always higher than those of corresponding bitumens; reversals may occur at a high maturity stage. The systematic differences between the compositions of the main aromatic hydrocarbons in bitumens and expelled oils could be predominantly controlled by the fractionation effect at a lower-temperature stage and differentiated decomposition at a higher-temperature stage during the hydrous pyrolysis of coal.



The overgrowth of macrophytes has become serious due to increasing eutrophication in shallow lakes. The primary degradation processes of macrophytes litter, including photodegradation and biodegradation, induce considerable patchiness in the concentration and bioavailability of dissolved organic matter (DOM). In this study we investigated the composition evolution of DOM derived from emergent aquatic plant litter, Phragmites australis, in microbial degradation, photodegradation, and the combination of bio- and photo-degradation. Results revealed that the effects of photo- and biodegradation on the composition difference of macrophyte litter-derived DOM during short- and long-term degradation phase were different. Although large changes in DOM were observed after five days of incubation, the abundance and chemical composition were similar in the three treatments. However, more concentration of DOM was produced by combined photo- and biodegradation at the long-term degradation phase, and the composition of DOM showed less lignin-like formulae, as well as less condensed aromatic and aromatic compounds when compared to sole treatments. More reactive oxygen species (ROS) were found under the combined treatments, thus the contents of refractory components (condensed aromatic- and aromatic compound groups) were reduced. This

study provide deeper insight into the fate of DOM and relevant biogeochemical processes in eutrophic lakes.



A novel method using multilateral wells to perform oil shale in-situ conversion process is proposed in this paper. This method constructs radial branches in upper and lower oil shale formation as injection and production wells. Hot fluids are injected from the injection wells, and pyrolyzed oil and gas are extracted by production wells. In this study, a 3D transient model coupling fluid flow, heat transfer and chemical process is established and implemented on COMSOL Multiphysics platform to investigate the oil shale in-situ conversion process. The temperature field, production characteristics and energy performance are characterized. Sensitivity of oil shale properties and operational parameters are analyzed. Influences of multilateral-well arrangements are studied. The simulation results indicate that the products are strongly dependent to oil shale temperature. The specific heat capacity, injection fluid temperature and injection mass flow rate can significantly influence production performance, while thermal conductivity has negligible effect. Multilateral wells with 5 branches, 60° branch angle and 40 m branch length show the best production performance among the computational cases. This study provides comprehensive insights and suggestions for the application of multilateral wells in oil shale in-situ conversion process.



A 2D-liquid chromatographic fractionation method was combined with direct infusion electrospray ionization Fourier transform-ion cyclotron resonance mass spectrometry to better resolve the high complexity of the organic material in atmospheric particles. The number of assigned molecular formulas increased by a factor of 2.3 for the fractionated sample (18 144) compared to a bulk sample analysis without fractionation (7819), while simultaneously allowing the identification of 71 240 isomeric compounds. Accounting for these isomers has an impact on the means and distributions of different descriptive sample parameters. More than 15 000 compounds were exclusively identified in the fractionated sample providing insights regarding the formation of organosulfates, reduced N-containing compounds, and polyaromatic compounds. Further, a new method for assigning organonitrates and poly-organonitrates based on Kendrick mass defect analysis is presented. The current study implicates that analytical separation leads to much more detailed insights into particle organics composition, while more commonly applied direct infusion MS studies can strongly underestimate composition complexity and lead to biased assignments of bulk organic properties. Overall, the particle organics composition is far more complex than previously shown, while separation through better chromatographic techniques helps to understand formation processes of atmospheric particle constituents.

Spyrou, M.A., Keller, M., Tukhbatova, R.I., Scheib, C.L., Nelson, E.A., Andrades Valtueña, A., Neumann, G.U., Walker, D., Alterauge, A., Carty, N., Cessford, C., Fetz, H., Gourvennec, M., Hartle, R., Henderson, M., von Heyking, K., Inskip, S.A., Kacki, S., Key, F.M., Knox, E.L., Later, C.,

Maheshwari-Aplin, P., Peters, J., Robb, J.E., Schreiber, J., Kivisild, T., Castex, D., Lösch, S., Harbeck, M., Herbig, A., Bos, K.I., Krause, J., 2019. Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes. Nature Communications 10, 4470.

https://doi.org/10.1038/s41467-019-12154-0

The second plague pandemic, caused by Yersinia pestis, devastated Europe and the nearby regions between the 14th and 18th centuries AD. Here we analyse human remains from ten European archaeological sites spanning this period and reconstruct 34 ancient Y. pestis genomes. Our data support an initial entry of the bacterium through eastern Europe, the absence of genetic diversity during the Black Death, and low within-outbreak diversity thereafter. Analysis of post-Black Death genomes shows the diversification of a Y. pestis lineage into multiple genetically distinct clades that may have given rise to more than one disease reservoir in, or close to, Europe. In addition, we show the loss of a genomic region that includes virulence-related genes in strains associated with late stages of the pandemic. The deletion was also identified in genomes connected with the first plague pandemic (541–750 AD), suggesting a comparable evolutionary trajectory of Y. pestis during both events.


https://doi.org/10.1134/S0965544119100104

Changes that occur at the molecular level in the composition of nitrogen compounds of a petroleum sample from the Yuzno-Yagunskoe field during ozonation have been studied by ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry in soft ionization modes. It has been found that N1Ox-containing products accumulate to form new classes of compounds, namely, N1O2, N1O3, N1O4, N1O5, N1O6, and N1O7, while N1 classes undergo degradation. Ozonation of 50% of the feedstock leads to a ~30% decrease in the number of identified empirical formulas of pyridine bases (N1 class).

Steinmann, J.W., Grammer, G.M., Brunner, B., Jones, C.K., Riedinger, N., 2020. Assessing the application of trace metals as paleoproxies and a chemostratigraphic tool in carbonate systems: A case study from the “Mississippian Limestone” of the midcontinent, United States. Marine and Petroleum Geology 112, 104061.


Trace metals have been successfully used to reconstruct geochemical seawater conditions of both modern and ancient environments. The majority of these efforts have been limited to marine shales, with little work on carbonate systems. Applying similar methods of trace metal analysis on carbonate-dominated rocks may provide valuable insight into the paleoseawater chemistry, such as redox state, and productivity, of ancient carbonate systems. This study evaluates the application of trace metals as paleoproxies in carbonate rocks. Middle-ramp wackestones to grainstones from the “Mississippian Limestone” in the Midcontinent were analyzed using inductively-coupled plasma mass spectrometry (ICP-MS) for both the carbonate-fraction and the bulk-fraction trace metal content. Our data show that productivity proxies, such as Cd and P, are captured within the carbonate-fraction and may reflect seawater chemistry of the system. High Cd, and moderate bionutrient (P, Ni, Zn) enrichments indicate primary productivity in the system, though it is difficult to quantify to what extent.

Vanadium, Cr, U, and Mo appear to be primarily associated with the bulk-fraction content and correlate well with Al content, indicating a detrital origin. Furthermore, V, U, and Mo show no significant enrichments, and Mo/Fe ratios correlate with those of shales from a modern oxic shelf. This suggests that anoxic or euxinic conditions in the water column were not present. Trace metal content of carbonate rocks have the potential to be used in paleoenvironmental reconstruction of carbonate systems, though challenges exist such as the lack of comparable carbonate trace metal data, bias of trace metal incorporation pathways into carbonates, and diagenetic alteration.



Methane clumped-isotope compositions provide a new approach to understanding the formational conditions of methane from both biogenic and thermogenic sources. Under some conditions, these compositions can be used to reconstruct the formational temperatures of the gas, and this capability can be applied to common subsets of both biogenic and thermogenic systems. Additionally, there are examples in which clumped-isotope compositions do not reflect gas-formation temperatures but instead mixing effects and kinetic phenomena; such kinetic effects also occur in common and recognizable subtypes of biogenic and thermogenic gases. Here we review the use of methane clumped-isotope measurements for understanding the origin of methane in the subsurface. We review methane clumped-isotope measurements from numerous biogenic and thermogenic natural gas reservoirs. We then place these measurements in the context of common frameworks for identifying the formational conditions of methane including the use of methane δ13C and δD values and C1/C2–3 ratios. Finally, we propose a framework for how methane clumped isotopes can be used to identify the origin of methane accumulations.


https://doi.org/10.1111/pala.12440

Palaeontology relies on the description of fossil morphologies to understand the evolutionary history of life on Earth. Yet much remains unknown about the impact of fossilization processes, even though these may introduce biases into palaeobiological interpretations. Here, we report the characterization of fossilized remains of the earliest known woody plant Armoricaphyton chateaupannense preserved either in 2D (as flat carbonaceous films) or in 3D (as organo‐mineral structures) in early Devonian shales (c. 407 Ma) of the Armorican Massif on the northern margin of Gondwana. To document the fine‐scale structure and the chemistry of the tracheids of this ancient plant, we used propagation phase contrast synchrotron radiation X‐ray microcomputed tomography (PPC‐SRμCT), transmission electron microscopy (TEM) and synchrotron‐based scanning transmission X‐ray microscopy (STXM) coupled with X‐ray absorption near edge structure (XANES) spectroscopy. PPC‐SRμCT enables digital visualization of cell walls in unprecedented detail for the specimens preserved in 3D revealing structures similar to those observed in extant lignified cells, thereby strongly suggesting that the earliest woody plant A. chateaupannense originally contained lignin compounds. STXM‐based XANES and TEM data show that, whatever the preservation modes (3D vs 2D), the remaining organic matter has a chemical composition rather typical of pyrobitumen compounds, raising the

possibility of an original source other than lignin. The pyrobitumen compounds also contains automorphic Ti‐nanominerals interpreted as a diagenetic feature. Altogether, the present study illustrates that anatomical and chemical preservations may not always be correlated.

Su, X., Wang, Q., Zhou, F., Si, Q., Song, J., Lin, H., 2019. Characteristics of graphite-like crystallites in coal with increasing coalification. International Journal of Oil, Gas and Coal Technology 22, 368-388.


This paper presents a study on the characteristics of graphite-like crystallites (GCs) in coals with different maximum vitrinite reflectance (Ro,max) which can be used to describe the rank of coal. Laser Raman spectroscopy (LRS), X-ray diffraction (XRD) and high-resolution transmission electron microscopy (HRTEM) were used in testing 17 coal samples with different ranks. Results show that the GCs in coal undertook through three consecutive processes including aromatisation, condensation and polymerisation. Five coalification upgrading yield to six stages that are corresponding to six different ranges of Ro,max. With the increasing coal rank, the GCs grow larger with improving quality and eventually evolve into graphite crystals. HRTEM observation also reveals that GCs in coal have undergone a graphitization process with increases in percentage, size, and order.

Suarez, C.A., Edmonds, M., Jones, A.P., 2019. Earth catastrophes and their impact on the carbon cycle. Elements 15, 301-306.


Carbon is one of the most important elements on Earth. It is the basis of life, it is stored and mobilized throughout the Earth from core to crust and it is the basis of the energy sources that are vital to human civilization. This issue will focus on the origins of carbon on Earth, the roles played by large-scale catastrophic carbon perturbations in mass extinctions, the movement and distribution of carbon in large igneous provinces, and the role carbon plays in icehouse–greenhouse climate transitions in deep time. Present-day carbon fluxes on Earth are changing rapidly, and it is of utmost importance that scientists understand Earth's carbon cycle to secure a sustainable future.

Suarez, C.A., Kohn, M.J., 2020. Caught in the act: A case study on microscopic scale physicochemical effects of fossilization on stable isotopic composition of bone. Geochimica et Cosmochimica Acta 268, 277-295.


Geochemical zoning in a partially fossilized Pleistocene artiodactyl metapodial was contrasted with a fully fossilized Cretaceous ceratopsian femur as distinct stages along the fossilization process to investigate the physicochemical effects of fossilization and fossilization mechanisms. Bone fragments were analyzed via laser ablation ICP-MS, FT-IR, and stable isotope microanalysis to determine zoning patterns in trace elements, relative carbonate content and collagen contents, and stable isotopes of both the CO3 and PO4 components (δ13CCO3, δ18OCO3, and δ18OPO4). The Pleistocene sample shows a pronounced step in U concentration from high values (up to 90 ppm) within 1 mm of the outer bone surface and inner medullary cavity to ppb-level concentrations typical of in-vivo bone in the interior (inner ∼6 mm). High U broadly coincides with reduced collagen, higher δ13CCO3, and lower δ18OCO3. Rare earth elements (REE), however, show typical exponential decreases from bone edges inward, and δ18OPO4 shows no clear trend. The Cretaceous bone shows high REE and U contents

throughout, a complete absence of collagen, and relatively uniform isotope compositions. The Pleistocene data, especially U zoning, implicate a diffusion-reaction (DR) fossilization mechanism, in which collagen degradation facilitates a recrystallization front that propagates as a front towards the bone interior, reducing OH-site CO3 content, and shifting δ13CCO3, δ18OCO3, and δ18OPO4. Disequilibrium O-isotope partitioning between the CO3 and PO4 components in the interior of the Pleistocene bone suggests that both the CO3 and PO4 components have exchanged with diagenetic waters, likely through abiotic and microbially-induced exchange, respectively. Strong partitioning between apatite and soil water, coupled with uptake of REE in apatite from surrounding sediment matrix during fossilization, leads to exponential decreases in concentrations, which are passively recorded in apatite in the bone interior. The Cretaceous data do not implicate a unique fossilization mechanism but instead reflect the consequences of protracted fossilization and the final state that the Pleistocene bone might eventually have reached had the bone not been excavated. That is, the Cretaceous bone fossilization history resulted in no collagen, reduced or no OH-site CO3, and more uniform isotopic compositions. The multi-analytical methods employed in this study may benefit studies of diagenetic alteration of other apatitic tissues, e.g., tooth enamel.



Dispersant application is a primary emergency oil spill response strategy and yet the efficacy and unintended consequences of this approach in marine ecosystems remain controversial. To address these uncertainties, ex situ incubations were conducted to quantify the impact of dispersant on petroleum hydrocarbon (PHC) biodegradation rates and microbial community structure at as close as realistically possible to approximated in situ conditions [2 ppm v/v oil with or without dispersant, at a dispersant to oil ratio (DOR) of 1:15] in surface seawater. Biodegradation rates were not substantially affected by dispersant application at low mixing conditions, while under completely dispersed conditions, biodegradation was substantially enhanced, decreasing the overall half-life of total PHC compounds from 15.4 to 8.8 days. While microbial respiration and growth were not substantially altered by dispersant treatment, RNA analysis revealed that dispersant application resulted in pronounced changes to the composition of metabolically active microbial communities, and the abundance of nitrogen-fixing prokaryotes, as determined by qPCR of nitrogenase (nifH) genes, showed a large increase. While the Gammaproteobacteria were enriched in all treatments, the Betaproteobacteria and different families of Alphaproteobacteria predominated in the oil and dispersant treatment, respectively. Results show that mixing conditions regulate the efficacy of dispersant application in an oil slick, and the quantitative increase in the nitrogen-fixing microbial community indicates a selection pressure for nitrogen fixation in response to a readily biodegradable, nitrogen-poor substrate.

Taubert, M., Grob, C., Crombie, A., Howat, A.M., Burns, O.J., Weber, M., Lott, C., Kaster, A.-K., Vollmers, J., Jehmlich, N., von Bergen, M., Chen, Y., Murrell, J.C., 2019. Communal metabolism by Methylococcaceae and Methylophilaceae is driving rapid aerobic methane oxidation in sediments of a shallow seep near Elba, Italy. Environmental Microbiology 21, 3780-3795.

https://doi.org/10.1111/1462-2920.14728

The release of abiotic methane from marine seeps into the atmosphere is a major source of this potent greenhouse gas. Methanotrophic microorganisms in methane seeps use methane as carbon and energy source, thus significantly mitigating global methane emissions. Here, we investigated microbial methane oxidation at the sediment–water interface of a shallow marine methane seep. Metagenomics and metaproteomics, combined with 13C‐methane stable isotope probing, demonstrated that various members of the gammaproteobacterial family Methylococcaceae were the key players for methane oxidation, catalysing the first reaction step to methanol. We observed a transfer of carbon to methanol‐oxidizing methylotrophs of the betaproteobacterial family Methylophilaceae, suggesting an interaction between methanotrophic and methylotrophic microorganisms that allowed for rapid methane oxidation. From our microcosms, we estimated methane oxidation rates of up to 871 nmol of methane per gram sediment per day. This implies that more than 50% of methane at the seep is removed by microbial oxidation at the sediment–water interface, based on previously reported in situ methane fluxes. The organic carbon produced was further assimilated by different heterotrophic microbes, demonstrating that the methane‐oxidizing community supported a complex trophic network. Our results provide valuable eco‐physiological insights into this specialized microbial community performing an ecosystem function of global relevance.

Thackeray, J.F., Scott, L., Pieterse, P., 2019. The Younger Dryas interval at Wonderkrater (South Africa) in the context of a platinum anomaly. Palaeontologia africana 54, 30-35.

https://hdl.handle.net/10539/28129

Wonderkrater in the Limpopo Province in South Africa is a late Quaternary archaeological site with peat deposits extending back more than 30 000 years before the present. Palaeoclimatic indices based on multivariate analysis of pollen spectra reflect a decline in temperature identifiable with the Younger Dryas (YD). A prominent spike in platinum is documented in aWonderkrater sample (5614) with a mean date of 12 744 cal yr BP using a Bayesian model, preceding the onset of the YD cooling event. The YD platinum spike at Wonderkrater is the first to be observed in Africa in the southern hemisphere, supplementing new discoveries from Patagonia in South America, in addition to more than 25 sites with such platinum anomalies in the northern hemisphere. The observations from South Africa serve to strengthen ongoing assessments of the controversial YD Impact Hypothesis, whereby it is proposed that a meteorite or cometary impact contributed to a decline in temperature, associated inter alia with dispersion of atmospheric dust, mammalian extinctions and cultural changes.

Tóth, S.Z., Yacoby, I., 2019. Paradigm shift in algal H2 production: Bypassing competitive processes. Trends in Biotechnology 37, 1159-1163.


Hydrogen is a promising energy carrier, but producing it sustainably remains a challenge. Green algae can produce hydrogen photosynthetically using their efficient but oxygen-sensitive hydrogenases. Recent strategies aiming to bypass competing processes provide a promising route for scaling up algal hydrogen production.



