Comparative Insights into Bacterial Endophytome and Antifungal Metabolites in Fusarium Wilt-Resistant and -Susceptible Banana Cultivars Unveil the Resistance Toward Fusarium oxysporum f. sp. cubense

India contributes 26% of global banana production, yet cultivation is severely threatened by Fusarium wilt (Fusarium oxysporum f. sp. cubense, Foc), necessitating sustainable, eco-friendly management strategies. This study evaluated the biocontrol potential of endophytic bacteria isolated from Foc-resistant and -susceptible banana cultivars. Isolates from the pseudostem, corm, and root of the resistant cultivar showed significantly greater inhibitory activity than those from the susceptible cultivar, underscoring the role of host genotype in shaping functionally competent endophytic communities. Among all isolates, Bacillus sp. from the corm of cv. Rose (AB) showed the highest mycelial inhibition of Foc (70.37–76.54%) in vitro. GC-MS-based metabolite profiling revealed a chemically diverse array of secondary metabolites, fatty acid esters, steroids, terpenoids, siloxanes, and nitrogenous compounds. Corm-associated endophytes exhibited membrane-disruptive and cytotoxic activity, while root-associated endophytes contributed protective, defense-modulatory effects. Halomonas sp. RoRo2 and B. subtilis RoC1 showed the highest inhibition in both agar-well and in planta assays, with unsaturated fatty acids and organic acid derivatives implicated as key antifungal effectors acting through multiple biochemical pathways. These findings identify metabolically versatile endophytes as promising candidates for developing efficient, environmentally compatible bioinoculants as sustainable alternatives to chemical control of Fusarium wilt in banana.