Multi-omics characterization of a rhizosphere-derived Bacillus cereus CBS-B5 strain reveals genomic stability, metabolic versatility, and biosafety-related genomic features for agricultural applications.

INTRODUCTION

Bacillus cereus strains have potential plant growth-promoting properties but may harbor virulence and antimicrobial resistance (AMR) determinants. This study characterized the rhizosphere-derived B. cereus CBS-B5 strain to assess its functional potential and biosafety-related features.

METHODS

CBS-B5, isolated from sugar beet rhizosphere, was characterized using an integrated multi-omics approach combining phenotypic assays, whole-genome sequencing, phylogenomic and comparative genomic analyses, and metabolomic profiling.

RESULTS

CBS-B5 exhibited visible growth under elevated salinity conditions, demonstrated recovery following heat stress exposure, and strong biofilm formation, but no detectable phosphate solubilization. Whole-genome sequencing revealed a 5.02 Mb genome with 35% GC content, 100% completeness, and 0.03% contamination. Phylogenomic analysis placed CBS-B5 within the B. cereus group. Comparative genomic and functional analyses indicated genomic stability, metabolic versatility, stress-adaptation potential, and diverse biosynthetic gene clusters. Genome plasticity was supported by the presence of mobile genetic elements and horizontal gene transfer events affecting approximately 16% of the proteome. Metabolomic analysis confirmed active metabolic processes, including nitrogen recycling, osmoprotection, and transformation of plant-derived compounds under laboratory conditions. Although virulence-associated genes, including nheABC, cytK, and inhA, and β-hemolytic activity were detected, AMR and virulence determinants showed limited potential for horizontal dissemination. Similarly, AMR genes exhibited low mobility potential and minimal phenotypic resistance beyond intrinsic traits.

DISCUSSION: Overall, CBS-B5 combines genomic stability, metabolic flexibility, and ecological adaptability. From a One Health perspective, the genomic analyses suggest a limited potential for horizontal dissemination of antimicrobial resistance and virulence determinants. However, the presence of chromosomally encoded toxin-associated genes and β-hemolytic activity indicates that additional biosafety evaluation is required before agricultural application.