Microbial communities of uranium contaminated groundwater :

Metagenomic insights

Group members:Pinaki SarRatul SahaSufia Kazy

Microbial communities from highly uranium-contaminated groundwater were sequenced using random shotgun sequencing-based strategy with the aim of addressing the following questions:

How does anthropogenic environmental change affect groundwater microbial community diversity and structure?

How does microbial community adapt to severe environmental changes such as heavy metal contamination?

Can molecular mechanisms responsible for such environmental changes be predicted from the metagenomic sequence?

Our questions• What are the dominant populations in the two

metagenomes obtained from ORFRC• What are the functional differences between

metagenomes? • How the phylogenetically abundant members are

functionally relevant?

Samplings location (ORFRC)

uranium, technetium-99 , nitrate, thorium, and volatile organic compounds such as acetone, methylene chloride, toluene, and tetrachloroethylene

Metagenomic statistics

1.00E+00

1.00E+01

1.00E+02

1.00E+03

1.00E+04

1.00E+05

1.00E+06

1.00E+07

1.00E+08

1.00E+09

Pristine U Contaminated

Phylogenetic distribution

Crenarchaeota

Euryarchaeota

Nanoarchaeota

Acidobacte

ria

Actinobacte

ria

Aquificae

Bactero

idetes

Caldithrix

Chlamydiae

Chlorobi

Chloroflexi

Chrysiogenetes

Cyanobacteria

Deferribacte

res

Dictyoglomi

Elusimicr

obia

Fibro

bacteres

Firmicu

tes

Fuso

bacteria

Gemmatimonadetes

Lentisp

haerae

Nitrosp

irae

Planctomyce

tes

Proteobacte

ria

Spiroch

aetes

Synergistetes

TM7

Tenericutes

Thermi

Thermodesu

lfobact.

..

Thermoto

gae

Verruco

microbia

1

10

100

1000

10000

100000

Ura Con FW67 Est CopiesOak Rid FW10 Est Copies

1

10

100

1000

10000

Ura Con FW67 Est Copies

Oak Rid FW10 Est Copies

0

500

1000

1500

2000

2500

Oak Rid FW10 Est CopiesUra Con FW67 Est Copies

1

10

100

1000

10000Ura Con FW67 Est Copies

Oak Rid FW10 Est Copies

Phylogenetic distribution of Xanthomonadaceae members

COGs from contaminated and pristine samples related to X. campestris

Cell cycle control, cell division, chromosome partitioning

Coenzyme transport and metabolism

Nucleotide transport and metabolism

Transcription

Defense mechanisms

Function unknown

Secondary metabolites biosynthesis, transport and catabolism

Lipid transport and metabolism

Replication, recombination and repair

Unknown

0 5 10 15 20 25

Gene Count

UnknownFunction unknown

Signal transduction mechanismsLipid transport and metabolism

Carbohydrate transport and metabolismCell wall/membrane/envelope biogenesis

General function prediction onlyTranscription

Amino acid transport and metabolismCoenzyme transport and metabolism

Translation, ribosomal structure and biogenesisCell motility

Energy production and conversionIntracellular trafficking, secretion, and vesicular transportCell cycle control, cell division, chromosome partitioning

Inorganic ion transport and metabolismPosttranslational modification, protein turnover, chaperones

Replication, recombination and repairSecondary metabolites biosynthesis, transport and catabolism

0 5 10 15 20 25 30 35 40

Gene Count

Contaminated sample Pristine sample

Distribution of protein coding genes with COGs within the contaminated samples

Amino acid transport and metabolism; 850

Carbohydrate transport and metabolism; 488

Cell cycle control, cell division, chromosome par-titioning; 113

Cell motility; 285

Cell wall/membrane/envelope biogenesis; 598

Chromatin structure and dynamics; 5

Coenzyme transport and metabolism; 397Cytoskeleton; 1

Defense mechanisms; 195

Energy production and conversion; 756

General function prediction only; 1008Inorganic ion transport and metabolism; 516

Intracellular trafficking, secretion, and vesicular transport; 395

Lipid transport and metabolism; 454

Nucleotide transport and metabolism; 175

Posttranslational modification, protein turnover, chaperones; 366

Replication, recombination and repair; 596

RNA processing and modification; 4

Secondary metabolites biosynthesis, transport and catabolism; 273

Signal transduction mechanisms; 525

Transcription; 607Translation, ribosomal structure and biogenesis; 410

Amino acid transport and metabolism; 9008Carbohydrate transport and metabolism;

