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Microbial Community Genomics at the JGI

Advancing Science with DNA Sequence. Microbial Community Genomics at the JGI. Susannah Green Tringe, PhD JGI Metagenome Program Lead. Talk outline. Metagenomics background and history JGI Metagenome Program Organization Project portfolio JGI Science: Wetlands metagenomics. Talk outline.

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Microbial Community Genomics at the JGI

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  1. Advancing Science with DNA Sequence Microbial Community Genomics at the JGI Susannah Green Tringe, PhD JGI Metagenome Program Lead

  2. Talk outline • Metagenomics background and history • JGI Metagenome Program • Organization • Project portfolio • JGI Science: Wetlands metagenomics

  3. Talk outline • Metagenomics background and history • JGI Metagenome Program • Organization • Project portfolio • JGI Science: Wetlands metagenomics

  4. Isolate (pure culture) Microbial community Genomics Metagenomics What is metagenomics?

  5. 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

  6. Metagenomics Sargasso Sea Soil Acid mine 1 10 100 1000 10000 Species complexity ?

  7. A Environmental Gene Tags (EGTs) Adaptive gene for habitat A Adaptive gene for habitat B Essential gene B

  8. Comparative metagenomics Tringe et al 2005

  9. COG5524: Bacteriorhodopsin COG1292: Choline- glycine betaine transporter COG3459: Cellobiosephosphorylase Tringe et al 2005

  10. Talk outline • Metagenomics background and history • JGI Metagenome Program • Organization • Project portfolio • JGI Science: Wetlands metagenomics

  11. User Programs Plants Fungi Microbes Metagenomes

  12. Program organization

  13. 2011- one super program • Science Programs • J. Bristow

  14. JGI sequence output 30 Tb 2012 projected: 47.1 Tb 40 Gb Sequence output (Gb) Fiscal Year

  15. JGI Project Portfolio

  16. FY13 Program Targets YTD

  17. Feedstock improvement Biomass degradation Fuels synthesis Poplar (Science) Sorghum bicolor (Nature) Switchgrass Miscanthus Pinustaeda Foxtail millet Brachypodiumdistachyon Trichodermareesei (PNAS) Postia placenta (PNAS) Termite gut (Nature) Cow rumen (Science) Leaf cutter ant garden Shipworm mollusk T. ethanolicus Pichiastipitus Biogas bioreactor Mixed alcohols bioreactor Butanol producing E coli Genomics for Bioenergy Biomass Cellulose Sugar CO2 Plants Pre-treatment Enzymes Microbes

  18. Termite metagenome Warnecke et al Nature 2007

  19. Biogeochemistry and bioremediation Enhanced Biological Phosphate Removal Sludge (Nat Biotech) Anammox bioreactors (EnvMicrobiol) Terephthalate degrading community (ISME) Gulf oil spill (ISME)

  20. Terephthalate-degrading community Lykidis et al, ISME 2011

  21. Carbon Cycling & Environment Permafrost metagenome (Nature) Wetlands metagenome Prairie soil metagenome Deep subsurface ecosystem Picoprymnesiophytes Lake Washington Methylotrophs (Science) (PNAS) (Nat Biotech)

  22. Talk outline • Metagenomics background and history • JGI Metagenome Program • Organization • Project portfolio • JGI Science: Wetlands metagenomics

  23. Why study wetlands? Wetlands store a lot of carbon (IPCC, 2000) …but their sequestration potential is uncertain (USGS, 2010)

  24. Peat island subsidence

  25. Wetland “carbon farming” CO2 CH4 O2 Lisamarie Windham-Myers

  26. Major microbial processes in wetland sediments • Plant biomass decomposition • Denitrification • Mn(IV) reduction • Fe(III) reduction • Sulfate reduction • Methanogenesis • Methane oxidation (aerobic or anaerobic) How do these processes impact “carbon farming”? Laanbroek, Annals of Botany

  27. Sampling site gradients A B C/L Site Methane flux Water inlet Does microbial community composition change with nutrient gradients, primary production and methane release? Water outflow Peat accretion Oxygen, Nitrate, Sulfate

  28. Sample Collection Caffrey & Kemp 1991

  29. Sequencing strategy Community composition Shotgun Metagenome Functional analysis Illumina shotgun sequencing 454 Titanium Pyrotag sequencing

  30. Wetland microbial communities February 2011 Site B Medium biomass accumulation -Similar results in August -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 Shaomei He

  31. Indicator OTUs MethanoregulaOTU DechloromonasOTU A, B, L Archaealmethanogen Correlates with CH4 production 170X coverage in one metagenome dataset Denitrifying Betaproteobacterium Correlates with nitrate abundance A RhizobialesOTU A Crenarchaeotasubphylum 2OTU Rhizome Bulk Alphaproteobacterium Known plant-associated bacteria Uncharacterized crenarchaeote Shaomei He

  32. Metagenome Sequencing and Assembly Shotgun data Contigs Assembly Singlets • More complex community, less assembly Shaomei He

  33. Relative gene family abundances Samples with more methanogenesisgenes have less dissimilatorysulfate/nitrate reduction genes Methane oxidation genes were more abundant in rhizomes Shaomei He

  34. Metagenome assembly Alphaproteobacteria ~850X Methanoregula ~170X G+C content Clostridia Draft methanogen genome 5 50 100 500 1000 10 Average read depth

  35. Single-copy phylogenetic marker COGs in finishedMethanomicrobial genomes Wetland OTU M. boonei High coverage and low redundancy of the draft genome

  36. Methanogenesis Pathways Acetoclastic Hydrogenotrophic Methylotrophic Red: present in wetland Methanoregula Grey: absent in wetland Methanoregula

  37. 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

  38. Questions?

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