Novel diversity of bacterial communities associated with bottlenose dolphin upper respiratory tracts

Bacterial microbiomes from mucus and breath of southern resident killer whales (Orcinus orca)

Opportunities to assess odontocete health are restricted due to their limited time at the surface, relatively quick movements and large geographic ranges. For endangered populations such as the southern resident killer whales (SKRWs) of the northeast Pacific Ocean, taking advantage of non-invasive samples such as expelled mucus and exhaled breath is appealing. Over the past 12 years, such samples were collected, providing a chance to analyse and assess their bacterial microbiomes using amplicon sequencing. Based on operational taxonomic units, microbiome communities from SRKW and transient killer whales showed little overlap between mucus, breath and seawater from SRKW habitats and six bacterial phyla were prominent in expelled mucus but not in seawater. Mollicutes and Fusobacteria were common and abundant in mucus, but not in breath or seawater, suggesting these bacterial classes may be normal constituents of the SRKW microbiome. Out of 134 bacterial families detected, 24 were unique to breath and mucus, including higher abundances of Burkholderiaceae, Moraxellaceae and Chitinophagaceae. Although there were multiple bacterial genera in breath or mucus that include pathogenic species (e.g. Campylobacter, Hemophilus, Treponema), the presence of these bacteria is not necessarily evidence of disease or infection. Future emphasis on genotyping mucus samples to the individual animal will allow further assessment in the context of that animal's history, including body condition index and prior contaminants burden. This study is the first to examine expelled mucus from cetaceans for microbiomes and demonstrates the value of analysing these types of non-invasive samples.

RESPIRATORY CHANGES IN STRANDED BOTTLENOSE DOLPHINS (TURSIOPS TRUNCATUS)

Lung function (breath duration, respiratory flow [V̇], and tidal volume [V_T]), and end-expiratory O₂ were measured in 19 adult bottlenose dolphins (Tursiops spp.) while at rest in water or beached for up to 10 min. The results show that inspiratory V_T, expiratory V_T, or inspiratory V̇ did not differ on land or in water. The average expiratory V̇ for all dolphins on land decreased by 16%, and the expiratory and total breath durations increased by 5% and 4%, respectively, compared with in water. There were temporal changes observed during beaching, where expired and inspired V_T and inspired V̇ decreased by 13%, 16%, and 9%, respectively, after 10 min on land. These data suggest that dolphins compensate for the effect of gravity by adjusting respiration to maintain alveolar ventilation and gas exchange, but during extended durations, the increased work of breathing may impede ventilation and gas exchange. Continuous monitoring of lung function and gas exchange may help prevent long-term damage during out-of-water medical procedures, optimize animal transport conditions, and improve survival during stranding events.

Highly abundant core taxa in the blow within and across captive bottlenose dolphins provide evidence for a temporally stable airway microbiota

Background

The analysis of blow microbiota has been proposed as a biomarker for respiratory health analysis in cetaceans. Yet, we lack crucial knowledge on the long-term stability of the blow microbiota and its potential changes during disease. Research in humans and mice have provided evidence that respiratory disease is accompanied by a shift in microbial communities of the airways. We investigate here the stability of the community composition of the blow microbiota for 13 captive bottlenose dolphins over eight months including both sick and healthy individuals. We used barcoded tag sequencing of the bacterial 16S rRNA gene. Four of the dolphins experienced distinct medical conditions and received systemic antimicrobial treatment during the study.

Results

We showed that each dolphin harboured a unique community of zero-radius operational taxonomic units (zOTUs) that was present throughout the entire sampling period (‘intra-core’). Although for most dolphins there was significant variation over time, overall the intra-core accounted for an average of 73% of relative abundance of the blow microbiota. In addition, the dolphins shared between 8 and 66 zOTUs on any of the sampling occasions (‘inter-core’), accounting for a relative abundance between 17 and 41% of any dolphin’s airway microbiota. The majority of the intra-core and all of the inter-core zOTUs in this study are commonly found in captive and free-ranging dolphins and have previously been reported from several different body sites. While we did not find a clear effect of microbial treatment on blow microbiota, age and sex of the dolphins did have such an effect.

