A systems biology approach to interactions and resource allocation in bioenergy-relevant microbial communities

The LLNL Biofuels Scientific Focus Area (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.

We seek to understand and predict ecological, biophysical, and biochemical dynamics of multi-taxa communities, as well as the metabolite fluxes that regulate trophic interactions. In our research, we focus 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. Our approach emphasizes 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.

News Highlights

May 28, 2021

Functional annotation tools webinar

SFA team members presented new annotation tools at KBase webinar

SFA team members Patrik D’haeseleer and Jeff Kimbrel presented the new annotation tools they developed for metabolic modeling at a KBase webinar.

ISME 2020 Award

Publication shortlisted for The ISME Journal 2020 Best Paper Award

A publication from 2020 led by SFA team members Erin Nuccio and Jennifer Pett-Ridge was shortlisted for the best paper of the year for its “outstanding quality and impact.”

Bacteria from soil

SFA team member interviewed on the JGI Podcast Genome Insider

In a recent episode of the JGI podcast Genome Insider, SFA team member Jennifer Pett-Ridge discussed DOE BER Genomic Sciences funded research.