Bio-organic fertilization is a widely used, eco-friendly, sustainable approach to increasing plant productivity in the agriculture and fruit industries. However, it remains unclear whether the promotion of fruit productivity is related to specific changes in microbial inoculants, the resident microbiome, and/or the physicochemical properties of rhizosphere soils.

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.

Ecosystem multifunctionality (EMF), a key metric reflecting soil health, has been proven to be positively influenced by organic amendments. Chinese herb residues (CHR), rich in bioactive compounds and with lower ecological risks, are regarded as a promising source for organic amendments. Therefore, we conducted a greenhouse experiment with four treatments: no fertilizer (CK), chemical fertilizer (CF), single application of CHR-OA (OA), and partially replacing chemical fertilizers with CHR-OA (OA-CF), aiming to explore the regulatory mechanism of CHR-OA addition to EMF. A total of 19 ecosystem functions, covering plant growth, pathogen suppression, soil physicochemical properties, and microbial diversity, were used to calculate EMF. The results showed that most of the above ecosystem functions were improved by adding CHR-OA, with the OA-CF possessing the highest EMF, followed by OA. Additionally, Lysobacter was enriched as a key genus. Further analysis revealed that Lysobacter drove EMF by influencing bacterial Simpson index, plant height, and root length, and this conclusion was confirmed in greenhouse verification experiments. Through this study, we have gained a clearer understanding of the prominent ecosystem functions provided by CHR-OA and the regulatory mechanism of EMF.

Carbohydrate-active enzyme (CAZyme) genes and their transcription factors (TFs) are crucial for the fermentation of lignocellulosic biomass to inhibit pathogen. However, the diversity of CAZyme genes and the complexity of TFs identification limit the efficient biovalorization of bio-resources. This study aimed to inhibit the pathogen Ralstonia solanacearum by fermenting two substrates (chrysanthemum and peanut stems) with Bacillus amyloliquefaciens, while employing multi-omics and machine learning to analyze key CAZyme genes as well as their TFs. The results showed that the water-soluble extracts (WSEs) from fermented chrysanthemum stem (days 6-7) exhibited strong antimicrobial activity. Glycosyl transferase (GT) and polysaccharide lyase (PL) gene sets were enriched significantly during chrysanthemum stem fermentation. Genes, encoding a UDP-glycosyltransferase (GT1) and a pectin lyase (PL1), were identified as key and correlated with the inhibition rate significantly. Through computational prediction, we further revealed the sigma factor RpoE as an indirect positive regulator of PL1 gene expression. Our study provides valuable insights into the identification of key CAZyme genes and the rapid discovery of their TFs, offering a foundation and promising direction for future optimization of fermentation technology.