Microbial Community Genomics at the JGI Susannah Green Tringe, PhD JGI Metagenome Program Advancing Science with DNA Sequence
Feb 24, 2016
Microbial Community Genomics at the JGI
Susannah Green Tringe, PhDJGI Metagenome Program Lead
Advancing Science with DNA Sequence
Talk outline
• Metagenomics background and history• JGI Metagenome Program
• Organization• Project portfolio
• JGI Science: Wetlands metagenomics
Talk outline
• Metagenomics background and history• JGI Metagenome Program
• Organization• Project portfolio
• JGI Science: Wetlands metagenomics
Isolate (pure culture)
Genomics
Microbial community
Metagenomics
What is metagenomics?
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
Metagenomics
1 10 100 1000 10000
Acid mine Sargasso Sea Soil
Species complexity
?
Adaptive gene for habitat AAdaptive gene for habitat BEssential gene
A
B
Environmental Gene Tags(EGTs)
Comparative metagenomics
Tringe et al 2005
COG3459:Cellobiose phosphorylase
COG5524: Bacteriorhodopsin
COG1292: Choline-glycine betaine transporter
Tringe et al 2005
Talk outline
• Metagenomics background and history• JGI Metagenome Program
• Organization• Project portfolio
• JGI Science: Wetlands metagenomics
User Programs
Plants Fungi Microbes Metagenomes
Program organization
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 GroupT. Woyke
Omics GroupK. Mavrommatis
Functional Annotation Group
N. Ivanova
Microbial Systems Group
S. Tringe
Metadata GroupD. Liolios
Comparative Analysis Systems
A. Chen
LANLP. Chain
Metagenome ProgramS. Tringe
Microbial ProgramT. Woyke
Major Collaborators
• DSMZ
• BIGELOW
Science ProgramsJ. Bristow
2004 2005 2006 2007 2008 2009 2010 2011 201210
100
1000
10000
100000
JGI sequence outputSe
quen
ce o
utpu
t (G
b)
Fiscal Year
40 Gb
30 Tb
2012 projected:47.1 Tb
JGI Project Portfolio
2008 2009 2010 2011 2012 (target)
2013 (target)
0
50
100
150
200
250
300
350
400Standard draft
Minimal draft
Metatranscriptome
Metatranscriptome counting
FY13 Program Targets
YTD
Genomics for Bioenergy
SugarCellulose
MicrobesEnzymesPlants
CO2
Pre-treatment
Biomass
Poplar (Science)Sorghum bicolor (Nature)SwitchgrassMiscanthusPinus taedaFoxtail milletBrachypodium distachyon
Feedstock improvement
Trichoderma reesei (PNAS)Postia placenta (PNAS)Termite gut (Nature)Cow rumen (Science)Leaf cutter ant gardenShipworm mollusk
Biomass degradation
T. ethanolicusPichia stipitus Biogas bioreactorMixed alcohols bioreactorButanol producing E coli
Fuels synthesis
Termite metagenome
Warnecke et al Nature 2007
Biogeochemistry and bioremediation
Enhanced BiologicalPhosphate RemovalSludge (Nat Biotech)
Anammox bioreactors(Env Microbiol)
Terephthalate degradingcommunity (ISME)
Gulf oil spill (ISME)
Terephthalate-degrading community
Lykidis et al, ISME 2011
Carbon Cycling & Environment
Picoprymnesiophytes
Lake Washington Methylotrophs
Prairie soil metagenome
Deep subsurface ecosystem
(Science)(PNAS) (Nat Biotech)
Permafrost metagenome(Nature)Wetlands metagenome
Talk outline
• Metagenomics background and history• JGI Metagenome Program
• Organization• Project portfolio
• JGI Science: Wetlands metagenomics
Why study wetlands?
Wetlands store a lot of carbon (IPCC, 2000)
…but their sequestration potential is uncertain (USGS, 2010)
Peat island subsidence
Wetland “carbon farming”
CO2
O2
CH4
LisamarieWindham-Myers
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”?
Sampling site gradients
PeataccretionOxygen,Nitrate,Sulfate
Methaneflux
Waterinlet
Wateroutflow
Site A B C/L
Does microbial community composition change with nutrient gradients, primary production and methane release?
Sample Collection
Caffrey & Kemp 1991
Illumina shotgun sequencing
Shotgun Metagenome
Community composition
454 Titanium Pyrotag sequencing
Functional analysis
Sequencing strategy
Wetland microbial communities
-Sampling site is major driver ofcommunity composition
-Sample type is next largest factor-Depth effect is subtle
Site LHigh biomassaccumulationSite A
Low biomassaccumulation
Site BMedium biomass
accumulation
February 2011
Shaomei He
-Similar resultsin August
Indicator OTUsDechloromonas OTUMethanoregula OTU
Archaeal methanogen Correlates with CH4 production
170X coverage in one metagenome dataset
Denitrifying BetaproteobacteriumCorrelates with nitrate abundance
A Rhizobiales OTU
AlphaproteobacteriumKnown plant-associated
bacteria
A Crenarchaeota subphylum 2 OTU
Uncharacterized crenarchaeote
A, B, L
RhizomeBulk
Shaomei He
Metagenome Sequencing and Assembly
More complex community, less
assembly
5.2 5.6 6 6.4 6.80%
5%
10%
15%
20%
25%
30%
Shannon diversity index from 16S pyrotag
Perc
ent r
eads
map
ped
to c
ontig
s
Shotgundata
Assembly
Contigs
Singlets
Shaomei He
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
Metagenome assemblyG
+C c
onte
nt
100 500 1000
Average read depth5 10 50
Alphaproteobacteria~850X
Methanoregula~170X
Clostridia
Draft methanogengenome
Single-copy phylogenetic marker COGs in finishedMethanomicrobial genomes
M. boonei
Wetland OTU
High coverage and low redundancy of the draft genome
Methanogenesis Pathways
HydrogenotrophicAcetoclastic Methylotrophic
Red: present in wetland MethanoregulaGrey: absent in wetland Methanoregula
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
Questions?