Deciphering the Distinct Associations of Rhizospheric and Endospheric Microbiomes with Capsicum Plant Pathological Status.

Exploring endospheric and rhizospheric microbiomes and their associations can help us to understand the pathological status of capsicum (Capsicum annuum L.) for implementing appropriate management strategies. To elucidate the differences among plants with distinct pathological status in the communities and functions of the endospheric and rhizospheric microbiomes, the samples of healthy and diseased capsicum plants, along with their rhizosphere soils, were collected from a long-term cultivation field. The results indicated a higher bacterial richness in the healthy rhizosphere than in the diseased rhizosphere (P < 0.05), with rhizospheric bacterial diversity surpassing endospheric bacterial diversity. The community assemblies of both the endospheric and rhizospheric microbiomes were driven by a combination of stochastic and deterministic processes, with the stochastic processes playing a primary role. The majority of co-enriched taxa in the healthy endophyte and rhizosphere mainly belonged to bacterial Proteobacteria, Actinobacteria, and Firmicutes, as well as fungal Ascomycota. Most of the bacterial indicators, primarily Alphaproteobacteria and Actinobacteria, were enriched in the healthy rhizosphere, but not in the diseased rhizosphere. In addition, most of the fungal indicators were enriched in both the healthy and diseased endosphere. The diseased endophyte constituted a less complex and stable microbial community than the healthy endophyte, and meanwhile, the diseased rhizosphere exhibited a higher complexity but lower stability than the healthy rhizosphere. Notably, only a microbial function, namely biosynthesis of other secondary metabolites, was higher in the healthy endophytes than in the diseased endophyte. These findings indicated the distinct responses of rhizospheric and endospheric microbiomes to capsicum pathological status, and in particular, provided a new insight into leveraging soil and plant microbial resources to enhance agriculture production.