Kojic acid and ε-poly-L-lysine suppress potato common scab and remodel the tuber-associated microbiome.

Potato common scab (PCS) is an economically important soil-borne disease whose occurrence is governed not only by pathogen virulence but also by the disease-associated microbiome and soil environment. However, studies on natural bioactive compounds have primarily focused on direct pathogen inhibition, whereas their roles in microbiome remodeling remain largely unexplored. Here, we investigated the antibacterial activity of kojic acid (KA) and ε-poly-L-lysine (ε-PL) against Streptomyces scabies and evaluated their effects on PCS severity and the tuber-associated microbiome. Both KA and ε-PL significantly inhibited the growth of Streptomyces scabies G9, with ε-PL exhibiting stronger in vitro antibacterial activity. Both treatments disrupted hyphal ultrastructure, increased membrane permeability, and triggered extensive transcriptional reprogramming involving cell envelope organization, central metabolism, membrane transport, and genetic information processing. Net-house and field trials showed that both compounds substantially reduced disease severity; significant yield increases were observed in the net-house trial, whereas no significant yield differences were detected among treatments in the field trial. Microbiome analyses revealed that both compounds improved the physicochemical properties and enzyme activities of tuber-associated soil, reshaped the composition and predicted functional profiles of the tuber-associated bacterial community, and reduced the relative abundance of pathogen-associated Streptomyces taxa. Correlation analyses revealed significant associations among soil environmental factors, pathogen-associated Streptomyces taxa, and disease occurrence. Collectively, these findings indicate that KA and ε-PL suppress PCS in association with direct antibacterial activity and remodeling of the tuber-associated bacterial community. This study provides insights into the potential roles of natural bioactive compounds in pathogen suppression and microbiome modulation.