Marine sediments harbor diverse Vibrio populations that play critical roles in benthic microbial ecology; however, the genomic determinants underlying the dominance of sediment-associated Vibrio taxa remain insufficiently characterized at the genome level. In this study, culture-based enumeration revealed Vibrio diabolicus as the dominant Vibrio species in marine sediment samples, providing ecological rationale for genome-resolved investigation. Because sediment-associated vibrio 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 V. diabolicus isolates (VdiabL2, VdiabL3, VdiabVA, and VdiabB48) 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 V. diabolicus references, while remaining clearly distinct from V. alginolyticus and V. parahaemolyticus references. Core-genome phylogenetic reconstruction resolved the sediment isolates into a coherent V. diabolicus 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 V. diabolicus populations. Together, these findings demonstrate that V. diabolicus 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 V. diabolicus populations and establishes a framework for future ecological and functional genomic investigations.
Esmaeil ALSaleh (2026) studied this question.