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Genomic Science Program

Systems Biology for Energy and the Environment

Department of Energy Office of Science. Click to visit main DOE SC site.

Genomic Science Program

Science Focus Area: Pacific Northwest National Laboratory (PNNL)

Phenotypic Response of the Soil Microbiome to Environmental Perturbations

Soil is a diverse ecosystem with microbial dark matter that remains to be discovered. Predicting microbial interactions in this complex system represents both an exciting frontier and a grand challenge with implications on the productivity and fertility of our nation’s soils. PNNL’s Soil Microbiome Science Focus Area (SFA) will result in a systems-level understanding of soil microbiome and phenotypic responses 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 our new local field site. Data, models, and methods will be captured and shared with the broader science community through the establishment of a Soil Microbiome Knowledgebase (SMK), a data management infrastructure 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

Co-Principal Investigator: 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


  • New Funding Announcement: DE-FOA-0002214 - Systems Biology Research To Advance Sustainable Bioenergy Crop Development
    Additional Information » [01/20]
  • New Funding Announcement: DE-FOA-0002215 - ESPCoR FOA 2215 Building EPSCOR-State/National Laboratory Partnerships
    Additional Information » [12/19]
  • New Funding Announcement: DE-FOA-0002217 – Computational Tool Development for Integrative Systems Biology Data Analysis Additional Information » [11/19]
  • New Funding Announcement: DE-FOA-0002173 – Early Career Research Program Additional Information » [11/19]
  • Now Available: Breaking the Bottleneck of Genomes: Understanding Gene Function Across Taxa report [9/19]
  • 2019 PI Meeting: Genomic Sciences Program Annual Principal Investigator Meeting February 24 - 27, 2019. Abstracts and More »
  • DOE Announces $64 Million for Plant and Microbe Research: U.S. Department of Energy announced $64 million in funding for 25 university-led genomics research projects on plants and microbes for bioenergy and bioproducts. [8/19]
    Read More »
  • $13.5 Million for New Bioimaging Approaches for Bioenergy: The U.S. Department of Energy announced $13.5 million in funding for six projects to develop new approaches to microscopic imaging of plants and microbes. [8/19]
    Read More »
  • More News and Announcements »

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