Persistence Control of Engineered Functions in Complex Soil Microbiomes

Science Focus Area: Pacific Northwest National Laboratory

• Principal Investigator: Robert Egbert¹
• Laboratory Research Manager: Vanessa Bailey¹
• Co-Investigators:Joshua Elmore¹, Pubudu Handakumbura¹, Jason McDermott¹, Bill Nelson¹, Young-Mo Kim¹, Ryan McClure¹, Jennifer Brophy², Adam Deutschbauer³, Adam Guss⁴, Carrie Harwood⁵, Devin Coleman-Derr⁶, Travis Wheeler⁷, Enoch Yeung⁸
• Participating Institutions:¹Pacific Northwest National Laboratory, ²Stanford University, ³Lawrence Berkeley National Laboratory, ⁴Oak Ridge National Laboratory, ⁵University of Washington, ⁶University of California– Berkeley, ⁷University of Arizona, ⁸University of California Santa–Barbara
• KBase Collaboration: Improved protein annotation using machine learning, multi-omics data integration, and structural prediction

Persistence Control in the Rhizosphere. Conceptually, persistence control engineering involves manipulating catabolic pathways to shift the environmental niche of a microbe. This SFA aims to increase the environmental persistence in the rhizosphere of sorghum (left) and to decrease persistence under scavenging environments, such as plant detritus and microbial necromass (right). Led by the Pacific Northwest National Laboratory (PNNL), the Persistence Control SFA team is investigating how genome edits to non-model bacteria isolated from sorghum specifically alters fitness under laboratory conditions, in the presence of other microbes from the sorghum rhizosphere, and in the rhizosphere using laboratory and field measurements. The establishment of persistence control engineering principles will advance the responsible deployment of engineered microbial systems in the environment. [Courtesy PNNL]

Summary

The responsible deployment of engineered microbial rhizosphere communities offers tremendous opportunity to sustainably generate productive and stress-tolerant biomass cropping systems. A critical obstacle to realizing this vision is understanding the fundamental principles that drive plant growth promotion and environmental persistence for engineered functions in the rhizosphere. Specifically, strategies to boost the environmental persistence and impact of engineered functions among complex rhizosphere microbial communities and restrict growth away from the plant have not been established. By establishing persistence control as an engineering discipline to manipulate environmental niches, the Science Focus Area (SFA) aims to develop programmable control of engineered microbes through genome engineering to promote colonization of a target plant’s rhizosphere but to diminish in bulk soil when the plant stops growing or microbes migrate away from the rhizosphere.

Persistence control engineering relies heavily on a fundamental understanding of genes that contribute to fitness in rhizosphere and bulk soil environments. For selected engineered non-model rhizosphere bacteria, the SFA integrates existing annotations of gene function and high-throughput functional genomics data to enforce persistence control by altering the bacteria’s environmental niche through the introduction and removal of critical catabolic pathways. Using the bioenergy crop sorghum as a model rhizosphere system, the Persistence Control SFA team is developing genome editing tools for non-model rhizosphere bacteria, computational tools to predict persistence phenotypes in a community environment, small synthetic microbial communities as a testbed for persistence control escape, and an experimental framework to conduct rhizosphere science at scales from the laboratory bench to the field.

These efforts to understand and control rhizosphere persistence will lead to more thorough annotation of genes that contribute to microbial metabolism in the rhizosphere.

2024 Abstracts