Conclusions

The airways of dolphins were colonized by an individual intra-core ‘signature’ that varied in abundance relative to more temporary bacteria. We speculate that the intra-core bacteria interact with the immune response of the respiratory tract and support its function. This study provides the first evidence of individual-specific airway microbiota in cetaceans that is stable over eight months.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-020-02076-z.

Pneumonia in endangered aquatic mammals and the need for developing low-coverage vaccination for their management and conservation

Anthropogenic activities can lead to several devastating effects on the environment. The pollutants, which include the discharge of effluents, runoffs in the form of different lethal and sub-lethal concentrations of pesticides, heavy metals, and other contaminants, can harm exposed fauna and flora. The aquatic environment is the ultimate destination for many pollutants which negatively affect aquatic biodiversity and even can cause a species to become extinct. A pollutant can directly affect the behavior of an animal, disrupt cellular systems, and impair the immune system. This harm can be reduced and even mitigated by adopting proper approaches for the conservation of the target biota. Among aquatic organisms, cetaceans, such as the Yangtze finless porpoise, Irrawaddy dolphin, Ganges River dolphin, Amazon River dolphin, and Indus River dolphin, are at a higher risk of extinction because of lack of knowledge and research, and thus insufficient information with respect to their conservation status, management, and policies. Pneumonia is one of the leading causes of mass mortalities of cetaceans. This article reviews the limited research reported on stress and pneumonia induced by pollution, stress-induced pneumonia and immunosuppression, pneumonia-caused mass mortalities of aquatic mammals, and vaccination in wildlife with a specific focus on aquatic mammals, the role of genomics in vaccine development and vaccination, and the major challenges in vaccine development for biodiversity conservation.

Cetacean morbillivirus in Humpback whales' exhaled breath

The humpback whale (HW; Megaptera novaeangliae) population that seasonally resides along the Brazilian coast concentrates in the Abrolhos Bank (Bahia and Espírito Santo states) for breeding during austral winter and spring. Cetacean morbillivirus (CeMV, Paramyxoviridae family) is currently one of the most significant biological threats to cetaceans worldwide with high infection and mortality rates. CeMV is pleiotropic yet it has special tropism for the respiratory, lymphoid and nervous system and is primarily transmitted by the aerogenous route. A new lineage of CeMV, the Guiana dolphin morbillivirus (GDMV), is known to affect cetaceans off Brazil. GDMV was first detected in a Guiana dolphin (Sotalia guianensis) stranded in the Abrolhos Bank region, in 2010. In addition to pathologic examinations on stranded HW, pathogen survey of free-ranging HW may provide valuable insight into the epidemiology of diseases. We hypothesized that HW in the Brazilian breeding ground could be exposed to CeMV. Thus, in the present study, we investigated the presence of CeMV in exhaled breath condensates (EBC) of HW in the Abrolhos Bank. Overall, 73 samples of EBC from 48 groups of HW were collected during the breeding seasons of 2011 (n = 16) and 2012 (n = 57). One sample failed to have the reference gene amplified and was excluded from the study. CeMV was detected by a RT-qPCR method in 2 EBC samples, representing 2 whale groups. Phylogenetic analysis of partial morbillivirus phosphoprotein gene showed 100% homology to GDMV. Our results show that HW in Brazil are infected by CeMV with a relative prevalence of 4.3% (2/47) and demonstrate the suitability of using EBC and RT-qPCR as a non-invasive tool for CeMV survey in free-ranging whales. This pioneer study provides scientific basis for non-invasive CeMV monitoring of HW, suggests HW may play a role in the dynamics of CeMV and raises concern for potential conservation implications for this species.

