Pan-Genome Provides Insights into Vibrio Evolution and Adaptation to Deep-Sea Hydrothermal Vents

Abstract

This study delves into the genomic features of 10 Vibrio strains collected from deep-sea hydrothermal vents in the Pacific Ocean, providing insights into their evolutionary history and ecological adaptations. Through sequencing and pan-genome analysis involving 141 Vibrio species, we found that deep-sea strains exhibit larger genomes with unique gene distributions, suggesting adaptation to the vent environment. The phylogenomic reconstruction of the investigated isolates revealed the presence of 2 main clades: The first is monophyletic, consisting exclusively of Vibrio alginolyticus, while the second forms a monophyletic clade comprising both Vibrio antiquarius and Vibrio diabolicus species, which were previously isolated from deep-sea vents. All strains carry virulence and antibiotic resistance genes related to those found in human pathogenic Vibrio species which may play a wider ecological role other than host infection in these environments. In addition, functional genomic analysis identified genes potentially related to deep-sea survival and stress response, alongside candidate genes encoding for novel antimicrobial agents. Ultimately, the pan-genome we generated represents a valuable resource for future studies investigating the taxonomy, evolution, and ecology of Vibrio species.

Keywords: Vibrio; antibiotic resistance genes; comparative genomics; deep-sea hydrothermal vents; pan-genome; virulence factors.

Fig. 1.

The pan-genome of the Vibrio genus: A) The boxplot reports the distribution of genome size of Vibrio representatives compared with EPRs. B) The proportion of core, shell, and cloud genes in the average Vibrio genome. C) The number of OGs for each pan-genome category is reported for each genome.

Fig. 2.

Phylogenomics of Vibrio: A) The phylogenetic analysis was conducted using a concatenated dataset of 380 single-copy genes, supported by 1,000 bootstrap replications. Nodes on the tree with bootstrap support values ≤ 80% are specifically noted. Clades containing EPRs are colored. B) Matrix reporting pairwise ANI values obtained for a dataset including members of the clade A, D, and all complete V. alginolyticus strains available. Colored bars denote clusters of genomes with ANI ≥ 95%. C) The phylogenetic analysis was conducted with core SNPs on the same dataset of panel B, with 1,000 bootstrap replicates. Support values ≤ 90% are reported. Clades are colored according to the ANI results.

Fig. 3.

Distribution of ARGs and VFs in Vibrio. A) Distribution of ARGs in EPRs compared with the rest of Vibrio. B) Phyletic pattern of ARGs found in EPRs within the Vibrio phylogeny. C) Distribution of VFs in EPRs compared with the rest of Vibrio. D) Phyletic pattern of VFs found in EPRs within the Vibrio phylogeny.

Fig. 4.

Distribution of biosynthetic clusters found in EPRs in the Vibrio phylogeny. The number of genes associated with each of the 4 classes of secondary metabolites (ectoine, beta-lactone, arylpolyene, and NI-siderophore) are reported across the Vibrio tree.

Fig. 5.

Top 60 genes enriched in deep-sea hydrothermal vents Vibrios: A) Phyletic pattern of the 60 genes most significantly enriched in the genomes of 12 Vibrio isolates from deep-sea hydrothermal vents. B) Distribution of KEGG terms from the 60 most enriched genes. C) Distribution of GO terms from the 60 most enriched genes.

Fig. 6.

In vitro bactericidal activity in hemocyte monolayers of the M. galloprovincialis and C. gigas. Percentages of survival of bacterial cells (106 CFU/mL) incubated on hemocyte monolayers for different periods of time (30 to 90 min), compared to values obtained at time 0.