Establishing Biogenicity and Paleoenvironments of Terrestrial Siliceous Stromatolites in Geothermal Settings

8/9/2019 Establishing Biogenicity and Paleoenvironments of Terrestrial Siliceous Stromatolites in Geothermal Settings

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ESTABLISHING BIOGENICITY AND PALEOENVIRONMENTS OF

TERRESTRIAL SILICEOUS STROMATOLITES IN GEOTHERMAL SETTINGS

KIM M. HANDLEY1AND KATHLEEN A. CAMPBELL

2

1Department of Earth and Planetary Science, University of California at

Berkeley, Berkeley, CA, U.S.A., and 2School of Geography, Geology, and

Environmental Sciences, University of Auckland, 23 Symonds St, Auckland

1142, New Zealand

1.Introduction

Siliceous stromatolites embody important records of past biological activity. The

biogenic-mineralogical laminated structures form within a range of geothermal settings and

physicochemical, hydrodynamic and biological regimes. Silica provides an excellent

medium for cellular preservation, due to its capacity to permineralize or encase microbial

cells with an X-ray amorphous cement (Francis et al., 1978). As such, it has rendered some

of the best microfossils in the geologic record. In particular, the Early Devonian Rhynie and

Windyfield cherts (Scotland) contain exceptionally clear and comprehensive examples of

fossilized early terrestrial plant, animal (arthropod) and microbial life, including detailed

preservation of internal structures, in addition to palaeoenvironmental information (Trewin,

1994; Fayers and Trewin, 2004). Although not displaying the same level and extent of

extemporary preservation, the internally laminated structures and/or filamentous characterof Devonian-aged Drummond Basin sinters (Australia) do exhibit a remarkable resemblance

to microfacies commonly found in contemporary hot spring environments, e.g. high-

temperature columnar and spicular, and lower-temperature stratiform, streamer and

pseudocolumnar stromatolites (Walter et al., 1996; Walter et al., 1998). The interpretation of

ancient siliceous deposits, however, becomes increasingly uncertain with the destructive

effects of extensive diagenetic overprinting on microfossils (e.g. Walter et al., 1980), and is

generally biased towards more enduring microfossil preservation in stromatolitic sinters

formed in lower-temperature systems where large sheathed cyanobacteria dominate.

2.MechanismsofFormationandDiagenesis


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2.1ENVIRONMENTALEFFECTSONSILICACHEMISTRY/MINERALOGY

Silica precipitates from hot spring waters as X-ray amorphous opal-A. The deposition of

soluble silica (or monomeric or polymeric silica) forms a dense, glass-like vitreous sinter

fabric, common in near-vent settings or acidic fluids (e.g. Handley et al., 2005; Schinteie et

al. 2007); whereas, porous granular sinter textures form where fast rates of polymerization

and/or aging are sufficient for colloid formation and deposition (White et al., 1956;

Rothbaum and Rohde, 1979; Mroczek et al., 2000). Higher silica saturations promote the

formation of smaller, more numerous colloids (Makrides et al., 1980). In mixed solutions

dense, cemented granular sinter develops by the precipitation of soluble silica at the point

where colloids join, where the negative radius of curvature has a low interfacial energy (Iler,

1979; e.g. Rodgers et al., 2002). Gels can form and settle in hot spring waters by

aggregation of colloids into networks either at alkaline pHs in the presence of salts, or at

acidic pHs where the ionic charge of colloids is small (Iler, 1979; e.g. White et al., 1956).Precipitation occurs owing to gravitational settling of large or aggregated colloids, silica

supersaturation, or the availability of substrates with small interfacial energies that lower the

activation energy required for nucleation. Aggregation of colloids may occur through

Brownian motion and London Forces (Hunter, 1993). Both precipitation and polymerization

of monomeric silica to form colloids also are driven by evaporation and cooling in menisci,

subaerially wicked water, and other subaerial water films or pooled water influenced by

hydrodynamic activity, such as splash or spray (Hinman and Lindstrom, 1996; Lowe et al.,

2001; Mountain et al., 2003). The rate of silica polymerization is pH dependant, and is

inhibited at pHs 5 and severely inhibited at pHs 9 (e.g. Brown and McDowell, 1983).