Host phylogeny and life history stage shape the gut microbiome in dwarf (Kogia sima) and pygmy (Kogia breviceps) sperm whales

Gut microbiomes perform crucial roles in host health and development, but few studies have explored cetacean microbiomes especially deep divers. We characterized the gut microbiomes of stranded dwarf (Kogia sima) and pygmy (K. breviceps) sperm whales to examine the effects of phylogeny and life stage on microbiome composition and diversity. 16S rRNA gene sequence analysis revealed diverse gut communities (averaging 674 OTUs) dominated by a few symbiont taxa (25 OTUs accounted for 64% of total relative abundance). Both phylogeny and life stage shaped community composition and diversity, with species-specific microbiome differences present early in life. Further analysis showed evidence of microbiome convergence with host maturity, albeit through different processes: symbiont 'accumulation' in K. sima and 'winnowing' in K. breviceps, indicating different methods of community assembly during host development. Furthermore, culture-based analyses yielded 116 pure cultures matching 25 OTUs, including one isolate positive for chitin utilization. Our findings indicate that kogiid gut microbiomes are highly diverse and species-specific, undergo significant shifts with host development, and can be cultivated on specialized media under anaerobic conditions. These results enhance our understanding of the kogiid gut microbiome and may provide useful information for symbiont assessment in host health.

Respiratory microbiota of humpback whales may be reduced in diversity and richness the longer they fast

Humpback whales endure several months of fasting while undertaking one of the longest annual migrations of any mammal, which depletes the whales’ energy stores and likely compromises their physiological state. Airway microbiota are linked to respiratory health in mammals. To illuminate the dynamics of airway microbiota in a physiologically challenged mammal, we investigated the bacterial communities in the blow of East Australian humpback whales at two stages of their migration: at the beginning (n = 20) and several months into their migration (n = 20), using barcoded tag sequencing of the bacterial 16S rRNA gene. We show that early in the fasting the whale blow samples had a higher diversity and richness combined with a larger number of core taxa and a different bacterial composition than later in the fasting. This study provides some evidence that the rich blow microbiota at the beginning of their fasting might reflect the whales’ uncompromised physiology and that changes in the microbiota occur during the whales’ migration.

Mollusk microbiota shift during Angiostrongylus cantonensis infection in the freshwater snail Biomphalaria glabrata and the terrestrial slug Phillocaulis soleiformis

In the present work, we reported for the first time the microbiome from Phyllocaulis soleiformis and Biomphalaria glabrata assessed using high-throughput DNA sequencing pre- and post-infection with the helminth parasite Angiostrongylus cantonensis. B. glabrata and P. soleiformis were experimentally infected with A. cantonensis. Fecal DNAs from control and infected groups were extracted and subjected to 16S rRNA high-throughput sequencing survey. No significant differences were found in the alpha diversity indexes in Phyllocaulis and Biomphalaria experiments independently. PCoA analysis using the unweighted UniFrac measures showed that both microbiotas behaved differently depending on the host. In Biomphalaria microbiota, control and infected groups were significantly different (p = 0.0219), while Phyllocaulis samples were not (p = 0.5190). The microbiome of P. soleiformis infected with A. cantonensis showed a significant decrease of Sphingobacterium and a substantial increase of Cellvibrio when compared to a control group. The microbiome of B. glabrata infected with A. cantonensis showed a significant decline in the abundance of Flavobacterium, Fluviicola, Nitrospira, Vogesella and an OTU belonging to the family Comamonadaceae, and a significant increase of Uliginosibacterium and an OTU belonging to the family Weeksellaceae when compared to a control group. Overall, the microbiome data reported here provided valuable information with regard to the diversity of bacterial communities that comprise the gut microbiome of gastropods. Furthermore, we report here the effect of the infection of the helminth A. cantonensis in the ratio and distribution of the fecal microbiome of the snails. Further studies are highly valuable in order to better understand those interactions by comparing different microbiome profiles and mollusk models. By now, we anticipate that ecological studies will take significant advantage of these advances, particularly concerning improving our understanding of helminth-microbiome-host interactions.