Pore surface heterogeneities and their associated lacunarity of major Indian shale gas reservoirs were analyzed using both gas adsorption and advanced image analysis. The experiments were carried on samples from priority Indian gas shales namely Cambay, Cauvery, Krishna-Godavari and Damodar Valley. An advanced watershed segmentation was adopted on the SEM images to understand the control of pore size on the porosity of shale formations. Further, 3D as well as 2D surface intensity maps were plotted from the SEM images applying the distance transformation technique. The fractal dimension D ranged from 2.55 to 2.78 for LPN2GA suggesting a high degree of complexity in their fractal pattern. The 3D surface intensity map is found to be useful in picturizing the anisotropy in shale brought about by preferential orientation of clay minerals. The results can be extended in understanding the behavior of gas flow within the complex pore systems as exhibited by shale.

Trontelj, P., Borko, Š., Delić, T., 2019. Testing the uniqueness of deep terrestrial life. Scientific Reports 9, 15188.

https://doi.org/10.1038/s41598-019-51610-1

Terrestrial life typically does not occur at depths greater than a few meters. Notable exceptions are massifs of fissured rock with caves and hollow spaces reaching depths of two kilometres and more. Recent biological discoveries from extremely deep caves have been reported as sensations analogous to wondrous deep sea creatures. However, the existence of unique deep terrestrial communities is questionable when caves are understood as integral parts of a bedrock fissure network (BFN) interconnecting all parts of a massif horizontally and vertically. We tested these two opposing hypotheses – unique deep cave fauna vs. BFN – by sampling subterranean communities within the 3D matrix of a typical karst massif. There was no distinction between deep core and shallow upper zone communities. Beta diversity patterns analysed against null models of random distribution were generally congruent with the BFN hypothesis, but suggested gravity-assisted concentration of fauna in deep caves and temperature-dependent horizontal distribution. We propose that the idea of a unique deep terrestrial fauna akin to deep oceanic life is unsupported by data and unwarranted by ecological considerations. Instead, the BFN hypothesis and local ecological and structural factors sufficiently explain the distribution of subterranean terrestrial life even in the deepest karst massifs.

Uritskiy, G., Getsin, S., Munn, A., Gomez-Silva, B., Davila, A., Glass, B., Taylor, J., DiRuggiero, J., 2019. Halophilic microbial community compositional shift after a rare rainfall in the Atacama Desert. The ISME Journal 13, 2737-2749.

https://doi.org/10.1038/s41396-019-0468-y

Understanding the mechanisms underlying microbial resistance and resilience to perturbations is essential to predict the impact of climate change on Earth’s ecosystems. However, the resilience and adaptation mechanisms of microbial communities to natural perturbations remain relatively unexplored, particularly in extreme environments. The response of an extremophile community inhabiting halite (salt rocks) in the Atacama Desert to a catastrophic rainfall provided the opportunity to characterize and de-convolute the temporal response of a highly specialized community to a major disturbance. With shotgun metagenomic sequencing, we investigated the halite microbiome taxonomic composition and functional potential over a 4-year longitudinal study, uncovering the dynamics of the initial response and of the recovery of the community after a rainfall event. The observed changes can be recapitulated by two general modes of community shifts—a rapid Type 1 shift and a more gradual Type 2 adjustment. In the initial response, the community entered an unstable intermediate state after stochastic niche re-colonization, resulting in broad predicted protein adaptations to increased water availability. In contrast, during recovery, the community returned to its

former functional potential by a gradual shift in abundances of the newly acquired taxa. The general characterization and proposed quantitation of these two modes of community response could potentially be applied to other ecosystems, providing a theoretical framework for prediction of taxonomic and functional flux following environmental changes.

Vajda, V., McLoughlin, S., Mays, C., Frank, T.D., Fielding, C.R., Tevyaw, A., Lehsten, V., Bocking, M., Nicoll, R.S., 2020. End-Permian (252 Mya) deforestation, wildfires and flooding—An ancient biotic crisis with lessons for the present. Earth and Planetary Science Letters 529, 115875.


Current large-scale deforestation poses a threat to ecosystems globally, and imposes substantial and prolonged changes on the hydrological and carbon cycles. The tropical forests of the Amazon and Indonesia are currently undergoing deforestation with catastrophic ecological consequences but widespread deforestation events have occurred several times in Earth's history and these provide lessons for the future. The end-Permian mass-extinction event (EPE; ∼252 Ma) provides a global, deep-time analogue for modern deforestation and diversity loss. We undertook centimeter-resolution palynological, sedimentological, carbon stable-isotope and paleobotanical investigations of strata spanning the end-Permian event at the Frazer Beach and Snapper Point localities, in the Sydney Basin, Australia. We show that the typical Permian temperate, coal-forming, forest communities disappeared abruptly, followed by the accumulation of a 1-m-thick mudstone poor in organic matter that, in effect, represents a ‘dead zone’ hosting degraded wood fragments, charcoal and fungal spores. This signals a catastrophic scenario of vegetation die-off and extinction in southern high-latitude terrestrial settings. Lake systems, expressed by laterally extensive but generally less than a few-metres-thick laminated siltstones, generally lacking bioturbation, hosting assemblages of algal cysts and freshwater acritarchs, developed soon after the vegetation die-off. The first traces of vascular plant recovery occur ∼1.6 m above the extinction horizon. Based on analogies with modern deforestation, we propose that the global fungal and acritarch events of the Permo-Triassic transition resulted directly from inundation of basinal areas following water-table rise as a response to the abrupt disappearance of complex vegetation from the landscape. The δ13Corg values reveal a significant excursion toward low isotopic values, down to ‰−31‰ (a shift of ∼4‰), across the end-Permian event. The magnitude of the shift at that time records a combination of changes in the global carbon cycle that were enhanced by the local increase in microbial activity, possibly also involving cyanobacterial proliferation. We envisage that elevated levels of organic and mineral nutrients delivered from inundated dead forests, enhanced weathering and erosion of extra-basinal areas, together with local contributions of volcanic ash, led to eutrophication and increased salinity of basinal lacustrine–lagoonal environments. We propose that the change in acritarch communities recorded globally in nearshore marine settings across the end-Permian event is to a great extent a consequence of the influx of freshwater algae and nutrients from the continents. Although this event coincides with the Siberian trap volcanic activity, we note that felsic–intermediate volcanism was extensively developed along the convergent Panthalassan margin of Pangea at that time and might also have contributed to environmental perturbations at the close of the Permian.

Valencia-Agami, S.S., Cerqueda-García, D., Putzeys, S., Uribe-Flores, M.M., García-Cruz, U.N., Pech, D., Herrera-Silveira, J., Aguirre-Macedo, L.M., García-Maldonado, Q.J., 2019. Changes in the bacterioplankton community structure from southern Gulf of Mexico during a simulated crude oil spill at mesocosm scale. Microorganisms 7.

https://doi.org/10.3390/microorganisms7100441

The southern Gulf of Mexico (sGoM) is highly susceptible to receiving environmental impacts due to the recent increase in oil-related activities. In this study, we assessed the changes in the bacterioplankton community structure caused by a simulated oil spill at mesocosms scale. The 16S rRNA gene sequencing analysis indicated that the initial bacterial community was mainly represented by Gamma-proteobacteria, Alpha-proteobacteria, Flavobacteriia, and Cyanobacteria. The hydrocarbon degradation activity, measured as the number of culturable hydrocarbonoclastic bacteria (CHB) and by the copy number of the alkB gene, was relatively low at the beginning of the experiment. However, after four days, the hydrocarbonoclastic activity reached its maximum values and was accompanied by increases in the relative abundance of the well-known hydrocarbonoclastic Alteromonas. At the end of the experiment, the diversity was restored to similar values as those observed in the initial time, although the community structure and composition were clearly different, where Marivita, Pseudohongiella, and Oleibacter were detected to have differential abundances on days eight–14. These changes were related with total nitrogen (p value = 0.030 and r2 = 0.22) and polycyclic aromatic hydrocarbons (p value = 0.048 and r2 = 0.25), according to PERMANOVA. The results of this study contribute to the understanding of the potential response of the bacterioplankton from sGoM to crude oil spills.

Välja, R., Kirsimäe, K., Koeberl, C., Boamah, D., Kirs, J., 2019. Incipient devitrification of impact melt particles at Bosumtwi crater, Ghana: Implications for suevite cooling history and melt dispersion. Meteoritics & Planetary Science 54, 2557-2572.


The petrographic, mineralogical, and geochemical compositions of the incipient devitrification products in impact melt fragments found in outer suevites at the Bosumtwi impact crater were studied to reconstruct the postimpact environmental constraints on the suevite formation and to refine its cooling history. Our study shows that devitrified melt/particles contain numerous microlitic crystals and crystal aggregates of different shapes derived from rapid cooling. The matrix of melt/particles in Bosumtwi suevites contains abundant Mg‐hercynite (pleonaste)‐type spinels with sizes rarely exceeding a few micrometers. High nucleation density of microlites suggests rapid crystallization under strong undercooling in the presence of abundant volatiles. Although the Bosumtwi impact event took place in a continental environment, the possible sources for elevated fluid/volatile content could have been the groundwater in the deeply weathered and fractured‐jointed Birimian basement, dewatering of abundant hydrous phases in weathered crust or hydrothermally altered basement, and the shale/phyllite–greywacke lithologies in the target rocks. Our results show that enough volatiles were present in the target rocks at the time of impact for the effective impact melt dispersion observed in Bosumtwi impactites.

van der Boon, A., van der Ploeg, R., Cramwinckel, M.J., Kuiper, K.F., Popov, S.V., Tabachnikova, I.P., Palcu, D.V., Krijgsman, W., 2019. Integrated stratigraphy of the Eocene-Oligocene deposits of the northern Caucasus (Belaya River, Russia): Intermittent oxygen-depleted episodes in the Peri-Tethys and Paratethys. Palaeogeography, Palaeoclimatology, Palaeoecology 536, 109395.


The sedimentary succession along the Belaya River (North Caucasus) provides a record of middle Eocene to Miocene sediments. This time interval is well known for its important climatic transitions (e.g., Middle Eocene Climate Optimum (MECO) and Eocene-Oligocene Transition (EOT)), and changes in basin configuration from Peri-Tethys to Paratethys. The Belaya section contains two intervals marked by oxygen-depleted sediments; the Eocene Kuma Formation of the Peri-Tethys and

the Oligocene Maikop Group of the Paratethys. Both are considered important source rocks for hydrocarbon exploration in the Black Sea and Caspian Sea. We present integrated stratigraphic results of the Belaya River section using calcareous nannoplankton biostratigraphy, magnetostratigraphy and 40Ar/39Ar dating. Furthermore, we investigate the geochemical character of the sediments using X-ray fluorescence (XRF) and stable carbon and oxygen isotopes. A middle Eocene age for the lower part of the succession is established from nannoplankton biostratigraphy. The Kuma Formation is dated between 42.1 and 38.4 Ma based on the assumption of constant sediment accumulation rates. A negative oxygen isotope excursion in the middle part of the Kuma Formation could be related to the MECO (~40 Ma). The onset of the Maikop Group is dated around the base of chron C13n at an age of ~33.7 Ma, close to the Eocene-Oligocene boundary. Based on geochemical results, we show that the Kuma Formation and Maikop Group correspond to two different episodes of intensified oceanic oxygen depletion in the succession. We hypothesise that oxygen-depletion as recorded in the Kuma Formation is linked to an increased nutrient input in the open marine Peri-Tethys due to widespread volcanism in the Neotethys subduction zone, while oxygen-depletion as recorded in the Maikop Group is linked to basin restriction caused by the eustatic sea-level fall straddling the Eocene – Oligocene boundary triggering stratified conditions in the semi-isolated Paratethys Sea.

Vasconcelos, M.A.R., Rocha, F.F., Crósta, A.P., Wünnemann, K., Güldemeister, N., Leite, E.P., Ferreira, J.C., Reimold, W.U., 2019. Insights about the formation of a complex impact structure formed in basalt from numerical modeling: The Vista Alegre structure, southern Brazil. Meteoritics & Planetary Science 54, 2373-2383.


We present the outcomes of simulations of the formation of the Vista Alegre impact structure, Paraná Basin, Brazil. The target comprised a thick sequence of volcanic rocks of predominantly basaltic composition of the Serra Geral Formation that had been deposited on top of sedimentary rocks (sandstones) of the Pirambóia/Botucatu formations. The cratering process was modeled using the iSALE shock physics code. Our best‐fit model suggests that (1) the crater was originally ~10 km in size; (2) it was formed in ~115 s by a stony projectile of 1000 m in diameter, for an assumed impact velocity of 12 km s−1; (3) target rocks underwent a peak pressure of ~20 GPa, in agreement with previous petrographic investigations of shock deformation. Furthermore, the model points out that the sedimentary strata below the layer of volcanic rocks were raised by ~650 meters at the central part of the crater, which resulted in the current partial exposure of the sandstones at the surface. The outcomes of our modeling suggest that parameters like cohesion and strength of the target rocks, after shock compression, determined the final morphology of the crater, especially the absence of a topographically prominent central peak. Finally, the results of the numerical modeling are roughly in agreement with gravity data over the structure, in particular with respect to the presence of the uplifted sedimentary strata, which are responsible for a low gravity signature at the center of the structure.

Velichko, N.V., Pinevich, A.V., 2019. Classification and identification tasks in microbiology: Mass spectrometric methods coming to the aid. Microbiology 88, 534-547.

https://doi.org/10.1134/S0026261719050151

Mass spectrometry (MS) methods furnish the clue to many microbiological applications including advanced studies on the diversity and classification of prokaryotes. Mass spectral data contribute to the polyphasic taxonomy which considers genotypic characters together with structure-functional and ecological traits. Additionally, these methods contribute to reliable and rapid identification of

microorganisms bypassing conventional manipulations which are materials and time consuming. MS based analyses of biomarkers can be performed at the level of whole cells, cell homogenates, subcellular fractions, and individual molecules. For this purpose, various MS methods can be employed, such as MALDI-TOF, ESI, SELDI, and BAMS. Of these, MALDI-TOF MS is the especially easy-to-use and rapid method with many analytical applications, primarily in proteomics which aims at comprehensive description of protein inventory in prokaryotes. An alternative for detection and comparison of biomarkers via MS is amplification and alignment of marker gene sequences. Two molecular approaches supplement each other under support of database resources. Microbiologists readily assimilate MS methods propelled by high performance analyzers and sensitive detectors. The review focuses at progressing application of MS methods in microbiology, with an emphasis on identification and comparative study of bacteria.

Venera-Pontón, D.E., Schmidt, W.E., Fredericq, S., 2019. Population structure of the red macroalga Botryocladia occidentalis (Børgesen) Kylin (Rhodymeniaceae, Rhodymeniales) in the Gulf of Mexico Before the Deepwater Horizon oil spill. Frontiers in Marine Science 6, 652. doi: 10.3389/fmars.2019.00652.

https://www.frontiersin.org/article/10.3389/fmars.2019.00652

Studies on the population structure of common widespread macroalgae in the Gulf of Mexico (GoMx) are scarce, and this knowledge gap limits our understanding on how disturbances affect the genetic diversity of macroalgae in this basin. The latter is due to the lack of a baseline that can be compared with allele frequency surveys conducted after a major disturbance such as the 2010 Deepwater Horizon oil spill (DWH), which leaked 780,000 m3 of crude oil in the vicinity of highly diverse macroalgal communities. Fortunately, quantitative assessments of the population structure pre-DWH can be accomplished for several macroalgae with dried specimens collected from research cruises conducted before 2010 in the offshore GoMx. Based on three markers (cytochrome c oxidase subunit I, COX II-III intergenic spacer, and the RuBisCO large subunit), this study reconstructed the allele frequencies pre-DWH for a GoMx-widespread macroalga, Botryocladia occidentalis, and revealed the existence of distinct populations in each of three distant regions of the GoMx: Florida Middle Grounds (FL), Campeche Banks (CB), and offshore Louisiana (LA). Population structure was assessed with exact tests of population differentiation and Analyses of Molecular Variance. FL harbored the most differentiated and genetically diverse population due to the presence and abundance of unique haplotypes. Interestingly, FL haplotypes were not closely phylogenetically related to each other and included the most divergent lineages of the entire GoMx; this phylogeographic pattern suggests a strong influence of migrants from the Caribbean on the FL population. Additionally, likelihood ratio tests with a small sample collected post-DWH indicated that the LA population underwent strong changes, showing statistically significant differences before (LA) vs. after (L2) the disaster. Whereas the LA population had affinity to CB, L2 showed a FL haplotype that, before the disaster, had never been reported in LA or CB. Such changes may not be permanent but rather a temporary response to disturbance; also, they may not necessarily be caused by the spilled oil but by other factors associated with the DWH.

Versteegh, G.J.M.V., 2, A J. P. Houben3,4, and KA. F. Zonneveld2 , Houben, A.J.P., Zonneveld, K.A.F., 2019. Better molecular preservation of organic matter in an oxic than in a sulphidic depositional environment: evidence from of Thalassiphora pelagica (Dinoflagellata, Eocene) cysts. Biogeosciences Discussions 2019, 1-24.


Anoxic sediments as compared to oxic settings encompass a much higher proportion of relatively labile and thus more reactive organic matter, naturally giving rise to condensation reactions (such as vulcanisation) transforming the original biomolecules into geomolecules. For the oxic environment where the labile, reactive, component is rapidly removed, such transformation and condensation is much less likely so that one would expect a structurally much better preservation of the more refractory initial biomolecules. To test this hypothesis, initially identical biomolecules need to be compared between different preservational environments. Here, we use the species specific morphology of organic microfossils to assure a single initial biosynthetic product (the cysts of the fossil dinoflagellate species Thallasiphora pelagica) for comparison. We assess the macromolecular structures of cysts from the Eocene (~ 40 Ma) sulphidic Rhine Graben and the oxic Kerguelen Plateau and compare them with each other and the structures of recent cysts. While between the sites the T. pelagica cysts are morphologically identical, pyrolysis gas chromatography mass spectroscopy and micro Fourier transform infra red analyses show that their macromolecular characteristics are strongly different. The cysts deposited in the sulphidic Rhine Graben show a strong contribution of long-chain aliphatic moieties and organic sulphur, absent in the material deposited on the oxic Kerguelen Plateau. Comparison with recent cyst walls suggests a much better molecular preservation for the oxic depositional environment, confirming our initial hypothesis. This leads to the conclusion that the best preservation of molecular structure is not necessarily where most organic matter gets preserved, which, in turn, is important for understanding the nature and fate of sedimentary organic matter.

Vieira, A.L., Nespeca, M.G., Pavini, W.D., Ferreira, E.C., Gomes Neto, J.A., 2019. A user-friendly Excel spreadsheet for dealing with spectroscopic and chromatographic data. Chemometrics and Intelligent Laboratory Systems 194, 103816.


