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.

Automated summary

Interactions between plants and neighboring microbial species play a crucial role in shaping the structure and function of plant microbiota. This study explores the molecular basis of these interactions by colonizing Arabidopsis leaves with nine plant-associated bacteria and analyzing their cotranscriptomes. The findings reveal common and distinct cotranscriptome signatures among plant-commensal pairs and identify genes enriched in the genomes of plant-associated bacteria that may contribute to their adaptation in the host environment.