Genome-wide analysis and growth-promoting potential of Burkholderia gladioli YNK-FB0053

Abstract

Introduction Sulfur-oxidizing bacteria can contribute to the conversion of reduced or organic sulfur pools into plant-available sulfate, thereby improving soil sulfur availability and supporting sustainable agricultural production. This study aimed to characterize the whole-genome features of the rapeseed rhizosphere strain Burkholderia gladioli YNK-FB0053, clarify its predicted genetic potential related to sulfur metabolism, nutrient mobilization, rhizosphere adaptation, and plant growth promotion, and validate selected functional traits through phenotypic and pot experiments. Methods Whole-genome sequencing of strain YNK-FB0053 was performed using combined Illumina NovaSeq short-read sequencing and PacBio Sequel third-generation single-molecule long-read sequencing, followed by genome assembly, quality assessment, and multi-database functional annotation. The complete genome sequence has been deposited in the GenBank database under accession number JBQPHS000000000. Assembly quality was evaluated using sequencing depth, read-mapping coverage, CheckM completeness/contamination, and BUSCO completeness. Genes predicted to be involved in sulfur metabolism, secondary metabolite biosynthesis, nutrient transformation, phytohormone production, and rhizosphere colonization were systematically identified. Biofilm formation assays, root colonization tests, and Chinese cabbage pot experiments were conducted to evaluate rhizosphere adaptability and plant growth-promoting effects. Results The final assembly consisted of two circular chromosomes totaling 8,148,635 bp, with a GC content of 68.07%. Illumina sequencing generated 996,434,009 bp of clean data with Q20 and Q30 values of 97.82 and 90.65%, respectively, while PacBio sequencing generated 548,213,285 bp of reads with an average read length of 10,518.29 bp and a reads N50 of 10,547 bp. The PacBio sequencing depth was 67.28 × , and both Illumina and PacBio reads showed 100% read-mapping coverage of the assembly. CheckM estimated genome completeness as 100%, with 1.68% contamination and 0% strain heterogeneity, while BUSCO analysis showed 100% complete single-copy BUSCOs. A total of 6,898 protein-coding genes were predicted, with an average coding gene length of 1,022.80 bp. Sulfur metabolism annotation identified sqr, Sox-related genes (soxA, soxB, soxC, soxD, and soxG), the cysPUWA sulfate/thiosulfate transport system, assimilatory sulfate reduction genes, and organic sulfur utilization genes, indicating a genetic basis for reduced sulfur oxidation, thiosulfate-related transformation, sulfate assimilation, and diverse sulfur-source utilization. In addition, genes associated with inorganic nitrogen transformation and assimilation, phosphate mobilization, zinc homeostasis, iron acquisition and siderophore-related processes, indole-3-acetic acid biosynthesis, biofilm formation, rhizosphere colonization, phenolic compound degradation, heavy metal resistance, and antibiotic resistance-related traits were also identified. Phenotypic assays showed that the strain formed wrinkled biofilms on MSgg medium within 24 h, with a biomass of 131.4 mg. After 3 days of inoculation, root colonization reached 3.8 × 109 CFU/g. Pot experiments showed that inoculation with YNK-FB0053 significantly increased SPAD value, plant height, and biomass of Chinese cabbage by 15–31%, and also improved plant and rhizosphere nutrient status. Conclusion Burkholderia gladioli YNK-FB0053 carries multiple genes predicted to participate in sulfur metabolism, nutrient mobilization, iron acquisition and siderophore-related processes, phytohormone biosynthesis, biofilm formation, and rhizosphere adaptation. Among these, sqr, Sox-related genes, sulfate/thiosulfate transport genes, assimilatory sulfate reduction genes, and organic sulfur utilization genes provide a focused genomic basis for its sulfur-related functional potential. Phenotypic assays confirmed its biofilm formation and root colonization ability, and pot experiments demonstrated that inoculation with YNK-FB0053 promoted the growth and nutrient status of Chinese cabbage under controlled greenhouse conditions. Together, these genome-based predictions and phenotypic results support YNK-FB0053 as a multifunctional plant growth-promoting bacterial resource with sulfur-related biofertilizer potential. However, genome-based functional predictions, particularly those related to nitrogen metabolism, iron acquisition and siderophore-related traits, phytohormone biosynthesis, antibiotic resistance, and biosafety, require additional targeted biochemical validation and risk assessment before field-scale agricultural application.