Polymerization is enhanced by the presence of silica or heterogeneous nuclei in solution

(White et al., 1956; Gallup, 1998). The rate and shorter induction periods before the onset of

polymerization are also favoured at large silica saturation ratios (silica

concentration/equilibrium concentration) (Krauskopf, 1956; White et al., 1956; Makrides etal., 1980), although this is somewhat counterbalanced by an increase in polymerization rate

with increasing temperature (Rothbaum and Rohde, 1979; Makrides et al., 1980). Saturation

increases rapidly with decreasing temperatures (Equation 1, Fournier and Rowe 1977).

Equilibrium concentration (ppm) = 10-731/T + 4.52 (1)

2.2ROLEOFBIOLOGICALTEMPLATESANDFOSSILIZATION

Surfaces wetted by hot spring waters are invariably coated by either visible

mesophilicthermophilic photosynthetic mats at temperatures below ~73C, and

microscopic thermophilichyperthermophilic biofilms above this temperature (Brock,

1978; Cady and Farmer, 1996). Microbial biofilms are pivotal in both stromatolite laminae

accretion and macrostructure development. Stromatolitic laminations are formed by changesin the rates or nature of microbial growth and silicification, while stromatolite morphologies


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are controlled to a large extent by microbial colonization patterns (e.g. Walter et al., 1972;

Brock, 1978; Jones et al., 1998; Handley et al., 2005; Schinteie, 2005). In the latter case, the

volume and spatial distribution of silica deposited is influenced by the high surface area

scaffolds of cells that often form irregular surface clusters, templates upon which

silicification occurs. The voluminous gelatinous matrix of exopolymeric substances (EPS)

that biofilm and mat forming microbes secrete around themselves (Hall-Stoodley et al.,

2004) is also prone to fossilization (e.g. Fig. 1; Weed, 1889; Westall et al., 2000; Handley et

al., 2008).

The affinity silica exhibits for biofilms appears to be passively induced, owing to either

smaller interfacial energies than the solution, or protonated functional sites on cell walls (or

sheaths) and within EPS (Urrutia & Beveridge, 1993; Westall et al., 1995). Even so, a

synchrotron-based Fourier-transform infrared study of cyanobacteria undergoing

silicification was able to demonstrate a physiological response to mineral encrustation,

involving a thickening of the polysaccharide sheath (Benning et al., 2004a,b). Higher ratesof silicification can arise during cellular lysis, where cell wall deterioration increases the

availability of functional groups as cytoplasmic material is released (Ferris et al., 1988).

Silicification of biofilm components can result in the long-term preservation of either

physical microfossils by encrustation, permineralization or replacement of cell walls and

cytoplasmic material (Westall et al., 1995; Toporski et al., 2002), or chemical or

biosignatures (e.g. lipids).

Figure 1. Scanning electron microscope (SEM) images of biofilms from a high-temperature stromatolitic sinter,Champagne Pool, Wairakei, New Zealand. (A) Unsilicified cells and desiccated EPS (left) overlying sinter. Silica

spherules of exposed sinter are visible on the right. (B) Silicified filamentous EPS (fine filaments) and cells (thick).

2.3PHYSICOCHEMICALANDHYDRODYNAMICEFFECTONSTROMATIOLITES

Siliceous stromatolites form distinct structures according to physicochemical and

hydrodynamic regime (Mountain et al., 2003; Lowe et al., 2001), and corresponding

changes in microbiota, which can change abruptly as conditions alter from subaqueous tosubaerial or with distance from vent, such as water cooling along outflow channels (Cassie

and Cooper, 1989; Walter et al., 1998; Lowe et al., 2001; Fernandez-Turiel et al., 2005;


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Childs et al., 2008). Neutral and alkaline pH waters tend to be dominated by photosynthetic

or non-photosynthetic prokaryotes, while acidic waters (< pH ~3) tend to inhabited by

acidophilic algae, such as Cyanidium caldarium, and acidophilic prokaryotes (e.g.

thermophilic Alicyclobacillus, Sulfobacillus, and Acidimicrobium bacteria) (Cassie and

Cooper, 1989; Jones et al., 2000; Johnson et al., 2003; Jones and Renaut, 2006; Schinteie et

al., 2007). Stromatolites formed from acidic waters are characteristically finely-laminated

with dense, vitreous sinter (Jones et al., 2000; Mountain et al., 2003; Jones and Renaut,

2006; Schinteie et al., 2007).

