Root development is maintained by specific bacteria-bacteria interactions within a complex microbiome

Plants grow within a complex web of species interacting with each other and with the plant via a wide repertoire of chemical signals. To model plant-microbe-microbe-environment interactions, we inoculated seedlings with a defined 185-member bacterial synthetic community (SynCom), and manipulated the abiotic environment to enable classification of the SynCom to modules of co-occurring strains. We deconstructed the SynCom based on these modules, identifying a single bacterial genus, Variovorax, which reverts phenotypic effects on root development induced by a wide diversity of bacterial strains and by the entire 185-member community. Variovorax use mechanisms related to auxin and ethylene manipulation to balance this ecologically realistic root community’s effects on root development. We demonstrate metabolic signal interference within a complex model community, defining Variovorax as determinants of bacteria-plant communication networks