Tobacco black shank disease significantly affects the composition and assembly of the genotype-associated microbial community in the rhizosphere

Tobacco black shank (TBS) disease is a soil-borne disease, and it is associated with the microbial community in the rhizosphere. However, the influence of tobacco genotype and TBS disease on the rhizospheric microbiome remains unknown. In this study, we investigated the severity of TBS disease, and characterized the rhizospheric bacterial and fungal community compositions of four tobacco varieties, including ZC208, YY87, YY85 and HD. The results showed that TBS disease drove the transformation of microorganisms from bacteria-dominated to fungi-dominated, and TBS disease increased the prevalence of beneficial microbiomes in the tobacco rhizosphere. Moreover, the influence of TBS disease on the rhizospheric microorganisms of resistant tobacco was lower than that on susceptible tobacco. Specifically, our findings suggested Taibaiella , Gemmatimonas , Rhodopirellula , Terrimonas and Lysobacter potential suppression roles of TBS disease, and Ensifer and Methanobacterium may play promoting roles in TBS disease progression. Our findings enhance the understanding of the microbial-mediated mechanism of TBS disease and provide novel insight for developing underlying microbial antagonists to manage soil-borne diseases. • The tobacco resistance to black shank disease in the same field were different from their genotypes. • Microbial composition and assembly in the rhizosphere are influenced by tobacco genotype and black shank disease. • The enrichment of beneficial microbiome in the rhizosphere of tobacco contributed to the suppression of black shank disease.