Control of tobacco Fusarium root rot by Bacillus amyloliquefaciens HN11 and its influence on the rhizosphere microbial community

Abstract BACKGROUND Over the past few decades, Fusarium root rot has gradually become the most prevalent soil‐borne disease affecting tobacco plants across various regions in China. Nevertheless, only a limited number of effective biological control agents are currently available for agricultural application. This study was designed to investigate the control efficacy of Bacillus amyloliquefaciens HN11 against tobacco Fusarium root rot, as well as its influence on soil microbial diversity and community structure. RESULTS Bacillus amyloliquefaciens HN11 was screened as a strain with superior control capacity, reducing the incidence of tobacco root rot in the field by 58%. Analysis of tobacco rhizosphere microbial communities revealed that HN11 inhibits the proliferation of pathogens such as some species of Fusarium , and interacts with symbiotic fungi including species of Conocybe , Pyrenochaetopsis , Echria , and arbuscular mycorrhizal fungi, facilitating a shift in fungal trophic modes from saprotroph to symbiotroph. In addition, it was found that HN11 significantly diminished the carbon metabolic function of bacteria, reduced the relative abundance of the dominant genera Sphingomonas and Gemmatimonas , altered the composition of soil bacterial communities while maintaining their diversity. Tracing the strain with green fluorescent labeling (HN11‐sfGFP) demonstrated its capability to colonize tobacco roots. Furthermore, based on the knockout of the core genes of the biosynthetic gene cluster responsible for different secondary metabolites of HN11, we hypothesized that bacillibactin siderophores can inhibit pathogenic fungi. The lack of difficidin and bacillaene may also be important in the inhibition of pathogenic fungi. CONCLUSIONS The interaction between Bacillus amyloliquefaciens HN11 and microbial communities in tobacco soil contributes to disease prevention and plant growth enhancement. © 2025 Society of Chemical Industry.