Antagonistic Bacterial Endophytes from Gingers and their Metabolite Mediated Interactions Against Pythium Soft Rot.

Soft rot is the most devastating disease affecting ginger, leading to production losses of 50–90%. While chemical fungicides can effectively control this disease, their extensive use presents environmental and health risks. As an eco-friendly alternative, we evaluated bacterial endophytes and their bioactive compounds from wild ginger relatives to manage the soft rot pathogens Pythium myriotylum and P. deliense. Fifty endophytic bacteria from the leaves, rhizomes, and stems of the selected wild ginger relatives were isolated, and their antagonistic activity toward P. myriotylum and P. deliense was assessed using dual culture tests, of which 30 isolates showed greater than 50% inhibition against P. myriotylum, while 27 showed greater than 50% inhibition of P. deliense. Ten potential endophytic isolates were identified based on 16 S rRNA gene sequencing. Based on the antifungal assay and minimum inhibitory concentrations (MIC), the bacterial extracts of Pseudacidovorax intermedius (NCC15), Rhizobium sp. (NCC17A), Pseudomonas sp. (NCZ1), B. amyloliquefaciens (CC11) and B. pumilus (KG6) were selected for further studies. Scanning electron microscopy (SEM) analysis showed that the bacterial metabolite extract caused significant abnormalities in the hyphae and spores of Pythium spp., with P. myriotylum being more severely affected than P. deliense. Metabolic profiling of crude methanolic extracts revealed the presence of several antifungal compounds. Among them, four metabolites—Pyrrolo[1,2-a] pyrazine-1,4-dione, hexahydro-3-(phenylmethyl), N-(3-Imidazol-1-yl-propyl)-N’-(4-isopropyl-phenyl)-oxalamide [1,2,4], Oxadiazole, 5-benzyl-3-(thiophen-2-yl), and 2,5-Cyclohexadien-1-one, 3,5-dihydroxy-4,4- dimethyl were selected and docked with major Pythium proteins, yielded high docking scores, suggesting that these compounds possess anti-Pythium activity.