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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)

A Systems Biology Approach to Interactions and Resource Allocation in Bioenergy-Relevant Microbial Communities

  • SFA Principal Investigator: Rhona Stuart1
  • Scientific Focus Area Manager for LLNL: Henry Shaw1
  • Participating Scientists: Xavier Mayali1, Jennifer Pett-Ridge1, Peter Weber1, Erin Nuccio1, Ali Navid1, Steven Blazewicz1, Michael Thelen1, Patrik D'Haeseleer1, Carol Zhou1, Eoin Brodie2, Trent Northen2, Mary Lipton3, Todd Lane4, Alfred Spormann5, Paul Zimba6, Sabeeha Merchant7, Christine Hawkes8, Kelly Craven9, Cullen Buie10 
  • Participating Institutions:  1Lawrence Livermore National Laboratory, 2Lawrence Berkeley National Laboratory, 3Pacific Northwest National Laboratory, 4Sandia National Laboratory, 5Stanford University, 6Texas A&M University-Corpus Christi, 7University of California, Los Angeles, 8University of Texas, Austin, 9Samuel R. Noble Foundation, 10Massachusetts Institute of Technology
  • Website:
  • KBase App: Adapting tools and functionalities in KBase to support a systems biology approach to understanding interactions in bioenergy-relevant microbial communities

The LLNL Biofuels SFA is focused on the community systems biology of microbial consortia that are closely associated with bioenergy-relevant plants and algae, with the ultimate goal of developing predictive models. Photosynthetic algal and plant systems have the unrivaled advantage of converting solar energy and CO2 into useful organic molecules. Their growth and efficiency are largely shaped and assisted by their surrounding ‘microbiome’—the groups of microorganisms that dwell in and around plants and algae and live off photosynthate, exopolymers, or exudates. The biogeochemical outcomes of these interactions--how specific taxonomic combinations affect energy and nutrient cycling pathways and are shaped by various environmental stressors--are fundamental concerns in the fields of microbial ecology and bioenergy production. This SFA seeks to understand and predict ecological, biophysical, and biochemical dynamics of multi-taxa communities, as well as the metabolite fluxes that regulate trophic interactions. Research activities are focused on microscale interactions between bacteria and algae in the phycosphere (the surface of algal cells) and between soil bacteria, fungi and plant roots in the rhizosphere as model systems. Projects emphasize microbial ecology, organismal interactions, quantitative isotope tracing of elemental exchanges, and effects of environmental regulation, using techniques that exploit unique LLNL capabilities to measure the microscale impacts of single cells on system scale processes.

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