Persistence Control SFA

Understanding the genetic determinants of environmental persistence, from microbe to community to ecosystem.

The Persistence Control of Engineered Functions in Complex Soil Microbiomes Science Focus Area (PerCon SFA), led by Dr. Robert Egbert at Pacific Northwest National Laboratory (PNNL), seeks to understand plant-microbiome interactions in bioenergy crops to establish plant-growth-promoting microbiomes within the rhizosphere. This vision requires uncovering exudate catabolism pathways from plant roots, eliminating genes that support fitness in bulk soil environments without decreasing rhizosphere fitness, and engineering rhizosphere niche occupation traits in phylogenetically distant bacteria. These efforts aim to increase our understanding of plant-microbe interactions and to extend high-throughput systems and synthetic biology tools to non-model microbes.

Collaborative Development Object

Improved protein annotation using machine learning, multi-omics data integration, and structural prediction

• Annotate with Snekmer Apply: Recodes, kmerizes (short protein sequences), and vectorizes curated protein sequences for machine learning training set(s) that represent targeted functional annotation profiles or to generate de novo clusters of protein families. (Released)
  • Demo Narrative in KBase

Additional Information

Meet the Members

SFA Manager: Tim Scheibe¹
SFA Principal Investigators: Robert Egbert¹
KBase Contacts: Chris Henry^2,3, Janaka Edirisinghe^2,3
Lead Developers: Jeremy Jacobson¹
Project Team Leads: William Nelson¹, Jason McDermott¹

Affiliations: ¹Pacific Northwest National Laboratory, ²Argonne National Laboratory, ³KBase

Resources

• PerCon SFA GitHub Repository
• Peptide Fingerprinting Predicts Function using Protein Annotation Tool – Research Highlight