Natural antimicrobial compounds (NACs) in the plant stem are crucial for replacing conventional synthetic pesticides in the control of soil-borne diseases, and microbial fermentation can enhance their concentration and bioactivity. In this study, the stems of 10 plant species were collected for fermentation by probiotic bacteria Bacillus amyloliquefaciens T-5 to identify the most effective plant resource for controlling tomato bacterial wilt disease and discover key NACs. Chrysanthemum stem was identified as an optimal fermentation substrate, as its water-soluble extracts (WSEs) significantly inhibited the growth of pathogenic Ralstonia solanacearum and effectively alleviated tomato wilt under greenhouse conditions. Key metabolites, primarily phenolic acids including 2-hydroxy-3-phenylpropanoic acid (PLA), 3-(4-hydroxyphenyl)-propionic acid (HPPA), and mandelic acid (MA), were determined by metabolomics, all of which significantly inhibited the growth of R. solanacearum at a concentration of 0.2 mM, with only HPPA effectively controlling tomato wilt. Thus, fermented chrysanthemum stem contains NACs that are effective against bacterial wilt, providing a green option for controlling soil-borne diseases.

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