A novel non-invasive tool for disease surveillance of free-ranging whales and its relevance to conservation programs

An evolutionary medicine perspective on the cetacean pulmonary immune system - The first identification of SP-D and LBP in the bottlenose dolphin (Tursiops truncatus)

Evolutionary medicine expresses the present status of biomolecules affected by past evolutionary events. To clarify the whole picture of cetacean pneumonia, which is a major threat to cetaceans, their pulmonary immune system should be studied from the perspective of evolutionary medicine. In this in silico study, we focused on cetacean surfactant protein D (SP-D) and lipopolysaccharide-binding protein (LBP) as two representative molecules of the cetacean pulmonary immune system. Sequencing and analyzing SP-D and LBP in the bottlenose dolphin (Tursiops truncatus) lung and liver tissue collected post-mortem elucidated not only basic physicochemical properties but also their evolutionary background. This is the first study to report the sequences and expression of SP-D and LBP in the bottlenose dolphin. Besides, our findings also suggest the direction of an evolutionary arms race in the cetacean pulmonary immune system. These results have important positive implications for cetacean clinical medicine.

Pathogen Exposure in White Whales (Delphinapterus leucas) in Svalbard, Norway

The Svalbard white whale (Delphinapterus leucas) population is one of the smallest in the world, making it particularly vulnerable to challenges such as climate change and pathogens. In this study, serum samples from live captured (2001−2016) white whales from this region were investigated for influenza A virus (IAV) antibodies (Abs) (n = 27) and RNA (n = 25); morbillivirus (MV) Abs (n = 3) and RNA (n = 25); Brucella spp. Abs; and Toxoplasma gondii Abs (n = 27). IAV Abs were found in a single adult male that was captured in Van Mijenfjorden in 2001, although no IAV RNA was detected. Brucella spp. Abs were found in 59% of the sample group (16/27). All MV and T. gondii results were negative. The results show that Svalbard white whales have been exposed to IAV and Brucella spp., although evidence of disease is lacking. However, dramatic changes in climate and marine ecosystems are taking place in the Arctic, so surveillance of health parameters, including pathogens, is critical for tracking changes in the status of this vulnerable population.

Evaluating beluga (Delphinapterus leucas) blow samples as a potential diagnostic for immune function gene expression within the respiratory system

Evaluating respiratory health is important in the management of cetaceans, which are vulnerable to respiratory diseases. Quantifying the expression of genes related to immune function within the respiratory tract could be a valuable tool for directly assessing respiratory health. Blow (exhale) samples allow DNA analysis, and we hypothesized that RNA could also be isolated from blow samples for gene expression studies of immune function. We evaluated the potential to extract RNA from beluga blow samples and tested whether transcripts associated with immune function could be detected with endpoint polymerase chain reaction. A total of 54 blow samples were collected from clinically healthy aquarium belugas (n = 3), and 15 were collected from wild belugas temporarily restrained for health assessment in Bristol Bay, Alaska (n = 9). Although RNA yield varied widely (range, 0-265.2 ng; mean = 85.8; SD = 71.3), measurable RNA was extracted from 97% of the samples. Extracted RNA was assessed in 1-6 PCR reactions targeting housekeeping genes (Rpl8, Gapdh or ActB) or genes associated with immune function (TNFα, IL-12p40 or Cox-2). Fifty of the aquarium samples (93%) amplified at least one transcript; overall PCR success for housekeeping genes (96/110, 87%) and genes associated with immune function (90/104, 87%) were similarly high. Both RNA yield and overall PCR success (27%) were lower for wild beluga samples, which is most likely due to the reduced forcefulness of the exhale when compared with trained or free-swimming belugas. Overall, the high detection rate with PCR suggests measuring gene expression in blow samples could provide diagnostic information about immune responses within the respiratory tract. While further study is required to determine if quantitative gene expression data from blow samples is associated with disease states, the non-invasive nature of this approach may prove valuable for belugas, which face increasing anthropogenic disturbances.

A Review of Non-Invasive Sampling in Wildlife Disease and Health Research: What’s New?

