Genomes of Vibrio spp. isolated from deep-sea hydrothermal vents highlight antibiotic resistance genes and ecological adaptation mechanisms

Deep-sea hydrothermal vents are extreme dynamic environments in which heterogeneous microbial communities engage with complex ecological relationships, constituting a promising source of novel bioactive molecules. Representatives of the Vibrio genus were collected from two of such sites (East Pacific Rise and Guyamas Basin, 2500 and 2000 meters depth, respectively), sampling from sediments, rock biofilms, mats and hydrothermal fluids. The genomes of 10 isolates were sequenced, assembled, and annotated with different functional databases and resources, focusing in particular on secondary metabolites production, antibiotic resistance, virulence, and adaptation to such extreme environments.To understand how these features compare with the genomic diversity of the Vibrio genus, we downloaded all representative genomes of Vibrio species (n=141), clustered the genes into orthologous groups with eggNOG, and used these to produce the Vibrio pan-genome. With this analysis it was possible not only to describe the evolutionary relationships between strains isolated from hydrothermal vents and the other Vibrio representatives, but also to highlight features enriched in genomes from deep-sea associated bacteria. For instance, we identified four antibiotic resistance genes (blaCARB, ampC, catC, tet35) in all 10 novel Vibrio isolates and a small subset of other vibrios, including deep-sea isolates (e.g. V. diabolicus, V. antiquarius). These genomes harbor both tet35 and a paralog, tet34, which is present in almost all Vibrio species, hinting that tet35 ancestrally evolved from tet34 duplication.In conclusion, our study represents a first attempt to screen features for Vibrio adaptation to deep-sea vents and reconstruct their evolutionary history.