LAUSR

Significance Inhibitory exometabolites produced by individual root-derived bacteria have been widely studied in plant protection against soil-borne pathogens. However, the prevalence of exometabolite production in root-associated bacterial communities and their ecological relevance for root microbiota establishment remains elusive. We characterized exometabolite-mediated binary interactions between taxonomically diverse root- and soil-derived bacteria. Using genetic and metabolomics approaches, we identified the antimicrobial 2,4-diacetylphloroglucinol (DAPG) and the iron chelator pyoverdine, which together explain most of the inhibitory activity of the highly antagonistic root-associated Pseudomonas brassicacearum. Microbiota reconstitution experiments with a defined bacterial community revealed their cofunctioning as root competence determinants by specifically affecting root microbiota establishment. In natural environments, these exometabolites likely serve as adaptive traits contributing to pseudomonad pervasiveness throughout the root microbiota.