Mechanisms of microbiota detente with the plant immune system

Plants grow in soil that is teeming with microbes. Because plants provide habitat and food, in the form of secreted sugars and amino acids, many soil bacteria evolved to colonize the plant root and shoot systems. Some plant-microbe interactions can lead to plant disease if the microbes can damage plant cells and tissue. However, other plant-microbe interactions can be neutral or even beneficial to the plant. The sum of the microbes that colonize and interact with plants is called the plant microbiome. This project addresses three important questions in plant microbiome research. First, how does common beneficial bacterium called Sphingomonas swim to and attach to the plant and how does this early colonization step evade activation of the plant immune system? Second, how do beneficial bacteria turn off the plant immune system? And third, how do beneficial microbes change their gene expression when they encounter a plant. This proposal includes training opportunities for undergraduate students and interfaces with the UNC Morehead Science Center to educate the public about the useful bacteria that may someday replace environmentally unfriendly diseases to combat plant disease and increase yields.This research will lead to understanding of how commensal microbes influence plant performance. This research uses collections of sequenced microbes that provide plant growth advantages or suppress or enhance immune responses; many are amenable to mechanistic studies during host interactions. This research will lead to the definition of single isolates or reduced complexity consortia of sequenced microbes that influence plant performance. These can be robustly deployed in re-colonization synthetic community microcosm experiments to define and iteratively test models of the principles that drive community formation and resiliency. The researchers use collections of sequenced microbes that provide plant growth advantages or suppress or enhance immune responses; many taxa are amenable to mechanistic studies during interactions with the host. The work moves beyond description of plant-associated microbial communities to generate and test mechanistic hypotheses. The aims are to: address the hypothesis that a core plant microbiota taxon uses flagellar switching during plant colonization and that this flagellar switching is monitored by the host immune system; dissect the function of two host transcription factors in immune system-microbiota détente; develop and deploy single-cell RNAseq and spatial transcriptomics for host and microbe in the context of defined synthetic bacterial communities to understand how host-commensal interactions shape microbe-microbe interactions on the plant. The research will contribute to predictive interventions that will modulate endogenous plant immune system function, increase plant health and productivity and facilitate carbon sequestration through the rational utilization of probiotic microbes and mixtures of microbes tuned to function in particular soils and local environments.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.