| Summary: | Ginger rhizome rot disease, caused by the pathogen <i>Bacillus</i><i>pumilus</i> GR8, could result in severe rot of ginger rhizomes and heavily threaten ginger production. In this study, we identified and characterized a new <i>Bacillus velezensis</i> strain, designated ATR2. Genome analysis revealed <i>B. velezensis</i> ATR2 harbored a series of genes closely related to promoting plant growth and triggering plant immunity. Meanwhile, ten gene clusters involved in the biosynthesis of various secondary metabolites (surfactin, bacillomycin, fengycin, bacillibactin, bacilysin, difficidin, macrolactin, bacillaene, plantazolicin, and amylocyclicin) and two clusters encoding a putative lipopeptide and a putative phosphonate which might be explored as novel bioactive compounds were also present in the ATR2 genome. Moreover, <i>B. velezensis</i> ATR2 showed excellent antagonistic activities against multiple plant pathogenic bacteria, plant pathogenic fungi, human pathogenic bacteria, and human pathogenic fungus. <i>B. velezensis</i> ATR2 was also efficacious in control of aphids. The antagonistic compound from <i>B. velezensis</i> ATR2 against <i>B.</i><i>pumilus</i> GR8 was purified and identified as bacillomycin D. In addition, <i>B. velezensis</i> ATR2 exhibited excellent biocontrol efficacy against ginger rhizome rot disease on ginger slices. These findings showed the potential of further applications of <i>B. velezensis</i> ATR2 as a biocontrol agent in agricultural diseases and pests management.
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