Untangling biological complexity to reveal drivers of root microbiome assembly

Plant microbiomes are assembled and modified through a complex milieu of biotic and abiotic factors. Despite dynamic and fluctuating contributing variables, specific host metabolites and immune responses are consistently identified as important mediators of microbial interactions. Mechanistic understanding of how these interactions combine to dictate microbiome establishment remains largely enigmatic. We aim to identify specific plant and microbial factors mediating plant-microbe and microbe-microbe interactions at the root interface. We use a range of experimental biotic complexities, from single strains to natural microbiomes, and host genetic mutants to gain both mechanistic and holistic understanding of how individual phenotypes scale-up to higher-order community dynamics. We combine characterized bacterial strains into synthetic communities to assess the impact of drought and plant-derived salicylic acid on microbiome establishment and maintenance in the model plant Arabidopsis thaliana. We find that individual bacterial strains have distinct phenotypes in the context of plant roots and these behaviors can be partially explained by salicylic acid biosynthesis. We also combine information from a large-scale metatranscriptomic dataset from natural poplar trees and experimental genetic manipulation assays in Arabidopsis seedlings to converge on a conserved role for transport of the plant metabolite myo-inositol in mediating host-microbe interactions. Our data suggests host control of this compound and resulting microbial behavior are important mechanisms at play surrounding the host metabolite myo-inositol. Together, these studies reveal that two common root exudates play distinct roles in root microbiome assembly and subsequently influence varying microbiome functioning and biodiversity across diverse plant hosts.