Interannual comparison of core taxa and community composition of the blow microbiota from East Australian humpback whales

Cetacean represent vulnerable species impacted by multiple stressors, including reduction in prey species, habitat destruction, whaling and infectious disease. The composition of blow microbiota has been claimed to provide a promising tool for non-invasive health monitoring aiming to inform conservation management. Still, little is known about the temporal stability and composition of blow microbiota in whales. We used East Australian humpback whales (Megaptera novaeangliae) as a model species and collected blow and control samples in August 2016 and 2017 for an interannual comparison. We analysed the blow by barcode tag sequencing of the bacterial 16S rRNA gene. We found that the microbial communities in 2016 and 2017 were statistically similar regarding alpha and beta diversity but distinct to seawater. Zero-radius operational taxonomic units (zOTUs) shared by both groups accounted for about 50% of all zOTUs present. Still, the large individual variability in the blow microbiota resulted in a small number of core taxa (defined as present in at least 60% of whales). We conclude that the blow microbiota of humpback whales is either generally limited and of transient nature or the reduced airway microbiota is the symptom of a compromised physiological state potentially due to the challenges of the whales' annual migration.

Characterization of the bacterial microbiome among free-ranging bottlenose dolphins (Tursiops truncatus)

Marine animals represent a dynamic and complex habitat for diverse microbial communities. The microbiota associated with bottlenose dolphins (Tursiops truncatus) are believed to influence their health status, but it remains poorly understood. We therefore characterized and compared the bacterial microbiome of bottlenose dolphins from six different anatomical sites that represent four different body systems (respiratory, digestive, reproductive, and integumentary). In this study, a total of 14 free-ranging bottlenose dolphins were sampled during the 2015 Sarasota Bay Dolphin Health Assessment. Bacterial diversity and abundance were assessed by PCR amplification of the hypervariable V3-V4 regions of the bacterial 16S rRNA gene for each sample, followed by sequencing on an Illumina MiSeq platform. Analysis showed that bottlenose dolphins harbor diverse bacterial communities with a unique microbial community at each body system. Additionally, the bottlenose dolphin bacterial microbiome was clearly distinct to the aquatic microbiome from their surrounding habitat. These results are in close agreement with other cetacean microbiome studies, while our study is the first to explore what was found to be a diverse bottlenose dolphin genital microbiome. The core bacterial communities identified in this study in apparently healthy animals might be informative for future health monitoring of bottlenose dolphins.

Pulmonary function testing as a diagnostic tool to assess respiratory health in bottlenose dolphins Tursiops truncatus

Pulmonary function testing was performed in 3 bottlenose dolphins Tursiops truncatus (1 female and 2 males) under managed care during a 2 yr period to assess whether these data provide diagnostic information about respiratory health. Pulmonary radiographs and standard clinical testing were used to evaluate the pulmonary health of each dolphin. The female dolphin (F1) had evidence of chronic pulmonary fibrosis, and 1 male (M2) developed pneumonia during the study. Pulmonary function data were collected from maximal respiratory efforts in water and from spontaneous breaths while beached. From these data, the flow-volume relationship, the flow measured between 25 and 75% of the expired vital capacity (mid forced expiratory flow, FEF25%-75%), and the percent of the vital capacity (VC) at the peak expiratory flow (%VCPEF), were evaluated and compared with the diagnostic assessment. For maximal respiratory manoeuvres in water, there were no differences in FEF25%-75% or %VCPEF, and the flow-volume relationship showed a consistent pattern for F1. Additionally, FEF25%-75% and %VCPEF decreased by 27 and 52%, respectively, and the flow-volume relationship showed clear flow limitations with emerging disease in M2. While spontaneously breathing on land, M2 also showed a 49% decrease in %VCPEF and changes in the flow-volume relationship, indicating flow limitations following the development of pneumonia. Based on these preliminary results, we suggest that pulmonary function testing should be given more attention as a non-invasive and possibly adjunctive diagnostic tool to evaluate lung health of dolphins under managed care and in the wild.

