Grant: Discovery Grants Program - Individual

Plant root-associated microbial communities (the rhizosphere microbiome) provide their plant hosts with diverse benefits including nutrient uptake and pathogen protection. In order to survive in the presence of a host, microbes must evade or suppress host immunity. At the same time, in order to avoid being overrun by microbes, the plant immune system must minimize the growth of non-adapted microbes. A major goal of my lab's research is to understand how the plant immune system excludes some microbes while allowing proliferation of beneficial microbiota. To identify bacterial genes required to suppress plant immunity and plant genes required to shape the rhizosphere microbiome, we use Pseudomonas fluorescens and the model plant Arabidopsis thaliana as a tractable rhizosphere microbiome model. Arabidopsis-P. fluorescens provides a system with molecular, genetic and biochemical tools to answer basic questions in host-microbiome interactions. This project proposal includes three complementary aims to study the bacterial and plant mechanisms that ultimately affect plant microbiome immune homeostasis. Objective 1: Determine how bacterial acidification of the rhizosphere suppresses plant immunity Pre-treatment of Arabidopsis roots with P. fluorescens will suppress a defense response upon subsequent challenge with a microbe-associated molecular pattern (MAMP) such as bacterial flagellin. Through forward genetic screens, we found that multiple bacterial acidification mechanisms work to suppress plant immunity. This objective describes characterization of the mechanisms by which altering the rhizosphere pH suppresses plant immunity. Objective 2: Determine how negative regulators of Salicylic Acid signaling shape the rhizosphere microbiome The plant hormone salicylic acid (SA) plays a central role in plant immunity, and also affects plant metabolism and development. Positive regulators of SA signaling have been shown to shape the rhizosphere microbiome structure and function. This objective is focused on characterizing the role of negative regulators of SA signaling in shaping plant metabolism and immune homeostasis in plant-microbiome interactions.  Objective 3: Characterize the role of HSM genes in the rhizosphere microbiome To identify plant genes that regulate the rhizosphere microbiome, we rescreened a collection of plant "hsm" mutants, which were originally identified as mutants impaired in hormone-immunity crosstalk. We identified 6 hsm mutants that support altered levels of P. fluorescens under gnotobiotic conditions. This aim focuses on characterizing the role of hsm genes in shaping the rhizosphere microbiome. These three complementary objectives will help determine how microbiota and their host strike a balance in immune homeostasis that ultimately results in establishment, tolerance and maintenance of a microbiome.