Genomic and functional characterization of Bacillus strains active against Fusarium graminearum

Fusarium species are among the most common and harmful fungal pathogens of cereals, able to synthesize a broad range of harmful mycotoxins, that they can accumulate in the kernels. The most important fungal disease is Fusarium Head Blight (FHB), caused by a complex of Fusarium species. Fusarium graminearum is the predominant species, able to produce deoxynivalenol (DON), a potent inhibitor of protein synthesis. The increasing demand for sustainable agriculture has driven research to find new eco-friendly strategies. This study aimed to identify new potential bacterial bio-control agents active against F. graminearum.

Thirty-six bacterial strains, belonging to Bacillus velezensis, B. amyloliquefaciens, B. subtilis, B. licheniformis, B. mojavensis, B. simplex, B. oleronius, B. pumilus, B. safensis, Priestia megaterium, and Peribacillus simplex, were selected. For each strain, antagonistic activity, by co-culture assay, and antifungal effect of bacteria filtrates were evaluated against five F. graminearum strains. All bacterial strains were molecularly characterized for the presence of genes associated with the production of antimicrobial molecules. In addition, ten selected strains were subjected to whole genome analyses.

Twenty-three strains exhibited antagonistic activity, achieving up to 75% mycelial growth inhibition. Furthermore, all B. velezensis strains, one strain of B. amyloliquefaciens, and B. mojavensis produced bioactive compounds that inhibited mycelial growth up to 64%. Co-culture assays demonstrated that all bacterial strains significantly reduced the ability of F. graminearum strains to produce DON up to 100%. Molecular analyses revealed the presence of genes encoding antimicrobial compounds in the majority of the bacterial strains. Genome analyses revealed the presence of a high number of secondary metabolite gene clusters (from 15 to 24), indicating a potential for secretion of multiple antimicrobial compounds. All strains shared genes devoted to the production of fengycin, surfactin, bacillibactin, mycosubtilin, bacillomycin D, bacillaene, and bacilysin, exhibiting, however, a distinct metabolite gene cluster profile. Bacillus velezensis strains presented the richest profiles, with N21.3 strain emerging as the most active against F. graminearum.

This study provides new Bacillus strains with antifungal activity and genomic traits that make them promising candidates for sustainable management of FHB and mycotoxin contamination in wheat.