Microbiota fingerprints within the oral cavity of cetaceans as indicators for population biomonitoring

The composition of mammalian microbiota has been related with the host health status. In this study, we assessed the oral microbiome of 3 cetacean species most commonly found stranded in Iberian Atlantic waters (Delphinus delphis, Stenella coeruleoalba and Phocoena phocoena), using 16S rDNA-amplicon metabarcoding. All oral microbiomes were dominated by Proteobacteria, Firmicutes, Bacteroidetes and Fusobacteria bacteria, which were also predominant in the oral cavity of Tursiops truncatus. A Constrained Canonical Analysis (CCA) showed that the major factors shaping the composition of 38 oral microbiomes (p-value < 0.05) were: (i) animal species and (ii) age class, segregating adults and juveniles. The correlation analysis also grouped the microbiomes by animal stranding location and health status. Similar discriminatory patterns were detected using the data from a previous study on Tursiops truncatus, indicating that this correlation approach may facilitate data comparisons between different studies on several cetacean species. This study identified a total of 15 bacterial genera and 27 OTUs discriminating between the observed CCA groups, which can be further explored as microbiota fingerprints to develop (i) specific diagnostic assays for cetacean population conservation and (ii) bio-monitoring approaches to assess the health of marine ecosystems from the Iberian Atlantic basin, using cetaceans as bioindicators.

Molecular footprints of inshore aquatic adaptation in Indo-Pacific humpback dolphin (Sousa chinensis)

The Indo-Pacific humpback dolphin, Sousa chinensis, being a member of cetaceans, had fully adapted to inshore waters. As a threatened marine mammal, little molecular information available for understanding the genetic basis of ecological adaptation. We firstly sequenced and obtained the draft genome map of S. chinensis. Phylogenetic analysis in this study, based on the single copy orthologous genes of the draft genome, is consistent with traditional phylogenetic classification. The comparative genomic analysis indicated that S. chinensis had 494 species-specific gene families, which involved immune, DNA repair and sensory systems associated with the potential adaption mechanism. We also identified the expansion and positive selection genes in S. chinensis lineage to investigate the potential adaptation mechanism. Our study provided the potential insight into the molecular bases of ecological adaptation in Indo-Pacific humpback dolphin and will be also valuable for future understanding the ecological adaptation and evolution of cetaceans at the genomic level.

Environmental Sources of Bacteria Differentially Influence Host-Associated Microbial Dynamics

These results provide valuable insights into the ecological influence of exogenous microbial exposure, as well as laying the foundation for improving aquarium management practices. By comparing data for dolphins from aquaria that use natural versus artificial seawater, we demonstrate the potential influence of aquarium water disinfection procedures on dolphin microbial dynamics.

Host-associated microbial dynamics are influenced by dietary and immune factors, but how exogenous microbial exposure shapes host-microbe dynamics remains poorly characterized. To investigate this phenomenon, we characterized the skin, rectum, and respiratory tract-associated microbiota in four aquarium-housed dolphins daily over a period of 6 weeks, including administration of a probiotic during weeks 4 to 6. The environmental bacterial sources were also characterized, including the animals’ human handlers, the aquarium air and water, and the dolphins’ food supply. Continuous microbial exposure occurred between all sites, yet each environment maintained a characteristic microbiota, suggesting that the majority of exposure events do not result in colonization. Small changes in water physicochemistry had a significant but weak correlation with change in dolphin-associated bacterial richness but had no influence on phylogenetic diversity. Food and air microbiota were the richest and had the largest conditional influence on other microbiota in the absence of probiotics, but during probiotic administration, food alone had the largest influence on the stability of the dolphin microbiota. Our results suggest that respiratory tract and gastrointestinal epithelium interactions with air- and food-associated microbes had the biggest influence on host-microbiota dynamics, while other interactions, such as skin transmission, played only a minor role. Finally, direct oral stimulation with a foreign exogenous microbial source can have a profound effect on microbial stability.

IMPORTANCE These results provide valuable insights into the ecological influence of exogenous microbial exposure, as well as laying the foundation for improving aquarium management practices. By comparing data for dolphins from aquaria that use natural versus artificial seawater, we demonstrate the potential influence of aquarium water disinfection procedures on dolphin microbial dynamics.

