Functions of T3SS-containing Proteobacteria and plant innate immunity in root microbiota establishment

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Natural soil harbors a rich diversity of microbes and a subset of these serve as seeding source for colonization of healthy plant roots. Although plants are known to influence the growth of root-associated bacteria through the process of root exudation, host mechanism(s) contributing to the establishment of a taxonomically structured bacterial assemblage, called the root microbiota, remain ill-defined. Plants are known to limit pathogen invasion by the activation of immune responses upon the detection of microbe-derived molecules by two classes of immune receptors that reside on the cell surface and inside plant cells. However, how plants with an intact immune system tolerate intimate colonization by root microbiota members is unknown. The Pseudomonadaceae family represents a taxonomic lineage of the core root microbiota. Our pilot experiments demonstrated a role of immune responses initiated by Arabidopsis thaliana cell surface-resident pattern recognition receptors (PRRs) in restricting the colonization of Pseudomonas commensals inside roots. By generating mutants of the Type III secretion system (T3SS) of these Pseudomonas commensals we have obtained preliminary evidence that the T3SS is needed for efficient root endosphere colonization. We hypothesize that some root microbiota members attenuate plant immunity and serve as keystone species that influence the structure of the root microbiota. We propose to use microbiota reconstitution experiments with increasingly complex synthetic bacterial communities to elucidate the role of the plant immune system in root microbiota establishment. In addition, we will conduct forward genetic experiments with partially immunocompromised A. thaliana to identify dysbiosis mutants of the root microbiota. Thus, this project will test whether the innate immune system of plants is needed for the establishment and maintenance of microbial homeostasis in healthy plants.