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

Fenghuan Yang ¹, Jie Zhang ¹, Huaying Zhang ², Guanghai Ji ³, Liexian Zeng ⁴, Yan Li ⁵, Chao Yu ¹, W G Dilantha Fernando ⁶, Wen Chen

Front Plant Sci. 2020 Jul 23;11:963. doi: 10.3389/fpls.2020.00963. eCollection 2020.

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.

See: https://pubmed.ncbi.nlm.nih.gov/32793250/

Figure 1: Compositional structure of the endophytic bacterial communities of rice leaves. (A) The hierarchical clustering of samples based on the relative abundance of dominant bacterial phyla; (B) The abundance of the Xanthomonas OTUs in BB-diseased and healthy leaves; (C) The relative abundance of the dominant bacterial genera recovered from BB-diseased or healthy leaves. AH-IH, healthy leaves of rice cultivars; AB-IB, BB leaves of rice cultivars used in this study.