A user-friendly interface was developed in Excel (Microsoft Office) to deal with spectroscopic and chromatographic data. The Excel spreadsheet includes baseline correction, area and height determination, and identification of variables that represent the maximum height. In addition, the user can quickly evaluate standardization methods and create databases by adding information to the library, where up to 300 peaks can be saved. In the present work, the application of the Excel spreadsheet is exemplified by analytical curves developed with gas chromatography, Raman spectroscopy and laser-induced breakdown spectroscopy (LIBS) data. The analytical parameters obtained by the Excel spreadsheet were compared with the results generated in different software, such as MATLAB (routine), Origin and ChromQuest. The coefficient of determination (R2) and root-mean-square error (RMSE) obtained from Excel spreadsheet were very similar to those from other software. The analytical curves were also submitted to analysis of variance (ANOVA) and, regarding the F-test, all presented values of Fcalculated greater than Fcritical. The relationship between the analytical responses from the Excel spreadsheet and other software showed a coefficient of correlation close to 1. Therefore, the proposed Excel interface is an attractive alternative to expensive software and provides easy handling for LIBS data. The spreadsheet and a short tutorial video are available in the electronic supplementary material (or in the link https://1drv.ms/f/s!AjTI1LyRsk35lYtYOvj6EGyXvFgWlQ).

Vinson, D.S., Blair, N.E., Ritter, D.J., Martini, A.M., McIntosh, J.C., 2019. Carbon mass balance, isotopic tracers of biogenic methane, and therole of acetate in coal beds: Powder River Basin (USA). Chemical Geology 530, 119329.


A multi-isotope (C, H, O) investigation of biogenic gas (δ13C−CH4, δ13C−CO2, δD−CH4) and coal bed waters (δD, δ18O, δ13C-DIC, δ13C-acetate) was conducted along a ∼25-km basinward sampling transect in the Powder River Basin (PRB) in Wyoming and Montana (USA) to address inconsistencies among isotope fingerprinting techniques and to apply mass balance isotope modeling to biogenic coalbed methane (CBM). Results include the first published compound-specific δ13C-acetate values from a natural biogenic CBM system, providing new constraints on acetate’s role in biogenic CH4 generation. Coal bed water chemistry is anoxic and dominated by Na+ and HCO3

−, with high alkalinity concentrations (14.8–33.0 meq/L). The deep basin interior environment contains sulfate-free, Na+−HCO3

−-dominated waters exhibiting signs of methanogenesis. CH4 and CO2 generally become 13C-enriched from the shallow basin edge to the deep basin interior (δ13C−CH4 −78.2 to −56.2‰ and δ13C−CO2 -24.7 to 4.7‰). Also, compound-specific δ13C-acetate is more positive in the basin interior compared to the basin edge setting (range −34.3 to −15.1‰). Using a steady-state mass balance isotope model, the observed variations in δ13C-CH4 and δ13C-CO2 can be explained in terms of the favorability of methanogenesis (fCH4) relative to heterotrophic bacterially-mediated non-methanogenic pathways, such as bacterial sulfate reduction, which compete with methanogenesis for substrates. At the basin interior, fCH4 exceeds 0.4, approaching its inferred limiting value hypothesized from the oxidation state of low-molecular weight compounds detected in PRB formation waters. Therefore, methanogenesis is likely a dominant biogeochemical pathway consuming substrates in the deeper coal beds. The basinward shift toward 13C-enriched acetate broadly indicates linkage between acetate, CH4, and CO2, and likely records acetate synthesis effects modified by methanogenic fractionation. These results suggest that acetate plays a role in methanogenesis in PRB coal beds (not necessarily a dominant role), while other C isotope and microbial evidence suggests that hydrogenotrophic methanogenesis is also a significant methane-producing pathway. The results of this study broadly suggest multiple viable methanogenic pathways and C cycling that affects acetate, a more complex view of coal bed geochemistry than implied by traditional C and H isotope fingerprinting of accumulated products (CH4, CO2) and coexisting water.


https://doi.org/10.1089/ast.2018.1961

A new technique that has applications for the detection of nonvolatile organics on Ocean Worlds has been developed. Here, liquid mixtures of fatty acids (FAs) and/or amino acids (AAs) are introduced directly into a miniature quadrupole ion trap mass spectrometer (QITMS) developed at Jet Propulsion Laboratory and analyzed. Two ionization methods, electron impact and chemical ionization (EI and CI, respectively), are compared and contrasted. Further, multiple CI reagents are tested to explore their potential to “soften” ionization of FAs and AAs. Both EI and CI yield mass spectra that bear signatures of FAs or AAs; however, soft CI yields significantly cleaner mass spectra that are easier to interpret. The combination of soft CI with tandem mass spectrometry (MS/MS) has also been demonstrated for AAs, generating “fingerprint” mass spectra of fragments from protonated parent ions. To mimic potential Ocean World conditions, water is used as the primary collision gas in MS/MS experiments. This technique has the potential for the in situ analysis of molecules in the cryogenic plumes of Ocean Worlds (e.g., Enceladus) and comets with the ultimate goal of detecting potential biosignatures.

Waltham, D., 2019. Intrinsic climate cooling. Astrobiology 19, 1388-1397.

https://doi.org/10.1089/ast.2018.1942

Lower heating of our planet by the young Sun was compensated by higher warming from factors such as greater greenhouse gas concentrations or reduced albedo. Earth's climate history has therefore been one of increasing solar forcing through time roughly cancelled by decreasing forcing due to geological and biological processes. The current generation of coupled carbon-cycle/climate models suggests that decreasing geological forcing—due to falling rates of outgassing, continent growth, and plate spreading—can account for much of Earth's climate history. If Earth-like planets orbiting in the habitable zone of red dwarfs experience a similar history of decreasing geological forcing, their climates will cool at a faster rate than is compensated for by the relatively slow evolution of their smaller stars. As a result, they will become globally glaciated within a few billion years. The results of this paper therefore suggest that coupled carbon-cycle/climate models account, parsimoniously, for both the faint young Sun paradox and the puzzle of why Earth orbits a relatively rare and short-lived star-type.

Wang, J., Gao, Z., Kang, Z., Zhu, D., Liu, Q., Ding, Q., Liu, Z., 2020. Geochemical characteristics, hydrocarbon potential and depositional environment of the Yangye Formation source rocks in Kashi sag, southwestern Tarim Basin, NW China. Marine and Petroleum Geology 112, 104084.


The Yangye Formation sequence is widely exposed in Kashi sag, Tarim Basin, NW China. To investigate geochemical characteristics and depositional environment of the Yangye Formation successions, 26 samples from an outcrop kzgs section in the north and 21 core samples from YD-1 well in the south were subjected to various geochemical analyses. The average TOC content is 1.87 wt % in the kzgs section and 1.36 wt % in the YD-1 well, and most samples have fairly high TOC contents (>1.0 wt %). Notably, samples in the YD-1 well are characterized by high S1, S2, HI and PG values, compared to those in the kzgs section. Based on pyrolysis data, organic matter (OM) in the kzgs section consists predominantly of type III kerogen with gas prone, whereas OM in the YD-1 well have oil/gas prone characters with dominating mixed type II/III and type III kerogen with minor type II kerogen. Tmax values (447–469 °C and 453–484 °C, respectively) imply that source rocks in the kzgs section are within peak to late mature stages, and samples in the YD-1 well contain late mature to post-mature OM, consistent with the results of Ro, PI, CPI, and biomarker maturity parameters. The distributions of n-alkane, isoprenoids, sterane and terpane, as well as carbon isotopes, suggest a predominance of algal, bacterial and planktonic OM, but with terrigenous higher plants influenced. However, samples in the kzgs section probably received more contributions of terrigenous and bacteria-reworked materials. Moreover, OM in the kzgs section was likely preserved in a suboxic, fresh/brackish condition, while OM from the YD-1 well was developed under a suboxic to oxygen-depleted, fresh with brackish influenced environment. There have distinct differences in organic richness, OM types and thermal maturity between the kzgs section and YD-1 well. Overall, the Yangye Formation in the whole Kashi sag still has fair to good hydrocarbon potential, and source rocks in the YD-1 well have more favorable potential to generate considerable oil and gas hydrocarbons.



In this study, the structural information and spatial properties of the Longkou kerogen model were obtained by using molecular simulation methods. The density evaluation of the molecular model was carried out to investigate the morphological properties of internal pore structures that are limited or

constrained by kerogen density. The density of the lowest-energy kerogen model is 1.01 g/cm3, which is consistent with its experimental value and close to the reference value for Green River Shale kerogen. Radial distribution function analysis indicated that the carbon skeleton of kerogen consists of significant amounts of sp2- and sp3-hybridized carbons. To further investigate the distribution characteristics of internal pore structures and provide valuable insights into the microstructures of the kerogen model, the morphology of pore volumes was created using Connolly surfaces. Meanwhile, a simplified mechanism model of kerogen pyrolysis was proposed based on the Mayer bond order analysis, which provided a strategy to accurately, quickly predict the cleavage behavior in the intrinsic structure of kerogen. This present study reveals inherent chemical features of kerogen and will aid in understanding the microscopic morphology characteristics of the pore network inside kerogen at the molecular level.

Wang, S., Chen, H., Zhang, X., 2020. Transformation of aromatic structure of vitrinite with different coal ranks by HRTEM in situ heating. Fuel 260, 116309.


Three vitrinite samples of different rank, denoted as V-YJL, V-AW, and V-J15, were investigated by in situ heating while in a High resolution transmission electron microscope (HRTEM) to study the aromatic structural transformations from 200 to 800 °C. Thermogravimetry coupled with Fourier transform infrared spectroscopy and mass spectrometry (TG-FTIR-MS) was employed to measure gaseous release from 30 to 900 °C. The relationships between aromatic structural transformations and gaseous release were also discussed in this work. The results showed that the rank of coal influenced the changes of aromatic layers. The change of naphthalene of low-rank coal (V-YJL, R = 0.61%) had four stages. For higher rank coals with R = 1.09% (V-AW) and R = 2.22% (V-J15), the changes of naphthalene had three and two stages, respectively. The increase in naphthalene content occurred at the same temperature with the release of CO2 and H2O, suggesting the increase of naphthalene probably caused by the decomposing of oxygen-containing functional groups. The noticeable change in 4 × 4 aromatic layers is from 650 to 750 °C, accompanying CH4 release, suggesting the increase of 4 × 4 aromatic layers may result from the break of bonds like aryl-methyl bonds or aryl-alkyl bonds.

Wang, T., David, J., 2019. Deep resistivity “turnover” effect at oil generation “peak” in the Woodford Shale, Anadarko Basin, USA. Petroleum Science 16, 972-980.

https://doi.org/10.1007/s12182-019-00370-8

The Devonian Woodford Shale in the Anadarko Basin is a highly organic, hydrocarbon source rock. Accurate values of vitrinite reflectance (Ro) present in the Woodford Shale penetrated by 52 control wells were measured directly. These vitrinite reflectance values, when plotted against borehole resistivity for the middle member of the Woodford Shale in the wells, display a rarely reported finding that deep resistivity readings decrease as Ro increases when Ro is greater than 0.90%. This phenomenon may be attributed to that aromatic and resin compounds containing conjugated pi bonds generated within source rocks are more electrically conductive than aliphatic compounds. And aromatic and resin fractions were generated more than aliphatic fraction when source rock maturity further increases beyond oil peak. The finding of the relationship between deep resistivity and Ro may re-investigate the previously found linear relationship between source rock formation and aid to unconventional play exploration.

Wang, T., Li, G., Aitchison, J.C., Ding, L., Sheng, J., 2019. Evolution of mid-Cretaceous radiolarians in response to oceanic anoxic events in the eastern Tethys (southern Tibet, China). Palaeogeography, Palaeoclimatology, Palaeoecology 536, 109369.


Oceanic anoxic events (OAEs) are well-known from their widespread black shale and carbon isotopic excursions in the (western and eastern) Tethys and Atlantic Ocean. However, the weakest link in the studies of the OAEs is biological evolution. Sedimentological, biostratigraphical and geochemical data from Albian to Coniacian strata in southern Tibet recorded turnover events and fluctuations in diversity of the radiolarian fauna within the eastern Tethys during OAE 1d and OAE 2. Abundant radiolarian fossils were obtained from the Gyabula Formation, with 93 species from 43 genera identified and assigned to the mid to Upper Cretaceous Acaeniotyle umbilicata, Archaeospongoprunum tehamaensis, Crucella cachensis, Alievium superbum, and Dictyomitra formosa zones. The association of carbon isotopic excursions, black shale and radiolarian turnover indicates extensive changes in the ocean-climate system. Nutrients are made increasing available to the marine plankton through submarine volcanic activity and rising sea-level, which were a likely cause of radiolarian turnover at/or near the OAEs. Active submarine tectonism-volcanism leads to the expansion of the hypoxic zone and may cause many deeper dwelling forms to become extinct whereas most of the shallower dwelling radiolarians survive. Radiolarian evolution thus provides a useful record with which to seek understand relationships between climate, paleoceanographic processes and plankton evolution.

Wang, Z., Juarez, D.L., Pan, J.-F., Blinebry, S.K., Gronniger, J., Clark, J.S., Johnson, Z.I., Hunt, D.E., 2019. Microbial communities across nearshore to offshore coastal transects are primarily shaped by distance and temperature. Environmental Microbiology 21, 3862-3872.

https://doi.org/10.1111/1462-2920.14734

Recent studies have focused on linking marine microbial communities with environmental factors, yet, relatively little is known about the drivers of microbial community patterns across the complex gradients from the nearshore to open ocean. Here, we examine microbial dynamics in 15 five-station transects beginning at the estuarine Piver's Island Coastal Observatory (PICO) time-series site and continuing 87?km across the continental shelf to the oligotrophic waters of the Sargasso Sea. 16S rRNA gene libraries reveal strong clustering by sampling site with distinct nearshore, continental shelf and offshore oceanic communities. Water temperature and distance from shore (which serves as a proxy for gradients in factors such as productivity, terrestrial input and nutrients) both most influence community composition. However, at the phylotype level, modelling shows the distribution of some taxa is linked to temperature, others to distance from shore and some by both factors, highlighting that taxa with distinct environmental preferences underlie apparent clustering by station. Thus, continental margins contain microbial communities that are distinct from those of either the nearshore or the offshore environments and contain mixtures of phylotypes with nearshore or offshore preferences rather than those unique to the shelf environment.

Wang, Z., Lin, M., Xiang, Y., Zeng, T., Dong, Z., Zhang, J., Yang, Z., 2019. Zr-induced thermostable polymeric nanospheres with double-cross-linked architectures for oil recovery. Energy & Fuels 33, 10356-10364.


For the purpose of ameliorating the temperature resistance of nanopolymer particles, a kind of hyper-cross-linked polymer, named Zr-AM/NVP/AMPS [main monomer acrylamide (AM), functional monomers N-vinylpyrrolidone (NVP), and 2-acrylamide-2-methylpropanesulfonic acid (AMPS)] with size varying from 100 to 170 nm and special double-cross-linked architectures, were prepared through inverse emulsion copolymerization of organic cross-linking agent N, N-methylene bis acrylamide (MBA), and metal cross-linking agent zirconium acetate (Zr) as a cross-linking system, ammonium persulfate (KPS) as the initiator for the first time. The surface morphology, pore structure, particle size distribution, cross-linking architecture and element distribution of nanoparticles were fully characterized with several means including SEM, TEM, LPSA, BET, FT-IR, 13CNMR, elemental analysis, and long-term thermal stability. The SEM, TEM, LPSA, and BET experimental results indicate that the nanopolymer particle exhibits regular spherical shape and smooth surface, has mesopores ranging from 4.9–7.1 nm with a typical diameter centered (BJH pore size distribution) at ∼5.7 nm. FT-IR, 13CNMR, and elemental analysis experimental results indicate that the monodisperse mesoporous networks nanopolymer particles were cross-linked by AM, AMPS, NVP, MBA, and Zr. Compared to the ordinary AM/NVP/AMPS nanoparticles, significantly enhanced high-temperature thermal stability was found under 150 °C. A core displacement experiment showed how the nanopolymer particles could effectively plug the porous media for water control and oil recovery improvement even after aging at 150 °C for three months. Oil recovery is increased by 13% on the basis of water flooding. Zr-AM/NVP/AMPS nanoparticles with double-cross-linked architectures can be a great help for petroleum engineers to better apply this deep profile control and flooding technology.

Ward, J.F., Verdel, C., Campbell, M.J., Leonard, N., Duc Nguyen, A., 2019. Rare earth element geochemistry of Australian Neoproterozoic carbonate: Constraints on the Neoproterozoic oxygenation events. Precambrian Research 335, 105471.


Carbonate successions are principal geochemical archives of the extraordinary environmental changes that occurred during the Neoproterozoic Era. In this study, we present a stratigraphic record of carbonate rare earth element (REE) compositions from Neoproterozoic and Cambrian strata in central and southern Australia. The new REE results provide insight into the redox conditions of the Neoproterozoic-Cambrian ocean, the influence of glacial meltwater on carbonate precipitation, and Neoproterozoic-Cambrian paleoenvironmental changes. High Ce/Ce* and low Y/Ho suggest that the major Neoproterozoic and Cambrian carbonate accumulations of central and southern Australia formed in restricted marine environments that were largely dysoxic. Elevated ∑REE of mid-Cryogenian and early Ediacaran carbonate from the Amadeus Basin (central Australia) and King Island (Tasmania), respectively, are interpreted to reflect increased detrital mineral flux following periods of Cryogenian glaciation. REE data from the basal Ediacaran Cumberland Creek Dolostone of King Island suggest a transient episode of ocean oxidation in the wake of the terminal Cryogenian glaciation, but the balance of evidence suggests dominantly low oxygen ocean conditions during carbonate deposition in the remainder of the Neoproterozoic Era. An apparent mismatch in timing between carbonate deposition in central and southern Australia versus previously proposed mid-to-late-Ediacaran oxygenation events based on geochemical results from strata of South China highlights what may be important factors in reconciling varied geochemical records of Neoproterozoic-Paleozoic ocean oxygenation.

Ware, T.B., Shin, M., Hsu, K.-L., 2019. Metabolomics analysis of lipid metabolizing enzyme activity. Methods in Enzymology 626, 407-428.


