From genome to field, biocontrol efficacy of Bacillus subtilis strain M10 against Rhizoctonia solani in common bean

Bacillus species are widely exploited in sustainable agriculture due to their capacity to suppress soil-borne pathogens and promote plant growth. In this study, we investigated Bacillus subtilis strain M10, isolated from hypersaline soil of Lake Magadi, Kenya, which previously demonstrated antagonistic activity against Rhizoctonia solani. We combined whole-genome sequencing with field-based evaluation to elucidate the genetic basis of its biocontrol potential and assess its agronomic performance. The assembled genome comprises of 4,024,855 bp with a G + C content of 43.74% and a BUSCO completeness score of 99.5%. In silico genome analyses predicted 13 biosynthetic gene clusters associated with non-ribosomal peptides, terpenes, and ribosomally synthesized and post-translationally modified peptides, alongside 10 genomic islands, two prophage regions, and 108 strain-specific genes. Functional annotation further suggested the presence of genes potentially involved in rhizosphere colonization, plant-microbe interactions, environmental stress tolerance, and antimicrobial resistance, although these roles remain to be experimentally validated. Field trials conducted under dry and rainy seasons demonstrated that strain M10 significantly reduced root rot severity 20–28% lowered wilting incidence 20–37% and increased grain yield by more than 56–75% compared with untreated controls. Collectively, these results establish B. subtilis strain M10 as a safe and effective biocontrol agent with strong potential for sustainable management of R. solani in common bean production.