Phenotypic Response of the Soil Microbiome to Environmental Perturbations

Science Focus Area: Pacific Northwest National Laboratory

  • Principal Investigators: Kirsten S. Hofmockel1
  • Laboratory Research Manager: Brian Thrall1
  • Co-Investigators: Janet K. Jansson1, Ryan McClure1, Christopher Anderton1, Mary Lipton1, Tom Metz1, Michelle Davison1, Jason McDermott1, Nikos Kyrpides2, Ari Jumpponen3, Hyun-Seob Song4, Steven Fransen5
  • Unfunded Collaborators: Leslie Shor6
  • Participating Institutions: 1Pacific Northwest National Laboratory, 2U.S. Department of Energy Joint Genome Institute, 3Kansas State University, 4University of Nebraska–Lincoln, 5Washington State University, 6University of Connecticut
  • Project Website:
  • Overview Brochure: Download PDF
  • KBase Collaboration: Metabolic network reconstruction of microorganisms and communities


Soil Microbiome.

Soil Microbiome. The Soil Microbiome SFA, led by Pacific Northwest National Laboratory, studies how changes in soil moisture influence the soil microbiome and metaphenome. The SFA team uses a variety of genome-enabled modeling approaches to determine reaction networks, interaction networks, and interkingdom interactions. [Reused under a Creative Commons license (CC BY 4.0) from Jansson, J. K. and K. S Hofmockel. 2018. “The Soil Microbiome — From Metagenomics to Metaphenomics,” Current Opinion in Microbiology 43, 162–68. DOI: 10.1016/j.mib.2018.01.013.]

Soil is a diverse ecosystem with microbial “dark matter” that remains to be discovered. Predicting microbial interactions in this complex system represents both an exciting frontier and a grand challenge, with implications for the productivity and fertility of the nation’s soils. The Pacific Northwest National Laboratory’s (PNNL) Soil Microbiome Science Focus Area (SFA) aims to develop a systems-level understanding of soil microbial and phenotypic responses to changing moisture through a tractable, spatially explicit examination of the molecular and ecological interactions occurring within and between microbial consortia in soil. PNNL is performing integrated experiments to confront both the scaling challenges and interkingdom interactions that regulate networks of biochemical reactions. High-resolution experimental data are being used to parameterize agent-based models. Genome-enabled predictions of spatially explicit microbial interactions are being validated in reduced-complexity microbial consortia using advanced chemical imaging and fluorescent probes unique to PNNL. Discoveries and outcomes from controlled experiments are being tested and validated in an irrigation field trial planted with tall wheatgrass, a bioenergy feedstock. Knowledge gained from this SFA is providing fundamental understanding of how enzymes, metabolites, and members of soil microbial consortia interact to decompose organic carbon. By revealing the genetic and genomic targets that regulate soil microbiome phenotypes, this research is enabling better predictions of how soil microbial reaction networks and related functions shift in response to changing resource availability and moisture regimes.