Lipids exert key structural, metabolic, and signaling functions in cells. Lipid diversity found in cells and tissues is regulated principally by metabolic enzymes whose activity is modulated posttranslationally to shape head group and fatty acyl composition of membrane lipids. Methodologies capable of monitoring in vivo changes in the lipidome are needed to assign substrate specificity of metabolic enzymes, which represents a key step toward understanding structure-function of lipids in living systems. The resulting lipid annotations also serve as important biomarkers for understanding mode of action for pharmacological agents targeting metabolic enzymes in cells and animal models. In this chapter, we describe a general metabolomics workflow to complement (chemo)proteomic efforts to modulate lipid pathways for basic science and translational applications.


https://doi.org/10.1038/s41467-019-12541-7

Oceanic emissions represent a highly uncertain term in the natural atmospheric methane (CH4) budget, due to the sparse sampling of dissolved CH4 in the marine environment. Here we overcome this limitation by training machine-learning models to map the surface distribution of methane disequilibrium (∆CH4). Our approach yields a global diffusive CH4 flux of 2–6TgCH4yr−1 from the ocean to the atmosphere, after propagating uncertainties in ∆CH4 and gas transfer velocity. Combined with constraints on bubble-driven ebullitive fluxes, we place total oceanic CH4 emissions between 6–12TgCH4yr−1, narrowing the range adopted by recent atmospheric budgets (5–25TgCH4yr−1) by a factor of three. The global flux is dominated by shallow near-shore environments, where CH4 released from the seafloor can escape to the atmosphere before oxidation. In the open ocean, our models reveal a significant relationship between ∆CH4 and primary production that is consistent with hypothesized pathways of in situ methane production during organic matter cycling.



This work targeted an asphaltenic tight formation and thoroughly investigated the effectiveness of supercritical CO2 (scCO2) injection in enhancing oil recovery. Particular attention was placed on the changes of rock petrophysical properties induced by asphaltene precipitation in porous media. Low-field Nuclear magnetic resonance (LF-NMR) spectrometer and SEM-EDS were employed to characterize the changes. The results indicated that high injection pressure was favorable for enhanced oil recovery (EOR) but accelerated asphaltene precipitation in formation. The precipitated asphaltenes notably reduced rock permeability and porosity, in which the large pores were more likely to be damaged. The wettability of rock surface was hardly altered with an exception of the inlet face. The results of this study supplement earlier observations and can provide insights into tight reservoirs EOR especially in the presence of asphaltenes.

Wei, H., Tang, Z., Yan, D., Wang, J., Roberts, A.P., 2019. Guadalupian (Middle Permian) ocean redox evolution in South China and its implications for mass extinction. Chemical Geology 530, 119318.


The Guadalupian mass extinction was a long-term biocrisis that started in the early Guadalupian Epoch (Permian Period). Many studies of the causes of the extinction have focused on the late Guadalupian, although the entire Guadalupian should be studied to address its origins. The selective nature of the species removed during the Guadalupian extinction also remains a puzzle. Here, we present pyrite framboid size distributions, pyrite-sulfur isotopic compositions, and C-N-S profiles for the entire Guadalupian from South China to develop a record of ocean redox evolution to help understand the selective extinction. Our results indicate that euxinia was mostly persistent in the deep-water platform basin throughout the Guadalupian, which triggered long-term Early and Middle Guadalupian shallow-water dysoxia and frequent episodic Late Guadalupian euxinia events that resulted in a gradual long-term Early and Middle Guadalupian diversity decrease and selective Late Guadalupian extinction. The combined effect of euxinia and global regression led to selective extinction of taxa that had weakly buffered respiratory physiology and high growth efficiency, such as brachiopods, large fusulinids, and giant bivalves.

Wei, L., Cook, A., Daigle, H., Malinverno, A., Nole, M., You, K., 2019. Factors controlling short-range methane migration of gas hydrate accumulations in thin coarse-grained layers. Geochemistry, Geophysics, Geosystems 20, 3985-4000.

https://doi.org/10.1029/2019GC008405

Natural gas hydrate is often found in marine sediment in heterogeneous distributions in different sediment types. Diffusion may be a dominant mechanism for methane migration and affect hydrate distribution. We use a 1-D advection-diffusion-reaction model to understand hydrate distribution in and surrounding thin coarse-grained layers to examine the sensitivity of four controlling factors in a diffusion-dominant gas hydrate system. These factors are the particulate organic carbon content at seafloor, the microbial reaction rate constant, the sediment grading pattern, and the cementation factor of the coarse-grained layer. We use available data at Walker Ridge 313 in the northern Gulf of Mexico where two ~3-m-thick hydrate-bearing coarse-grained layers were observed at different depths. The results show that the hydrate volume and the total amount of methane within thin, coarse-grained layers are most sensitive to the particulate organic carbon of fine-grained sediments when deposited at the seafloor. The thickness of fine-grained hydrate free zones surrounding the coarse-grained layers is most sensitive to the microbial reaction rate constant. Moreover, it may be possible to estimate microbial reaction rate constants at other locations by studying the thickness of the hydrate free zones using the Damköhler number. In addition, we note that sediment grading patterns have a strong influence on gas hydrate occurrence within coarse-grained layers.

Wei, S., Cui, H., Zhang, Y., Su, X., Dong, H., Chen, F., Zhu, Y., 2019. Comparative evaluation of three archaeal primer pairs for exploring archaeal communities in deep-sea sediments and permafrost soils. Extremophiles 23, 747-757.

https://doi.org/10.1007/s00792-019-01128-1

16S rRNA gene profiling is a powerful method for characterizing microbial communities; however, no universal primer pair can target all bacteria and archaea, resulting in different primer pairs which may impact the diversity profile obtained. Here, we evaluated three pairs of high-throughput sequencing primers for characterizing archaeal communities from deep-sea sediments and permafrost soils. The results show that primer pair Arch519/Arch915 (V4–V5 regions) produced the highest alpha diversity estimates, followed by Arch349f/Arch806r (V3–V4 regions) and A751f/AU1204r (V5–V7 regions) in both sample types. The archaeal taxonomic compositions and the relative abundance estimates of archaeal communities are influenced by the primer pairs. Beta diversity of the

archaeal community detected by the three primer pairs reveals that primer pairs Arch349f/Arch806r and Arch519f/Arch915r are biased toward detection of Halobacteriales, Methanobacteriales and MBG-E/Hydrothermarchaeota, whereas the primer pairs Arch519f/Arch915r and A751f/UA1204r are biased to detect MBG-B/Lokiarchaeota, and the primers pairs Arch349f/Arch806r and A751f/UA1204r are biased to detect Methanomicrobiales and Methanosarcinales. The data suggest that the alpha and beta diversities of archaeal communities as well as the community compositions are influenced by the primer pair choice. This finding provides researchers with valuable experimental insight for selection of appropriate archaeal primer pairs to characterize archaeal communities.

Wellman, C.H., Graham, L.E., Lewis, L.A., 2019. Filamentous green algae from the Early Devonian Rhynie chert. PalZ 93, 387-393.

https://doi.org/10.1007/s12542-019-00456-z

A relatively neglected element of the biota of the Lower Devonian Rhynie chert Lagerstätte are filamentous green algae exceptionally preserved by silicification. Palynological processing of sediments associated with the cherts has yielded palynomorphs that we also interpret as the remains of filamentous green algae and one such taxon is described herein. Cells occur individually, in masses or joined end-to-end as an unbranched filament. The cells are characterised by end walls that form a ‘collar’ structure and inner bodies interpreted as reproductive structures. Because of a lack of preserved characters taxonomic precision is limited, although we suggest the fossils are most likely either zygnematalean or oedogonialean algae that inhabited ponds or lakes and were either attached to substrates and/or free-floating.

Whittle, R.J., Witts, J.D., Bowman, V.C., Crame, J.A., Francis, J.E., Ineson, J., 2019. Nature and timing of biotic recovery in Antarctic benthic marine ecosystems following the Cretaceous–Palaeogene mass extinction. Palaeontology 62, 919-934.

https://doi.org/10.1111/pala.12434

Taxonomic and ecological recovery from the Cretaceous–Palaeogene (K–Pg) mass extinction 66 million years ago shaped the composition and structure of modern ecosystems. The timing and nature of recovery has been linked to many factors including palaeolatitude, geographical range, the ecology of survivors, incumbency and palaeoenvironmental setting. Using a temporally constrained fossil dataset from one of the most expanded K–Pg successions in the world, integrated with palaeoenvironmental information, we provide the most detailed examination of the patterns and timing of recovery from the K–Pg mass extinction event in the high southern latitudes of Antarctica. The timing of biotic recovery was influenced by global stabilization of the wider Earth system following severe environmental perturbations, apparently regardless of latitude or local environment. Extinction intensity and ecological change were decoupled, with community scale ecological change less distinct compared to other locations, even if the taxonomic severity of the extinction was the same as at lower latitudes. This is consistent with a degree of geographical heterogeneity in the recovery from the K–Pg mass extinction. Recovery in Antarctica was influenced by local factors (such as water depth changes, local volcanism, and possibly incumbency and pre‐adaptation to seasonality of the local benthic molluscan population), and also showed global signals, for example the radiation of the Neogastropoda within the first million years of the Danian, and a shift in dominance between bivalves and gastropods.

Williams, B.T., Cowles, K., Bermejo Martínez, A., Curson, A.R.J., Zheng, Y., Liu, J., Newton-Payne, S., Hind, A.J., Li, C.-Y., Rivera, P.P.L., Carrión, O., Liu, J., Spurgin, L.G., Brearley, C.A., Mackenzie, B.W., Pinchbeck, B.J., Peng, M., Pratscher, J., Zhang, X.-H., Zhang, Y.-Z., Murrell, J.C., Todd, J.D., 2019. Bacteria are important dimethylsulfoniopropionate producers in coastal sediments. Nature Microbiology 4, 1815-1825.

https://doi.org/10.1038/s41564-019-0527-1

Dimethylsulfoniopropionate (DMSP) and its catabolite dimethyl sulfide (DMS) are key marine nutrients1,2 that have roles in global sulfur cycling2, atmospheric chemistry3, signalling4,5 and, potentially, climate regulation6,7. The production of DMSP was previously thought to be an oxic and photic process that is mainly confined to the surface oceans. However, here we show that DMSP concentrations and/or rates of DMSP and DMS synthesis are higher in surface sediment from, for example, saltmarsh ponds, estuaries and the deep ocean than in the overlying seawater. A quarter of bacterial strains isolated from saltmarsh sediment produced DMSP (up to 73 mM), and we identified several previously unknown producers of DMSP. Most DMSP-producing isolates contained dsyB8, but some alphaproteobacteria, gammaproteobacteria and actinobacteria used a methionine methylation pathway independent of DsyB that was previously only associated with higher plants. These bacteria contained a methionine methyltransferase gene (mmtN)—a marker for bacterial synthesis of DMSP through this pathway. DMSP-producing bacteria and their dsyB and/or mmtN transcripts were present in all of the tested seawater samples and Tara Oceans bacterioplankton datasets, but were much more abundant in marine surface sediment. Approximately 1 × 108 bacteria g−1 of surface marine sediment are predicted to produce DMSP, and their contribution to this process should be included in future models of global DMSP production. We propose that coastal and marine sediments, which cover a large part of the Earth’s surface, are environments with high levels of DMSP and DMS productivity, and that bacteria are important producers of DMSP and DMS within these environments.

Wong, K., Mason, E., Brune, S., East, M., Edmonds, M., Zahirovic, S., 2019. Deep carbon cycling over the past 200 million years: A review of fluxes in different tectonic settings. Frontiers in Earth Science 7, 263. doi: 10.3389/feart.2019.00263.

https://www.frontiersin.org/article/10.3389/feart.2019.00263

Carbon is a key control on the surface chemistry and climate of Earth. Significant volumes of carbon are input to the oceans and atmosphere from deep Earth in the form of degassed CO2 and are returned to large carbon reservoirs in the mantle via subduction or burial. Different tectonic settings (e.g., volcanic arcs, mid-ocean ridges, and continental rifts) emit fluxes of CO2 that are temporally and spatially variable, and together they represent a first-order control on carbon outgassing from the deep Earth. A change in the relative importance of different tectonic settings throughout Earth’s history has therefore played a key role in balancing the deep carbon cycle on geological timescales. Over the past 10 years the Deep Carbon Observatory has made enormous progress in constraining estimates of carbon outgassing flux at different tectonic settings. Using plate boundary evolution modeling and our understanding of present-day carbon fluxes, we develop time series of carbon fluxes into and out of the Earth’s interior through the past 200 million years. We highlight the increasing importance of carbonate-intersecting subduction zones over time to carbon outgassing, and the possible dominance of carbon outgassing at continental rift zones, which leads to maxima in outgassing at 130 and 15 Ma. To a first-order, carbon outgassing since 200 Ma may be net positive, averaging ∼50 Mt C yr–1 more than the ingassing flux at subduction zones. Our net outgassing curve is poorly correlated with atmospheric CO2, implying that surface carbon cycling processes play a significant role in modulating carbon concentrations and/or there is a long-term crustal or lithospheric storage of carbon which

modulates the outgassing flux. Our results highlight the large uncertainties that exist in reconstructing the corresponding in- and outgassing fluxes of carbon. Our synthesis summarizes our current understanding of fluxes at tectonic settings and their influence on atmospheric CO2, and provides a framework for future research into Earth’s deep carbon cycling, both today and in the past.

Woo, J.E., Jang, Y.-S., 2019. Metabolic engineering of microorganisms for the production of ethanol and butanol from oxides of carbon. Applied Microbiology and Biotechnology 103, 8283-8292.

https://doi.org/10.1007/s00253-019-10072-1

The utilized biomass is an important consideration for sustainable biofuel production. To avoid competing with food needs, researchers have turned their attention to non-food lignocellulosic biomasses as potential feedstocks for biofuel production. However, the saccharification of a lignocellulosic biomass produces a large amount of lignin as waste. To overcome this hurdle, biomass gasification has been suggested as an alternative to saccharification. During biomass gasification, oxides of carbon (CO, CO2) and hydrogen are produced as a major product. Accordingly, microorganisms capable of utilizing these oxides of carbon have gained attention as hosts for the production of biofuels, such as ethanol and butanol. In this work, we reviewed the Calvin cycle and Wood-Ljungdahl pathway for utilizing oxides of carbon in cyanobacteria and acetogens, respectively, and discussed the metabolic engineering strategies that may be used to produce ethanol and butanol from oxides of carbon through these routes.

Wordsworth, R., Kerber, L., Cockell, C., 2019. Enabling Martian habitability with silica aerogel via the solid-state greenhouse effect. Nature Astronomy 3, 898-903.

https://doi.org/10.1038/s41550-019-0813-0

The low temperatures and high ultraviolet radiation levels at the surface of Mars today currently preclude the survival of life anywhere except perhaps in limited subsurface niches4. Several ideas for making the Martian surface more habitable have been put forward, but they all involve massive environmental modification that will be well beyond human capability for the foreseeable future. Here, we present a new approach to this problem. We show that widespread regions of the surface of Mars could be made habitable to photosynthetic life in the future via a solid-state analogue to Earth’s atmospheric greenhouse effect. Specifically, we demonstrate via experiments and modelling that under Martian environmental conditions, a 2–3 cm-thick layer of silica aerogel will simultaneously transmit sufficient visible light for photosynthesis, block hazardous ultraviolet radiation and raise temperatures underneath it permanently to above the melting point of water, without the need for any internal heat source. Placing silica aerogel shields over sufficiently ice-rich regions of the Martian surface could therefore allow photosynthetic life to survive there with minimal subsequent intervention. This regional approach to making Mars habitable is much more achievable than global atmospheric modification. In addition, it can be developed systematically, starting from minimal resources, and can be further tested in extreme environments on Earth today.



Polycyclic aromatic hydrocarbons (PAHs) are a large category of ubiquitous persistent environmental pollutants, some of them have strong carcinogenicity to human and animals. These pollutants can

easily enter the river through multiple ways including rainfall, dry deposition and water washout, and deposit in the sediment. However, it is easy for them to re-enter the river water and pollute water sources, as well as aquatic animals and plants, bringing potential harm to human health. Therefore, it is requisite to accurately analyze the PAHs in sediment. In this review, the analytical methods of PAHs in sediment, focused on the methods of sample extraction, purification, concentration and determination, are summarized.

Wu, W., Xu, Y., Hou, S., Dong, L., Liu, H., Wang, H., Liu, W., Zhang, C., 2019. Origin and preservation of archaeal intact polar tetraether lipids in deeply buried sediments from the South China Sea. Deep Sea Research Part I: Oceanographic Research Papers 152, 103107.


Intact polar lipids-glycerol dibiphytanyl glycerol tetraethers (IPL-GDGTs) are assumed to be degraded to core lipids (CL) upon cell death, which thus can serve as markers for live archaea in marine deep biosphere. However, the degradation models of sedimentary IPL-GDGTs suggested that they are mainly fossil compounds and can be preserved over geological timescales. Here we investigated the CL- and IPL-GDGTs from deeply buried sediments (0.1–485 mbsf, ~7.3 Ma) in the South China Sea (SCS). The depth profiles of IPL-GDGT concentrations paralleled those of CL-GDGTs. The sea surface temperatures (SST) derived from CL- and IPL-TEX86 ranged 23.1–28.8 °C and 22–33.3 °C, respectively. They are close to the SST in the SCS, suggesting that CL- and IPL-GDGTs mostly originate from pelagic archaea. The composition and distribution of the IPL-GDGTs differed among the polar headgroups. Hexose-phosphohexose (HPH)-GDGTs were dominated by GDGT-0, monohexose (1G)-GDGTs were mainly composed of GDGT-0 and crenarchaeol, and dihexose (2G)-GDGTs consist primarily of GDGT-2 and crenarchaeol isomer. The compositions of HPH-, 1G- and 2G-GDGTs are similar to those in previously studied water column samples, supporting that sedimentary IPL-GDGTs predominantly derive from the water column. HPH-GDGT abundances fast declined to be undetectable at ~31 mbsf (~0.6 Ma) while 1G- and 2G-GDGTs dominated the deeply buried sediments, indicating that GDGTs with glycosidic headgroups are better preserved versus GDGTs with phosphorous headgroups over geological timescales. Our results demonstrate that IPL-GDGTs, especially glycosidic GDGTs, are not suitable as biomarkers for live archaea in the deep biosphere.

