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 will be incorporated into the existing Gapfill Metabolic Model App in KBase, leveraging the ongoing ModelSEEDpy development by the KBase team. (in development)

Additional Information

Meet the Members

SFA Principal Investigators: Kirsten S. Hofmockel¹
KBase Contact: Chris Henry^2,3, Janaka Edirisinghe^2,3
Lead Developers: David ML Brown Jr¹, Hyun-Seob Song⁴
Project Team Leads: Jason McDermott¹, William Nelson¹, Firnaaz Ahamed⁴
Affiliations: ¹Pacific Northwest National Laboratory, ²Argonne National Laboratory, ³KBase, ⁴University of Nebraska-Lincoln

Resources

• PNNL Soil Microbiome SFA Project Website
• GitHub Repository – coming soon