Fungal phytopathogens cause major crop losses worldwide and are traditionally managed with chemical fungicides. However, excessive use of fungicides promotes resistance, affects non-target organisms, and raises environmental and food safety concerns. Bacterial strains with strong antifungal activity represent a sustainable alternative for biocontrol development. In a previous study, three bacterial strains (Pseudomonas protegens MH2, Pseudomonas koreensis CNI3, and Pseudomonas sp. R3) showed high inhibitory activity against plant pathogenic fungi, including Phomopsis sp., Botryosphaeria sp., and Harpophora maydis (unpublished data). To elucidate the molecular mechanisms underlying their antifungal activity, whole-genome sequencing was combined with functional annotation and secondary metabolite mining using antiSMASH. Biosynthetic gene clusters (BGCs) were compared across strains to identify metabolites potentially responsible for antifungal effects.
Strain MH2 exhibited strong inhibition (≥70% mycelial inhibition) of Phomopsis sp. and Botryosphaeria sp. and encoded a diverse set of BGCs, including those for 2,4-diacetylphloroglucinol, pyoluteorin, pyrrolnitrin, orfamide-type lipopeptides, phenazines, hydrogen cyanide, and multiple siderophores. Strain CNI3 inhibited H. maydis and Botryosphaeria sp. and carried clusters for NRPS, PKS, WLIP-like lipopeptides, siderophores, betalactones, and hydrogen cyanide. Strain R3, active only against H. maydis, contained a smaller arsenal of BGCs, notably pyoverdine-like siderophores, hydrogen cyanide, arylpolyenes, and betalactones. Comparative analysis indicated that MH2 and CNI3 harbor unique NRPS/PKS clusters absent in R3, potentially explaining their broader antifungal spectra.
The genomic profiles of these strains reveal multiple antifungal determinants, with MH2 emerging as the most promising candidate for biocontrol development due to its broad activity and rich biosynthetic repertoire. These results provide a genomic basis for the antifungal potential of these isolates and establish a foundation for integrative transcriptomic, metabolomic, and functional studies to characterize their mechanisms and biotechnological applications.
