Comparative genomics links ecological dominance and genome plasticity in sediment-derived <i>Vibrio diabolicus</i>

Marine sediments harbor diverse <i>Vibrio</i> populations that play critical roles in benthic microbial ecology; however, the genomic determinants underlying the dominance of sediment-associated <i>Vibrio</i> taxa remain insufficiently characterized at the genome level. In this study, culture-based enumeration revealed <i>Vibrio diabolicus</i> as the dominant <i>Vibrio</i> species in marine sediment samples, providing ecological rationale for genome-resolved investigation. Because sediment-associated <i>vibrio</i> species, often responds rapidly to environmental fluctuations and organic enrichment in coastal ecosystems, their distribution and genomic characteristics may also reflect changes in sediment microbial community structure and local environmental conditions. Four sediment-derived <i>V. diabolicus</i> isolates (Vdiab_L2, Vdiab_L3, Vdiab_VA, and Vdiab_B48) were subjected to whole-genome sequencing and comparative genomic analysis alongside closely related reference genomes. Average nucleotide identity (ANI) analyses confirmed species-level assignment, with all isolates exhibiting ANI values exceeding 95% relative to <i>V. diabolicus</i> references, while remaining clearly distinct from <i>V. alginolyticus</i> and <i>V. parahaemolyticus</i> references. Core-genome phylogenetic reconstruction resolved the sediment isolates into a coherent <i>V. diabolicus</i> lineage, consistent with ANI-based relationships and demonstrating strong concordance between whole-genome similarity metrics and evolutionary history inferred from conserved genes. Pangenome analysis revealed a relatively small, conserved core genome accompanied by a dominant accessory gene pool composed primarily of shell and cloud genes, indicative of an open pangenome structure. Accessory gene clustering and presence-absence profiling further highlighted strain-specific genomic heterogeneity within the species. Importantly, this study focuses specifically on comparative genomic structure rather than comparative functional genomics, aiming to establish a genome-level evolutionary framework for sediment-associated <i>V. diabolicus</i> populations. Together, these findings demonstrate that <i>V. diabolicus</i> combines ecological dominance in marine sediments with extensive genomic plasticity, a combination likely facilitating persistence and adaptation within heterogeneous benthic environments. This study provides a comprehensive comparative genomic baseline for understanding sediment-associated <i>V. diabolicus</i> populations and establishes a framework for future ecological and functional genomic investigations.