5941Cell cycle control, cell division, chro-

mosome partitioning; 1146

Cell wall/membrane/envelope biogenesis; 7777

Coenzyme transport and metabolism; 4299

Defense mechanisms; 2126

Energy production and conversion; 7066

Function unknown; 7782

General function prediction only; 12302Inorganic ion transport and metabolism; 4176

Intracellular trafficking, secretion, and vesicular transport; 3590

Lipid transport and metabolism; 4293

Nucleotide transport and metabolism; 2824

Posttranslational modification, protein turnover, chaperones; 4304

Replication, recombination and repair; 6867

Secondary metabolites biosynthesis, transport and catabolism; 2752

Signal transduction mechanisms; 6973

Transcription; 6276

Translation, ribosomal structure and biogenesis; 6649

Distribution of protein coding genes with COGs within the pristine samples

Protein coding genes detected within the contaminated samples connected to KEGG pathways

Amino Acid Metabolism; 618

Carbohydrate Metabolism; 575

Energy Metabolism; 472

Membrane Transport; 361Lipid Metabolism; 258

Metabolism of Cofactors and Vitamins; 256

Signal Transduction; 244

Xenobiotics Biodegradation and Metabol-ism; 235

Metabolism of Other Amino Acids; 193

Nucleotide Metabolism; 182

Translation; 157Replication and Repair; 125Folding, Sorting and Degradation; 77Biosynthesis of Other Secondary Metabolites; 58Transcription; 16

Protein coding genes detected within the pristine samples connected to KEGG pathways

Amino Acid Metabolism; 5911Biosynthesis of Other Secondary Metabolites;

576

Carbohydrate Metabolism; 5398

Cell Communication; 6

Cell Growth and Death; 599

Cell Motility; 703

Energy Metabolism; 3982

Environmental Adaptation; 114Folding, Sorting and Degradation; 1049

Lipid Metabolism; 1908

Membrane Transport; 3006Metabolic Diseases; 95

Metabolism; 15990

Metabolism of Cofactors and Vitamins; 2531

Metabolism of Other Amino Acids; 1662

Metabolism of Terpenoids and Polyketides; 1404

Nervous System; 4Nucleotide Metabolism; 2684

Replication and Repair; 1663

Signal Transduction; 1856Transcription; 313

Translation; 2552Transport and Catabolism; 269 Xenobiotics Biodegradation and Metabolism; 2002

Func_id Func_nameOak_Ridge_Pristine_Groundwater_FRC_FW301_geneCount

Uranium_Contaminated_Groundwater_FW1

06

Uranium_Contaminated_Groundwater_FW106_pva

lue

Uranium_Contaminated_Groundwater_FW106_geneC

ountA RNA processing and modification 69 0 5.00E-01 4B Chromatin structure and dynamics 59 -0.27 3.94E-01 5C Energy production and conversion 7066 -5.65 yellow 8.07e-09 yellow 756D Cell cycle control, cell division, chromosome partitioning 1146 -0.92 1.80E-01 113E Amino acid transport and metabolism 9008 -4.02 yellow 2.87e-05 yellow 850F Nucleotide transport and metabolism 2824 0.04 4.84E-01 175G Carbohydrate transport and metabolism 5941 -1.67 4.78E-02 488H Coenzyme transport and metabolism 4299 -1.34 8.99E-02 397I Lipid transport and metabolism 4293 -2.38 yellow 8.57e-03 yellow 454J Translation, ribosomal structure and biogenesis 6649 -0.03 4.89E-01 410K Transcription 6276 -2.46 yellow 7.04e-03 yellow 607L Replication, recombination and repair 6867 -3.76 yellow 8.35e-05 yellow 596M Cell wall/membrane/envelope biogenesis 7777 -1.1 1.35E-01 598N Cell motility 2267 -1.86 3.14E-02 285O Posttranslational modification, protein turnover, chaperones 4304 -1.42 7.76E-02 366P Inorganic ion transport and metabolism 4176 -5.40 yellow 3.31e-08 yellow 516Q Secondary metabolites biosynthesis, transport and catabolism 2752 -2.28 pink 1.13e-02 pink 273R General function prediction only 12302 -2.73 yellow 3.19e-03 yellow 1008S Function unknown 7782 -1.05 1.47E-01 734T Signal transduction mechanisms 6973 -0.65 2.57E-01 525U Intracellular traffi cking, secretion, and vesicular transport 3590 -2.29 pink 1.09e-02 pink 395V Defense mechanisms 2126 -1.47 7.06E-02 195W Extracellular structures 1 0 5.00E-01 0Z Cytoskeleton 54 0 5.00E-01 1