Simple Summary

The interest in wildlife research has increased in the last decades as more scientists work within a One Health framework that regards human, livestock and wildlife health as connected entities. To minimise the impact of research on wildlife, collecting samples with as little disturbance of the animals as possible is important. In our review, we assess the use of so-called non-invasive sampling and summarise which samples can be used successfully when carrying out research on wildlife diseases and health status. Our results show that interest in minimally invasive sampling has steadily increased since the 2010s. Topics able to employ these methods include disease research, but also stress and other hormone assessments, pollution studies, and dietary studies. At the moment, such methods are mainly used to collect samples from land mammals, however, they can also be used in a wide range of other animals. Ever more capable analytical methods will allow for an even wider use of such “animal-friendly” sampling methods.

Abstract

In the last decades, wildlife diseases and the health status of animal populations have gained increasing attention from the scientific community as part of a One Health framework. Furthermore, the need for non-invasive sampling methods with a minimal impact on wildlife has become paramount in complying with modern ethical standards and regulations, and to collect high-quality and unbiased data. We analysed the publication trends on non-invasive sampling in wildlife health and disease research and offer a comprehensive review on the different samples that can be collected non-invasively. We retrieved 272 articles spanning from 1998 to 2021, with a rapid increase in number from 2010. Thirty-nine percent of the papers were focussed on diseases, 58% on other health-related topics, and 3% on both. Stress and other physiological parameters were the most addressed research topics, followed by viruses, helminths, and bacterial infections. Terrestrial mammals accounted for 75% of all publications, and faeces were the most widely used sample. Our review of the sampling materials and collection methods highlights that, although the use of some types of samples for specific applications is now consolidated, others are perhaps still underutilised and new technologies may offer future opportunities for an even wider use of non-invasively collected samples.

Insights on Gut and Skin Wound Microbiome in Stranded Indo-Pacific Finless Porpoise (Neophocaena phocaenoides)

The gut microbiome is a unique marker for cetaceans’ health status, and the microbiome composition of their skin wounds can indicate a potential infection from their habitat. Our study provides the first comparative analysis of the microbial communities from gut regions and skin wounds of an individual Indo-Pacific finless porpoise (Neophocaena phocaenoides). Microbial richness increased from the foregut to the hindgut with variation in the composition of microbes. Fusobacteria (67.51% ± 5.10%), Firmicutes (22.00% ± 2.60%), and Proteobacteria (10.47% ± 5.49%) were the dominant phyla in the gastrointestinal tract, while Proteobacteria (76.11% ± 0.54%), Firmicutes (22.00% ± 2.60%), and Bacteroidetes (10.13% ± 0.49%) were the dominant phyla in the skin wounds. The genera Photobacterium, Actinobacillus, Vibrio, Erysipelothrix, Tenacibaculum, and Psychrobacter, considered potential pathogens for mammals, were identified in the gut and skin wounds of the stranded Indo-Pacific finless porpoise. A comparison of the gut microbiome in the Indo-Pacific finless porpoise and other cetaceans revealed a possible species-specific gut microbiome in the Indo-Pacific finless porpoise. There was a significant difference between the skin wound microbiomes in terrestrial and marine mammals, probably due to habitat-specific differences. Our results show potential species specificity in the microbiome structure and a potential threat posed by environmental pathogens to cetaceans.

First Unmanned Aerial Vehicle Observation of Epimeletic Behavior in Indo-Pacific Humpback Dolphins

Simple Summary

In this study, we reported a case of epimeletic behavior in Indo-Pacific humpback dolphin. Using a combination of drone and conventional photography, we were able to comprehensively document individual body condition, swimming pattern, and group behavior during the epimeletic event. Our research highlighted the application of drones in wildlife research to provide important insights into the health, behavior, and ecology of free-ranging populations.

Abstract

Epimeletic behavior has been reported in various species of cetaceans and sometimes in wild populations during vessel-based surveys. Epimeletic behavior in cetaceans involves complex social interactions which have been described using observational and acoustic studies. The recent advances in unmanned aerial vehicle (UAV) technology allowed its application in wildlife research and frequently in cetaceans in conjunction with vessel-based surveys. This article is the first report of intraspecific epimeletic behavior of Indo-Pacific humpback dolphins (Sousa chinensis) in Hong Kong waters using a combination of UAV- and vessel-based photography. Using both techniques, we were able to observe and qualitative analyze the individual body condition, group behavior, and swimming pattern during the epimeletic event. This study highlighted that UAVs can be used to observe the complex social behaviors and interactions of cetaceans from the aerial angle while keeping a minimal level of disturbance to the animals. Aerial footage can also be quantitatively analyzed to provide further insights on the group behaviors of cetaceans. The application allows efficient assessment of health, behavior, and ecology of wild animals, offering valuable opportunities for researchers working on free-ranging populations.

