Rhizobium nepotum Z-21 induces systemic resistance in chili against Fusarium wilt: insights from metabolomic profiling and molecular docking

Fusarium wilt is a devastating plant disease that causes significant yield losses worldwide. Biocontrol agents represent a sustainable alternative for Fusarium wilt management. In this study, three rhizospheric bacterial strains from Rhizobium and Bacillus genera were evaluated for managing Fusarium wilt in chili plants. Rhizobium nepotum strain Z-21 isolated from the rhizosphere of Vicia faba significantly reduced Fusarium wilt severity, showing a disease index of 26.2% that was 67.9% lower than the pathogen alone treatment. Additionally, Z-21 significantly increased shoot length (62.93%), root length (136.16%), and dry biomass (42.42%), compared to the negative control. We elucidated metabolomic mechanisms underlying Z-21-induced systemic resistance in chili plants. Z-21 increased total phenolic compounds by 37.54% and enhanced activities of peroxidase and polyphenol oxidase enzymes by 2.12-fold and 1.78-fold, respectively, compared to the pathogen control. Ultra-performance liquid chromatography tandem triple quadrupole mass spectrometry (UPLC-QQQ-ESI-MS) revealed that strain Z-21 effectively altered the metabolomic profile of chili plants. The application of Z-21 significantly increased the levels of numerous metabolites in chili plants that were reduced by Fusarium wilt infection. Metabolites present in the culture filtrates of Z-21 were identified by GC/MS analysis and used as ligands in molecular docking analysis. In-silico molecular docking analysis showed that di-2-ethylhexyl phthalate (DEHP) and 2,2'-methylenebis-6-t-butyl-4-methylphenol (MBBM) had the highest docking scores towards defence-related receptor kinase proteins. To our knowledge, this is the first report of Rhizobium nepotum as a biocontrol agent against Fusarium wilt in chili through induced systemic resistance (ISR).