Daniel Drell, Ph.D.Biological Systems Science DivisionOffice of Biological and Environmental Research U.S. Department of Energy

October 9, 2009

NRC Designing the Microbial Commons

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Steve Koonin, Undersecretarry for Science

Advanced Scientific Computin

g Research

Fusion EnergyScience

s

High Energy Physic

s

Basic Energy Science

s

Climate and Environmental SciencesMichael Kuperberg

Acting Director

Biological Systems Science

Sharlene WeatherwaxDirector

Biological and Environmenta

l Research (BER)

Anna PalmisanoAssociate Director

Nuclear

Physics

Steven Chu, Secretary, Department of Energy

William Brinkman, Director, Office of Science

Provide the foundational science for:

Developing biofuels as major, secure, and sustainable national energy resources

Understanding potential effects of greenhouse gas emissions on Earth’s climate and biosphere and the implications of these emissions for our energy future

Predicting the fate and transport of contaminants in the subsurface environment at DOE sites

Developing new tools to explore the interface of biological and physical sciences

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Biological generation of energy compounds (biofuels) e.g. Hydrogen, Ethanol

Biogeochemistry of legacy wastes (metals, radionuclides, toxic chemicals, etc.)

Carbon Dioxide Capture and Sequestration

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Biological Systems Science Division: Genome Sciences

(Knowledgebase)Bioenergy Research CentersImagingRadiobiologyEthical, Legal, and Social Issues (ELSI)User Facilities (JGI)

Climate and Environmental Sciences Division: Climate and Environmental Sciences Division: Atmospheric Systems ResearchAtmospheric Systems ResearchEnvironmental Systems ScienceEnvironmental Systems ScienceClimate and Earth Systems ModelnigClimate and Earth Systems ModelnigUser Facilities (ARM, EMSL)User Facilities (ARM, EMSL)

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THE MICROBE PROJECT INTERAGENCY WORKING GROUP Daniel Drell (Chair) DOE Frederick Pearce DOD Ann Lichens-Park (Exec Sec) USDA Robert Foster DOD Joanne Tornow NSF James Lindsay USDA Maria Giovanni NIH Kevin Anderson DHS James Anderson NIH C. Jacobs-Young OSTP Kay Marano Briggs DOI Gerard Stelma EPA Michael Broder EPA Linda Chrisey ONR Valentina Di Francesco NIH J. Eugene LeClerc FDA Pamela McInnes NIH Shawn McLaughlin NOAA Dale Nordenberg CDC

Member agencies:DOE, CSREES/USDA, NSF, ARS/USDA, NIAID/NIH, NIDCR/NIH, NIGMS/NIH, EPA, FDA, USGS/DOI, ONR/DOD, NOAA, CDC, DST/DOD, DHS, OSTP

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THE MICROBE PROJECT INTERAGENCY WORKING GROUP “Maximize the opportunities

offered by genome-enabled microbial science to benefit science and society through coordinated interagency efforts to promote research, infrastructure development, education and outreach.”Goals for ResearchGoals for Research11. Functional GenomicsFunctional Genomics2. Proteomics2. Proteomics..3. Comparative Genomics3. Comparative Genomics4. Microbe-Host and Microbe-Microbe 4. Microbe-Host and Microbe-Microbe InteractionsInteractions5. 5. Microbial ForensicsMicrobial Forensics6. Environmental Genomics6. Environmental Genomics

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http://www.jgi.doe.gov

“User facility providing high-throughput DNA sequencing & analysis in support of DOE missions in alternative energy, carbon cycling & bioremediation.”

Targets sequence-based projects of high scientific merit

Focus on DOE relevance

JGI organizes peer-review, allocation ~50% of capacity

Approved for sequencing (2005-2009) 174 bacterial & archaeal isolates 33 metagenomes 45 fungi, algae 20 euk pilots & EST projects 17 plant & animal WGS

http://www.jgi.doe.gov/CSP/

http://img.jgi.doe.gov/cgi-bin/pub/main.cgi

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

QuickTime™ and aTIFF (LZW) decompressor

are needed to see this picture.

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JGI Science ProgramsPlants

Dan RokhsarJeremy Schmutz

Jerry Tuskan

FungiScott BakerAlla Lapidus

Igor Gregoriev

ProkaryoticIsolates

Tanja WoykeNikos KypidesJonathan Eisen

MetagenomesPhil HugenholtzSusannah TringeNikos Kyrpides

10IMG, IMG/M

Capillary[75]

1.8 Mb/day

700 bp reads

$1000/Mb

Plant WGS,Metagenomes,

Clones

454/Roche[9]

600 Mb/day

400 bp reads

$30/Mb

Microbe WGS,Metagenomes,

ESTs

Solexa/Illumina[8]

1500 Mb/day

35 bp reads

$10/Mb

Re-sequencing,Transcript mapping

ABI 3730

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JJGI

http://www.genomesonline.org/ Published Complete Genomes 1110 Archaeal complete genomes111 Bacterial Ongoing Genomes: 3342 Eukaryotic Ongoing Genomes 1165 Metagenomes 200 Total: 5928

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Insects

Mammals

MarsupialsBirds

MollusksRuminants

Compost

Decomposing wood chipsBioenergy Metagenomes at the JGI

JGI GEBA

Populus trichocarpa black cottonwood

Chlamydomonas reinhardtii chlorophyte alga Physcomitrella patens bryophyte mossSorghum bicolor sorghumGlycine max soybeanPanicum virgatum switchgrassMiscanthus x giganteus miscanthusVolvox carteri multicellular green algaArabidopsis lyrata Lyrate rockcressSelaginella moellendorffii lycophyte fernBrachypodium distachyon false purple brome

