Sclerotinia spp. causing root rot of Panax ginseng in Northeast China and its potential biocontrol by Bacillus amyloliquefaciens FS6

Sclerotinia root rot is one of the most destructive soilborne diseases in ginseng (Asian ginseng) production regions in China. To identify the causal pathogens, 409 Sclerotinia isolates were recovered from ginseng plants at 11 plantations in Jilin, Heilongjiang, and Liaoning Provinces in China from 2018 to 2021. Based on morphological characteristics, sequence analyses of the internal transcribed spacer region and the beta-tubulin gene, as well as a phylogenetic analysis, the isolates were identified as S. nivalis ( n = 268), S. ginseng ( n = 114), and S. sclerotiorum ( n = 27). S. nivalis and S. sclerotiorum were found on fields growing Panax ginseng for the first time in China. Bacillus amyloliquefaciens FS6 (CGMCC 9538) exerted significant antifungal effects on all three Sclerotinia spp. by inhibiting in vitro mycelial growth by 85%, resulting in deformed and broken hyphae and dissolving sclerotia; on average, >73% inhibition (sclerotia formation) was achieved by FS6. Notably, the germination of sclerotia was inhibited for up to 20 days post-treatment in the fermentation broth (FB) of FS6 at concentrations of 4 × 10 6 to 4 × 10 8 CFU·mL −1 . Using those FS6 FB concentrations in vitro resulted in control efficacy of 43.48% to 100.00% against Sclerotinia root rot. Field trials in 2021 and 2022 showed that 10 7 to 10 8 CFU·mL −1 FS6 FB sprayed on ginseng leaves three times every 7 days exhibited a promising control effect against S. nivalis , with a control efficiency ranging from 53.00% to 73.51% 15 days after the third application. This study clarified that Sclerotinia root rot affecting Asian ginseng in Northeast China is caused by three species of Sclerotinia , for which B. amyloliquefaciens FS6 is a promising biocontrol agent. IMPORTANCE Sclerotinia root rot typically causes substantial losses in ginseng yield. This study aims to identify the types of pathogens that cause ginseng sclerotinia rot and their distribution in various production areas. This study is the first to report S. nivalis as a dominant species causing sclerotinia root rot in Asian ginseng cultivated in China. The most effective method for the prevention and control of sclerotinia root rot is biological control. Our findings suggest that B. amyloliquefaciens FS6 could be a promising way to control sclerotinia disease prevalent in commercial ginseng plantations in China.