<i>Bacillus subtilis</i> ge28, a potential biocontrol agent for controlling rust rot in <i>Panax ginseng</i> caused by <i>Cylindrocarpon destructans</i>

<italic>Panax ginseng</italic> is a traditional herbal medicine used worldwide. Rust rot caused by <italic>Cylindrocarpon destructans</italic> infects the root of <italic>P. ginseng</italic> and usually results in severe yield losses and quality deterioration. Quality control of <italic>P. ginseng</italic> is crucial to ensure its medicinal value. However, the increasing application of chemical fungicides for controlling severe epidemics of diseases including rust rot in ginseng-producing regions every year has led to significant environmental pollution, fungicide residues in harvested ginseng, and an increased risk of phytopathogen resistance. In this study, an endophytic <italic>Bacillus subtillis</italic> strain, temporarily named ge28, which has shown strong antagonistic activity to <italic>C. destructans</italic>, was isolated from healthy roots of <italic>P. ginseng</italic>. <italic>In vitro</italic> and pot experiments showed fermentation and the supernatant of ge28 exhibited significant biocontrol efficacy on rust rot. The whole genome of ge28 was 4,065,429 bp, containing 4,162 functional genes. Furthermore, three clusters of non-ribosomal peptide synthetase genes conferring the synthesis of lipopeptides, a group of secondary metabolites exhibiting antagonistic properties, including surfactin, fengycin, and bacillibactin, were identified through genome analysis. Surfactin and fengycin were confirmed to be present in the supernatant of ge28 by UPLC-ESI-QTOF-MS analysis. In conclusion, this study demonstrated that the ge28 strain possesses substantial biocontrol potential against the rust rot of <italic>P. ginseng</italic>, and its antagonistic mechanisms were preliminarily clarified. These results should accelerate the utilization of ge28 to enhance the yield and quality of <italic>P. ginseng</italic> through reduced fungicide application.