Wu, X., Ni, C., Chen, Y., Zhu, J., Li, K., Zeng, H., 2019. Source of the Upper Paleozoic natural gas in the Dingbei area, Ordos Basin, China. Journal of Natural Gas Geoscience 4, 183-190.

http://www.sciencedirect.com/science/article/pii/S2468256X1930046X

The Dingbei area is an important exploration area in the Ordos Basin for SINOPEC, and natural gas exploration in the Upper Paleozoic strata in the area achieved a great breakthrough in recent years. However, the origin and source of natural gas are weakly studied, wherein there is no consensus on whether the Upper Paleozoic gas in the basin has experienced large-scale lateral migration. Studies on the geochemical characteristics of natural gas indicate that the Upper Paleozoic natural gas in the Dingbei area is typically dry gas with the dryness coefficient (C1/C1-5) ranging from 0.977 to 0.986, and the δ13C1, δ13C2, and δD1 values range from −30.6‰ to −28.6‰, −25.9‰ to −24.1‰, and −191‰ to −177‰, respectively. The above has positive carbon and hydrogen isotopic sequence between CH4 and C2H6. Carbon and hydrogen isotope compositions of alkane gas suggest that the Upper Paleozoic gas in the Dingbei area is typically coal-derived gas. The calculated RO values according to the two-stage fractionation mode of coal-derived gas are consistent with the measured RO values of the Upper Paleozoic source rocks; this indicates that the Upper Paleozoic gas in the Dingbei area was mainly

derived from in-situ source rocks in the Taiyuan and Shanxi formations. In comparison to the Dingbei area, natural gas from the Daniudi gas field in northeastern Ordos Basin displays lower δ13C1, C1/C1-5, and C1/C2+3 values and higher C2/C1 ratios, suggesting the lower maturity of source rocks rather than migration effect. The Upper Paleozoic natural gas in the Ordos Basin has not experienced large-scale lateral migration.

Xiao, C.-T., Wei, G.-Q., Song, Z.-Y., Xiao, Y.-P., Yang, W., Dong, M., Huang, Y.-F., Gao, D., 2019. Petrography and origin of the Lower Ordovician microbial carbonates in the Songzi Area of Hubei Province, middle Yangtze region, China. Petroleum Science 16, 956-971.

https://doi.org/10.1007/s12182-019-0346-2

This study is the first systematic assessment of the Lower Ordovician microbial carbonates in Songzi, Hubei Province, China. This paper divides the microbial carbonates into two types according to growth patterns, namely nongranular and granular. The nongranular types include stromatolites, thrombolites, dendrolites, leiolites and laminites; the granular types are mainly oncolites and may include a small amount of microbiogenic oolite. According to their geometric features, the stromatolites can be divided into four types: stratiform, wavy, columnar and domal. Additionally, dipyramidal columnar stromatolites are identified for the first time and represent a new type of columnar stromatolite. The thrombolites are divided into three types: speckled, reticulated and banded. The grazing gastropod Ecculiomphalus and traces of bioturbation are observed in the speckled and reticulated thrombolites. This paper considers these two kinds of thrombolites to represent bioturbated thrombolites. These findings not only fill gaps in the field of domestic Ordovician bioturbated thrombolites but also provide new information for the study of thrombolites. Based on the analysis of the sedimentary characteristics of microbialites, the depositional environments of the various types of microbialites are described, and the distribution patterns of their depositional environments are summarized. The relationship between the development of microbialites and the evolution and radiation of metazoans during the Early to Middle Ordovician is discussed. Consistent with the correspondence between the stepwise and rapid radiation of metazoans and the abrupt reduction in the number of microbialites between the late Early Ordovician and the early Middle Ordovician, fossils of benthonic grazing gastropods (Ecculiomphalus) were found in the stromatolites and thrombolite of the study area. It is believed that the gradual reduction in microbialites was related to the rapid increase in the abundance of metazoans. Grazers not only grazed on the microorganisms that formed stromatolites, resulting in a continuous reduction in the number of stromatolites, but also disrupted the growth state of the stromatolites, resulting in the formation of unique bioturbated thrombolites in the study area. Hydrocarbon potential analysis shows that the microbialites in the Nanjinguan Formation represent better source rocks than those in the other formations.

Xiao, H., Li, M., Wang, W., You, B., Liu, X., Yang, Z., Liu, J., Chen, Q., Uwiringiyimana, M., 2019. Identification, distribution and geochemical significance of four rearranged hopane series in crude oil. Organic Geochemistry 138, 103929.


Four rearranged hopane series were simultaneously detected in oils from the Muglad Basin, one of several rift basins on the Central African Shear Zone (CASZ). The series are identified as having the structure of 17α(H)-diahopane (D series), 18α(H)-neohopane (Ts series), early eluting rearranged hopane (E series) and 21-methyl-28-norhopanes (Nsp series). The four rearranged hopane series exhibit strong positive correlations. The slope and intercept of the linear equation in plots of

C29D/C29H vs C30D/C30H are 1.10 and 0.003 respectively, possibly implying identical biological origins and formation mechanisms. The relatively low slope (<0.80) and intercept (<0.07) in both C30E/C30H vs C30D/C30H and C29Nsp/C29H vs C29D/C29H suggest that E and Nsp series have similar biological origins as D series, but form at a slower rate following different rearrangement mechanisms. Both the Nsp and E series require the shifting of two methyl groups from their precursors, whereas the D series have only one methyl migration from C-18 to C-17. The extremely high values of slope (1.42) and intercept (0.427) in a plot of C29Ts/C29H vs C29D/C29H probably indicates that the Ts series is more easily generated than other rearranged hopane series and possibly has multiple biological sources, such as contributions from diplopterol and/or diploptene. Furthermore, C30E, C30D, C29Nsp and Ts are enriched relative to regular hopanes in severely biodegraded oil samples owing to their greater resistance to microbial degradation, and/or additional sources of rearranged hopanes from bacterially reworked terrigenous organic matter. Based on relative Gibbs free energies (ΔG) calculated by density functional theory (DFT), the thermodynamic stabilities of C30 isomers follow the order C30D > C30H > C30E.

Xiao, S., Chen, Z., Zhou, C., Yuan, X., 2019. Surfing in and on microbial mats: Oxygen-related behavior of a terminal Ediacaran bilaterian animal. Geology 47, 1054-1058.

https://doi.org/10.1130/G46474.1

Geochemical evidence suggests that terminal Ediacaran (ca. 551–539 Ma) oceans experienced expansive anoxia and dynamic redox conditions, which are expected to have impacted animal distribution and behaviors. However, fossil evidence for oxygen-related behaviors of terminal Ediacaran animals is poorly documented. Here, we report a terminal Ediacaran trace fossil that records redox-regulated behaviors. This trace fossil, Yichnus levis new ichnogenus and new ichnospecies, consists of short and uniserially aligned segments of horizontal burrows that are closely associated with microbial mats. Thin-section analysis shows that the trace-making animal moved repeatedly in and out of microbial mats, with mat-burrowing intervals interspersed by epibenthic intermissions. This animal is hypothesized to have been a bilaterian exploring an oxygen oasis in microbial mats. Such intermittent burrowing behavior reflects challenging and dynamic redox conditions in both the water column and microbial mats, highlighting the close relationship between terminal Ediacaran animals and redox dynamics.

Xiao, W., Wang, Y., Liu, Y., Zhang, X., Shi, L., Xu, Y., 2019. Predominance of hexamethylated 6-methyl branched glycerol dialkyl glycerol tetraethers in the Mariana Trench: Source and environmental implication. Biogeosciences Discussions 2019, 1-36.


Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are useful molecular indicators for organic carbon (OC) source and paleoenvironment. Their application in marine environments, however, is complicated because of the mixed terrestrial and marine contributions to brGDGTs. Here, we employ two dimensional (2D) ultrahigh-performance liquid chromatography-mass spectrometry (UHPLC-MS) to analyze brGDGTs in sediments from the Challenger Deep, Mariana Trench, the deepest ocean in the absent of terrestrial influence. The unique feature is the absence of 5-methyl brGDGTs, and the strong predominance of hexamethylated 6-methyl brGDGT (IIIa') (73.4 ±2.4 % of total brGDGTs). The brGDGTs-reconstructed pH is 8.22 ± 0.07, close to seawater pH. This, combined with characteristics of δ13C (− 19.82 ± 0.25 %), OC / TN ratio (6.72 ± 0.84), branched and isoprenoid tetraether (BIT) index (0.03 ± 0.01) and the acyclic hexa-/pentamethylated brGDGTs ratio (7.13 ± 0.98), strongly suggest that brGDGTs are of autochthonous products from benthic bacteria or

planktonic bacteria. The compiling of literature data reveals that enhanced fractional abundance of hexamethylated 6-methyl brGDGTs is common in diverse continental margins when the marine influence became intensified. This may reflect an adaption of brGDGTs-producing bacteria to weak alkaline seawater and low ambient temperature. Based on the global dataset, the cross plot of acyclic hexa-/pentamethylated brGDGTs ratio and fractional abundance of brGDGT-IIIa' is an effective approach to distinguish the terrestrial vs. marine provenance of brGDGTs.

Xie, J., Jia, T., Gong, S., Liu, N., Nie, G., Pan, L., Zhang, X., Zou, J.-J., 2020. Synthesis and thermal stability of dimethyl adamantanes as high-density and high-thermal-stability fuels. Fuel 260, 116424.


Alkyl-adamantane fuels are appealing for aerospace vehicles due to their high density, good low-temperature performance and thermal stability. Here we reported a facile route to synthesize dimethyl-adamantane fuels via solvent-free rearrangement. The thermodynamic preference of six products (dimethyl-adamantane isomers) was revealed by Density Functional Theory (DFT) calculation and experiment, and the reaction pathway was further discussed. The reaction conditions including catalyst, catalyst dosage, temperature, and solvent were optimized, with the dimethyl-adamantane yield of 88.7%. We synthesized two typical dimethyl-adamantane fuels (with different compositions of isomers) by adjusting the reaction conditions and then evaluated their properties. It is found the two fuels show different fuel properties (e.g., density, heating value, thermal stability) due to the difference in methyl substitution position, although both with high density and good low-temperature fluidity. Specifically, the dimethyl-adamantane with methyl on the tertiary carbon shows better thermal stability than JP-10 and decalin. This work presents dimethyl-adamantanes as good high-density and high-thermal-stability fuels, and suggests the position of methyl substitution on adamantane has considerable effect on their properties.

Xie, L., Sun, Y., Uguna, C.N., Li, Y., Snape, C.E., Meredith, W., 2019. Thermal cracking of oil under water pressure up to 900 bar at high thermal maturities: 2. Insight from light hydrocarbon generation and carbon isotope fractionation. Energy & Fuels 33, 9546-9558.


In this study, pyrolysis experiments were conducted with a saturate-rich Tertiary source rock-derived oil from the South China Sea basin using a fixed-volume pressure vessel at temperatures from 350 to 425 °C for 24 h (0.92–1.85% Easy R0) to investigate pressure effects up to 900 bar on the generation and stable carbon isotopic fractionation of light hydrocarbons in the C6–C7 range. The results demonstrate that the pressure retards oil cracking to light hydrocarbons, but the retardation depends on the thermal evolution. In the peak oil to early wet gas stage (350 and 373 °C, 0.92–1.15% Easy R0), the light hydrocarbon generation is low but it is still suppressed by increasing pressure. In the late stages of the wet gas window (390, 405, and 425 °C, 1.35–1.85% Easy R0), the light hydrocarbon generation is suppressed significantly from 200 to 470 bar, followed by promotion and promotion-suppression as pressure is increased up to 900 bar. Meanwhile, the distributions of branched alkanes, cycloalkanes, and aromatic hydrocarbons are pressure-dependent. The medium to high pressures result in increasing Mango K1 values and toluene/n-C7 ratios and decreasing n-C7/methylcyclohexane ratios, suggesting that pressure benefits the occurrence of cyclization and aromatization during oil cracking, probably involving bimolecular reaction pathways. Preferential aromatization and isomerization with increasing pressure lead to significant carbon isotopic fractionations of aromatic hydrocarbons and branched alkanes as up to 4‰ and 2‰, respectively. However, stable carbon isotopic compositions of cycloalkanes show almost no fractionation under pressurized cracking.

Therefore, caution must be taken with respect to the application of light hydrocarbon-derived parameters in deep petroleum reservoirs usually at high temperatures and pressures. The carbon isotopes of branched alkanes and aromatic hydrocarbons could be potential measures to identify the pressure effects, while carbon isotopes of cycloalkanes could be an effective index for oil–oil/oil–source correlations.



Gas hydrates are the largest carbon sink on the earth and have an important impact on global climate and the environment. We studied theδ34S,δ13C, major trace elements and P –Fe dates at station 973-4 which acquired from the cold seep area of the Taixinan Basin. The results showed that during the Last Glacial Maximum (LGM), Younger Dryas (YD), and the Last Deglaciation, Gas hydrate inventory (GHI) was significantly reduced. And during the LGM, anaerobic oxidation of methane played an important role in preventing methane from leaking into seawater and the atmosphere. Because that there was no acidification of seawater or increase in PCO2. Meanwhile, rapid rate of sediment accumulation caused by isobaric flow provided accumulated material for Anaerobic Oxidation of Methan (AOM) during the LGM. The rapid rate of sediment accumulation also created a good environment for the formation of PCFA and vivianite below the sulfate methane transition zone (SMTZ). And according to changes of elements with depth, we conclude that the effect of methane anaerobic oxidation on redistribution of elemental P–Fe is divided into three processes: SMTZ rapid movement (material accumulation); SMTZ gradually stable; and SMTZ fixation process. In this paper, the effects of sedimentary evolution and hydrate evolution on AOM are studied in detail, which is of great significance for further understanding of anaerobic oxidation of methane.

Xu, A., Chen, Z., Qu, Y., Tian, Y., Shu, C., Zheng, X., Li, G., Yan, W., Zhao, M., 2019. Cold-water corals in a cold seep area on the northern continental slopes of the South China sea and their isotopic characteristics. Deep Sea Research Part I: Oceanographic Research Papers 152, 103043.


Cold-water corals (CWCs) were found to occur in association with authigenic carbonates in a cold seep area on the northern continental slopes of the South China Sea (SCS). The taxa identified were: Balanophyllia (Balanophyllia) sp., Balanophyllia (Eupsammia) sp., Lochmaeotrochus sp., Enallopsammia sp., Crispatotrochus sp.1 and Crispatotrochus sp.2. The δ13C (−7.36‰ to −1.15‰, V-PDB) and 87Sr/86Sr ratios (0.709126–0.709184) indicated that CWC aragonite skeletons had been precipitated from seawater without the involvement of seeping fluids. The presence and growth of CWCs on the slopes of the submarine seamounts in the south-western (SW) Dongsha area could be directly linked with the hard substrates provided by exhumed hydrocarbon-imprinted authigenic carbonates and fed by the food particles enhanced by high-velocity internal tides and near-bottom currents. A multi-step process for CWC colonization was proposed that encompassed cold-seepage processes as a driver for hard-substrate generation of CWC, as well as the subsequent settlement and maintenance of CWC larvae under the persistent influence of bottom currents.

Xu, L., Frank, A.B., Lehmann, B., Zhu, J., Mao, J., Ju, Y., Frei, R., 2019. Subtle Cr isotope signals track the variably anoxic Cryogenian interglacial period with voluminous manganese accumulation and decrease in biodiversity. Scientific Reports 9, 15056.

https://doi.org/10.1038/s41598-019-51495-0

Earth’s atmosphere experienced a step of profound oxygenation during the Neoproterozoic era, accompanied by diversification of animals. However, during the Cryogenian period (720–635 million years ago) Earth experienced its most severe glaciations which likely impacted marine ecosystems and multicellular life in the oceans. In particular, large volumes of Mn and Fe accumulated during the interglacial intervals of the Cryogenian glaciations, indicating large anoxic marine metal reservoirs. Here we present chromium isotope-, rare earth element-, and redox-sensitive trace element data of sedimentary rocks from the interglacial Datangpo Formation deposited between the Sturtian and Marinoan glaciations in South China, in an attempt to investigate the oxidation state of the oceans and atmosphere. Both the Cr isotope and trace element data indicate mainly anoxic water conditions with cryptic oxic surface water incursions after the Sturtian glaciation. Glacial-fed manganese precipitated as manganese carbonate in anoxic basins, and the non-fractionated δ53Cr record of −0.10 ± 0.06‰ identifies anoxic conditions with a cryptic component of slightly fractionated Cr isotope composition in manganese ore, in line with distinctly fractionated Mo isotope composition. Both the manganese carbonate ore and the black shales exhibit very low redox-sensitive element concentrations. Our study demonstrates that the oxygenation of the seawater, and inferably of the atmosphere, at the beginning of the Cryogenian interglacial interval was much subdued. The post-glacial rebound then allowed the Ediacaran biological diversity.

Xu, S., Shi, W., Yu, Q., Wang, X., 2019. Capillary introduction mass spectrometry coupled with selective cryotrapping for analysis of volatile compounds in water. Analytical Methods 11, 5237-5242.

http://dx.doi.org/10.1039/C9AY01669D

Capillary introduction mass spectrometry (CI-MS) has been recently developed for the direct analysis of volatile organic compounds (VOCs) in liquid samples. It exhibits the merits of simple structure, easy operation, and minimal sample consumption. For CI-MS analysis of aqueous solutions, the injection rate is generally a few microliters per minute. As the dominant component of the solution, water is drawn into the instrument together with the dissolved solutes, and it may reduce the ionization efficiency of the analytes and cause spectral interference. This proof of concept study aims to improve sampling efficiency by coupling CI with cryotrapping to implement selective removal of water. With the use of a cryotrap cooled by drikold, water vapor is effectively condensed to cause more than 90% reduction of its ion signal, whereas the detection of other components is less affected. Therein, the ion signals of the dissolved air are only slightly reduced, and the ethanol and toluene signals decrease by less than 50%. The chamber pressure drops substantially during the cryotrapping CI process, enabling a high injection rate of liquid samples to improve the detection efficiency of the uncondensed analytes. In addition, to prevent the solution from freezing at the capillary outlet in vacuum, an appropriate high voltage is applied onto the sample to initiate an electrospray (ES) at the capillary tip and increase the injection rate. On the basis of this cryotrapping ES-CI strategy, the MS detection sensitivity for ethanol in water can be improved by 29.5 times compared with conventional CI-MS, and the detection limit of the established instrument can be greatly reduced. In conclusion, selective cryotrapping is a simple and practical method to promote CI-MS analysis of VOCs in water.



