Genomic and Functional Characterization of the Endophytic Bacillus siamensis Strain BACIII with Plant Growth-Promoting and Antifungal Activity

Abstract

Endophytic bacteria of the Bacillus subtilis species complex are known for plant growth promotion and antifungal activity, although strain-specific traits remain poorly understood. This study characterized the Bacillus siamensis strain BACIII, isolated from asymptomatic soybean roots in a charcoal rot-affected area, using whole-genome analysis and phenotypic assays. Genome sequencing identified BACIII as Bacillus siamensis and revealed a metabolically versatile genome containing twelve biosynthetic gene clusters linked to antimicrobial compounds such as difficidin, fengycin, and surfactin. Additionally, genomic islands associated with mobile elements, regulation, and stress response suggest adaptive potential. Inoculation with the BACIII strain significantly accelerated germination and increased early growth, biomass accumulation, and chlorophyll content in soybean and sunn hemp (p < 0.05), whereas no significant effects were observed in cotton or sunflower, indicating host-dependent responses. In vitro assays demonstrated consistent inhibition of several phytopathogenic fungi, including Sclerotinia sclerotiorum, Fusarium spp., and Macrophomina phaseolina, with variable intensity. Overall, BACIII combines host-specific plant growth promotion with broad antifungal activity, supporting its potential for biological control in sustainable agriculture.