Microbiomes of pathogenic vibrio species elucidate environmental and planktonic associations

Many species of coastal vibrio bacteria can infect humans, representing an emerging health threat linked to increasing seawater temperatures. Vibrio interactions with the planktonic community impact coastal ecology and human infection potential, yet are poorly understood, particularly regarding eukaryotic associations. We quantified pathogenic Vibrio species, including V. cholerae, V. parahaemolyticus, and V. vulnificus, and two virulence-associated genes for one year at five coastal sites in Southern California using digital droplet PCR. We then profiled associated prokaryotic and eukaryotic communities, including vibrio-specific communities, using next-generation sequencing and both culture dependent and independent methodologies. Pathogenic vibrio species were abundant and inhabited distinct species-specific environmental niches driven by temperature and salinity. Taxonomic resolution played a key role in determining associations for both Vibrio species and other community members, with broader taxonomic grouping masking potentially important functionally relevant interactions. For example, low-salinity vibrio species were associated with eukaryotic copepods and chitin-exuding diatom genera, while higher salinity species associated with genera lacking chitin. Associations were often linked to shared environmental preferences, clarifying ecological relationships and highlighting prospective model systems for future mechanistic studies. Our study establishes a new comprehensive workflow for examining environmental pathogen microbiomes, offers insights into conflicting results from previous studies while elucidating new functionally relevant associations, and facilitates future environmentally realistic model laboratory studies.