Commonly observed associations between stromatolite structures, microbiota and

temperature are defined by changes in photosynthetic bacteria at 73C (neutralalkaline

pHs). At low temperatures ( 30-35C) Calothrix mats commonly form shrub or stratiform

palisade structures; at mid temperatures (~35-59C) Phormidium-dominated cyanobacterial

mats (often tufted) tend to prevail and are associated with the formation of conical, fenestral

bubble mat or palisades stromatolites, marked by finer filaments than Calothrix; and atmidhigh temperatures (~60-73C) laminated stratiform structures typically develop from

mats populated by Chloroflexus and Synechococcus (Walter et al., 1972; Brock, 1978;Walter, 1976; Cady and Farmer, 1996; Walter et al., 1998; Jones et al., 2002; Lynne and

Campbell, 2004; Fernandez-Turiel et al., 2005). Non-photosynthetic biofilms at high

temperatures (> 73C) form columnar or spicular stromatolites, otherwise known as

geyserite (Castenholz, 1969; Walter, 1976). The laminae thickness between mat and

biofilm forming stromatolites differs between visually recognizable in the former to micron-

scale in the latter, and sinter is more likely to be dense and vitreous when precipitated at

high temperatures (Weed, 1889; Walter, 1976; Cady and Farmer, 1996; Braunstein and

Lowe, 2001; Handley et al., 2005).

Stromatolite type is further controlled to a significant degree by a wide range of

pontential hydrodynamic settings (Lowe et al., 2001). Splash, spray or fluctuating water

levels (surging or even gentle ripples), for example, are most frequently associated withproximal vent sites, including geyser vents, and spicular or columnar geyserite (Walter,

1976; Jones et al., 1998; Braunstein and Lowe, 2001; Mountain et al., 2003). Free-forming

pisoliths, ooids and oncoids are a common subaqueous feature of turbulent geyser/vent

pools, generated by multidirectional rolling motion (Walter, 1976; Jones and Renaut, 1997).

In outflow channels, stromatolites are affected by flow rates. Midtemperature columnar

stromatolites will form when subjected to a various water flow conditions and water depths

(Walter et al., 1972). Calothrix mats are apt to form palisades with thin sheet flow, but

develop pustular mats with shrub-like structures in deeperwater (Walter et al., 1998). On

the other hand, at low to high temperature regimes higher velocity flow can result in the

formation of streamer fabrics comprising massive collections of silicified filamentous forms

elongated in the direction of flow (Walter et al., 1998; Smith et al., 2003).


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2.4DIAGENESIS

Similar to wood petrification and diagenesis of siliceous marine sediments (e.g. Wise

and Weaver, 1974; Oehler, 1975; Stein, 1982), siliceous sinter undergoes a series of

mineralogic and morphologic changes once deposited. Fresh sinter comprises noncrystalline

microspheres of opal-A, which transform to noncrystalline, aligned nanospheres-upon-

microspheres of opal-A/CT, then to paracrystalline lepispheres or dumbbells of opal-CT,

various types of nanostructures of opal-C and eventually to blocky microcrystalline quartz

(Fig. 2; e.g. Herdianita et al., 2000; Campbell et al., 2001; Lynne and Campbell, 2004;

