A Gnotobiotic Rice Pathosystem Reveals How the Microbiome Suppresses Rice Blast Disease

Abstract

Rice blast disease caused by the hemibiotrophic fungal pathogen Magnaporthe oryzae poses a major threat to global rice production, creating an urgent need for sustainable disease management strategies. Because plant-associated microbiomes can contribute to pathogen suppression and host defense, their role in rice blast resistance is of considerable interest. However, interactions among M. oryzae, rice, and the rice microbiome remain poorly understood. Using a gnotobiotic rice pathosystem, we investigated how microbiome colonization influences host responses to infection and how bacterial community structure changes following pathogen challenge. Microbiome colonization significantly reduced blast disease severity, while differential abundance analyses identified infection-associated shifts in bacterial community composition, including enrichment of Brevibacillus-associated taxa. Functional characterization of cultured endophytes revealed plant growth-promoting traits and antagonistic activity against M. oryzae. Two synthetic communities assembled from healthy- and infected-derived isolates significantly reduced disease severity, demonstrating that disease suppression can be recapitulated using simplified microbial communities. Interestingly, axenically grown plants exhibited elevated basal expression of multiple defense-associated genes but greater disease severity and reduced chitin-induced ROS production compared with holoxenic plants. In contrast, microbiome-colonized plants displayed enhanced ROS responsiveness and reduced disease, suggesting that the rice microbiome promotes a more effective and regulated immune state rather than simply increasing defense activation. Together, these findings advance our understanding of rice-microbiome-M. oryzae interactions and establish a tractable experimental platform for mechanistic studies of microbiome-mediated disease suppression.