An Analytical Technology Platform to Identify Symbiotic Interactions Between PGPR and Root Microbiome Members from Biofuel Feedstocks

The overall goal of this STTR proposal is to establish a commercial microwell technology for high-throughput screening and characterization of interactions that are critical to plant growth promoting rhizobacteria (PGPR) survival and function. PGPR can be used to improve crop stress tolerance by enhancing root function; providing nutrient uptake, nitrogen fixation, hormone regulation, and suppression of soil-borne pathogens. Treating crops with PGPR is a viable approach for economical and sustainable plant production. However, a major bottleneck to PGPR commercialization comes from poor survival and performance of PGPR strains when used in existing formulations. An improved understanding of critical PGPR interactions with native rhizosphere microbiome members will inform the development of more consistent and effective PGPR formulations. The technology platform consists of a microwell array system that forms 104 - 105 unique combinations between a fluorescently-modified test species and a defined collection of root microbiome members isolated from plant rhizosphere, then screens each well for survival and growth of the test species. Cellular material in wells that show symbiotic or antagonistic interactions with the test species is removed for genomic analysis to identify the members influencing the test species function. The goal of the Phase I proposal is to provide the existing microwell technology with new capabilities that are key to its commercial pathway. Objective 1 will adapt the technology towards screening interactions of known PGPR species in Populus rhizosphere networks. Objective 2 will develop a user-friendly, highly-automated image analysis tool that can rapidly quantify large data sets generated by the platform to identify wells containing important PGPR interactions. The software accessory is expected to dramatically enhance the utility of the existing microwell tool, moving it towards a marketable product. The project will also leverage a well-established collaboration with colleagues working in the DOE-funded Plant Microbe Interfaces Project at Oak Ridge National Laboratory to meet these objectives.