Effects of root rot on microbial communities associated with goji berry (Lycium barbarum) in the Qaidam Basin, China

Goji berry (Lycium barbarum) is an important cash crop in China. However, in recent years its yield has been threatened by root rot caused by fungal pathogens. The infection significantly alters the structure and function of the plant microbiome. Thus, knowledge of the responses of the plant microbiome is a prerequisite for the bio-control of fungal pathogens. In the present study, the microbial communities of healthy, diseased, and wild goji berries were studied by amplicon sequencing. We found different responses of the microbial communities in different goji berry organs to the fungal pathogen. Moreover, higher microbial community abundance and diversity in the wild goji berry plant parts were observed, implying more complex and diverse ecological functions. At the same time, some potential beneficial bacteria were enriched in the diseased goji berry roots, consistent with the 'cry to help' hypothesis in plant roots. Moreover, intra-kingdom co-occurrence network analysis revealed higher positive correlations in bacterial than in fungal networks, implying an unstable bacterial network. In the inter-kingdom networks, most of the hubs (with high degree and closeness centrality values) were bacterial, indicating the important role of bacteria in the interaction under stress. In addition, of the 54 fungal strains isolated from the diseased goji berry roots, 42.6% were identified as Fusarium spp.; hence, it is a potential pathogen for subsequent research on the control of root rot in goji berries. The results of this study provide new perspectives on the biological control of root rot in goji berries.