Temporal and Regional Variability in the Skin Microbiome of Humpback Whales along the Western Antarctic Peninsula

The skin is the first line of defense between an animal and its environment, and disruptions in skin-associated microorganisms can be linked to an animal's health and nutritional state. To better understand the skin microbiome of large whales, high-throughput sequencing of partial small subunit rRNA genes was used to study the skin-associated bacteria of 89 seemingly healthy humpback whales (Megaptera novaeangliae) sampled along the Western Antarctic Peninsula (WAP) during early (2010) and late (2013) austral summers. Six core groups of bacteria were present in 93% or more of all humpback skin samples. A shift was observed in the average relative abundances of these core bacteria over time, with the emergence of four additional core groups of bacteria that corresponded to a decrease in water temperature, possibly caused by season- or foraging-related changes in skin biochemistry that influenced microbial growth, or other temporal factors. The skin microbiome differed between whales sampled at several regional locations along the WAP, suggesting that environmental factors or population may also influence the whale skin microbiome. Overall, the skin microbiome of humpback whales appears to provide insight into animal- and environment-related factors and may serve as a useful indicator for animal health or ecosystem alterations.

IMPORTANCE The microbiomes of wild animals are currently understudied but may provide information about animal health and/or animal-environment interactions. In the largest sampling of any marine mammal microbiome, this study demonstrates conservation in the skin microbiome of 89 seemingly healthy humpback whales sampled in the Western Antarctic Peninsula, with shifts in the bacterial community composition related to temporal and regional variability. This study is important because it suggests that the skin microbiome of humpback whales could provide insight into animal nutritional or seasonal/environment-related factors, which are becoming increasingly important to recognize due to unprecedented rates of climate change and anthropogenic impact on ocean ecosystems.

Exhaled breath condensate methods adapted from human studies using longitudinal metabolomics for predicting early health alterations in dolphins

Monitoring health conditions is essential to detect early asymptomatic stages of a disease. To achieve this, blood, urine and breath samples are commonly used as a routine clinical diagnostic. These samples offer the opportunity to detect specific metabolites related to diseases and provide a better understanding of their development. Although blood samples are commonly used routinely to monitor health, the implementation of a relatively noninvasive technique, such as exhaled breath condensate (EBC) analysis, may further benefit the well-being of both humans and other animals. EBC analysis can be used to track possible physical or biochemical alterations caused by common diseases of the bottlenose dolphin (Tursiops truncatus), such as infections or inflammatory-mediated processes. We have used an untargeted metabolomic method with liquid chromatography-mass spectrometry analysis of EBC samples to determine biomarkers related to disease development. In this study, five dolphins under human care were followed up for 1 year. We collected paired blood, physical examination information, and EBC samples. We then statistically correlated this information to predict specific health alterations. Three dolphins provided promising case study information about biomarkers related to cutaneous infections, respiratory infections, dental disease, or hormonal changes (pregnancy). The use of complementary liquid chromatography platforms, with hydrophilic interaction chromatography and reverse-phased columns, allowed us to detect a wide spectrum of EBC biomarker compounds that could be related to these health alterations. Moreover, these two analytical techniques not only provided complementary metabolite information but in both cases they also provided promising diagnostic information for these health conditions. Graphical abstract Collection of the exhaled condensed breath from a bottlenose dolphin from U.S. Navy Marine Mammal Program (MMP).

Extensive Core Microbiome in Drone-Captured Whale Blow Supports a Framework for Health Monitoring

