Microbial Community Genomics at the JGI Susannah Green Tringe,
PhD JGI Metagenome Program Lead Advancing Science with DNA
Sequence
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Talk outline Metagenomics background and history JGI Metagenome
Program Organization Project portfolio JGI Science: Wetlands
metagenomics
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Talk outline Metagenomics background and history JGI Metagenome
Program Organization Project portfolio JGI Science: Wetlands
metagenomics
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Isolate (pure culture) Genomics Microbial community
Metagenomics What is metagenomics?
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Why metagenomics? Vast uncultivated phylogenetic diversity
hints at a potential reservoir of untapped functional diversity
Ecologically important processes nutrient cycling Pharmacologically
valuable compounds antibiotics Industrially useful enzymes
cellulases
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Metagenomics 110100100010000 Acid mine Sargasso SeaSoil Species
complexity ?
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Adaptive gene for habitat A Adaptive gene for habitat B
Essential gene A B Environmental Gene Tags (EGTs)
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Comparative metagenomics Tringe et al 2005
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COG3459: Cellobiose phosphorylase COG5524: Bacteriorhodopsin
COG1292: Choline- glycine betaine transporter Tringe et al
2005
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Talk outline Metagenomics background and history JGI Metagenome
Program Organization Project portfolio JGI Science: Wetlands
metagenomics
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User Programs PlantsFungiMicrobesMetagenomes
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Program organization
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Scientific Advisory Board 1. Cameron Currie, University of
Wisconsin 2. Ed DeLong, MIT 3. Jed Fuhrman, University of Southern
California 4. George Garrity, MSU 5. Steve Hallam, University of
British Columbia 6. Bob Landick, Great Lakes BRC 7. Folker Meyer,
Argonne National Laboratory 8. Nancy Moran, Yale University 9. Mary
Ann Moran, University of Georgia 10. Karen Nelson, JCVI 11. Rich
Roberts, NEB 12. Doug Rusch, J. Craig Venter Institute 13. Ramunas
Stepanauskas, Bigelow Laboratory 14. Niels van der Lelie, RTI 15.
Phil Hugenholtz, University of Queensland 2011- one super program
Prokaryote Super Program N. Kyrpides Single Cells Group T. Woyke
Omics Group K. Mavrommatis Functional Annotation Group N. Ivanova
Microbial Systems Group S. Tringe Metadata Group D. Liolios
Comparative Analysis Systems A. Chen LANL P. Chain Metagenome
Program S. Tringe Microbial Program T. Woyke Major Collaborators
DSMZ BIGELOW Science Programs J. Bristow
Terephthalate-degrading community Lykidis et al, ISME 2011
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Carbon Cycling & Environment Picoprymnesiophytes Lake
Washington Methylotrophs Prairie soil metagenome Deep subsurface
ecosystem (Science) (PNAS) (Nat Biotech) Permafrost metagenome
(Nature) Wetlands metagenome
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Talk outline Metagenomics background and history JGI Metagenome
Program Organization Project portfolio JGI Science: Wetlands
metagenomics
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Why study wetlands? Wetlands store a lot of carbon (IPCC, 2000)
but their sequestration potential is uncertain (USGS, 2010)
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Peat island subsidence
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Wetland carbon farming CO 2 O2O2 CH 4 Lisamarie
Windham-Myers
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Major microbial processes in wetland sediments Plant biomass
decomposition Denitrification Mn(IV) reduction Fe(III) reduction
Sulfate reduction Methanogenesis Methane oxidation (aerobic or
anaerobic) Laanbroek, Annals of Botany How do these processes
impact carbon farming?
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Sampling site gradients Peat accretion Oxygen, Nitrate, Sulfate
Methane flux Water inlet Water outflow Site ABC/L Does microbial
community composition change with nutrient gradients, primary
production and methane release?
Wetland microbial communities -Sampling site is major driver of
community composition -Sample type is next largest factor -Depth
effect is subtle Site L High biomass accumulation Site A Low
biomass accumulation Site B Medium biomass accumulation February
2011 Shaomei He -Similar results in August
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Indicator OTUs Dechloromonas OTUMethanoregula OTU Archaeal
methanogen Correlates with CH 4 production 170X coverage in one
metagenome dataset Denitrifying Betaproteobacterium Correlates with
nitrate abundance A Rhizobiales OTU Alphaproteobacterium Known
plant-associated bacteria A Crenarchaeota subphylum 2 OTU
Uncharacterized crenarchaeote A, B, L Rhizome Bulk Shaomei He
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Metagenome Sequencing and Assembly More complex community, less
assembly Shotgun data Assembly Contigs Singlets Shaomei He
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Relative gene family abundances Samples with more
methanogenesis genes have less dissimilatory sulfate/nitrate
reduction genes Methane oxidation genes were more abundant in
rhizomes Shaomei He
Single-copy phylogenetic marker COGs in finished
Methanomicrobial genomes M. boonei Wetland OTU High coverage and
low redundancy of the draft genome
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Methanogenesis Pathways
HydrogenotrophicAcetoclasticMethylotrophic Red: present in wetland
Methanoregula Grey: absent in wetland Methanoregula
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Conclusions Metagenomics provides a means to study uncultivated
communities of microbes Recent advances in sequencing technologies
allow us to explore these communities at unprecedented depth
Complex communities found in soils and sediments still present
significant challenges to genome reconstruction Appropriate library
construction, sequencing and analysis methods enable greater
functional insight into complex communities
