Natural variation in Arabidopsis thaliana root responses to microbiota-derived Pseudomonas strains

Plant roots are consistently colonized by specific microbial taxa in nature, but little is known about how plants perceive and respond to these core microbiota members at a molecular level. To identify genetic factors involved in plant interactions with the microbiota, we leveraged natural variation in Arabidopsis thaliana root responses to microbiota-derived Pseudomonas isolates. A. thaliana accession Van-0 shows root system architecture (RSA) changes when grown with the majority of microbiota-derived Pseudomonas isolates. The RSA changes mediated by Pseudomonas are maintained in a bacterial community context. By contrast, many of these isolates do not trigger RSA changes in accession Col-0. Pseudomonas R569 also triggers strong transcriptional changes in Van-0 roots, while the response in Col-0 is comparatively minor. Through a forward genetic screen, we identified a gene in R569 that is required for the bacterial activity. Additionally, we identified a plant quantitative trait locus (QTL) associated with the RSA changes. Genetically, the QTL appears to contain multiple genes involved in the root responses to R569. We have identified one of these genes, EXO7E2, which is required for the root responses in Van-0, and are currently validating additional candidate genes. Taken together, we have uncovered a signalling pathway involving genetic factors in both a plant host and a microbiota member, linking microbiota functioning with plant growth.