Persistence Control of Engineered Functions in Complex Soil Microbiomes

Science Focus Area: Pacific Northwest National Laboratory

  • Principal Investigator: Robert Egbert1
  • Laboratory Research Manager: Brian Thrall1
  • Co-Investigators:Janet Jansson1, Christer Jansson1, Jason McDermott1, Joshua Elmore1, Bill Nelson1, Ernesto Nakayasu1, Vivian Lin1, Ryan McClure1, Pubudu Handakumbura1, Adam Deutschbauer2, Adam Guss3, Carrie Harwood4, Devin Coleman-Derr5, Enoch Yeung6
  • Participating Institutions: 1Pacific Northwest National Laboratory, 2Lawrence Berkeley National Laboratory, 3Oak Ridge National Laboratory, 4University of Washington, 5University of California– Berkeley, 6University of California Santa–Barbara
  • KBase Collaboration: Improved protein annotation using machine learning, multi-omics data integration, and structural prediction
biosystems design diagram

Biosystems Design. Persistence control engineering for biomass cropping systems requires a fundamental understanding of how genetics determine cellular function at the single organism, microbial community, and ecosystem scales. Led by Pacific Northwest National Laboratory (PNNL), the Persistence Control SFA is exploring how environmental niches can be sculpted using the mechanisms of genome reduction and metabolic addiction to drive secure rhizosphere community design for robust biomass cropping in challenging environments. [Courtesy PNNL]


The potential to employ genome-scale engineering to design synthetic rhizosphere microbiomes offers tremendous opportunity to sustainably generate highly productive and stress-tolerant biomass cropping systems. A critical obstacle to realizing this vision is understanding the fundamental principles that drive the performance and persistence of engineered functions in rhizosphere microbiomes under challenging conditions, notably those characterized by nutrient limitation and drought. Furthermore, predictive tools are needed to assess the risks associated with the deployment or unintended release of engineered microbes in plant ecosystems. Recent advances in functional genomics, genome editing, plant microbiome science, chemical biology, and machine learning provide an opportunity to meet these challenges through the discovery and validation of genetic elements that control microbiome function in rhizosphere environments.

The long-term vision of the Persistence Control Science Focus Area (SFA) at Pacific Northwest National Laboratory (PNNL) is to develop a fundamental understanding of the factors governing the persistence of engineered microbial functions in rhizosphere environments. The SFA will use this understanding to establish design principles to control the environmental niche of native rhizosphere bacteria through genome reduction and metabolic addiction to plant root exudates. The team’s model ecosystem is the rhizosphere of the bioenergy crop sorghum. Researchers are identifying gene targets that confer conditional persistence phenotypes by developing genetic tools for phylogenetically diverse sorghum rhizosphere bacteria; investigating the contribution of genetic, metabolic, and spatial factors to the escape of persistence control; and establishing methodologies to design and implement bacterial metabolic addictions that enforce obligate host-microbiome symbioses.

Research directly addresses objectives of the Secure Biosystems Design activity within the Genomic Science Program by (1) understanding the genetic determinants of cellular behavior in complex soil-plant biosystems, (2) developing data-driven genome-editing approaches to control the fitness of engineered organisms outside the laboratory, and (3) establishing innovative biosystems design approaches to increase the resilience of plant ecosystems through persistence control engineering of rhizosphere communities.