The Genomic Science Program: Microbial Communities and the Carbon Cycle

Transcription

1 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

2 National Academies Report: A New Biology for the 21 st 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. 2 BER GenomicScience

3 DOE Genomic Science Program A mission-inspired fundamental research approach 3 BER GenomicScience

4 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 4 BER GenomicScience

5 5 BER GenomicScience

6 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 6 BER GenomicScience Overview

7 7 BER GenomicScience 7

8 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: carboncycle/ 8 BER GenomicScience

9 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 9 BER GenomicScience Overview

10 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) 10 BER GenomicScience Overview

11 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) 11 BER GenomicScience Overview

12 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) 12 BER GenomicScience Overview

13 Visit the new Genomic Science Program website genomicscience.energy.gov 13 BER GenomicScience