Mimulus guttatus monkeyflowerManihot esculenta c assavaPrunus persica peachSetaria italica foxtail milletCapsella rubella Pink Shepherd’s purseAquilegia coerulea Goldsmith columbine Gossypium raimondii diploid cottonEucalyptus grandis rose gumPhaseolus vulgaris Common beanZea mays (Mo17 inbred) maize

Plant Genomes

Single Cell Projects at the JGI

Single Cell Projects at the JGI

GEBAOscillospira

guilliermondii

Roderick Mackie (U of Illinois)

Frank Roberto (Idaho Natl Lab)

LSP 2007Archaeal viral community

Howard Ochman (U of Arizona)

R&D 2008Green Sharpshooter

Symbionts

Eddy Rubin (DOE JGI)

R&D 2009 Cow Rumen Community

GEBATermite Gut Community

Phil Hugenholtz (DOE JGI)

DOEM 2004Glomus intraradices

Gerald Tuskan (Oakridge Natl Lab)

Ramunas Stepanauskas (Bigelow Lab)

DOEM 2007Marine Flavobacteria sp.

GEBATagetibacter soli Ellin

5290

Catherine Osborne (UC Berkeley)

CSP 2009Shipworm symbionts

CSP 2009Hoatzin crop microbiome

Daniel Distel (Ocean Genome Legacy)Maria Dominguez-Bello (UPR Rio Piedras)

BESC 2008Clostridium pasteurianum BC1

Daniel van der Lelie (Brookhaven Natl Lab)Tanja WoykeTanja Woyke16

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100,000 Great Prairie metagenomic project , ~100 Gbp

Termite hindgut, 62 Mbp62

1,000,000

Potential Future Projects:Terabase Projects

Increasing Scale of Metagenomic Projects in the JGI’s Future

1 Terabase: 1 trillion (1012) base pairs

Eubacteria: 120 Plant (Eucalyptus) 1 Fungal: 37 Total: 158

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Integrated Microbial Genomes (IMG): http://img.jgi.doe.gov/cgi-bin/pub/main.cgiIntegrated Microbial Genomes: Microbiome Samples: http://img.jgi.doe.gov/cgi-bin/m/main.cgiIMG is a data management and analysis platform, containing draft and completed genomes, from the JGI and elsewhere in the public domain, providing tools and viewers for analyzing genes and genomes, singly or comparatively, and generate GenBank formatted files.

EMSL Capabilities Nuclear Magnetic Resonance &

EPR

Mass Spectrometry Kinetics & Reactions Molecular Science Computing Subsurface Flow and Transport Deposition and Microfabrication Spectroscopy & Diffraction

Science Themes Biological Interactions and

Dynamics Biogeochemistry and Subsurface

Science Interfacial Processes 20

http://www.emsl.pnl.gov/emslweb/

GTL Data and Information Sharing Policy• The Office of Biological and Environmental Research (OBER) will

require that all publishable information resulting from GTL funded research must conform to community recognized standard formats when they exist, be clearly attributable, and be deposited within a community recognized public database(s) appropriate for the research conducted. Furthermore, all experimental data obtained as a result of GTL funded research must be kept in an archive maintained by the Principal Investigator (PI) for the duration of the funded project. Any publications resulting from the use of shared experimental data must accurately acknowledge the original source or provider of the attributable data.

JGI Data Release Policy (http://genome.jgi-psf.org/pages/data-usage-policy.jsf):

•Immediate release of raw reads; •“reserved analyses” are discouraged (for up to but not more than 12 months) when they would compete with scientific aims of the project PI

To accelerate research on the integration, cross referencing, genertion and ongoing curation of derived data to make the genomic/biological communities more effective.

To provide a variety of interfaces, suitable for both first time and more experienced users and to provide useful applications and interfaces.

To leverage best-in-class existing tools, standards, protocols and database technologies and to stimulate development of new and improved tools.

http://genomicsgtl.energy.gov/compbio/

A Knowledgebase Workshop to define Needs and provide Recommendations

Held May 28-30, 2008 in Washington DC and Chaired by

Jim Frederickson and Rick Stevens

Office of Science Financial Assistance Funding Opportunity Announcement

DE-FOA-0000143 Computational Biology and Bioinformatic

Methods to Enable a Systems Biology Knowledgebase There are four objectives that may be addressed by applicants

responding to this FOA:

(1)develop methods to integrate together multiple data types, (2)develop new methods to infer and curate (meta)genomic functional annotations (3)develop methods to couple multiple cellular pathways and processes and (4)develop new methods to model whole cellular processes. Preapplication due to DOE by 4:30 p.m., Eastern Time, November 5, 2009.Closing Date for Applications: Jan 29, 2010    Program Manager: Susan K. Gregurick, susan.gregurick@science.doe.gov http://www.sc.doe.gov/grants/FOA-0000143.html

Genomics of Energy & EnvironmentGenomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms

Http://www.jgi.doe.gov/meetings/usermeeting

Rita Colwell, Chairman of Canon US Life Sciences; U Maryland Cristina Cuomo, Broad Institute; Evan Delucia, University of Illinois at Urbana-Champaign; Richard Flavell, Ceres; Dennis Hedgecock, University of Southern California; Jay Keasling, CEO DOE Joint BioEnergy Institute; Richard Jorgensen, iPlant™ Collaborative, University of Arizona; Madhu Khanna, University of Illinois at Urbana-Champaign Steve Knapp, University of Georgia; Tom Mitchell-Olds, Duke University; Steve Moose, University of Illinois at Urbana-Champaign; Joseph Noel, Salk Institute for Biological Studies; Forest Rohwer, San Diego State University; Steven Savage, Cirrus Partners; Gary Stacey, University of Missouri; Jim Tiedje, Michigan State University; Detlef Weigel, Max Planck Institute for Developmental Biology