ROD1-controlled immune activation reshapes the rice phyllosphere microbiome

Abstract

The phyllosphere microbiome contributes to plant disease resistance, but how immune activation reshapes rice leaf-associated bacterial communities remains unclear. Here, we investigated the rice rod1 (resistance of rice to diseases 1) mutant, which exhibits spontaneous defense activation, using host transcriptome analysis and 16S rRNA profiling across two field sites. rod1 exhibited reduced bacterial alpha diversity, altered community composition, and co-occurrence networks with lower connectivity but stronger modularity. Although taxonomic responses differed between Hainan and Shanghai, predicted functions consistently shifted toward phenylpropanoid metabolism and reactive oxygen species (ROS) scavenging. Representative rod1-associated isolates showed strain-dependent responses to p-coumaric acid (CA) and H2O2, with CA partially alleviating H2O2-induced growth inhibition. Selected isolates and a synthetic community (SynCom) also suppressed Magnaporthe oryzae mycelial growth in vitro and reduced fungal colonization in rice plants. These findings suggest that ROD1-mediated immune homeostasis shapes the rice phyllosphere by coupling changes in defense status, the oxidative environment, and microbial functional potential.