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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 (LLNL)

Microbes Persist: Systems Biology of the Soil Microbiome

  • Lead Investigator: Jennifer Pett-Ridge1
  • Laboratory Research Manager: Henry Shaw1
  • LLNL SFA Team: Steve Blazewicz1, Yongqin Jiao1, Stephanie Malfatti1, Karis McFarlane1, Erin Nuccio1, Brian Souza1, Ben Stewart1, Rhona Stuart1, Peter Weber1, Mavrik Zavarin1
  • Collaborators: Eoin Brodie2, Peter Nico2, Jinyun Tang2, Mary Firestone3, Jill Banfield3, Bruce Hungate4, Paul Dijkstra4, Christina Schaedel4, Ben Koch4, Matt Sullivan3, Ljiljana Paša-Tolic6
  • Postdocs/Students: Rachel Neurath1,3, Keith Morrison1, Evan Starr3, Alexa Nicholas3
  • Participating Institutions:  1Lawrence Livermore National Laboratory, 2Lawrence Berkeley National Laboratory, 3University of California at Berkeley, 4Northern Arizona University, 5Ohio State University, 6Environmental and Molecular Sciences Laboratory/Pacific Northwest National Laboratory (EMSL/PNNL)
  • KBase App: Microbes Persist: Building a KBase Foundation for Microbial and Viral Ecogenomics in Soil

Microorganisms play key roles in soil carbon turnover and stabilization of persistent organic matter via their metabolic activities, cellular biochemistry, and extracellular products. Microbial residues are also 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 SFA is that microbial cellular-chemistry, functional potential, and ecophysiology fundamentally shape soil carbon persistence—this will be characterized via stable isotope probing (SIP) of genome resolved metagenomes. Studies will focus on soil moisture as a 'master controller' of microbial activity and mortality, since altered precipitation regimes are predicted across the temperate U.S.

The LLNL Soil Microbiome SFA’s ultimate goal is to determine how microbial soil ecophysiology, population dynamics, and microbe-mineral-organic matter interactions regulate the persistence of microbial residues under changing moisture regimes.

Objectives include:

  • Apply SIP-metagenomics to delineate how changing water regimes shape activity of individual microbial populations and expression of ecophysiological traits that affect the fate of microbial and plant C.
  • Identify and quantify mechanisms of mortality in the soil microbiome (focusing on phage lysis and water stress) and their contribution to C 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 C persistence.
  • Synthesize genome-scale ecophysiological trait data, population-specific growth and mortality, and SOM chemistry to build models of microbial functional guilds and SOM turnover, to predict the long-aspired connection between soil microbiomes and fate of soil C.

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