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

Science Focus Area: Lawrence Livermore National Laboratory

  • Principal Investigator: Rhona Stuart1
  • Co-Investigators: Xavier Mayali1, Ali Navid1, Erin Nuccio1, Jennifer Pett-Ridge1, Peter Weber1, Jeff Kimbrel1, Patrik D’Haeseleer1, Ty Samo1, Steven Blazewicz1, Eoin Brodie2, Trent Northen2, Todd Lane3, Sabeeha Merchant4, Christine Hawkes5, Cullen Buie6, Rene Boiteau7, Kelly Craven8
  • Participating Institutions:  1Lawrence Livermore National Laboratory, 2Lawrence Berkeley National Laboratory, 3Sandia National Laboratories, 4University of California–Berkeley, 5North Carolina State University, 6Massachusetts Institute of Technology, 7Oregon State University, 8Samuel R. Noble Foundation
  • Project Website: bio-sfa.llnl.gov
  • KBase Collaboration: Tools and functionality to support a systems biology approach to understanding interactions in bioenergy-relevant microbial communities
diagram: Microbe-crop interactions

Microbe-crop interactions are explored using advanced imaging approaches such as nanoscale imaging mass spectrometry paired with stable isotope tracing (called nanometer-scale stable isotope probing or NanoSIP, with example images shown in the center circles). [Courtesy LLNL; NanoSIP portion of the image reprinted by permission from Nuccio et al, 2013. “An arbuscular mycorrhizal fungus significantly modifies the soil bacterial community and nitrogen cycling during litter decomposition,” Environmental Microbiology 15(6), 1870–1881. DOI: 10.1111/1462-2920. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.]


This Science Focus Area (SFA) examines the community systems biology of microbial consortia closely associated with bioenergy-relevant plants and algae, with the ultimate goal of developing predictive models to understand how these systems will respond to external stimuli. Photosynthetic algal and plant systems are unrivaled in their ability to convert solar energy and carbon dioxide (CO2) into useful organic molecules. The growth and photosynthetic efficiency of plants and algae are largely shaped and assisted by the microbial communities (heterotrophic symbionts) that dwell in and around them and are sustained by their primary productivity. SFA research aims to understand phototroph-symbiont interactions that shape biomass productivity, crop robustness, the balance of resource fluxes (carbon, nutrients, water), and the functionality of the surrounding microbiome. The project’s overarching hypothesis is that different heterotrophic symbionts not only have differential effects on host productivity but can also change the entire system’s resource economy—a critical metric for sustainable bioenergy cultivation. Research focuses on interactions in two model systems: (1) bacteria and algae in the phycosphere (the surface of algal cells) and (2) soil bacteria, fungi, and plant roots in the rhizosphere (the soil surrounding plant roots) and endosphere (all of a plant’s endophytes). Of particular interest is understanding how microscale interactions affect larger-scale parameters such as plant robustness and sustainability. Consequently, the SFA’s approach encompasses single-cell measurements using, for example, quantitative isotope tracing of elemental exchanges between members of the model systems, as well as system-scale omics measurements. The focus is on two research areas: advanced computational modeling to integrate results and develop refined hypotheses, and new methods development to push the envelope of what can be measured and modeled at the single-cell level and how those results can be scaled.