Development of biocontrol agents for cotton verticillium wilt using microbiome analysis

Verticillium wilt is one of the most devastating diseases of cotton. However, effective biocontrol strains are still lacking. The aim of this study is to inform the selection of effective biocontrol strains by comparing the microbiomes of healthy and diseased cotton plants. Our results revealed that Verticillium dahliae V991 (V991) is the causal agent of cotton Verticillium wilt, significantly altering the bacterial and fungal communities in the roots, rhizosphere and bulk soil. Compared to the diseased cotton in the V991 inoculation group (D), the healthy cotton in the V991 inoculation group (H) and the control cotton in the V991 non-inoculation group (C) both suppressed Verticillium and Fusarium and enriched taxa of Bacilli , Clostridia , Archacosporales , Glomerales , unclassified Basidiomycota and unclassified Glomeromycota in the roots, both enriched Burkholderiales in the rhizosphere soil, both enriched Archaeosporales and Verrucomicrobiota in the bulk soil. A total of 20 strains were screened for antagonism to V991, most of them were isolated from the roots of the C group. Bacillus amyloliquefaciens M9 (BM), which was screened from the rhizosphere soil, exhibited the strongest antifungal activity, whereas Bacillus cereus R19 (BR), which was screened from the root, exhibited weaker antifungal activity. Pot experiments showed that the application of BR and BM (10 ⁹ CFU/mL) reduced the disease incidence by 44.44% and 33.33%, respectively, compared to the control. Field experiments showed that BR reduced the disease incidence by 88.46%, while BM reduced it by 50.01%. These results demonstrate the effectiveness of comparative microbiome analysis in guiding the selection of highly effective biocontrol strains.