Integrated Genomic and Metabolomic Analysis Reveals the Biocontrol Potential of Endophytic Bacillus velezensis NS13 Against Fusarium spp. in Lonicera macranthoides

Fusarium spp. are major fungal pathogens causing root rot. They exhibit a broad host range and high pathogenicity, leading to yield losses, reduced quality, and plant mortality. Current control measures rely primarily on chemical pesticides, with few sustainable biological options available. This study compared rhizosphere microbial diversity between healthy and diseased Lonicera macranthoides, revealing increased pathogenic fungi (Fusarium, Plectosphaerella, p < 0.01) and reduced beneficial fungi (Trichoderma, Chao1/Shannon, p < 0.05) in diseased plants. An endophytic Bacillus velezensis strain, NS13, was isolated from healthy roots. Plate confrontation assays showed strong inhibition of Fusarium oxysporum from L. macranthoides and other Fusarium species (F. solani, F. graminearum, F. fujikuroi). The 3.95 Mb genome encoded 4,060 proteins, including 96 biocontrol-related genes. AntiSMASH identified 15 secondary metabolite biosynthetic gene clusters, with five linked to antifungal, three to antibacterial activity, and seven potentially novel compounds. LC–MS/MS metabolomics detected multiple antifungal metabolites, including cyclic dipeptides, fatty acid amides (e.g., erucamide), and oleanolic acid. These results demonstrate soil microbial dysbiosis in L. macranthoides affected by root rot and confirm the broad-spectrum anti-Fusarium potential of NS13, highlighting its promise as a biocontrol resource against Fusarium pathogens in medicinal plants.