Multi-omics dissection of Bacillus atrophaeus mediated antagonism against Wilsonomyces carpophilus in wild apricot

• Multi-omics profiling elucidates B. atrophaeus antagonism against W. carpophilus . • Genome analysis reveals diverse biosynthetic gene clusters for biocontrol. • Antagonistic interaction triggers arginine/proline metabolic reprogramming. • Functional linkage established between srfABCD cluster and surfactin production. The development of green and targeted biocontrol agents requires a comprehensive understanding of the biocontrol potential of microbial strains and their interaction mechanisms with pathogens. In this study, we addressed the challenge of managing Wilsonomyces carpophilus by employing an integrative genomics and metabolomics approach to elucidate the antagonistic mechanisms of Bacillus atrophaeus XHG-1–3 m2. Genomic analysis rev ealed the presence of a complete srfABCD gene cluster along with diverse antimicrobial enzyme systems. Metabolomic profiling indicated that the strain undergoes metabolic reprogramming under interaction conditions, leading to the activation of arginine and proline biosynthesis while suppressing central carbon and phosphorus metabolism. This metabolic shift redirects resources toward the production of antimicrobial compounds. The fermentation broth exhibited a notable accumulation of amino acids, peptides, and alkaloids, achieving a peak inhibition rate of 79.38 % against the pathogen on day 5. A functional correlation was established between the key metabolite surfactin and the srfABCD gene cluster, confirming its pivotal role from both genetic and metabolic perspectives. Collectively, our findings demonstrate that B. atrophaeus XHG-1–3 m2 exerts biocontrol activity through metabolic reprogramming and the synergistic production of surfactin and other antimicrobial compounds. These results provide a molecular framework for developing targeted biocontrol strategies against fungal diseases in fruit trees.