Abundance Profile

PhylumDomain Phylum/Class No. Of Genomes

No. Of Hits 30%

% Hits 30%No. Of Hits

60%% Hits

60%No. Of

Hits 90%% Hits 90%

Archaea Crenarchaeota 39 (2) 4 (2) 0.09% 0% 0%Archaea Euryarchaeota 79 (6) 5 (4) 0.11% 2 (2) 0.05% 0%Bacteria Acidobacteria 7 (4) 7 (4) 0.16% 4 (3) 0.09% 0%Bacteria Actinobacteria 280 (39) 37 (31) 0.84% 26 (13) 0.59% 0%Bacteria Aquificae 13 (2) 2 (2) 0.05% 0% 0%Bacteria Bacteroidetes 187 (11) 16 (10) 0.37% 2 (2) 0.05% 0%Bacteria Chlorobi 12 (6) 5 (4) 0.11% 8 (5) 0.18% 0%Bacteria Chloroflexi 18 (10) 12 (9) 0.27% 3 (3) 0.07% 0%Bacteria Chrysiogenetes 1 (1) 3 (1) 0.07% 1 (1) 0.02% 0%Bacteria Cyanobacteria 64 (14) 13 (12) 0.30% 12 (6) 0.27% 0%Bacteria Dictyoglomi 2 (1) 1 (1) 0.02% 0% 0%Bacteria Bacilli 568 (8) 7 (7) 0.16% 1 (1) 0.02% 0%Bacteria Clostridia 231 (15) 15 (12) 0.34% 4 (4) 0.09% 0%Bacteria Erysipelotrichi 16 (1) 0% 1 (1) 0.02% 0%Bacteria Gemmatimonadetes 1 (1) 3 (1) 0.07% 0% 0%Bacteria Nitrospirae 2 (1) 2 (1) 0.05% 0% 0%Bacteria Planctomycetes 11 (5) 1 (1) 0.02% 5 (4) 0.11% 0%Bacteria Alphaproteobacteria 255 (95) 182 (75) 4.15% 118 (58) 2.69% 6 (2) 0.14%Bacteria Betaproteobacteria 179 (104) 354 (86) 8.08% 539 (90) 12.30% 18 (15) 0.41%Bacteria Deltaproteobacteria 57 (38) 78 (35) 1.78% 35 (16) 0.80% 0%Bacteria Epsilonproteobacteria 81 (2) 2 (2) 0.05% 0% 0%Bacteria Gammaproteobacteria 636 (163) 837 (123) 19.11% 1422 (111) 32.46% 44 (5) 1.00%Bacteria Magnetococci 1 (1) 1 (1) 0.02% 0% 0%Bacteria Zetaproteobacteria 1 (1) 12 (1) 0.27% 8 (1) 0.18% 0%Bacteria Spirochaetes 60 (3) 4 (3) 0.09% 0% 0%Bacteria Synergistetes 13 (2) 1 (1) 0.02% 1 (1) 0.02% 0%Bacteria Thermi 19 (5) 6 (4) 0.14% 4 (3) 0.09% 0%Bacteria Thermodesulfobacteria 2 (2) 2 (2) 0.05% 0% 0%Bacteria Verrucomicrobia 9 (4) 5 (4) 0.11% 2 (2) 0.05% 0%Bacteria unclassified<span style='color:red'title='Taxon data unavailable'>N/A</span> (1)2 (1) 0.05% 1 (1) 0.02% 0%

Eukaryota Arthropoda 19 (3) 3 (3) 0.07% 0% 0%Eukaryota Ascomycota 54 (4) 3 (3) 0.07% 1 (1) 0.02% 0%Eukaryota Basidiomycota 9 (1) 0% 1 (1) 0.02% 0%Eukaryota Chlorophyta 3 (1) 3 (1) 0.07% 0% 0%Eukaryota Streptophyta 7 (1) 4 (1) 0.09% 0% 0%Eukaryota unclassified eukaryotes 9 (1) 1 (1) 0.02% 0% 0%

Plasmid:Bacteria Alphaproteobacteria 56 (2) 5 (2) 0.11% 2 (1) 0.05% 0%Plasmid:Bacteria Betaproteobacteria 38 (4) 10 (3) 0.23% 2 (2) 0.05% 0%Plasmid:BacteriaGammaproteobacteria 402 (6) 8 (5) 0.18% 1 (1) 0.02% 0%Plasmid:Bacteria unclassified 16 (4) 2 (1) 0.05% 8 (4) 0.18% 0%

- Unassigned - 397 9.061858 2055 46.9071 4269 97.443506

Family Composition

0

100

200

300

400

500

600

Family

No.

of H

its

Species Composition

93%

5%2%

Frateuria Unknown Xanthomonas axonopodis Xanthomonas campestris

…..and more questions………..

Conclusion