Functional genomics of the plant microbiome

Plant root-associated microbial communities (“rhizosphere microbiome”) influence plant growth and defense. Closely-related bacteria can have dramatically different effects on plant health and range from pathogenic to mutualistic. Using Pseudomonas fluorescens and related species and Arabidopsis as a tractable rhizosphere microbiome model, we are using a combination of comparative genomics and high-throughput phenotyping to identify the genomic basis of microbiome function. We have used these approaches to identify the bacterial genomic basis of opportunistic pathogenesis as well as modulation of plant immunity. Collectively, this work has revealed mechanisms by which members of the microbiota affect the health of their hosts.