Lynne et al., 2007; Jones and Renaut, 2007). Silica residues, also found in some acidic

geothermal areas, are destructional rather than constructional in origin, and form smaller,

irregular microspheres of opal-A owing to acidification and remobilization of silica from

surrounding country rock (Rodgers et al., 2002; 2004). Using electron backscatter

diffractometry, Lynne et al. (2007) have shown that crystallographic restructuring of sinteroccurs before the silica mineral phase transformations which, in turn, precede nano- to

micron-scale morphological changes within the sinter matrix. In other words,

crystallographic axes realign at a fine-scale in the direction of the next most mineralogically

mature silica phase prior to any sign (by XRD or SEM imaging) that the deposit is about to

change to the next phase. The spectrum of opal to quartz transitions that occur during

diagenesis is now understood to proceed at variable rates depending on environmental

conditions, including changes in the water table, pH, heat, and composition (e.g. organic

content, carbonate, iron, etc.) (Herdianita et al., 2000; Guidry and Chafetz , 2003; Lynne et

al., 2006; 2007).


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Figure 2. Silica encrustation and patchy diagenesis of filamentous palisdade fabrics from Holocene sinters of the

Taupo Volcanic Zone, New Zealand. (A) Recently silicified filamentous mat (< 60 years old) from HB2 spring,

Tokaanu. Filaments still preserve orange-brown organic pigmentation despite being silicified and overgrown by apeloidal sinter horizon. Photo by Kristy Nicholson. (B) SEM image of filamentous mat encrusted by opal-Amicrospheres. HB2 spring, Tokaanu. Image by Kristy Nicholson. (C) Patchy quartzose diagenesis (white solid

areas) of palisade laminae from the late Pleistocene Umukuri sinter. Porous areas show opal-CT preservation offilaments. (D) Detail of Umukuri filament filled in and encrusted by opal-CT bladed lepispheres. From Lynne and

Campbell (2003).

Diagenesis affects microbial fabrics in at least two main ways. First, if silicification is

early, and subsequent diagenetic modification not too severe, rapidly mineralizing hot

spring deposits can serve as excellent archives for biological signatures in the geologic

record, and even form lagersttte (e.g., Trewin, 1996; Guido et al., in review). Second,

recrystallization and reprecipitation of silica phase minerals from opal to quartz can easily

obscure and even destroy biofabrics (e.g., Cady and Farmer, 1996; Walter et al., 1996;

Campbell et al., 2001; Lynne and Campbell, 2003; Jones et al. 2004). Trichome and sheath

diameters of cyanobacteria, for example, fill in or become encrusted with silica minerals,

such that fine filaments from mid-temperature sinter aprons are difficult to distinguish from

coarse filaments of low-temperature apron areas. However, many sinter deposits do not

undergo diagenesis uniformly (e.g., Campbell et al., 2001; Lynne et al. 2008). Patches oforiginal macrofabrics are good targets to search for micro-scale preservation of biosignals in


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sinters, including microbial micro-tufts, laminae, filaments, and micro-bubbles from

photosynthetic degassing within stromatolitic macrostructures (e.g., Guido and Campbell,

2009). Current research is focused on identifying the (micro)environmental factors that

contribute to the rate at which diagenesis proceeds and the causes of spatial variability in the

quality of sinter fabric preservation in the geologic record (e.g. Campbell and Lynne, 2006).

3.Analyticaltechniques

3.1SAMPLINGANDPRESERVINGFRESHSINTERDEPOSITS

A large part of the ability to interpret stromatolites preserved in the geologic record

derives from understanding modern systems. Numerous sedimentological and

microbiological studies document the geochemical and hydrodynamic conditions affectinggrowth in relation to the mineralogical and microbiological textures formed (Walter et al.,

1972; Walter, 1976; Cady et al. 1996; Hinman and Lindstrom, 1996; Jones and Renaut,

1997; Jones et al., 1998), aiding interpretations of relict deposits (e.g. White et al., 1989;

Walter et al., 1996; Walter et al., 1998; Campbell et al., 2001). The approach to

understanding actively forming siliceous stromatolites includes a small subset of

experimental growth studies designed to examine the transitional phases in stromatolite

accretion. Doemel and Brock (1974; 1977) conducted light filtration experiments and added

silicon carbide to the surfaces of nodular mats (alkaline hot spring waters, 4670C,

