The Genomic Science Program:
Microbial Communities and the
Carbon Cycle
Joseph Graber, Ph.D.
Program Manager
Department of Energy, Office of Biological &
Environmental Research
April 26, 2011
Office
of Science
Office of Biological
and Environmental Research
National Academies Report:
“A New Biology for the 21st Century”
“Systems biology seeks a deep
quantitative understanding of complex
biological processes through dynamic
interaction components that may
include multiple molecular, cellular,
organismal, population, community,
and ecosystem functions. It builds on
foundational large-scale cataloguing
efforts (e.g. genomics, proteomics,
metabolomics, etc.) that specify the
“parts list” needed for constructing
models. The models relate the
properties of parts to the dynamic
operation of the systems they
participate in.”
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BER GenomicScience
Department of Energy • Office of Science • Biological and Environmental Research
DOE Genomic Science Program
A mission-inspired fundamental research approach
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BER GenomicScience
Department of Energy • Office of Science • Biological and Environmental Research
DOE Biological & Environmental
Research Missions
•  Understand complex biological, climatic, and environmental
systems across spatial and temporal scales.
•  BER provides the foundational science to:
–  Support the development of biofuels as major, secure, and sustainable
national energy resources
–  Understand the potential effects of greenhouse gas emissions on
Earth’s climate and biosphere and the implications of these emissions
for our energy future
–  Predict the fate and transport of contaminants in the subsurface
environment at DOE sites
–  Develop new tools to explore the interface of biological and physical
sciences
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BER GenomicScience
Department of Energy • Office of Science • Biological and Environmental Research
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BER GenomicScience
Department of Energy • Office of Science • Biological and Environmental Research
Microbes, the Carbon Cycle,
and Climate
•  Effects of changing climate conditions on
biological carbon cycle processes will
heavily influence the stability of carbon
stored in ecosystems and types of GHGs
released during degradation
•  The role of microbial communities in
mediating many critical carbon cycle
processes remains poorly understood, and
microbially-mediated processes are only
minimally represented in carbon cycle
models
•  Elimination of "black boxes" requires new
research to link structural and functional
characterization of microbial communities
with quantitative measurement of carbon
cycle processes
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BER GenomicScience
BER
Overview
Department of Energy • Office of Science • Biological and Environmental Research
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BER GenomicScience
Department of Energy • Office of Science • Biological and Environmental Research
DOE Report on Carbon Cycling &
Biosequestration
Report from the March, 2008 DOE
Workshop on Carbon Cycling &
Biosequestration
Identifies priorities for fundamental
research on biological aspects of the
global carbon cycle and biosequestration
of carbon in ecosystems
Emphasizes multidisciplinary research
and knowledge integration across
microbiology, plant biology, ecosystem
science, biogeochemistry, oceanography,
and modeling efforts
Available at: http://genomicscience.energy.gov/
carboncycle/
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BER GenomicScience
Department of Energy • Office of Science • Biological and Environmental Research
Biological Systems Research on the Role of
Microbial Communities in Carbon Cycling
2010 Genomic Science Program FOA:
•  Systems-level studies on regulatory and metabolic
networks of microbes and microbial consortia
involved in biogeochemical cycling of carbon
•  Development of molecular –omics approaches to
understand how shifts in environmental variables
impact microbial community structure and function
related to carbon cycling processes in terrestrial
ecosystems
•  Development of techniques for imaging and
analysis of microbially- mediated carbon cycling
processes at submicron scales of resolution
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BER GenomicScience
BER
Overview
Department of Energy • Office of Science • Biological and Environmental Research
Microbial Functional Traits: Predicting Response
& Resilience of Decomposition to Global Change
Steve Allison, UC Irvine
•  Use metagenomic analysis to examine
impact of water and nitrogen availability on
fungal, bacterial, and archaeal community
structure in a California grasslands
ecosystem
•  Characterize distribution of extracellular
enzymes involved in decomposition
processes amongst major microbial taxa
•  Develop quantitative models of decomposition based on trait/taxon
relationships and validate predictions using manipulative field
experiments
•  Collaborators: Mike Goulden, Adam Martiny, Jennifer Martiny, and
Kathleen Treseder (UC Irvine) and Eoin Brodie (LBNL)
BER GenomicScience
10 BER
Overview
Department of Energy • Office of Science • Biological and Environmental Research
Syntrophic Interactions and Mechanisms
Underpinning Anaerobic Methane Oxidation
Victoria Orphan, Cal Tech
•  Understand key physiological and ecological
factors impacting the rate and magnitude of
methane oxidation by microbial consortia
under anoxic conditions
•  Develop advanced techniques for
visualization, isotopic tracing, and
proteogenomic analysis of intact consortia
•  Characterize carbon, nitrogen, and sulfur metabolism of diverse
consortial types under conditions favoring different terminal electron
accepting pathways
•  Collaborators: Chris House (Penn State), Jeff Grethe & Mark Ellisman
(UC San Diego), Bob Hettich (ORNL)
BER GenomicScience
11 BER
Overview
Department of Energy • Office of Science • Biological and Environmental Research
Metagenomics-Enabled Predictive Understanding
of Temperature Sensitivity of Soil Carbon
Decomposition to Climate Warming
Jizhong Zhou, Univ. Oklahoma
•  Examine shifts in soil microbial community
structure/function as a result of elevated
temperatures
•  Construct a high throughput –omics pipeline
for metagenomics and metatrascriptomics
using a combination of pyrosequencing and
Geochip screening
•  Develop a network model to predict microbial control points of
ecosystem carbon cycling processes in responses to climate change
•  Collaborators: Jim Tiedje (Michigan State), Yiqi Luo & Zhile He (Univ.
Oklahoma), Ted Schuur (Univ. Florida), Kostas Konstantinidis (Georgia
Tech)
BER GenomicScience
12 BER
Overview
Department of Energy • Office of Science • Biological and Environmental Research
Visit the new Genomic Science Program
website
genomicscience.energy.gov
13 BER GenomicScience
Department of Energy • Office of Science • Biological and Environmental Research