Genomic insights into three Bacillus strains for biocontrol of tobacco black shank disease.

Tobacco black shank, primarily caused by the pathogenic oomycete Phytophthora nicotianae, severely hampers tobacco production. In the present study, three bacterial strains (YC2158, YC2177 and YC2228) exhibiting significant inhibitory activity against P. nicotianae were isolated from the rhizosphere soil of disease-resistant tobacco plants. Using 16s rDNA sequencing and phylogenetic analyses, they were identified as belonging to the genus Bacillus. Comprehensive genomic analyses revealed that YC2158, YC2177 and YC2228 were closely related to B. velezensis strain BvL03, B. velezensis strain HAB-2, and B. subtilis strain LBUM979, respectively. The three Bacillus species demonstrated a high abundance of genes encoding carbohydrate-active enzymes, polyketide synthases, and lipopeptides, all of which may contribute to their inhibitory activity against P. nicotianae. The inhibitory mechanisms were likely associated with enhanced transcriptional activities, as well as amino acid and carbohydrate transport and metabolism in tobacco plants. The sublancin coding gene, introduced by the insertion of a prophage sequence into the YC2228 genome, endows it with biocontrol functions. Secondary metabolite gene cluster analysis identified 12 biocontrol-related clusters, 5 of which were conserved across the 3 Bacillus strains. These findings suggest that these strains might be inducing systemic resistance in tobacco plants against black shank disease. Moreover, three gene clusters shared between two known potato black shank pathogenic bacteria were identified, indicating a potential connection to pathogenicity factors associated with the disease. This study underlines the significance of Bacillus spp. as biocontrol agents in managing tobacco black shank disease and provides insights into the genetic foundations of their disease resistance mechanisms.