Bacterial Blight Induced Shifts in Endophytic Microbiome of Rice Leaves and the Enrichment of Specific Bacterial Strains With Pathogen Antagonism

The endophytic microbiome plays an important role in plant health and pathogenesis. However, little is known about its relationship with bacterial blight (BB) of rice caused byXanthomonas oryzaepv.oryzae(Xoo). The current study compared the community compositional structure of the endophytic microbiota in healthy and BB symptomatic leaves of rice through a metabarcoding approach, which revealed BB induced a decrease in the alpha-diversity of the fungal communities and an increase in the bacterial communities. BB-diseased rice leaves were enriched with saprophytic fungi that are capable of decomposing plant cell walls (e.g. Khuskiaspp. andLeptosphaerulinaspp.), while healthy rice leaves were found to be significantly more abundant with plant pathogens or mycotoxin-producing fungi (e.g. Fusarium,Magnaporthe, andAspergillus). The endophytic bacterial communities of BB-diseased leaves were significantly enriched withPantoea,Pseudomonas, andCurtobacterium, strains.Pantoeasp. isolates from BB leaves are identified as promising candidates for the biocontrol of BB for their ability to inhibitin vitrogrowth ofXoo, suppress the development of rice BB disease, and possess multiple PGP characteristics. Our study revealed BB-induced complexed changes in the endophytic fungal and bacterial communities of rice leaves and demonstrated that BB-associated enrichment of some endophytic bacterial taxa,e.g. Pantoeasp. isolates, may play important roles in suppressing the development of BB disease in rice.