Dysbiosis of the rice leaf phyllomicrobiome induced by Magnaporthe oryzae infection: evidence from metabarcoding and microbiome imprinting.

Abstract

Rice blast, caused by Magnaporthe oryzae, remains a major constraint to global rice production, typically presenting as necrotic lesions on infected leaves. To investigate the bacterial communities associated with these lesions, we employed a novel "Microbiome Imprinting-Metabarcoding" approach, which generated comprehensive microbial datasets (203.34 Mb) from two blast-infected rice cultivars, aromatic Pusa Basmati 1 (PB1) and non-aromatic VL Dhan 85. Metabarcoding analysis revealed the consistent presence of several dominant bacterial genera, including Pantoea, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Pseudomonas, and Chryseobacterium, across both cultivars. Notably, bacterial diversity was reduced in blast lesions compared to healthy phylloplane tissues. Lesion samples comprised 28 genera (Shannon Diversity Index: 1.66; Chao1 richness: 326.86), whereas healthy leaves harbored 48 genera (Shannon Diversity Index: 1.98; Chao1 richness: 361.82). Linear discriminant effect size (LEfSe) analysis identified specific genera such as Bifidobacterium, Desemzia, Acidovorax, and Mucilaginibacter that were uniquely associated with the dysbiotic microbial communities in infected tissues. Core microbiome analysis further revealed ten genera shared between both cultivars, with Pantoea and Allorhizobium emerging as the most abundant. These findings offer new insights into the composition and dynamics of lesion-associated bacterial communities in rice blast and highlight potential microbial targets for the development of improved disease management strategies.