Fundamental Concepts, Knowledge Gaps and Key Concerns Relating to Welfare and Survival of Stranded Cetaceans

Wildlife management can influence animal welfare and survival, although both are often not explicitly integrated into decision making. This study explores fundamental concepts and key concerns relating to the welfare and survival of stranded cetaceans. Using the Delphi method, the opinions of an international, interdisciplinary expert panel were gathered, regarding the characterisation of stranded cetacean welfare and survival likelihood, knowledge gaps and key concerns. Experts suggest that stranded cetacean welfare should be characterised based on interrelated aspects of animals’ biological function, behaviour, and mental state and the impacts of human interventions. The characterisation of survival likelihood should reflect aspects of stranded animals’ biological functioning and behaviour as well as a 6-month post-re-floating survival marker. Post-release monitoring was the major knowledge gap for survival. Welfare knowledge gaps related to diagnosing internal injuries, interpreting behavioural and physiological parameters, and euthanasia decision making. Twelve concerns were highlighted for both welfare and survival likelihood, including difficulty breathing and organ compression, skin damage and physical traumas, separation from conspecifics, and suffering and stress due to stranding and human intervention. These findings indicate inextricable links between perceptions of welfare state and the likely survival of stranded cetaceans and demonstrate a need to integrate welfare science alongside conservation biology to achieve effective, ethical management at strandings.

Drone Surveys Are More Accurate Than Boat-Based Surveys of Bottlenose Dolphins (Tursiops truncatus)

Generating accurate estimates of group sizes or behaviours of cetaceans from boat-based surveys can be challenging because much of their activity occurs below the water surface and observations are distorted by horizontal perspectives. Automated observation using drones is an emerging research tool for animal behavioural investigations. However, drone-based and boat-based survey methods have not been quantitatively compared for small, highly mobile cetaceans, such as Delphinidae. Here, we conduct paired concurrent boat-based and drone-based surveys, measuring the number of individuals in 21 groups and the behaviour within 13 groups of bottlenose dolphin (Tursiops truncatus). We additionally assessed the ability to detect behaviour events by the drone that would not be detectable from the boat. Drone-derived abundance counts detected 26.4% more individuals per group on average than boat-based counts (p = 0.003). Drone-based behaviour observations detected travelling 55.2% more frequently and association in subgroups 80.4% more frequently than boat-based observations (p < 0.001 for both comparisons). Whereas foraging was recorded 58.3% and resting 15.1% less frequently by the drone than by boat-based surveys, respectively (p = 0.014 and 0.024). A considerable number of underwater behaviours ranging from individual play activities to intra- and inter-species interactions (including those with humans) were observed from the drone that could not be detected from the boat. Our findings demonstrate that drone surveys can improve the accuracy of population counts and behavioural data for small cetaceans and the magnitude of the discrepancies between the two methods highlights the need for cautious interpretation of studies that have relied on boat-derived data.

Zoonotic Blood-Borne Pathogens in Non-Human Primates in the Neotropical Region: A Systematic Review

Background: Understanding which non-human primates (NHPs) act as a wild reservoir for blood-borne pathogens will allow us to better understand the ecology of diseases and the role of NHPs in the emergence of human diseases in Ecuador, a small country in South America that lacks information on most of these pathogens. Methods and principal findings: A systematic review was carried out using PRISMA guidelines from 1927 until 2019 about blood-borne pathogens present in NHPs of the Neotropical region (i.e., South America and Middle America). Results: A total of 127 publications were found in several databases. We found in 25 genera (132 species) of NHPs a total of 56 blood-borne pathogens in 197 records where Protozoa has the highest number of records in neotropical NHPs (n = 128) compared to bacteria (n = 12) and viruses (n = 57). Plasmodium brasilianum and Trypanosoma cruzi are the most recorded protozoa in NHP. The neotropical primate genus with the highest number of blood-borne pathogens recorded is Alouatta sp. (n = 32). The use of non-invasive samples for neotropical NHPs remains poor in a group where several species are endangered or threatened. A combination of serological and molecular techniques is common when detecting blood-borne pathogens. Socioecological and ecological risk factors facilitate the transmission of these parasites. Finally, a large number of countries remain unsurveyed, such as Ecuador, which can be of public health importance. Conclusions and significance: NHPs are potential reservoirs of a large number of blood-borne pathogens. In Ecuador, research activities should be focused on bacteria and viruses, where there is a gap of information for neotropical NHPs, in order to implement surveillance programs with regular and effective monitoring protocols adapted to NHPs.

