Comparative genomic analysis of cassava rhizospheric Bacillus subtilis using integrated in vitro and in silico approaches with enterobacterial repetitive intergenic consensus (ERIC) sequences

Abstract

Background: Bacillus subtilis is a beneficial rhizobacterium extensively used in agriculture and industry due to its abilities in promoting plant growth and decomposing organic matter. To enhance its application potential, precise genetic characterization of native strains, particularly those associated with crop rhizospheres, is crucial. Methods and results: This study focused on B. subtilis isolates obtained from the cassava rhizosphere. Genetic diversity among the isolates was assessed using the Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR method. Genomic DNA was extracted and amplified, with ERIC-PCR effectively differentiating strains based on unique banding patterns. Whole-genome sequencing and database comparisons further validated the strain identities and revealed significant genetic variation. While a few isolates shared high similarity (≥ 99.5%), the majority exhibited lower similarity levels (< 70%), indicating considerable genomic diversity. Several genes—spoVAF, spoVAEA, spoVAEB, spoVAD, hisIE, hisF, hisA, rsbRB, thiW, ispA, and thiX—were identified as potential markers for strain differentiation and functional characterization. Conclusions: ERIC-PCR proved to be a reliable and efficient method for discriminating B. subtilis strains from the cassava rhizosphere. The observed genetic diversity suggests a rich reservoir of functional traits among native strains, offering new opportunities for targeted applications in plant-microbe interactions, such as biofertilization and biocontrol. These findings provide a foundation for the strategic use and further study of B. subtilis in sustainable agriculture. Clinical trial number: Not applicable.