Yellowstone National Park) to demonstrate the mechanism of stromatolite formation in

siliceous hot springs. Rapid lamina accretion occurred during aerobic respiration at night via

upward migration of phototrophic Chloroflexusaurantiacus. Hinman and Lindstrom (1996)

used silicon carbide markers to demonstrate seasonal effects on the silicification of

photosynthetic bubble mats. Other studies have employed artificial substrates to gauge

stromatolite growth rates (e.g. Mountain et al., 2003; Handley et al., 2005). Furthermore,

multiple time point sampling enabled tracking of the formation of microstromatolitc spicular

sinter from Champagne Pool (75C; New Zealand), from its origins as microcolonies of

filamentous thermophilic prokaryotes, and its development through recurrent recolonization

(Handley et al., 2005). By examining varying effects of water level and hydrodynamics

(ripples) on substrates, the study also demonstrated the subtle balance between silica

deposition and microbial growth rates required for spicule formation.

An important consideration for field sampling is the ability to capture the transient

nature of stromatolite surfaces, and hence the different laminae forming events, which

typically alternate between porous (evidently microbe-rich) and non-porous (evidently

microbe-poor/abiotic) sinter development (e.g. Cady and Farmer, 1996; Mountain et al.,

2003). The outcome of studies in which freshly deposited sinters are imaged also depends

strongly on the choice of method used for sample preservation and analysis. Simple air

drying of sinter samples post-collection, and without fixation is sufficient to preserve largenumbers of (silicified) microbial cells at sinter surfaces (e.g. Jones et al., 1997).


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Occasionally localized films of desiccated EPS are also apparent (e.g. Jones et al., 1997).

However, these biofilms are generally present in an altered state, owing to cellular decay,

dehydration, and potential microbial contamination (e.g. fungal overgrowths), such that it is

not possible to fully and accurately interpret their impact on stromatolite formation. The

choice of biological fixative also has an effect on overall biofilm integrity. Garland et al.

(1979) found that a combination of fixative and mucopolysaccharide stain resulted in better

preservation of EPS and hence also retention of cells bound by the EPS, although the choice

of stain clearly influenced the polysaccharide morphology.

3.2ANALYSISOFFRESHLYDEPOSITEDSINTER

Multiple imaging methods have been employed to examine (sub)micron-scale textures

and microbialmineral associations in siliceous stromatolites. For freshly deposited sinter,

the effect of the analytical technique on biofilm integrity, and the nature of the target data(i.e. textural versus compositional) are important considerations. Scanning electron

microscopy (SEM) is the core tool for examining textures and fabrics at a high resolution.

Many, although not all, biological features are clearly distinguishable from the mineral

matrix. The vacuum under which samples are placed in traditional SEM causes the collapse

of poorly or unsilicified microbial cells, owing to the evaporation of water. This problem

can be overcome by first substituting water for a fluid with a low surface tension prior to

drying, such as liquid CO2 via the critical-point drying method or hexamethyldisilazane(Anderson, 1951, 1952; Fratesi et al., 2004). Critical-point drying has been used to preserve

the three-dimensional character of microbial cells on freshly deposited sinters from a range

of physicochemical regimes, notably assisting in cell identification and interpretation of

their roles in forming high-temperature and acidic microstromatolites (Cady and Farmer,

1996; Handley et al., 2005; Schinteie et al., 2007).

Other techniques are better suited to imaging the biofilms in their natural or near-naturalform. Both cryo-SEM and environmental SEM (ESEM) enable analyses of cells and EPS in

a hydrous three-dimensional state, through either flash-freezing biofilms and maintaining

them at liquid nitrogen temperatures, or analyzing them under a pressurized and humid

atmosphere of air, respectively. In a cryo-SEM study of a partially silicified cyanobacterial

mat from Orakei Korako, New Zealand, morphologically well-preserved cells were shown

to not only be bound together in a tight fibrillar mesh of EPS, but also to contain fibrillar

cytoplasmic material (Lynne and Campbell, 2003). In ESEM, the gelatinous character of

