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Genomic Science Program

Systems Biology for Energy and the Environment

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Genomic Science Program

Science Focus Area (Completed Project): Pacific Northwest National Laboratory (PNNL)

Principles of Microbial Community Design

The PNNL Foundational Science Focus Area (FSFA) is a multidisciplinary team of investigators at four institutions who seek to identify fundamental principles governing microbial community structure and function and from which higher order properties (e.g., resistance and resilience) emerge. To identify candidate design principles, we will initially examine autotrophic microbial communities found in diverse extreme environments. By combining field studies with experi­ments using simplified consortia and isolates from those environments, we will identify common attributes across the different systems. The reduced complexity of our model systems allows us to use derived genome sequence data, which enables use of multiple omics analyses to test underlying mechanistic relationships. This, in turn, provides a foundation for building models of community metabolism, spatial relationships, and regulatory and interaction networks. These models will be used iteratively with targeted experiments to predict the dynamic behavior of communi­ties and understand how higher-order community properties arise. Future work will be aimed at confirming identi­fied design principles using more complex natural systems, then applying these principles to engineer new microbial communities with predictable behavior. Knowing the fundamental rules and basic underlying principles governing the functioning of complex, interacting cellular systems can guide the engineering of stable microbial communities for sustainable cost-efficient production of biofuels, and inform­ing science and policy associated with environmental steward­ship and climate change. Our research plan supports DOE goals to achieve a predictive under­standing of mi­crobes and microbial communities and to provide foundational knowledge that can be used as a basis for rational design of microbial systems.

Scientific Focus Area Manager for PNNL: Janet Jansson1

SFA Technical Co-Managers: Jim Fredrickson1 and Margaret Romine1

Participating Scientists: Alex Beliaev1, Haluck Beyena1,3, Bill Inskeep1,4, Steve Lindemann1, Mary Lipton1, Matt Marshall1, Jason McDermott1, Tom Metz1, James Moran1, Bill Nelson1, Andrei Ostermann2, Dmitry Rodianov2, Hyun-Seob Song1, Steven Wiley1, and Aaron Wright1

Participating Institutions: 1Pacific Northwest National Laboratory, Richland, Washington 99352; 2Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road,  La Jolla, CA 92037; 3Washington State University, 2710 Crimson Way, Richland, Washington 99354;  4Montana State University, Bozeman, MT 59717

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