Science Focus Area: Pacific Northwest National Laboratory
- Principal Investigator: Kirsten S. Hofmockel1
- Laboratory Research Manager: Jon Magnason1
- Co-Investigators: Nikos Kyrpides2, Hyun-Seob Song3, Steven Norberg4
- Participating Institutions: 1Pacific Northwest National Laboratory, 2U.S. Department of Energy Joint Genome Institute, 3University of Nebraska—Lincoln, 4Washington State University
- Project Website: pnnl.gov/projects/soil-microbiome
- Overview Brochure: Download PDF
- KBase Collaboration: Omics-enabled global gapfilling (OMEGGA) for phenotype-consistent metabolic network reconstruction of microorganisms and communities
SummaryThe soil microbiome is vital to ecological health and sustainability. It is involved in all major terrestrial nutrient cycles and thus influences plant production, atmospheric gas flux, carbon sequestration, and water quality. Through a complex web of inter- and intraspecies interactions, soil microbial metabolism supports soil organic matter transformations that are essential for sustaining life on Earth.
Pacific Northwest National Laboratory’s (PNNL) Soil Microbiome Science Focus Area (SFA) is using a cross-scale empirical and modeling approach to understand how enzymes, metabolites, and microbial consortia interact to control carbon cycling and sequestration. This approach will enable prediction of how these reaction networks and related functions shift in response to changing moisture regimes.
The SFA reconciles vast differences in scale and complexity by relating coarse metrics to molecular techniques and bridging organisms to metaphenomes to gain a predictive understanding of soil microbial communities and their function. Researchers use a genome-resolved, soil-derived, microbial consortium, paired with intermediate-scale modeling and empirical experiments, to identify biochemical and metabolic interactions that mediate soil microbiome functions identified under field conditions. Discoveries and outcomes from controlled experiments are being tested and validated in an irrigation field trial planted with tall wheatgrass, a potential bioenergy feedstock.
This SFA provides a comprehensive understanding of metabolic interactions and phenotypes from cellular to field scales. This understanding enables a mechanistic representation of microbial processes in multiscale models of integrated microbiome function. Results are providing much-needed information for discovering principles that translate from the lab to the field.
By providing a genomic understanding of the microbial metaphenomes measured throughout the rhizosphere and horizons of soil ecosystems, this work will help define biological paradigms that enable researchers to harness the soil microbiome’s functional capacity.