EPS is readily apparent (e.g. estuarine biofilm, Little et al., 1991; various terrestrial

biofilms, Douglas, 2005; sinter surface biofilm, Handley et al., 2008). Cryo-SEM tends to

illustrate the polysaccharide backbone of EPS, and can demonstrate the succession of

structures formed throughout matrix desiccation and contraction, i.e. (1) the three-

dimensional matrix, (2) two-dimensional films, and finally (3) fibrillar (e.g. siliceous hot

spring biofilm; Handley et al., 2008). Real-time dehydration studies of the EPS matrix also

can be undertaken by sublimation of ice in cryo-SEM (Fig. 3), and evaporation by

decreasing the atmospheric pressure in ESEM (Handley et al., 2008, Fig 5A-D). In this


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manner, effects of natural and post-collection dehydration can be simulated, and features

typically obscured by EPS may then be exposed.

Figure 3. EPS dehydration in cryo-SEM. (A) Cells of the marine bacterium Marinobacter santoriniensis embeddedin EPS. (B) Rod-shaped cell morphology evident after further ice sublimation.

Transmission electron microscopy (TEM) permits visualization of the ultra-structural

level detail of extra- and intra-cellular components. In sinter studies, TEM has been

performed at ambient temperatures following alcohol dehydration, embedding and ultrathin-

sectioning (although forms of cryo-TEM are also possible) to examine the nature of cellular-

level silicification, and the process of microfossil formation. Results indicate the pattern of

microfossil formation is dependent on the microbial community and thereby also the

geothermal setting. For example, cells within a Chloroflexus mat, which had been

undergoing silicification in a hot spring in Strokkur, Iceland, were encrusted extracellularly

by silica spherules, and within the cytoplasm only when cells appeared to have lysed

(Konhauser and Ferris, 1996). In a similar TEM study, sheaths of the cyanobacterium,

Calothrix were shown to effectively exclude silica, resulting in extracellular silicification

(Phoenix et al., 2000). In comparison, Handley et al. (2005) showed small, unsheathed

filamentous cells from a thermophilic hot spring biofilm tended to be silicified both intra-

and extra-cellularly. Both these silicified cellular fractions remained clearly distinct from

one another. Nonetheless, Lalonde et al. (2005) revealed a curious lack of cell-associated

silicification in experiments with the thermophilic Aquificales bacterium

Sulfurihydrogenibium azorense. Silica aggregated within the protein-rich EPS that was

expressed in response to environmental silica, but remote from cell surfaces.

In addition to textural characterizations are methods that enable clear identification of

mineralogical (discussed below) and biofilm compositions. Confocal laser scanning

microscopy (CLSM) combines two- or three-dimensional imagining with target specific

fluorescent staining (e.g. DNA, RNA, EPS) or autofluorescence (e.g. silica). One recent

study of siliceous stromatolites employed CLSM to obtain compositional data, and to

examine spatial associations of sinter and biofilm components in their hydrated state(Handley et al., 2008). Use of CLSM illustrated the prevalence and wide distribution of


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biofilm EPS, supporting observations from SEM analyses that mineralization of EPS creates

silicified films at the sinter surface or fibrillar structures that contribute to stromatolite

formation and textures.

Molecular phylogenetic techniques have largely replaced phenotypic analyses in order to

investigate the complexity of bacterial and archaeal community compositions, and identify

uncultured organisms. The use of both techniques has revealed correlations between

phylogeny and geothermal regime, and hence stromatolite type, and tentatively imply

function where closely related cultivated representatives exist. This is particularly important

for diverse non-photosynthetic communities, where phylogeny cannot be determined by

light microscopy. Non-photosynthetic, thermophilic communities identified on sinters

deposited from several thermal springs in Yellowstone National Park, Iceland and New

Zealand, based on 16S rRNA gene analyses, for example, were found to be abundant in

unclassified bacteria (i.e. with no near relatives in culture); organisms related to

Thermotogales, Thermus spp., Saccharomonospora glauca, gammaproteobacteria, and theAquificales bacteria Thermocrinis ruber and Aquifexpyrophilus (H2, S2O3