The pulmonary system is a common site for bacterial infections in cetaceans, but very little is known about their respiratory microbiome. We used a small, unmanned hexacopter to collect exhaled breath condensate (blow) from two geographically distinct populations of apparently healthy humpback whales (Megaptera novaeangliae), sampled in the Massachusetts coastal waters off Cape Cod (n = 17) and coastal waters around Vancouver Island (n = 9). Bacterial and archaeal small-subunit rRNA genes were amplified and sequenced from blow samples, including many of sparse volume, as well as seawater and other controls, to characterize the associated microbial community. The blow microbiomes were distinct from the seawater microbiomes and included 25 phylogenetically diverse bacteria common to all sampled whales. This core assemblage comprised on average 36% of the microbiome, making it one of the more consistent animal microbiomes studied to date. The closest phylogenetic relatives of 20 of these core microbes were previously detected in marine mammals, suggesting that this core microbiome assemblage is specialized for marine mammals and may indicate a healthy, noninfected pulmonary system. Pathogen screening was conducted on the microbiomes at the genus level, which showed that all blow and few seawater microbiomes contained relatives of bacterial pathogens; no known cetacean respiratory pathogens were detected in the blow. Overall, the discovery of a shared large core microbiome in humpback whales is an important advancement for health and disease monitoring of this species and of other large whales. IMPORTANCE The conservation and management of large whales rely in part upon health monitoring of individuals and populations, and methods generally necessitate invasive sampling. Here, we used a small, unmanned hexacopter drone to noninvasively fly above humpback whales from two populations, capture their exhaled breath (blow), and examine the associated microbiome. In the first extensive examination of the large-whale blow microbiome, we present surprising results about the discovery of a large core microbiome that was shared across individual whales from geographically separated populations in two ocean basins. We suggest that this core microbiome, in addition to other microbiome characteristics, could be a useful feature for health monitoring of large whales worldwide.

Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea

Marine mammals play crucial ecological roles in the oceans, but little is known about their microbiotas. Here we study the bacterial communities in 337 samples from 5 body sites in 48 healthy dolphins and 18 healthy sea lions, as well as those of adjacent seawater and other hosts. The bacterial taxonomic compositions are distinct from those of other mammals, dietary fish and seawater, are highly diverse and vary according to body site and host species. Dolphins harbour 30 bacterial phyla, with 25 of them in the mouth, several abundant but poorly characterized Tenericutes species in gastric fluid and a surprisingly paucity of Bacteroidetes in distal gut. About 70% of near-full length bacterial 16S ribosomal RNA sequences from dolphins are unique. Host habitat, diet and phylogeny all contribute to variation in marine mammal distal gut microbiota composition. Our findings help elucidate the factors structuring marine mammal microbiotas and may enhance monitoring of marine mammal health.

Pathogen surveillance in wild bottlenose dolphins Tursiops truncatus

The number and prevalence of diseases is rapidly increasing in the marine ecosystem. Although there is an increase in the number of marine diseases observed world-wide, current understanding of the pathogens associated with marine mammals is limited. An important need exists to develop and apply platforms for rapid detection and characterization of pathogenic agents to assess, prevent and respond to disease outbreaks. In this study, a broad-spectrum molecular detection technology capable of detecting all sequenced microbial organisms, the Lawrence Livermore Microbial Detection Array, was used to assess the microbial agents that could be associated with wild Atlantic dolphins. Blowhole, gastric, and fecal samples from 8 bottlenose dolphins were collected in Charleston, SC, as part of the dolphin assessment effort. The array detected various microbial agents from the dolphin samples. Clostridium perfringens was most prevalent in the samples surveyed using the microarray. This pathogen was also detected using microbiological culture techniques. Additionally, Campylobacter sp., Staphylococcus sp., Erwinia amylovora, Helicobacter pylori, and Frankia sp. were also detected in more than one dolphin using the microarray, but not in culture. This study provides the first survey of pathogens associated with 3 tissue types in dolphins using a broad-spectrum microbial detection microarray and expands insight on the microbial community profile in dolphins.

Humpback whale populations share a core skin bacterial community: towards a health index for marine mammals?

