Response of the Endophytic Microbiome in Cotinus coggygria Roots to Verticillium Wilt Infection

Verticillium wilt caused by <i>Verticillium dahliae</i> Kleb. is a lethal soil-borne fungal disease of <i>Cotinus coggygria</i>. The plant endophytic microbiome plays an important role in maintaining plant health and disease resistance, but it is unclear how the endophytic microbiome of <i>C. coggygria</i> roots varies in response to Verticillium wilt occurrence. In this study, the endophytic microbial diversity, community composition, dominant species, and co-occurrence network of <i>C. coggygria</i> under Verticillium wilt-affected and healthy conditions were assessed using Illumina sequencing. Compared with healthy plants, the bacterial alpha diversity indices of Verticillium wilt-affected plants decreased significantly, while the fungal alpha diversity indices showed obvious increases. The relative abundance of dominant taxa including Proteobacteria, Actinobacteriota, Ascomycota, and Basidiomycota at the phylum level, as well as Gammaproteobacteria, Thermoleophilia, Dothideomycetes, and Agaricomycetes at the class level, differed significantly between Verticillium wilt-affected and healthy plants. Co-occurrence networks revealed that the fungal network of Verticillium wilt-affected roots was denser with more negative interactions, which may be relevant to functional changes from reciprocity to competition in the microbial community, in response to <i>V. dahliae</i> infection. The results enhanced our understanding on the relationships between the endophytic microbiome and Verticillium wilt, which could provide information for the management of this disease in <i>C. coggygria</i>.