Cofunctioning of bacterial exometabolites drives root microbiota establishment

Soil-dwelling microbes are the principal inoculum for the root microbiota, but our under-standing of microbe-microbe interactions in microbiota establishment remains fragmen-tary. We tested 39,204 binary interbacterial interactions for inhibitory activities in vitro, allowing us to identify taxonomic signatures in bacterial inhibition profiles. Using genetic and metabolomic approaches, we identified the antimicrobial 2,4-diacetylphloroglucino l (DAPG) and the iron chelator pyoverdine as exometabolites whose combined func-tions explain most of the inhibitory activity of the strongly antagonistic Pseudomonas brassicacearum R401. Microbiota reconstitution with a core of Arabidopsis thaliana root commensals in the presence of wild -type or mutant strains revealed a root niche-specific cofunction of these exometabolites as root competence determinants and drivers of pre-dictable changes in the root-associated community. In natural environments, both the corresponding biosynthetic operons are enriched in roots, a pattern likely linked to their role as iron sinks, indicating that these cofunctioning exometabolites are adaptive traits contributing to pseudomonad pervasiveness throughout the root microbiota.