Microbes are now well regarded for their important role in mammalian health. The microbiology of skin--a unique interface between the host and environment--is a major research focus in human health and skin disorders, but is less explored in other mammals. Here, we report on a cross-population study of the skin-associated bacterial community of humpback whales (Megaptera novaeangliae), and examine the potential for a core bacterial community and its variability with host (endogenous) or geographic/environmental (exogenous) specific factors. Skin biopsies or freshly sloughed skin from 56 individuals were sampled from populations in the North Atlantic, North Pacific and South Pacific oceans and bacteria were characterized using 454 pyrosequencing of SSU rRNA genes. Phylogenetic and statistical analyses revealed the ubiquity and abundance of bacteria belonging to the Flavobacteria genus Tenacibaculum and the Gammaproteobacteria genus Psychrobacter across the whale populations. Scanning electron microscopy of skin indicated that microbial cells colonize the skin surface. Despite the ubiquity of Tenacibaculum and Psychrobater spp., the relative composition of the skin-bacterial community differed significantly by geographic area as well as metabolic state of the animals (feeding versus starving during migration and breeding), suggesting that both exogenous and endogenous factors may play a role in influencing the skin-bacteria. Further, characteristics of the skin bacterial community from these free-swimming individuals were assembled and compared to two entangled and three dead individuals, revealing a decrease in the central or core bacterial community members (Tenacibaculum and Psychrobater spp.), as well as the emergence of potential pathogens in the latter cases. This is the first discovery of a cross-population, shared skin bacterial community. This research suggests that the skin bacteria may be connected to humpback health and immunity and could possibly serve as a useful index for health and skin disorder monitoring of threatened and endangered marine mammals.

Temporal stability and species specificity in bacteria associated with the bottlenose dolphins respiratory system

We demonstrate that the exhaled breath condensate, or 'blow', from marine mammals can be used to examine respiratory associated microbial communities using non-invasive sampling methods. Blow samples from two species of bottlenose dolphin, Tursiops truncatus and T. aduncus, along with hybrid offspring, were examined using molecular microbial ecology methods. A temporal analysis revealed that microbial community structure of each individual remained distinct from other individuals over a two-month period, indicting strong host specificity. The taxonomic composition of samples, based on pyrosequencing of the V1-V3 regions of the 16S rRNA gene, from 24 healthy individuals was dominated by the Cardiobacteraceae lineage of Gammaproteobacteria, comprising on average 52% of sequences in all samples. Sequences in this taxa were associated with novel clades that contain only sequences from dolphin respiratory tracts. Other genera that likely form part of the core biota include the Saccharospirillaceae (Gammaproteobacteria), Arcobacter (Epsilonproteobacteria), Hydrogenimonaceae (Epsilonproteobacteria), Halotalea (Gammaproteobacteria), Aquimarina (Flavobacteria) and Helococcus (Clostridia). Significant differences between samples from different species were observed only at the species/ strain level, driven by the relative contributions of strains from the most common phylogenetic lineages. Analysis of communities associated with hybrid animals provides tentative evidence for a paternal role in community assembly. Clear overlap was observed with data collected by capture and swabbing of bottlenose dolphins blowholes, indicating this method provides a novel non-invasive alternative to monitoring marine mammal population health.

Humpback whales harbour a combination of specific and variable skin bacteria

Investigations of marine mammal skin-associated microbiota are limited to cultivation-based studies of lesioned individuals, resulting in a lack of understanding about the composition of 'normal' skin-associated microbial communities, their variation among individuals, and whether or not the microbial communities change with host health or environmental exposures. In this study, bacterial communities associated with the skin of 19 North Pacific humpback whales (Megaptera novaeangliae), including skin from three health-compromised individuals, were examined using small subunit ribosomal RNA gene-based culture-independent techniques. These analyses revealed that the skin-associated bacteria were significantly different from free-living bacterial communities in the surrounding seawater. Two novel groups within the Flavobacteriaceae family of the Bacteroidetes phylum were found to be associated with multiple whales, including a species within the Tenacibaculum genus that associated with 95% of the individuals. Statistical analyses revealed that a group of eight 'healthy' whales harboured similar microbial communities, while the health-compromised and other 'healthy' animals harboured communities that were unique to the specific animal. These results describe two components of the whale skin bacterial community: a specific and potentially co-evolved fraction, and a more variable microbial community fraction that may offer a diagnostic-type tool for investigating the health and life-related events of these endangered animals.