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Genomic Science Program

Systems Biology for Energy and the Environment

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Genomic Science Program

Science Focus Area: Lawrence Livermore National Laboratory

Microbes Persist: Systems Biology of the Soil Microbiome

  • Principal Investigator: Jennifer Pett-Ridge1
  • Co-Investigators:  Steve Blazewicz1, Yongqin Jiao1, Jeff Kimbrel1, Stephanie Malfatti1, Karis McFarlane1, Erin Nuccio1, Brian Souza1, Peter Weber1, Mavrik Zavarin1, Mary Firestone2, Jill Banfield2, Bruce Hungate3, Paul Dijkstra3, Christina Schaedel3, Ben Koch3, Egbert Schwartz3, Eoin Brodie4, Peter Nico4, Jinyun Tang4, Matt Sullivan5, Ljiljana Paša-Tolic6
  • Participating Institutions: 1Lawrence Livermore National Laboratory, 2University of California–Berkeley, 3Northern Arizona University, 4Lawrence Berkeley National Laboratory, 5Ohio State University, 6Pacific Northwest National Laboratory
  • Collaborations: Peter Kennedy, University of Minnesota; Asmeret Asefaw Berhe, University of California–Merced; Lawrence Berkeley National Laboratory and the DOE Systems Biology Knowledgebase (KBase)
  • KBase App: Microbes Persist: Building a KBase Foundation for Microbial and Viral Ecogenomics in Soil


The Microbes Persist SFA at Lawrence Livermore National Laboratory (LLNL) seeks to gain a foundational and predictive understanding of the interacting biological, biogeochemical, and physical factors that control soil carbon turnover and persistence. Because of the vast complexity of soils, the multi-institutional team includes experts in a number of disciplines such as soil microbiology, ecophysiology and biogeochemistry, metagenomics and viral ecology, organic matter–mineral chemistry, isotope and compound-specific mass spectrometry, and multiscale modeling. [Courtesy LLNL]

Microorganisms play key roles in soil carbon turnover and the stabilization of persistent organic matter via their metabolic activities, cellular biochemistry, and extracellular products. Soil microbes also provide rich elemental and genetic resources to their predators, including phages, bacteria, and microfauna. The resulting microbial residues are thought to be primary ingredients of soil organic matter (SOM), a pool critical to Earth’s soil health and climate. The central hypothesis of this Science Focus Area (SFA) is that microbial cellular chemistry, functional potential, and ecophysiology fundamentally shape soil carbon persistence. The SFA team is testing this concept by characterizing the capabilities of the “active” microbiome and virome, using stable isotope-informed approaches to scale from metagenomes and viromes to computational models that span the trait and systems scales. Rainfall and soil water act as “master controllers” of microbial transformations, interactions, and SOM stabilization processes. With Earth system models projecting major changes in precipitation in many regions, the SFA’s ultimate goal is to determine how microbial ecophysiology, population dynamics, and microbe-mineral interactions regulate the persistence of soil microbial residues under changing moisture regimes.

Specific objectives include:

  • Apply stable isotope probing (SIP) metagenomics to delineate how changing water regimes shape the activity of individual microbial populations and expression of ecophysiological traits that affect the fate of microbial and plant carbon.
  • Identify and quantify mechanisms of mortality in the soil microbiome (focusing on phage lysis, bacterial predators, and water stress) and their contributions to carbon turnover and the biochemistry of microbial residues.
  • Measure how the soil microbiome and its products (cell envelope, extracellular polymeric substances, exo-enzymes) interact with contrasting mineral assemblages to control both short- and long-term soil carbon persistence.
  • Synthesize genome-scale ecophysiological trait data, population-specific growth and mortality information, and SOM chemistry to build models of microbial functional guilds and SOM turnover, and to predict the long-aspired connection between soil microbiomes and the fate of soil carbon.

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