Dissecting the cotranscriptome landscape of plants and their microbiota

Interactions between plants and neighboring microbial species are fundamental elements that collectively determine the structure and function of the plant microbiota. However, the molecular basis of such interactions is poorly characterized. Here, we colonize Arabidopsis leaves with nine plant‐associated bacteria from all major phyla of the plant microbiota and profile cotranscriptomes of plants and bacteria six hours after inoculation. We detect both common and distinct cotranscriptome signatures among plant–commensal pairs. In planta responses of commensals are similar to those of a disarmed pathogen characterized by the suppression of genes involved in general metabolism in contrast to a virulent pathogen. We identify genes that are enriched in the genome of plant‐associated bacteria and induced in planta , which may be instrumental for bacterial adaptation to the host environment and niche separation. This study provides insights into how plants discriminate among bacterial strains and lays the foundation for in‐depth mechanistic dissection of plant–microbiota interactions. Synopsis The molecular basis of interactions between plants and commensal microbial species is poorly characterized. This study reveals common and distinct cotranscriptome signatures among plant–commensal bacteria pairs. The transcriptomes of commensals are distinct from that of a virulent pathogen and similar to that of a disarmed pathogen. Plant immunity appears to inhibit the metabolic activity of commensal bacteria. Commensal genes associated with plant colonization tend to be induced during interactions with plants. Transcriptome responses of plants and interacting microbiota members are incongruent. Graphical Abstract The molecular basis of interactions between plants and commensal microbial species is poorly characterized. This study reveals common and distinct cotranscriptome signatures among plant–commensal bacteria pairs.