microbial communities of uranium contaminated groundwater : metagenomic insights
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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
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