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

Abstract

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 by Xanthomonas oryzae pv. 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. Khuskia spp. and Leptosphaerulina spp.), while healthy rice leaves were found to be significantly more abundant with plant pathogens or mycotoxin-producing fungi (e.g. Fusarium, Magnaporthe, and Aspergillus). The endophytic bacterial communities of BB-diseased leaves were significantly enriched with Pantoea, Pseudomonas, and Curtobacterium, strains. Pantoea sp. isolates from BB leaves are identified as promising candidates for the biocontrol of BB for their ability to inhibit in vitro growth of Xoo, 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. Pantoea sp. isolates, may play important roles in suppressing the development of BB disease in rice.

The microbiota of the grapevine holobiont: A key component of plant health

“…Note, however, that the microbial shift could either be the direct cause of the decline or the consequence of the impact of another stress (with an indirect cause and effect relationship). This hypothesis was confirmed by studies mainly carried out on annual plants [152] , [153] , [154] as well as on some perennial plants too (shifts in the microbiota linked to horse chestnut bleeding canker disease in [155] , to olive knot disease in [156] , to huanglongbing in citrus in [157] or to acute oak decline in [158] ).…”

Plant–Microbiome Crosstalk: Dawning from Composition and Assembly of Microbial Community to Improvement of Disease Resilience in Plants

“…For example, invasion of Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of rice bacterial blight, negatively regulated the endophytic microbial diversity of rice plants by reducing alpha-diversity of the fungal communities, Xoo infection helped rice plants to acquire disease combating beneficial microbes that subsequently elicited the disease-suppressive mechanisms in the plants [38]. However, the composition, interactions, and functions of endophytic bacterial communities in protecting plants from pathogen attack under adverse environmental conditions remain unclear.…”

Endophytic Fungi: Biological Control and Induced Resistance to Phytopathogens and Abiotic Stresses

“…Finally, perspectives are presented to better understand how the endophytic fungi area should evolve in the coming years. Although endophytic bacteria can also act to protect plants against biotic [ 25 , 26 , 27 ] and abiotic stresses, this is not the focus of this review.…”