Molecular Comparison of Two Bacillus velezensis Strains from Grapevine Reveals Candidate Genomic Determinants of Differential Efficacy Against Downy Mildew

Intensive use of synthetic fungicides to control grapevine downy mildew raises interconnected concerns for human health, environmental safety, and food quality—a challenge that biological control agents (BCAs) are well positioned to address. Among bacterial BCAs, Bacillus velezensis shows strong biocontrol potential, but efficacy varies substantially among conspecific strains, complicating rational strain selection. Whole-genome comparative analysis of two strains with contrasting efficacy against Plasmopara viticola (BLG_B2 and BLG_B4) identified four HIGH-impact variants present exclusively in the ineffective strain BLG_B2, predicted to cause loss of function of glycerol kinase (glpK), the antimicrobial peptide resistance regulator yxdJ, a c-di-GMP phosphodiesterase, and the ribonuclease yeeF. In other Bacillus strains, three of these genes are linked to surfactin biosynthesis, antimicrobial peptide detoxification and the motility-to-biofilm transition; they are therefore proposed as candidate determinants of the biocontrol deficit of BLG_B2, whose causal role remains to be tested. These results show that whole-genome comparison of conspecific BCA strains can generate testable hypotheses on the genomic basis of differential biocontrol efficacy.