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Genomic Science Program

Systems Biology for Energy and the Environment

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Genomic Science Program

Science Focus Area: Pacific Northwest National Laboratory (PNNL)

Phenotypic Response of the Soil Microbiome to Environmental Perturbations

Soil is a complex ecosystem that boasts some of the most diverse communities of microbes on Earth. These microbes play an important role in the cycling of soil carbon, nitrogen, and other nutrients. Predicting microbial interactions in this complex system represents both an exciting frontier and a grand challenge with implications on soil productivity, fertility, and carbon storage.

PNNL’s Soil Microbiome Science Focus Area (SFA) is developing a systems-level understanding of how soil microbial communities respond to and affect changing environmental conditions. Specifically, SFA researchers are studying the microbiome’s response to changing moisture through a tractable, spatially explicit examination of the molecular and ecological interactions occurring within and between microbial consortia, with identification of sentinel biomarkers in complex, live soil systems. Integrated experiments are designed to confront both the scaling challenges and inter-kingdom interactions that regulate networks of biochemical reactions. Agent-based models will be parameterized using high- resolution experimental data, and predictions will be tested in soils using advanced chemical imaging and fluorescent probes unique to PNNL to reveal spatially explicit microbial interactions.

Discoveries and outcomes from controlled experiments will be tested and validated in the field, using moisture gradient experiments at a local field site. Data, models, and methods will be captured and shared with the broader science community through the establishment of a soil microbiome database that leverages existing PNNL tools and resources to encourage sharing of data and results. Knowledge gained from this SFA will provide fundamental understanding for how enzymes, metabolites, and microbial consortia interact to decompose organic carbon and enable prediction of how these reaction networks and related functions shift in response to changing moisture regimes.

Laboratory Research Manager: Charlette Geffen

Principal Investigator: Janet K. Jansson and Kirsten S. Hofmockel


Pacific Northwest National Laboratory: Hyun-Seob Song, Erin Baker, Hans Bernstein, Mary Lipton, Jason McDermott, Tom Metz, Ryan Renslow, and Aaron Wright

Kansas State University: Ari Jumpponen

Lawrence Berkeley National Laboratory-Joint Genome Institute: Nikos Kyrpides

Washington State University: Steven Fransen


Overview Brochure: Download PDF

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