Cultivar-dependent variation of the cotton rhizosphere and endosphere microbiome under field conditions. Cotton_rhiz_endo_wilt

Verticillium wilt caused by Verticillium dahliae is a common soil-borne disease worldwide, affecting many economically important crop species. Soil microbes, particularly in the rhizosphere, and endophytes can influence plant disease development. We investigated rhizosphere microbiomes in relation to cotton cultivars with differential susceptibility to Verticillium wilt. Soil samples from nine cotton cultivars (three resistant and six highly susceptible) were assessed for the density of V. dahliae microsclerotia using a wet-sieving plating method; plants were assessed for disease development. We used amplicon sequencing to profile both bacterial and fungal communities in rhizosphere and endosphere. Unlike wilt severity, wilt inoculum density did not differ significantly among resistant and susceptible cultivars. Overall, there were no significant association of within-sample microbial (alpha) diversity indices with wilt susceptibility. In contrast, there were clear differences in the overall rhizosphere and endosphere microbial communities, particularly bacteria, between resistant and susceptible cultivars. Many rhizosphere and endosphere bacterial and fungal groups (OTUs) differed in their relative abundance between resistant and susceptible cultivars. These OTUs included groups from several well-known taxonomy groups with beneficial microbes, such as Bacillales, Pseudomonadales, Rhizobiales and Trichoderma, which were more abundant in the rhizosphere and/or endosphere of resistant cultivars. These findings suggested that specific rhizosphere and endosphere microbes may contribute to coton resistance to V. dahliae.