2-and/or S

0

oxidizing); and the archaea Sulfolobales, Thermoplasmatales, Thermoproteales andDesulfurococcales (Reysenbach et al., 1994; Huber et al., 1998; Inagaki et al., 2001; Blank

et al., 2002; Meyer-Dombard et al., 2005; Benning and Tobler, 2008; Childs 2008). Smith et

al. (2003) used molecular phylogenetic techniques to identify bacteria responsible for

forming large swaths of siliceous streamer fabric in a geothermal power station effluent

drain. The community was found not to be dominated by a single organism, but to contain a

variety of bacteria, including relatives of the thermophilic betaproteobacterium,

Hydrogenophilus sp. (H2-oxidizing), Chloroflexi and cyanobacteria. Bacterial communities

have also successfully been identified from within sinter deposited years previously using

16S rRNA gene analysis (e.g. Neilan et al., 2002).

In environmental microbial ecology there is also increasing accessibility and application

of metagenomics, transcriptomics and proteomics, as well as specific gene expressionstudies to community analysis, permitting detailed assessment of community structure, and

gene and protein expression (Maron et al., 2007; Bertin et al. 2008). Research groups have

already begun applying these powerful techniques to microbial mats in hot spring systems.

In a study by Bhaya et al. (2007), genomic sequencing of two dominant, but ecologically

dissimilarSynechococcus strains (i.e. ecotypes) from hot springs in Yellowstone National

Park revealed differences in phosphate and nitrogen pathways, indicating the strains had

developed different nutrient requirements. In comparing these sequences to metagenomic

data from mats the authors also found greater strain-level variation in the Synechococcus

populations at lower rather than higher temperatures, and identified a distinct population

with genes for Fe(II) uptake and assimilation. In another study, the expression of oxygenic

versus anoxygenic photosynthesis and nitrogen fixation genes was examined in a

thermophilic microbial mat (Tibet) (Lau and Pointing, 2009). Results showed a clear

vertical transition, from sequences that indicate phototrophic and nitrogen-fixingchemolithoautotrophic bacteria at the surface, to those indicating anoxygenic phototrophs

with depth. In a similar study, Steuno et al. (2006) determined gene sequences specific to


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Synechococcus ecotypes in a microbial mat (Octopus Spring, Yellowstone National Park).

From these they tracked the expression of the Synechococcus genes throughout the day and

night, depicting, for example, a decline in photosynthesis and respiration in the evening, and

an increase in nitrogen fixation toward the end of the day as photosynthesis declined and

anoxia encroached in the mats.

3.3ANALYSISOFMODERNTOANCIENTTERRESTRIALHOTSPRINGDEPOSITS

Certain analytical techniques are equally applicable to both modern and ancient sinters,

such as mineralogical analyses of sinter and textural characterizations of sinter and

microfossils. X-ray diffraction, used primarily in this context to differentiate between silica

polymorphs, is complemented by RAMAN spectroscopy and thermal analysis in tracking

sinter crystallinity and maturity (Herdianita et al., 2000; Lynne et al. 2005; 2008). As for

freshly deposited sinter, SEM underpins textural characterizations of fossil stromatoliticlaminae and microbes. Optical light microscopy of thin sections of (micro)stromatolite cross

sections is important for obtaining a well-contrasted overview of micro-stromatolitic

laminations, and microfossils particularly laminae-forming microfossils from low- or

mid-temperature deposits (e.g. Braunstein, 1999; Jones et al., 2000; Campbell et al., 2001;

Lynne and Campbell, 2003; Handley et al., 2005; Guido and Campbell, 2009; Guido et al.,

in review). Microfossils can also be detected in high-temperature deposits by light

microscopy where cells have been enlarged by silica encrustation, but only to a very limited

extent (Handley et al., 2005). SEM is particularly important when imaging the small

diameter cells typical of (hyper)thermophiles.

Refractory lipids provide a long-surviving source of information on members of

eukaryotic, bacterial and archaeal microbial assemblages, as opposed to DNA which is more

readily degraded. Studies of modern and recently relict sinters prove the efficacy of the

method for interpreting lipid signatures in ancient sinters, and to explore differences in lipid preservation. Up to genera-level resolution of bacteria has been inferred from lipid

compositions in modern hot spring settings, based on lipid profiles of pure cultures.

