NADPH oxidase RBOHD is required for microbiota homeostasis in leaves

The plant microbiota consists of a multitude of microorganisms that affect plant health and fitness. However, it is currently unclear how the plant shapes its leaf microbiota and what role the plant immune system plays in this process. Here, we tested Arabidopsis thaliana mutants with defects in different parts of the immune system for an altered bacterial community assembly using a gnotobiotic system. While higher order mutants in receptors that recognize microbial features and in defense hormone signaling showed significant microbial community alterations, the absence of NADPH oxidase RBOHD caused the most remarkable change in the composition of the microbiota. The rbohD knockout resulted in an enrichment of specific bacteria. Among these, we identified opportunistic pathogens that colonized wild-type plants asymptomatically but caused disease in rbohD plants. Strain dropout experiments revealed that the lack of RBOHD unlocks the pathogenicity of individual microbiota members driving dysbiosis in rbohD plants. For full protection, healthy plants require both a functional immune system and a microbial community. Our results show that the NADPH oxidase RBOHD is essential for microbiota homeostasis and emphasizes the importance of the plant immune system in controlling the leaf microbiota.