Bioprospecting Honey-Derived Microorganisms for the Biological Control of Phytopathogens

Microbial biological control agents are a sustainable alternative to synthetic pesticides, yet their widespread application is limited by a lack of environmental resilience of commercial products. To address this, we exploited honey—a stringent ecological niche—as a reservoir for stress-tolerant bacteria. In this study, the bioprospection utilizing five types of commercially available honeys yielded a collection of 53 bacteria and 10 fungi. All bacterial isolates were evaluated for antimicrobial activity against a laboratory-standard bacterium and yeast, and six economically relevant phytopathogenic microorganisms. Initial screening with standard laboratory organisms proved to be an efficient method to detect strains with antimicrobial potential, correlating significantly with further phytopathogen inhibition (Spearman’s r = 0.4512, p = 0.0005). Two promising strains, M2.7 and M3.18, were selected for quantitative dual-culture assays along with molecular identification using 16S rDNA and gyrA gene sequencing, classifying them as Bacillus velezensis. These strains exhibited high inhibitory effects against the pathogens (p > 0.001), often with equivalent efficacy to the commercial biocontrol strain, and also induced significant phytopathogen hyphal deformities, such as increased septation and swelling. These findings support honey as a viable source of robust biocontrol agents, offering a sustainable strategy to substitute or complement current agrochemicals.