Dissecting the co-transcriptome landscape of plants and microbiota members

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 monocolonized Arabidopsis leaves with nine plant- associated bacteria from all major phyla of the plant microbiota and profiled co- transcriptomes of plants and bacteria. We detected both common and distinct co- transcriptome signatures among plant-commensal pairs. In planta responses of commensals were similar to those of a disarmed pathogen characterized by the suppression of genes involved in general metabolism in contrast to a virulent pathogen. We identified 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.