The structural transformation of layered double hydroxides (LDHs) plays an important role in a variety of natural environmental behaviors. As one of the important ways of structure transformation in LDHs, the structure memory effect closely interacted with humic acid (HA). However, the role of functional groups in HA is unclear because its structure is relatively complex. Therefore, seven representative small molecules of single or double aromatic compounds were selected to explore their influence on the regeneration of different LDHs, thereby revealing key function groups in HA. As a result, ortho-benzene compounds could more effectively affect the regeneration of LDHs than other model compounds. For these compounds, the aliphatic chain length and aromatic ring size have little effect on regeneration of LDHs. However, increasing the number of carboxyl or hydroxyl groups affected the results, although all of them accelerated the regeneration rate of LDHs. Additionally, LDHs during the regeneration have a positive adsorption effect on both o-carboxyl and o-hydroxyl aromatic compounds; however, they have shown different effects on the regeneration of LDHs. Phthalic acid revealed no effect on the structure and crystallinity of regenerated LDH, while catechol inhibited the regeneration process and decreased the crystallinity of regenerated LDHs. The effects of o-hydroxyl aromatic compounds, such as catechol, are also dependent upon the type of LDHs. They have an inhibitory effect on the crystallinity of the regenerated Mg–LDH within a short time or with a high concentration but have no effect on its morphology. Although o-hydroxyl aromatic compounds have no effect on the crystallinity of regenerated Ca–LDH, the crystal growth was suppressed. This is due to the difference in the regeneration processes between two LDHs. These results provide a more detailed theoretical basis for understanding the influence of HA on the structural transformation of LDHs or even other minerals, such as hydroxides, in the environment.

Xue, H., Zhang, J., Han, S., Sun, M., Yan, X., Li, H., 2019. Effect of asphaltenes on the structure and surface properties of wax crystals in waxy oils. Energy & Fuels 33, 9570-9584.


Asphaltenes, as the most polar component of crude oils, may interact with wax molecules during the wax crystallization, thus changing wax precipitation characteristics and wax crystal structure and affecting the gelation behavior of crude oils. In the present work, waxy model oils of variable asphaltene contents (0–0.20 wt %) were prepared in order to systematically examine the effect of asphaltenes on the wax precipitation characteristics and the gelation behavior of waxy oils and to look into the structure and the surface electrical properties of wax crystals formed in oils of different asphaltene contents. By means of differential scanning calorimetry and multiple rheometries, it was found that asphaltenes play a significant role in inhibiting the precipitation of wax crystals and delaying the gelation, as well as in weakening the strength of the gel structure. It was observed by polarized optical microscopy that as the asphaltene content increases, the size of wax crystals gradually decreases, and the shape of wax crystals transforms from rodlike into elliptical. Furthermore, both the average aspect ratio and the average perimeter of wax crystals decrease, while the boundary box fractal dimension increases, demonstrating that the morphology of wax crystals becomes more complex. Based on the X-ray diffraction (XRD) pattern, the grain size obtained with the Scherrer equation presents a descending trend with the increase of asphaltenes. It could be inferred that the reduction of grain size is one of the reasons leading to the smaller sizes of wax crystals. The XRD result also showed that with higher asphaltene content, the lattice parameter c of wax crystals obviously increases, indicating that the conformation of wax crystals gets more

disordered, which results in the weakening of gel strength, corresponding to the decline of the measured yield stress of the waxy oil gel. With higher asphaltene content, the zeta potential of wax crystals goes up, which indicates that with more negative charges adsorbed on the wax crystal surfaces, stronger electrostatic double layers have formed. The greater electrostatic repulsion among wax crystals would interfere with the growth and aggregation of wax crystals, thus holding up the gelation of waxy oils.

Xue, J., Bai, Y., Liu, H., 2019. Recent advances in ambient mass spectrometry imaging. TrAC Trends in Analytical Chemistry 120, 115659.


The emerging ambient mass spectrometry imaging (MSI) enables to acquire molecular images and information directly on the sample surface under the atmospheric environment without labelling and staining. The appealing and unique advantages of ambient MSI drive the active development of novel ambient ionization techniques and their wide applications in different research areas. This paper first gives the overview of ambient ionization techniques capable of MSI from different point of view, including the ion source setup, the desorption/extraction, the spatial resolution etc. On this basis, some critical issues during ambient MSI, for example, spatial resolution, compounds identification, matrix effects, quantitative analysis, sensitivity and specificity etc., are discussed in detail. After briefly introducing the frontier three-dimensional ambient MSI, the applications of ambient MSI in different field are summarized, focusing on various types of analytes (e.g., proteins, lipids, natural produces, polymers etc.). Finally, the challenges and the perspectives of ambient MSI are concluded and proposed.

Yang, X., Liang, Q., Chen, Y., Wang, B., 2019. Alteration of methanogenic archaeon by ethanol contribute to the enhancement of biogenic methane production of lignite. Frontiers in Microbiology 10, 2323. doi: 10.3389/fmicb.2019.02323.


Bioconverting coal to methane is a green and environmental friendly method to reuse waste coal. In this study, heterologous bacteria were used for the gas-producing fermentation of lignite under laboratory conditions, simultaneously, different concentrations of ethanol added into the culture to investigate the effect of ethanol on gas production and microbial flora structure. Results show that when the ethanol concentration was 1%, the best methanogenesis was achieved at 44.86 mL/g, which was twice the gas production of 0% ethanol. Before and after gas fermentation, the composition and structure of the coal changed, the volatile matter and fixed carbon increased, and the ash decreased. The absorbance value at characteristic peaks of all functional groups decreased, new peaks were generated at 2,300/cm, and the peak value disappeared at 3,375/cm. Thus, microorganisms interacted with coal, consumed it, and produced new materials. The microbial flora changes during gas production were tracked in real time. 0.5 and 1% ethanol did not obviously change the bacterial communities but strongly influenced the archaeon communities, thereby changed the methane production pathway. In the absence of ethanol, Methanosarcina was continuously increasing with the extension of fermentation time, this pathway was the nutrient type of acetic acid. When ethanol was added, Methanobacterium gradually increased, the pathway was mainly hydrotropic type. In summary, adding ethanol can increase the coalbed methane production, change the structure and composition of coal, and facilitate the interaction of microbe with coal. Therefore, the methanogenic archaeon changes could help improve the methane-producing ability of lignite in the presence of ethanol.

Yao, Y.-N., Wu, L., Di, D., Yuan, Z.-C., Hu, B., 2019. Vibrating tip spray ionization mass spectrometry for direct sample analysis. Journal of Mass Spectrometry 54, 772-779.

https://doi.org/10.1002/jms.4429

In this work, a vibrating tip spray ionization source was developed for direct mass spectrometric analysis of raw samples under voltage-free condition. A solid tip was mounted on a vibrator, and the solid tip was placed on the front of MS inlet. Liquid, viscous, and bulk solid samples could be directly loaded on the tip-end surface, and then a drop of solvent at microliter level was subsequently loaded on the tip for dissolution and extraction of analytes, and a vibrator was then started to atomize and ionize the analytes under ambient condition. We demonstrated vibrating tip spray mass spectrometry in various applications, including food safety, pharmaceutical analysis, and forensic science. Furthermore, in situ analysis of biological tissues and in vivo analysis of living plants were conveniently performed, due to voltage-free. Different vibration frequencies and solvent compositions were investigated. The analytical performances, including sensitivity, reproducibility, and linear range, were investigated. The ionization process and mechanism were also discussed in this work.

Yashchenko, I.G., Polishchuk, Y.M., 2019. Classification approach to assay of crude oils with different physicochemical properties and quality parameters. Petroleum Chemistry 59, 1161-1168.

https://doi.org/10.1134/S0965544119100116

An approach to crude oil assay based on the consistent application of two heterogeneous classifications of oils is proposed: according to the quality index and physicochemical parameters. The methodological issues of the classification approach to oil analysis, implemented in the form of a two-stage procedure, are described. The approach is illustrated by an example of analysis of the characteristics features of different types of tight oils in Russia. The analysis used data from 25.190 oil samples with abnormal properties and 10 500 oil samples with complex modes of occurrence. At the first stage, the analysis has been carried out using the classification of tight oils according to the quality index; as a result, the oils were divided into three homogeneous classes: low, medium, and high quality oils. At the second stage of the analysis, the classification of oils by physicochemical characteristics has been used, taking into account the density; viscosity; sulfur, resin, asphaltene, wax, vanadium, nickel, and light end contents; gas saturation of oil; etc. The analysis made it possible to establish the characteristic features of the physicochemical properties of tight oils belonging to different quality classes.


https://doi.org/10.1007/s12517-019-4795-0

An integrated petrological and geochemical analysis of surface and drilled oil sands from the Middle Jurassic Yan’an Formation in the southern Ordos Basin was conducted to investigate the petrophysical properties, organic matter origin/type, and thermal maturity and their relation to environmental conditions during sediment deposition. Petrographic analysis (thin section, scanning electron microscopy (SEM), and porosity and permeability determination) of the oil sand was

performed to establish the relationships between porosity and permeability and bulk density, reservoir quality index (RQI), normalized porosity index (NPI), and flow zone indicator (FZI). Geochemical analyses include oil extraction, column chromatography, and gas chromatography–mass spectrometry (GC-MS). The strong correlation between RQI and permeability (R2 = 0.98) reveals that porosity has a good correlation with RQI. The positive correlations between porosity and permeability and NPI and RQI (R2 = 0.77 and R2 = 0.65, respectively) show that the studied rocks contain many large pores with pore-to-pore throat connection structures that enhance permeability, which is further supported by the relatively high connection coefficient between NPI and RQI (R2 = 0.65). The organic matter in the Yan’an Formation is mainly composed of oil-prone type I kerogen indicated by the recovery of a large amount of crude oil rich in saturated hydrocarbon fractions from the extracted oil. The biomarker signatures of the analyzed oil (nC13-nC35, Pr/n-C17 and Ph/n-C18, and low C27/C29 regular sterane) reveal predominantly land plant materials as organic input sources based on the average concentration of αααC27:C28:C29 sterane 20R of approximately 38%, 22%, and 40%, respectively, and on high values of tricyclic terpane/αβC30 hopane and regular sterane/αβC30 hopane. Deposition within a lacustrine paleoenvironment under anoxic conditions enhanced organic matter preservation in the area based on the low Pr/Ph ratios (average 0.74), low αβC31-22R-hopane/αβC30 hopane ratios, and high C26/C25 tricyclic terpane ratios, as well as the presence of gammacerane and low water salinity. Biomarker maturity parameters (e.g., C32 homohopane 22S/(22S + 22R), moretane/hopane, and C29 sterane 20S/(20S + 20R) ratios and CPI) show that the extracted oil sand entered the early oil window stage.

Yonkofski, C., Tartakovsky, G., Huerta, N., Wentworth, A., 2019. Risk-based monitoring designs for detecting CO2 leakage through abandoned wellbores: An application of NRAP’s WLAT and DREAM tools. International Journal of Greenhouse Gas Control 91, 102807.


As geologic CO2 storage (GCS) moves towards industrial-scale deployment, strategies must be developed to ensure long-term environmental risks related to potential leakage are managed. One approach to is to perform risk-based subsurface monitoring targeting early leak detection. Early detection is particularly important to address the risk associated with leakage along legacy wells. The challenge in risk-based monitoring is that leakage impacts are expected to be small in comparison with the footprint of the stored CO2 plume and could occur over considerable depths, ranging from the storage formation up to surficial aquifers. Here we demonstrate the application workflow of two of the National Risk Assessment Partnership’s (NRAP) computational tools, WLAT (Wellbore Leakage Analysis Tool) and DREAM (Designs for Risk Evaluation and Management), to a hypothetical CO2 storage site based on a study area in the Midwestern United States. By incorporating site specific wellbore integrity analyses, results show how fluid leakage may be estimated, evaluated, and monitored in terms of risk. For the selected site, three monitoring wells were ultimately needed to detect all possible CO2 leaks and six monitoring wells were needed to minimize time to leak detection. Such analyses inform stakeholders about long-term liability and monitoring costs of GCS projects.



In situ oil shale conversion experiments have revealed that to efficiently obtain shale oil, factors such as heating temperature, products, and matter thermal evolution of organic matter during heating need to be optimized. In this study, oil shales from China were subjected to retorting experiments involving eight heating steps. During steps I-II (≤300 °C), the expelled product is mainly water, the hydrocarbon generation potential (PP) of the samples was extremely high, and the organic matter was in the immature to low-mature stage. The oil shale produced a large amount of oil in steps III–VI (300–475 °C), and the TOC contents and S2 of the shale showed the greatest decreases during these steps. The analysis data suggest that the organic matter entered the mature stage during these steps. After heating to 400 °C and expelling a large amount of oil and gas, the PP decreased gradually. From 475 to 520 °C (steps VII–VIII), only a small amount of gas was produced and the organic matter had almost no PP in the high- and over-mature stages. Based on our experimental results, in situ conversion of oil shale the final heating temperature should be ~440 °C. These constraints require further field testing to be properly optimized.



Nanopore plays a crucial role in shale gas adsorption, and its characteristics and evolution are significant for the evaluation of shale reservoirs with strong heterogeneity. In this study, transitional coal-bearing shale samples from the south margin of North China were selected for investigation of pore structure characteristics and evolution mechanism. Results indicated that nanopores of the studied shales are fractal with strong heterogeneity. The higher fractal dimension leads to larger surface area and micropore volume of shale samples. The abundant terrigenous material and limited hydrocarbon generation and expulsion are favorable for the development of intraP pores in clay, so that the Organic matter (OM) pores are poorly developed and are partially filled with clay minerals and pyrite framboids. Shale samples having higher levels of clay content and lower levels of quartz content tend to develop more heterogeneous micropores, producing a more complex pore structure in shale. The evolution of nanopore in studied shales is simultaneously determined by the coupling relationship between clay content and the thermal maturation of OM. In the early oil and low clay content stage, the low degree of the thermal evolution of OM leads to generation of less acidic fluid during the decarboxylation of kerogen, resulting in a weak physical combination and chemical corrosion between OM and clay minerals, with the macropores taking the main place in the pore structure. In the main to late oil and medium clay content stage, hydrocarbon generation of OM leads to the development of pores in kerogen and the gradual generation of more acidic fluids that dissolve clay minerals, so that the mesopores are dominant. In the wet gas and high clay content stage, increases in hydrocarbon generation intensity and clay mineral content cause development of more complexes of OM and clay, with a large number of micropores produced in shale reservoirs.

Yu, Q., Xu, G., Liang, H., Xu, F., Liang, J., Wang, D., 2019. A research into the crude oil geochemistry and oil-source correlation by means of gas chromatography and gas chromatography–mass spectrometry: a case study of the Laizhou Bay Sag, Bohai Bay Basin, China. Arabian Journal of Geosciences 12, 634.

https://doi.org/10.1007/s12517-019-4815-0

Laizhou Bay Sag in the south of Bohai Bay Basin is a petroliferous province and hot study area for oil explorers and geologists. Oil-source correlation is of great importance in the study of the petroleum system, for it contributes to the selection of favorable exploration sites. Previously, much

attention has been paid to the study of the third member of the Shahejie Formation (E2s3 Fm.). The contribution of the fourth member of the Shahejie Formation (E2s4 Fm.) to the petroleum accumulation often failed to get adequate attention, which resulted in some difficulties in exploiting this area. In view of this, in our research, in the light of the theory of molecular organic geochemistry, the geochemical characteristics of 19 crude oil and 8 source rock samples (cuttings) from the study area are analyzed by means of gas chromatography (GC) and gas chromatography–mass spectrometry (GC–MS). On the basis of the analysis of oil composition and 16 biomarker parameters of saturated fractions, the following findings are generated: (a) the crude oil of Laizhou Bay Sag can be classified into three oil families: oil family A, oil family B, and oil family C. (b) the E2s4 source rocks were deposited in a low-alkalinity, hypersaline lacustrine environment under heavily reducing condition in which carbonates or evaporites were being precipitated and the organic matter is planktonic-organism-sourced (e.g., dinoflagellate-sourced); (c) oil family A, with medium maturity, is generated from the E2s3 FM. Oil family B, with low maturity, is generated from the E2s4 FM. Oil family C is the mixtures of oil family A and B oil. (d) A set of specific system has been established for the effective evaluation of the source and properties of the oil from the study area.

Yu, T., Zhang, M., Kang, D., Zhao, S., Ding, A., Lin, Q., Xu, D., Hong, Y., Wang, L., Zheng, P., 2019. Characteristics of microbial communities and their correlation with environmental substrates and sediment type in the gas-bearing formation of Hangzhou Bay, China. Frontiers in Microbiology 10, 2421. doi: 10.3389/fmicb.2019.02421.


Shallow gas is a kind of natural gas buried in shallow strata, generally, with methane as the main component, endowing it a potential energy resource while also a potential risk to the safety of ground engineering and environment. Microbial activity is usually regarded as an important driving force to generate shallow gas via metabolizing the environmental substrates. Therefore, the research on the microbial communities will be helpful to reveal the distribution of shallow gas in the gas-bearing formation. In this study, 30 sediment samples below the seabed in Hangzhou Bay (China) from depths of 1.5 m to 55 m were collected to investigate their microbial community, environmental characteristics and sediment type (clay or sand). It turned out that the presence of shallow gas had a good correlation with the distribution of archaea rather than bacteria, with the dominant microbe of Bathyarchaeota, Thaumarchaeota, and Euryarchaeota in the formation. Methanosarcinaceae and ANME-1a with the capacity of methane metabolism occupied high proportions. The correlation analysis and redundancy analysis (RDA) suggested that ammonium was a key environmental substrate to indicate the microbial community in the formation. The sediment type was proposed to shape environmental substrates in the formation, thus further affecting the microbial communities. The clay strata were demonstrated to have an important role in the generation and distribution of shallow gas, and more attention should be paid in terms of its resource discovery and engineering safety assessment.



The aim of this research work was to determine the molecular compositional changes of dissolved organic matter (DOM) taken from different phases of the hyperthermophilic composting (HTC) process. The DOM samples were extracted by the standard protocol of C18 extraction methodology,

and then analyzed by electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS). The profiles of negative ion mass spectrum and DOM molecular formulas of the four HTC samples were reported. Data related to the molecular compositional changes of DOM during HTC were also presented. Further interpretation and discussion on these datasets can be found in the related article entitled “Molecular insights into the transformation of dissolved organic matter during hyperthermophilic composting using ESI FT-ICR MS” [1].

Yuan, J., Elektorowicz, M., Chen, Z., Segun, G.A., Vakili, M., Zhong, L., Wang, B., Zhu, J., Wu, Y., 2019. Simulation and computer modeling of asphaltene in different solvents on oil-water interfaces using a molecular dynamic methodology. Journal of Molecular Graphics and Modelling 93, 107450.


