Captive bottlenose dolphins and killer whales harbor a species-specific skin microbiota that varies among individuals

Abstract

Marine animals surfaces host diverse microbial communities, which play major roles for host’s health. Most inventories of marine animal surface microbiota have focused on corals and fishes, while cetaceans remain overlooked. The few studies focused on wild cetaceans, making difficult to distinguish intrinsic inter- and/or intraspecific variability in skin microbiota from environmental effects. We used high-throughput sequencing to assess the skin microbiota from 4 body zones of 8 bottlenose dolphins (Tursiops truncatus) and killer whales (Orcinus orca), housed in captivity (Marineland park, France). Overall, cetacean skin microbiota is more diverse than planktonic communities and is dominated by different phylogenetic lineages and functions. In addition, the two cetacean species host different skin microbiotas. Within each species, variability was higher between individuals than between body parts, suggesting a high individuality of cetacean skin microbiota. Overall, the skin microbiota of the assessed cetaceans related more to the humpback whale and fishes’ than to microbiotas of terrestrial mammals.

Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin

“…In addition, it underscores that although killer whale skin is influenced by the local environment (Romano‐Bertrand, Licznar‐Fajardo, Parer, & Jumas‐Bilak, ), it represents a unique ecosystem that is separate from that of the surrounding habitat. Concordant with our results, a study of the microbiome of four captive killer whales and the sea water from their pool found that the skin microbiota were more diverse and phylogenetically distinct from the sea water microbial community (Chiarello et al., ). Killer whales are highly social mammals (Baird, ; Ford, ), and thus, they are likely to have a high potential for horizontal transfer of microbes between individuals during contact (Nelson et al., ).…”

“…DNA was extracted from epidermal biopsies collected by firing a lightweight dart with a sterilized stainless steel cutting tip from a sterilized projector (e.g., Barrett-Lennard, Smith, & Ellis, 1996;Palsbøll, Larsen, & Hansen, 1991) at the flank of the killer whale. As a study on captive killer whales found low variability in the taxonomic composition of the skin microbiome from different body sites (Chiarello, Villéger, Bouvier, Auguet, & Bouvier, 2017), small variation in the exact location on the flank from which the biopsy was taken should not bias our results. Biopsies were stored in sterile tubes at −20°C.…”

“…General separation by sequencing approach (i.e., shotgun versus amplicon) was not observed: for instance, amplicon‐ and shotgun‐sequenced human samples grouped together (Figure a,b). It is therefore possible that the separation of the captive study samples is due to either the use of a specific 16S target locus or other factors associated with captive versus wild environments (note that the pool was filled with sea water from the Mediterranean Sea; Chiarello et al., ).…”

“…This approach allowed us to compare the composition of the free‐ranging killer whale skin microbiome to other marine mammal skin microbiota and to a number of potential contaminating and environmental sources. We obtained data from public repositories and included microbial communities reflecting the marine environment (ocean water from Southern Ocean and the North Pacific, Sunagawa et al., ), other marine mammal skin (captive bottlenose dolphins Tursiops truncatus and killer whales along with the respective pool water samples and free‐ranging humpback whales, Bierlich et al., ; Chiarello et al., ), likely contaminants such as human skin and gut (Lloyd‐Price et al., ; Meisel et al., ; Oh et al., ) and laboratory contamination from commonly used reagents (sterile water, Salter et al., ) (Supporting Information Table ). We attempted to specifically select sources that were obtained with the shotgun sequencing approach to avoid potential locus‐specific effects that can produce distinct microbiome profiles in amplicon‐based studies.…”

“…Ocean and the North Pacific, Sunagawa et al, 2015), other marine mammal skin (captive bottlenose dolphins Tursiops truncatus and killer whales along with the respective pool water samples and freeranging humpback whales, Bierlich et al, 2018;Chiarello et al, 2017), likely contaminants such as human skin and gut (Lloyd-Price et al, 2017;Meisel et al, 2016;Oh et al, 2014) and laboratory contamination from commonly used reagents (sterile water, Salter et al, Table S2). We attempted to specifically select sources that were obtained with the shotgun sequencing HOOPER ET AL.…”