Analyses of various refractory polar lipids (e.g. monoglycosyl, diglycosyl andsulfoquinosovyl diglycerides, and phosphatidyl glycerol, 2-methylbacteriohopanepolyols

and methylalkanes) have been used to distinguish among bacterial genera present in a

modern thermophilic Cyanobacterial mat at Octopus Spring, Yellowstone National Park

(Ward et al., 1994; Jahnke et al., 2004). Meanwhile, lipids indicative of novel organisms,

thermophiles, archaea, bacteria, and the bacterial genus Roseiflexus and orderAquificales

were identified from silicified microbial communities within several high-temperature

sinters from the Taupo Volcanic Zone, New Zealand (Pancost et al., 2005). Kaur et al.,

(2008) examined concentrations of bacterial and archaeal diether lipids, of a similar

chemical structure and expected level of preservation, in order to determine temporal

changes in community structures in a sinter accumulated over a 900 years (Champagne

Pool). Their results suggested a dramatic transition in the relative abundances of bacterial

and archaeal communities.


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4.Summaryandsignificanceofhotspringsandtheirdeposits

The attraction of hot springs settings is both in the extreme microbial life they host, and

in their capacity to act as time capsules of palaeoecological and palaeoenvironmental

information. Hot springs lure microbiologists to the discovery of novel enzymes, notably

those that are thermostable (e.g. Turner et al., 2007). Arguably the most famous case is that

of the isolation of thermophilic Thermus aquaticus from a hot spring in Yellowstone

National Park, followed by the isolation of thermostable Taq polymerase from T. aquaticus

a DNA polymerase widely used in polymerase chain reactions for DNA amplification

(Brock and Freeze, 1969; Chien et al., 1976). In addition, the sinter deposited in many

thermal springs is valued for preserving traces of microbial life deep into the geological

record, and as such render insights into early forms of life on Earth (e.g. Trewin et al., 1994;

Walter et al., 1998). However, there is also much interest in the application of terrestrial

stromatolite studies to the search for fossilized life on Mars (e.g. Cady et al., 2003; DesMarias et al., 2008). Convincing evidence now exists for siliceous hot spring deposits on

Mars. The Mars Reconaissance Orbiter (MRO) High Resolution Imaging Science

Experiment (HiRISE) detected geomorphic features closely resembling terrestrial thermal

features on Earth, including a large fracture system, and aligned spring-like elliptical

mounds with central vents, terracing and concentric zoning of color ( composition) (Allen

and Oehler, 2008). Meanwhile, silica-rich deposits were also discovered on Mars by the

Spirit rover, and were found in conjunction with volcanic deposits (e.g. basalt, tephra and

hydrated ferric sulphates), giving strong indication for the siliceous material to have formed

under (low-pH acid-sulfate) hydrothermal conditions (Squyres et al., 2008).

Future research on terrestrial hot springs will likely involve increased emphasis on

genomic, transcriptomic, and proteomic studies to establish the intricacies of microbial

communities and their metabolisms, and better understand the ecology of these systems as

analogues for early forms of life. Even so, detecting and interpreting biosignatures presentin stromatolites necessitates that data from a manifold of approaches be taken into account,

i.e. studies of modern sinters to identify relationships between environmental conditions and

microbes that affect the overall morphological and internally laminated construction of

stromatolites; microbial community information (phylogenetic and functional); and the

underlying causes of the differential effects of diagenesis. This also includes examining the

processes of biofilm silicification and fossilization, which can involve both cells and EPS,

and can also be fraught by inconsistencies, such as species-specific fossilization biases (e.g.

Westall, 1997; Westall et al., 2000; Handley et al., 2008). Considering the wider physical

context of sinters, namely stromatolitic patterns in relict deposits that match microfacies in

modern hot springs settings, and other potential non-morphological evidence such as lipid

biomarkers, is especially important for avoiding potential misapplication of a biological

origin to abiotic structures, e.g. filament-like mineral inclusions (Hofman and Farmer,

2000).


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Establishing Biogenicity and Paleoenvironments of Terrestrial Siliceous Stromatolites in Geothermal Settings