Molecular dynamics (MD) simulations were used to study the thermodynamic properties of asphalt binder components, namely asphaltene, and other solvents, such as pentane or toluene, before and after adding pentane or toluene. The two systems were compared by MD simulation under lots of molecules, temperature and pressure to predict their internal energy, structure, and density as a function of time or distance between molecules. Then the simulation results of the two systems were analyzed and compared to determine the influence of different solvents on asphaltene aggregation behavior. The results show that the asphaltenes with pentane or toluene in the two systems have different structure and dynamic characteristics and will produce different precipitation and aggregation characteristics. The aggregation behavior of asphaltene at water - oil interface with or without pentane or toluene was studied. The relationship between the molecular structure and the aggregation of asphaltene in different solvents was investigated.

Yuan, Y., Rezaee, R., Al-Khdheeawi, E.A., Hu, S.-Y., Verrall, M., Zou, J., Liu, K., 2019. Impact of composition on pore structure properties in shale: Implications for micro-/mesopore volume and surface area prediction. Energy & Fuels 33, 9619-9628.


Pore structure properties such as pore volume, surface area, and pore size distribution (PSD) are the key petrophysical parameters in shales that control storage capacity, hydraulic conductivity, and the gas adsorption in potential. The nature of pore volume, surface area, and PSD are largely dependent on shale composition, which is highly heterogeneous in different formations. However, the quantitative effects of the clay content and total organic carbon (TOC) content on micropore and mesopore structural properties have not been fully explored yet. Here, we quantified the impact of clay and TOC contents on micro-/mesopore volume, surface area, and PSD using three shale formations with large compositional variations. The results indicate that clay and TOC contents synchronically influence the shale micro-/mesopore structure properties, but they function in different pore size ranges. The micropores are predominantly contributed by organic matter pores. For the first time, we discover that the mesopores ranging between 2 and 17 nm are primarily controlled by clay mineral pores, and the pores larger than 17 nm contain both clay and organic matter pores. We further develop four new equations to predict micropore volume, mesopore volume, micropore surface area, and mesopore surface area as a function of clay and TOC contents on the basis of the data collected from the three different shale types. The statistical analysis shows that our developed correlations are capable of predicting the pore structure properties in our investigated formations with acceptable accuracy. The newly established equations provide insightful implications for the precise formation evaluation in downhole practices.

Zak, D., Roth, C., Unger, V., Goldhammer, T., Fenner, N., Freeman, C., Jurasinski, G., 2019. Unraveling the importance of polyphenols for microbial carbon mineralization in rewetted riparian peatlands. Frontiers in Environmental Science 7, 147. doi: 10.3389/fenvs.2019.00147.

https://www.frontiersin.org/article/10.3389/fenvs.2019.00147

There have been widespread attempts to rewet peatlands in Europe and elsewhere in the world to restore their unique biodiversity as well as their important function as nutrient and carbon sinks. However, changes in hydrological regime and therefore oxygen availability likely alter the abundance of enzyme-inhibiting polyphenolic compounds, which have been suggested as a “latch” preventing large amounts of carbon from being released into the atmosphere by microbial mineralization. In recent years, a variety of factors have been identified that appear to weaken that latch including not only oxygen, but also pH. In minerotrophic fens, it is unknown if long-term peat mineralization during decades of drainage and intense agricultural use causes an enrichment or a decline of enzyme-inhibiting polyphenols. To address this, we collected peat samples and fresh roots of dominating plants (i.e., the peat parent material) from the upper 20 cm peat layer in 5 rewetted and 6 natural fens and quantified total phenolic content as well as hydrolysable and condensed tannins. Polyphenols from less decomposed peat and living roots served partly as an internal standard for polyphenol analysis and to run enzyme inhibition tests. As hypothesized, we found the polyphenol content in highly decomposed peat to be eight times lower than in less decomposed peat, while condensed tannin content was 50 times lower in highly degraded peat. In addition, plant tissue polyphenol contents differed strongly between peat-forming plant species, with the highest amount found in roots of Carex appropinquata at 450 mg g−1 dry mass, and lowest in Sphagnum spp. at 39 mg g−1 dry mass: a 10-fold difference. Despite large and clear differences in peat and porewater chemistry between natural and rewetted sites, enzyme activities determined with Fluorescein diacetate (FDA) hydrolysis and peat degradation were not significantly correlated, indicating no simple linear relationship between polyphenol content and microbial activity. Still, samples with low contents of polyphenols and condensed tannins showed the highest microbial activities as measured with FDA.

Zeldes, B.M., Loder, A.J., Counts, J.A., Haque, M., Widney, K.A., Keller, L.M., Albers, S.-V., Kelly, R.M., 2019. Determinants of sulphur chemolithoautotrophy in the extremely thermoacidophilic Sulfolobales. Environmental Microbiology 21, 3696-3710.

https://doi.org/10.1111/1462-2920.14712

Species in the archaeal order Sulfolobales thrive in hot acid and exhibit remarkable metabolic diversity. Some species are chemolithoautotrophic, obtaining energy through the oxidation of inorganic substrates, sulphur in particular, and acquiring carbon through the 3‐hydroxypropionate/4‐hydroxybutyrate (3‐HP/4‐HB) CO2‐fixation cycle. The current model for sulphur oxidation in the Sulfolobales is based on the biochemical analysis of specific proteins from Acidianus ambivalens, including sulphur oxygenase reductase (SOR) that disproportionates S° into H2S and sulphite (SO3

2−). Initial studies indicated SOR catalyses the essential first step in oxidation of elemental sulphur, but an ancillary role for SOR as a ‘recycle’ enzyme has also been proposed. Here, heterologous expression of both SOR and membrane‐bound thiosulphate‐quinone oxidoreductase (TQO) from Sulfolobus tokodaii ‘restored’ sulphur oxidation capacity in Sulfolobus acidocaldarius DSM639, but not autotrophy, although earlier reports indicate this strain was once capable of chemolithoautotrophy. Comparative transcriptomic analyses of Acidianus brierleyi, a chemolithoautotrophic sulphur oxidizer, and S. acidocaldarius DSM639 showed that while both share a strong transcriptional response to elemental sulphur, S. acidocaldarius DSM639 failed to upregulate key 3‐HP/4‐HB cycle

genes used by A. brierleyi to drive chemolithoautotrophy. Thus, the inability for S. acidocaldarius DSM639 to grow chemolithoautotrophically may be rooted more in gene regulation than the biochemical capacity.

Zhakupbekova, A., Baimatova, N., Kenessov, B., 2019. A critical review of vacuum-assisted headspace solid-phase microextraction for environmental analysis. Trends in Environmental Analytical Chemistry 22, e00065.


Vacuum-assisted headspace solid-phase microextraction (Vac-HSSPME) is an emerging analytical technique, which further advances HSSPME by providing lower detection limits of analytes with poor volatility at shorter extraction times. This review discusses the theoretical aspects and possibilities of the Vac-HSSPME technique for analysis of environmental samples. Optimization of key parameters, currently available equipment and methods for quantification of organic pollutants in water and soil are considered. Key problems and limitations of the technique are discussed along with possible approaches for its future development. The technique has a well-developed theory, which could be used for modeling of the extraction process, faster method development, and optimization. Wider application of the technique is limited by the lack of automation, which, however, seems possible to develop and implement by manufacturers of commercial multi-purpose autosamplers for gas chromatography instruments. It has been shown that Vac-HSSPME allows decreasing cross-contamination of samples from the laboratory air, which is advantageous for identification and quantification of trace environmental pollutants. Simple equipment for the technique makes it possible to apply for on-site sample preparation and analysis of environmental samples.



The role of O2 in the evolution of early animals, as represented by some members of the Ediacara biota, has been heavily debated because current geochemical evidence paints a conflicting picture regarding global marine O2 levels during key intervals of the rise and fall of the Ediacara biota. Fossil evidence indicates that the diversification the Ediacara biota occurred during or shortly after the Ediacaran Shuram negative C‐isotope Excursion (SE), which is often interpreted to reflect ocean oxygenation. However, there is conflicting evidence regarding ocean oxygen levels during the SE and the middle Ediacaran Period. To help resolve this debate, we examined U isotope variations (δ238U) in three carbonate sections from South China, Siberia, and USA that record the SE. The δ238U data from all three sections are in excellent agreement and reveal the largest positive shift in δ238U ever reported in the geologic record (from ~ −0.74‰ to ~ −0.26‰). Quantitative modeling of these data suggests that the global ocean switched from a largely anoxic state (26%–100% of the seafloor overlain by anoxic waters) to near‐modern levels of ocean oxygenation during the SE. This episode of ocean oxygenation is broadly coincident with the rise of the Ediacara biota. Following this initial radiation, the Ediacara biota persisted until the terminal Ediacaran period, when recently published U isotope data indicate a return to more widespread ocean anoxia. Taken together, it appears that global marine redox changes drove the rise and fall of the Ediacara biota.

Zhang, J., Zhou, L., Zhou, J., Xiao, D., Han, G., Zhao, M., Fu, L., Li, H., Lou, D., Wang, H., 2019. Control of the Mesozoic tectonic movement on the hydrocarbon generation and evolution of Upper Paleozoic coal-measure source rocks in the Huanghua Depression, Bohai Bay Basin. Natural Gas Industry 39, 1-10.


Recently, great discoveries have been made on the primary gas reservoirs related to the Upper Paleozoic coal measure in the inner buried hills of Gangbei, Wumaying and Qibei in the Huanghua Depression of the Bohai Bay Basin, which reveals a huge oil and gas resource potential in this depression. In order to deepen the understanding of the controlling factors of the Mesozoic tectonic movement in the Huanghua Depression on the hydrocarbon generation of Upper Paleozoic coal-measure source rocks, we analyzed the Mesozoic tectonic system and evolution, the basin migration process and the geochemical characteristics and hydrocarbon generation history of coal-measure source rocks by means of structural analysis, burial–thermal history analysis, core slice observation and basin hydrocarbon generation simulation. In addition, the influences of the subsidence, migration and magmatic activity of Mesozoic basins on the hydrocarbon generation of coal-measure source rocks were studied. And the following research results were obtained. First, in the Huanghua Depression, there were multi-stage and multi-type tectonic movements in the Mesozoic, and the main tectonic events include Triassic craton uplift-subsidence movement, Jurassic differential depression-compression–torsion movement, Cretaceous volcanic activity and extensional uplift movement. Second, the basin migration process is from south to north, and the Kongdian uplift is an important boundary of South and North migration. Third, the Upper Paleozoic coal-measure source rocks in the Huanghua Depression experience two hydrocarbon generation processes, and there are early hydrocarbon reservoirs. Fourth, the Upper Paleozoic coal measure in the Cangdong Sag reached the effective hydrocarbon generation threshold at the end of Late Jurassic, and the Upper Paleozoic coal-measure source rocks in the Qikou Sag reached the hydrocarbon generation threshold at the end of Early Cretaceous. Fifth, the control of the Mesozoic tectonic movement on the primary hydrocarbon generation and evolution of source rocks is mainly embodied in two aspects. On the one hand, basin migration events in the Mesozoic dominate the primary hydrocarbon generation sequence of source rocks. And on the other hand, local heating events of magmatic rocks accelerate the hydrocarbon generation and abnormal maturation of organic matter in source rocks. In conclusion, the research results define the control factors of the Mesozoic tectonic movement on the primary hydrocarbon generation and evolution of Upper Paleozoic coal-measure source rocks, and can be used as reference for researching the Mesozoic tectonic movement and the hydrocarbon generation and evolution of coal measure, restoring the protobasins and conducting oil and gas exploration in North China.

Zhang, K., Liu, R., Liu, Z., Li, B., Han, J., Zhao, K., 2020. Influence of volcanic and hydrothermal activity on organic matter enrichment in the Upper Triassic Yanchang Formation, southern Ordos Basin, Central China. Marine and Petroleum Geology 112, 104059.


Based on the field investigation of oil shales in the southern Ordos Basin, detailed observations, and systematic sample analyses of core samples from a well that penetrated an oil shale, the influence of volcanic and hydrothermal activity on the Chang 8–Chang 7 members of the Yanchang Formation on organic matter (OM) enrichment was geochemically and petrologically analyzed. According to maceral analyses and rock pyrolysis, the kerogen types of the samples in the study area are widely distributed. Those of the oil shale with the highest OM abundance are mostly type II-I, and are immature or in a stage of low-maturity. Six layers of tuff and tuffaceous mudstone were identified by core observation and element characteristics; they are characterized by higher total rare earth element

(∑REE) and δCe values and Th contents, and lower (La/Yb)N and δEu values. Mineral assemblages of anhydrite–pyrite–marcasite and relevant diagrams of the elemental geochemistry confirmed the existence of hydrothermal deposits. The high Yn/Hon and U/Th ratios and total sulfur (TS) contents indicate that the Chang 7 Member experienced four episodes of intense hydrothermal activity. Early in the Chang 73 Member, volcanic ash and hydrothermal fluids brought in a large amount of nutrients, which not only increased primary productivity, but also increased the salinity of the water column, enhanced anoxia in the sedimentary environment of the lake bottom, promoted the preservation of OM, and finally formed the oil shale layer with the richest OM. However, the strong volcanic eruption in the late Chang 73 Member led to changes in the regional climate, causing it to dry and become colder and resulting in a decrease of primary productivity. Earthquakes triggered by volcanism resulted in turbidite deposits, which destroyed the preservation and diluted the enrichment of OM. This study reveals in detail the influence of volcanic and hydrothermal activity on OM enrichment during the evolution of the basin, and thereby deepens our theoretical understanding of OM enrichment.


https://doi.org/10.1093/molbev/msz167

Cholesterol plays essential roles in animal development and disease progression. Here, we characterize the evolutionary pattern of the canonical cholesterol biosynthesis pathway (CBP) in the animal kingdom using both genome-wide analyses and functional experiments. CBP genes in the basal metazoans were inherited from their last common eukaryotic ancestor and evolutionarily conserved for cholesterol biosynthesis. The genomes of both the basal metazoans and deuterostomes retain almost the full set of CBP genes, while Cnidaria and many protostomes have independently experienced multiple massive losses of CBP genes that might be due to the geologic events during the Ediacaran period, such as the appearance of an exogenous sterol supply and the frequent perturbation of ocean oxygenation. Meanwhile, the indispensable utilization processes of cholesterol potentially strengthened the maintenance of the complete set of CBP genes in vertebrates. These results strengthen both biotic and abiotic roles in the macroevolution of a biosynthesis pathway in animals.



Thermal dissolution and alkanolyses of the extraction residue (ER) from Baiyinhua lignite were successively processed in cyclohexane, CH3OH, CH3CH2OH, and (CH3)2CHOH at 300 °C to afford soluble portions (SPs) 1–4. The oxygen-containing aromatics (OCAs) in the SPs were analyzed with a gas chromatograph/mass spectrometer (GC/MS) and quadrupole exactive orbitrap mass spectrometer (QEOTMS) with atmosphere pressure chemical ionization source in positive-ion mode (PIM) and negative-ion mode (NIM), while carbon types and oxygen functional groups in ER were characterized with a solid-state 13C nuclear magnetic resonance and X-ray photoelectron spectrometer, respectively. The results show that the aromatics contain 2 aromatic rings (ARs) and 2 substituents on average. -OH group is the dominant existing form of oxygen on the ER surface. Arenols and esters are the most abundant OCAs identified with GC/MS in the SPs. For O1-O6 class species detected with QEOTMS, O1-O2 class species detected in PIM and O2-O4 class species

detected in NIM are predominant. The oxygen species detected in PIM mainly appear in >C-O-C<, -CO-C<, and furan rings, but they were mainly detected in the forms of -OH and -COOH in NIM.


https://doi.org/10.1029/2018JG004917

Terrestrial vegetation, as the key component of the biosphere, has a greening trend since the beginning of this century. However, how this substantial greening translated to global gross carbon sequestration or gross primary production (GPP) is not clear. Here we investigated terrestrial GPP dynamics and the respective contributions of climate change and vegetation cover change (VCC) from 2000 to 2015. We adopted a remote sensing based data-driven model, which was calibrated based on the global eddy flux data set (FLUXNET2015) and Moderate Resolution Imaging Spectroradiometer vegetation index data (Collection 6). A series of simulation experiments were conducted to disaggregate the effects of climate and VCC. We found a much weaker increase in global GPP (0.08%/year; P = 0.07) when compared with the global greening rate (0.23%/year; P < 0.001). The positive effect of VCC on GPP was reduced by 53% due to climate stress. Enhanced global GPP were largely contributed by nonforests, especially croplands. However, tropical forests, once a major driver of the global GPP increase, negatively contributed to global GPP trend due to warming-induced moisture stress and deforestation. Given the limited potential of cropland carbon storage due to harvest and consumption, the contrasting GPP changes (i.e., cropland GPP increase vs. forest GPP reduction) may have shifted the distribution of the land carbon sink. Our study highlights the potential vulnerability of terrestrial gross carbon sequestration under climate and land use changes and has important implications in the global carbon cycle and climate warming mitigation.



The product distribution and organic sulfur removal during direct pyrolysis and hydropyrolysis of oil shale kerogen were investigated via reactive molecular dynamics (RMD) simulations with reactive force field (ReaxFF). Two structural models for direct pyrolysis and hydropyrolysis of kerogen were constructed about kerogen extracted from Longkou oil shale to investigate the impact of H2 at different temperatures on the product distribution and reaction processes of oil shale. The experimental results show that hydropyrolysis could increase light shale oil (the most important product in shale oil industry), and improve the removal rate of organic sulfur simultaneously. It was found that comparing to the direct pyrolysis, hydropyrolysis can provide more H free radicals to participate in the reaction and therefore promoting the pyrolytic reaction of kerogen. In addition, hydropyrolysis greatly promoted the desulfurization due to the contribution to the production of H2O molecules, and the transfer of sulfur to the gas products requires the participation of H2O molecules. This work is an intensive study on hydropyrolysis mechanism at different temperatures at the atomic level. These conclusions could be helpful for the clean utilization technology of oil shale industry.

Zhao, W., Hu, S., Guo, X., Li, J., Cao, Z., 2019. New concepts for deepening hydrocarbon exploration and their application effects in the Junggar Basin, NW China. Petroleum Exploration and Development 46, 856-865.


The Junggar Basin is one of the major petroliferous basins with abundant oil and gas resources in onshore China. Around 2010 and thereafter, the hydrocarbon exploration for finding giant fields in the basin faced tough difficulties: in the northwestern margin area, no significant breakthrough has been made for long since seeking to “escape from the step-fault zone and extend to the slope area”; in the central part, the exploration for large lithologic-stratigraphic reservoirs stood still; since the discovery of the Kelameili gas field, no important achievement has been made in gas exploration. Under the guidance of “whole sag-oil-bearing” theory in the petroliferous basin, and based on the long-term study and thinking of the petroleum accumulation conditions and characteristics, the authors proposed several new concepts, i.e., a “thrust-induced second-order fault step” hiding under the northwestern slope area; six “hydrocarbon migrationward surfaces” favorable for hydrocarbon accumulation; promising natural gas resource. These concepts have played an important role in the discoveries of Wells Mahu1 and Yanbei1 as well as the confirmation and expansion of Permian-Triassic billion-ton-scale petroliferous areas in Mahu. The fairway of new discoveries has also appeared for natural gas exploration in Wells Fu26, Gaotan1 and Qianshao2, suggesting that the surrounding regions of the highly matured source kitchen are of high possibility to form gas accumulations.

