Soil Microbiome SFA

A systems-level approach to understanding  microbial response to changing soil conditions

The Phenotypic Response of the Soil Microbiome to Environmental Perturbations (a.k.a. Soil Microbiome) Science Focus Area, led by Dr. Kirsten Hofmockel at Pacific Northwest National Laboratory (PNNL) uses cross-scale empirical and modeling experiments to identify phenotypic elements underpinning community metabolism, metaphenomes expressed under drought, and the implications for carbon use efficiency.

Collaborative Development Projects

Omics-enabled global gapfilling (OMEGGA) for phenotype-consistent metabolic network reconstruction of microorganisms and communities

OMEGGA offers a new concept of gapfilling (i.e., adding additional reactions to draft metabolic networks) method to improve model predictions by identifying biologically relevant and optimal gapfilling solutions in a computationally efficient way through simultaneous integration of complementary annotation pipelines, diverse ‘omics’ data, and multiple phenotype growth observations. OMEGGA will be tested using data from non-model organisms and consortia such as the Model Soil Consortia-2 (MSC-2) and associated isolated organisms developed by PNNL’s Soil Microbiome SFA. OMEGGA is incorporated in ModelSEED2 Build Prokaryotic and Improved Gapfill Metabolic Models in KBase, leveraging ongoing ModelSEEDpy development by the KBase team. (Released)

Additional Information

Meet the Members

SFA Principal Investigators: Kirsten S. Hofmockel1
KBase Contact: Chris Henry2,3, Janaka Edirisinghe2,3
Lead Developers: David ML Brown Jr1, Hyun-Seob Song4
Project Team Leads: Jason McDermott1, William Nelson1, Jeremy R Jacobson1, Aimee Kessell4, Hugh McCullough4
Affiliations: 1Pacific Northwest National Laboratory, 2Argonne National Laboratory, 3KBase, 4University of Nebraska-Lincoln