Zhao, X., Zhou, L., Pu, X., Jin, F., Shi, Z., Xiao, D., Han, W., Jiang, W., Zhang, W., Wang, H., 2019. Favorable formation conditions and enrichment characteristics of lacustrine facies shale oil in faulted lake basin: a case study of Member 2 of Kongdian Formation in Cangdong sag, Bohai Bay Basin Acta Petrolei Sinica 40, 1013-1029.


Different from the North American marine facies shale oil, the China lacustrine facies shale oil presents very complex geological characteristics. It is urgently required to find out whether the geological conditions are suitable for the formation of lacustrine facies shale oil, and how to locate the enrichment zones of shale oil. This paper takes the Member 2 of Kongdian Formation of Cangdong sag in the Huanghua depression of Bohai Bay Basin as an example to explore the main controlling factors and enrichment characteristics of lacustrine facies shale oil. Comprehensively using the 635.8 m cores from Well G108-8, GD12 and GD14, analytical test data of more than 12 000 pieces of core samples, as well as well testing and pilot production data of 20 wells, the accumulation mechanism of lacustrine facies shale oil have been analyzed in terms of source rock, sedimentary texture and thermal evolution. The study shows that widely distributed, multi-type and high abundance organic matter, composition of highly brittle minerals, high-density laminaed structure and moderate thermal evolution are the main factors for shale oil formation and enrichment. The lacustrine shale strata are classified into four types of tectonic facies, i.e., laminated felsic shale, lamellar diamictic shale, thinly laminated limy dolomite shale and thick laminated limy dolomite shale. It has been confirmed that laminated felsic shale and lamellar diamictic shale in the moderate thermal evolution stage have the best tectonic facies, and the S1

*/TOC is greater than 135 mg/g. This has revealed the shale oil enrichment characteristic of "favorable tectonic facies and transcendence effect of retained hydrocarbon". The new understanding can effectively guide shale oil exploration. Thus, Well GD1702H achieved the highest daily oil production of 61 m3; the natural flow well has been producing over 416 days, and the production is basically stabilized at 17 m3/d. Two horizontal

wells, GD1701H and GD1702H, have a cumulative output exceeding 14 000 tons, proving that the lacustrine facies shale oil in the eastern China has a good potential for industrial development.


https://doi.org/10.1007/s12182-019-0345-3

A Canadian in situ oilsands bitumen-derived vacuum residue (VR) was subjected to supercritical fluid extraction and fractionation (SFEF) into 13 extractable fractions and an unextractable end-cut and characterized by positive- and negative-ion electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The results of negative-ion ESI FT-ICR MS showed that the N1 class species was the most abundant and the multifunctional group compounds, such as N1O1, N1O2, N1S1, N1S2, and N2 class species became abundant as the SFEF fraction became heavier. In positive-ion ESI mode, the relative abundance of N1 class species decreased gradually in the heavy SFEF fractions while that of multifunctional group compounds increased. The relative abundance of N4V1O1 increased dramatically in heavy fractions and the end-cut. The distributions of polar heteroatom species of VR derived from oilsands bitumen were similar with those of VR derived from the Venezuela Orinoco extra heavy oil.


https://doi.org/10.1029/2018JG004743

Ongoing climate change is making the large pool of organic matter (OM) stored in Arctic permafrost vulnerable to mobilization; thus, garnering a deeper understanding of molecular transformations within the abundant pool of soil OM, specifically humic substances, is crucial. Here we present the first high-resolution mass-spectrometry examination of molecular compositions of humic acid (HA) and fulvic acid (FA) isolated from organic-rich deep yedoma (Pleistocene age ice-rich permafrost) and alas (thermokarst deposit formed during permafrost thaw) cores. The FA fractions were dominated by oxygen-rich unsaturated compounds, whereas the HA fractions were mostly composed of relatively reduced saturated and aromatic moieties. A substantial increase in contribution of both CHO-only and N-containing aliphatic compounds was observed in the HA fractions of the yedoma OM with depth, whereas the alas HA fractions were depleted in aliphatics but enriched with condensed and hydrolyzable tannins. The observed differences in compositional space of the immobile OM stored in the deep yedoma versus alas deposits were consistent with evolution of OM during thermokarst lake genesis, implying intense microbial degradation of N-rich OM released from the yedoma deposits and accumulation of highly degraded, plant-derived OM. The patterns of molecular transformations of OM were apparent in compositional space of the least degraded HA fractions as compared to much more oxidized FA fractions. This shows great promise of molecular exploration of the alkali-extracted OM, comprising up to 50% of the total organic carbon in deep permafrost both for paleoreconstructions and predictions of climate feedback to released OM due to permafrost thaw.

Zhou, B., Zhao, Y., Dai, Q., 2019. Application of comprehensive multiphase NMR to characterize organic matter in clay and atmospheric particulates. ACS Earth and Space Chemistry 2, 2276-2286.


The molecular composition of organic matter (OM) and its interaction with minerals play important roles in regulating the fate of carbon and pollutants in soil and in the atmosphere. Clay minerals such as montmorillonite processed with bacteria can imitate the microbial interactions occurring in more complex natural environmental media such as soil and atmospheric particulates. Here, we characterize OMs in multiple phases for bacteria-inoculated montmorillonite clay and atmospheric particulates collected in China. In addition to the traditional 13C cross-polarization magic angle spinning nuclear magnetic resonance (CPMAS NMR) experiments, this study, for the first time, applies both one- and two-dimensional comprehensive multiphase (CMP) NMR to these critical environmental issues. The CMP NMR experimental spectra show that the main OM components in these samples are aliphatics, carbohydrates, and aromatics. These CMP NMR spectra also reveal the biochemical interactions between microbes and clay minerals by identifying the metabolites. CMP NMR can further investigate the states, interfacial/surficial interactions, and dynamics at the molecular/atomic levels since diffusion/relaxation (T2)-edited experiments can distinguish OM with differing sizes and mobilities. Therefore, the mechanism at the atomic/molecular level for environmental biogeochemical interactions can be efficiently probed by CMP NMR experiments. This paper concludes that CMP NMR is a powerful and innovative tool for crucial environmental studies at the molecular/atomic scale, providing not only the composition, phase, and structural identifications but also the interfacial/surficial interaction dynamics involved in environmental geochemical processes.



Two main challenges exist in enhancing oil recovery rate from tight oil reservoirs, namely how to create an effective complicated fracture network and how to enhance the imbibition effect of fracturing fluid. In response to the challenges, through modeling experiment in laboratory and evaluation of field application results, a set of integrated efficient fracturing and enhanced oil recovery (EOR) techniques suitable for tight oil development in China has been proposed. (1) Fracturing with temporary plugging agents to realize stimulation in multiple clusters, to form dense fracture network, and thus maximizing the drainage area; (2) Supporting induced fractures with micro-sized proppants during the prepad fluid fracture-making stage, to generate dense fracture network with high conductivity; (3) Using the liquid nanofluid as a fracturing fluid additive to increase oil-water displacement ratio and take advantage of the massive injected fracturing fluid and maximize the oil production after hydraulic fracturing.

Zhou, J., Wu, J., Ma, L., Abuduwaili, J., 2019. Late Quaternary environmental change record in biomarker lipid compositions of Lake Ebinur sediments, Northwestern China. International Journal of Earth Sciences 108, 2361-2371.

https://doi.org/10.1007/s00531-019-01767-x

Late Quaternary paleoclimate records from arid regions help us understand the response of ecological systems to natural climate change to place recent changes in a longer-term perspective. In this research, a biogeochemical analysis of a sediment core from Lake Ebinur, Xinjiang, allowed us to infer the climate and environmental changes in the late Quaternary in arid northwestern China. The combined lipid biomarkers and bulk biogeochemical properties (TOC, δ13Corg) revealed moderately wet conditions from 34 to 28 ka, favoring the growth of terrestrial vegetation. The subsequent period from 28 to 13 ka was dominated by aquatic plants, algae and microbes, indicating cold and dry conditions. Ameliorated regional moisture conditions were deduced from the higher carbon preference index (CPI) and from δ13Corg values from 13 to 3.6 ka. The optimum climate conditions occurred from 9 to 5 ka. Several climatic events also exist in the Lake Ebinur records with a wide distribution into other regions. Our biogeochemical-based paleoclimate and paleoenvironmental reconstruction is generally synchronous with sedimentary records from mid-latitude Eurasia and the NGRIP ice core record, which probably has a certain linkage with the 45°N summer insolation. We propose that summer insolation conditions in the northern hemisphere might have an impact on the climate and environmental changes in arid northwestern China in the late Quaternary.

Zhou, T., Che, G., Ding, L., Sun, D., Li, Y., 2019. Recent progress of selective adsorbents: From preparation to complex sample pretreatment. TrAC Trends in Analytical Chemistry 121, 115678.


Sample pretreatment is an important part for qualitative and quantitative analysis of targets in analytical chemistry. With the rapid development of adsorbents in material science, selective adsorbents have been found particularly practical in sample pretreatment due to their resistance to complex matrix interference. Selective adsorbents concern formation of selective recognition sites, involving diverse interactions and distinct size/shape matching cavities for targets, which can selectively extract targets from complex real samples. In this review, selective adsorbents constructed in recent years have been summarized, involving molecularly imprinted polymers (summarizing from faced typical challenges, such as template leakage, low adsorption capacity, poor resistance to macromolecular interference and difficulty in aqueous recognition) and non-imprinted selective adsorbents (discussing from representative types of adsorbents with selectivity). Meanwhile, we concentrate on the application of selective adsorbents in complex sample pretreatment. Finally, a conclusion and a brief assessment of future developments in this area are revealed.

Zhou, X., Kamal, M.S., 2019. Experimental study on the relationship between carbonate reservoir quality index and dynamic parameters of chemical solutions for oil recovery practice. Energy & Fuels 33, 9747-9758.


Understanding the complex variation in dynamic characterizations of chemical solutions on the surface of rock related to different carbonate reservoir qualities is one of the most challenging subjects in enhancing the oil recovery process because pore distribution, pore structure, and petrophysical properties of carbonate reservoir have many differences. Carbonate reservoirs usually have heterogeneity, a wide range of pore levels, and petrophysical parameters. This research aims to investigate systematically and explain the interrelationship between reservoir quality indexes (RQI) or flow zone indicator and dynamic characterization of chemical solutions. The interrelationship derived can be applied to enhance oil recovery in carbonate reservoirs. Several laboratory studies were completed using carbonate core plugs and reservoir brine at reservoir conditions for dynamic characterization of chemical solutions for the potential application of enhanced oil recovery: (1) the

evaluation of resistance factor (RF), residual resistance factor (RRF), and injectivity (I) of a sulfonated polymer and (2) dynamic adsorption and desorption of an amphoteric surfactant. The RQIs of carbonate core plugs are in the range of 0.74–1.91 μm. Based on the results of this study, we found that the dynamic characterizations of chemical solutions depend on the RQI. The results from a sulfonated polymer solution injection tests show that RF and RRF increase with a decrease in RQI for both solutions of 0.1 and 0.2 wt % polymer. However, there is a critical frontal velocity for such a polymer solution of 0.2 wt %. When the frontal velocity is more than critical frontal velocity, RRF has similar values with increase in front velocity. Liquid permeability loss at a concentration of 0.2 wt % is higher than that in the case of 0.1 wt %. This paper provides a comprehensive overview of dynamic characterization of an amphoteric surfactant and sulfonated polymer for carbonate reservoir rocks with RQI and presents insights and large potential for application of chemically enhanced oil recovery in carbonate reservoirs.



To investigate the effect of functional groups in coal on volatiles evolution, eight coal samples with different ranks were pyrolyzed in a novel in-situ pyrolysis photoionization time-of-flight mass spectrometer (Py-PI-TOF MS). Soft ionization were adopted to enable the fragment-free detection of volatiles generated from initial pyrolysis products. Temperature-evolved profiles of main products are visible via scanning of the ion current of individual compound measured during the pyrolysis processes. The obtained mass spectra of volatiles from pyrolysis of eight coal samples reveal predominantly molecular ions with four categories: alkenes, benzenes, phenols and diphenols. Furthermore, the analysis of different coal samples demonstrates that both alkyl and oxygen-containing groups attached on the benzene rings can reduce the peak temperatures of main products’ evolution, and the effect of oxygen-containing group is stronger than that of alkyl group. The difference of peak temperature with maximum evolution, which is used as an indicator to measure the effect of the functional groups, were correlated with carbon content and volatile content of coal samples. The influence degree of functional groups on evolution temperature was found to be negative correlated with the carbon content and positive correlated with the volatile content, respectively. Based on the experimental observations and theoretical calculations, the overall results allowed to reveal the influence of the functional groups on the volatile organic compounds during coal pyrolysis. Analogous to reported setups with online studies of coal pyrolysis, Py-PI-TOF MS may be a good option for monitoring the evolution characteristics and reaction pathways of coal pyrolysis process.

Zirks, E., Krom, M.D., Zhu, D., Schmiedl, G., Goodman-Tchernov, B.N., 2019. Evidence for the presence of oxygen-depleted sapropel intermediate water across the Eastern Mediterranean during sapropel S1. ACS Earth and Space Chemistry 3, 2287-2297.


In the Eastern Mediterranean Sea (EMS), natural climate-driven changes that impacted its physical circulation and created deep-water anoxia have led to periods of distinctive deposits referred to as sapropels. The most recent sapropel event (S1) occurred between ∼6 and 10.8 kyr BP. Use of a global climate model has suggested that there was a previously unrecognized mid-depth (500–1800 m) water mass present at that time. Here, a broad review of cores previously analyzed from across the

EMS was undertaken to determine if the field evidence was compatible with the presence of this intermediate water mass. The proxy records document a widespread oxygenated interruption centered around 8.2 ka BP in water depths between 500 and 1800 m, but not present in shallower or deeper water. We attribute this pattern to the formation and spread of a water mass, which we refer to as Sapropel Intermediate Water (SIW). It is shown that this water mass was formed in the Aegean Sea and became more depleted in oxygen, to anoxicity but not euxinicity, as it flowed west to the Adriatic and east across the Levantine basin. The rate of formation and flow of this water mass was estimated to be slow but not zero. An evolving oxygen minimum zone in the SE Levantine basin is posited where oxygen was depleted first in shallower water and expanded with time into deeper water. The presence of SIW obviates the need for the previously suggested thin anoxic blanket, since the 1300 m-thick SIW can be fully deoxygenated in 200–500 years.

Zou, C., Pan, S., Horsfield, B., Yang, Z., Hao, S., Liu, E., Zhang, L., 2019. Oil retention and intrasource migration in the organic-rich lacustrine Chang 7 shale of the Upper Triassic Yanchang Formation, Ordos Basin, central China. American Association of Petroleum Geologists Bulletin 103, 2627-2663.

http://archives.datapages.com/data/bulletns/2019/11nov/BLTN17052/bltn17052.html

The Zhang 22 well was drilled in the Ordos Basin, penetrating the Chang 7 Member of the Triassic Yanchang Formation, which, cumulatively, has more than 80 m (>260 ft) of black organic-rich shale of oil window maturity. Using 76 samples collected every 1 m (3 ft) from the well, the effects of stratigraphic fractionation and petroleum expulsion within five intervals of the Chang 7 shale were qualitatively and quantitatively documented. The organic-rich intervals 1, 2, and 5, having an average total organic carbon (TOC) of 6.79 wt. % and pyrolyzable hydrocarbon potential of 9.40 mg/g rock (i.e., the amount of hydrocarbons generated by pyrolysis between 300°C and 650°C [S2]), are defined as “generative units” in the Chang 7 shale system, compared to the “in-source reservoirs” or “sweet spots” (i.e., the third and fourth intervals), which contain a lower average TOC of 4.19 wt. % and an average S2 value of 7.17 mg/g rock, but the highest amount of free oil (average total oil of 7.35 mg/g rock). Geochemical and molecular compositions display distinctive differences between samples from these source and reservoir groupings. For example, bitumens from the generative units proportionally possess lower saturated hydrocarbons (56%–66%) than those from the in-source reservoirs (up to 81%). The proportions of aromatic and polar compounds in the generative units are accordingly higher than in their counterpart. The individual molecular weight distribution of sample extracts displays more light-end moieties being enriched in the generative units. By applying the compositional mass balance calculation, the overall and compound-specific expulsion efficiencies in the in-source reservoirs are abnormally negative compared to the positive values in the generative intervals. This finding, in conjunction with the effects of the preferential retention of aliphatic hydrocarbons and the differential expulsion of light molecular weight compounds in the in-source reservoirs, indicates a short-distance intrasource migration of generated petroleum into the sweet-spot intervals (intervals 3 and 4) from the overlying units (intervals 1 and 2) and the underlying interval 5. Furthermore, when quantifying the total amount of retained petroleum in the shale system, an amended assessment has been introduced to overcome the systematic misestimations if only unextracted values for the amount of thermally extractable hydrocarbons volatilized at 300°C (mg HC/g rock) were considered. Thus, the oil crossover effect, temperature at which the rate of S2 generation is at maximum shift phenomenon, and the hydrogen index being shifted to higher values after extraction all account for identifying intervals 3 and 4 as the in-source reservoirs. In this study, we have not only identified a set of promising in-source targets for shale oil exploration and production, but we also presented the chemical and molecular composition for these shale oils. We have additionally speculated for the intrasource migration model and further discussed the different expulsion efficiencies in the shale system upon the compositional mass balance calculation as well as

the stratigraphic fractionation on differentiating the chemical compositions during migration. The improved oil quality by fractionation, the extra storage potential derived from microfossil quartz, the weak adsorptive affinity of oil to organic matter, and the good shale susceptibility to hydraulic fracturing all give a promising prospective for exploring and producing shale oil from the Chang 7 shale system in the Ordos Basin.

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eaogorg.files.wordpress.com€¦ · Web viewGEOCHEMISTRY ARTICLES – October 2019. Analytical Chemistry. Mironov, N.A., Milordov, D.V., Abilova, G.R., Yakubova, S.G., Yakubov,