Is Harbor Porpoise (Phocoena phocoena) Exhaled Breath Sampling Suitable for Hormonal Assessments?

Simple Summary

The progress of animal welfare in wildlife conservation and research calls for more non-invasive sampling techniques. In cetaceans, exhaled breath condensate (blow)—a mixture of cells, mucus and fluids expelled through the force of a whale’s exhale—is a unique sampling matrix for hormones, bacteria and genetic material, among others. Especially the detection of steroid hormones, such as cortisol, is being investigated as stress indicators in several species. As the only native cetacean in Germany, harbor porpoises (Phocoena phocoena) are of special conservation concern and research interest. So far, strandings and live captures have been the only method to obtain samples from free-ranging individuals, and novel, non-invasive monitoring methods are desirable for this small cetacean species. Hence, three different blow collection devices were tested on harbor porpoises. All samples were analyzed for cortisol using a commercially available immunosorbent assay. The most suitable protocol for sampling, storage and processing is using a sterile 50 mL centrifuge tube. This pilot study shows that cortisol can be detected in the exhale of harbor porpoises, thus paving the way for future studies and most likely successful non-invasive small cetacean health monitoring through blow.

Abstract

Over the last decades, exhaled breath sampling has been established for laboratory analysis in various cetacean species. Due to their small size, the usability of respiratory vapor for hormone assessments was questionable in harbor porpoises (Phocoena phocoena). This pilot study compared three different blow collection devices for their suitability in the field and during laboratory processing: a sterile petri dish covered by a Nitex membrane, as well as sterile 50 mL centrifuge tubes with or without manganese(II) chloride as a stabilizer. Collected exhales varied between three, five or ten, depending on feasibility. Hormones were extracted through an ether mix, followed by centrifugal evaporation and cortisol analysis using an immunoassay. Although close to the lower end of the assay’s dynamic range, the ELISA produced results (n = 110, 0.102–0.937 ng/mL). Hence, a simple 50 mL centrifuge tube was determined as the best suited blow collection device, while three consecutive exhales proved sufficient to yield results. These findings are promising regarding the suitability of exhaled breath as a matrix for future endocrine and immune system-related studies in harbor porpoises. If further advanced, blow sampling can become an important, non-invasive tool for studying and monitoring health, stress levels and diseases in harbor porpoises.

Streptococcal Infections in Marine Mammals

Marine mammals are sentinels for the marine ecosystem and threatened by numerous factors including infectious diseases. One of the most frequently isolated bacteria are beta-hemolytic streptococci. However, knowledge on ecology and epidemiology of streptococcal species in marine mammals is very limited. This review summarizes published reports on streptococcal species, which have been detected in marine mammals. Furthermore, we discuss streptococcal transmission between and adaptation to their marine mammalian hosts. We conclude that streptococci colonize and/or infect marine mammals very frequently, but in many cases, streptococci isolated from marine mammals have not been further identified. How these bacteria disseminate and adapt to their specific niches can only be speculated due to the lack of respective research. Considering the relevance of pathogenic streptococci for marine mammals as part of the marine ecosystem, it seems that they have been neglected and should receive scientific interest in the future.

Assessing the Behavioural Responses of Small Cetaceans to Unmanned Aerial Vehicles

Unmanned Aerial Vehicles (UAVs), or drones, have recently emerged as a relatively affordable and accessible method for studying wildlife. Vertical Take-off and Landing (VTOL) UAVs are appropriate for morphometric, behavioural, abundance and demographic studies of marine mammals, providing a stable, nonintrusive and highly manoeuvrable platform. Previous studies using VTOL UAVs have been conducted on various marine mammal species, but specific studies regarding behavioural responses to these devices are limited and scarce. The aim of this study was to evaluate the immediate behavioural responses of common (Delphinus delphis) and bottlenose (Tursiops truncatus) dolphins to a VTOL UAV flown at different altitudes. A multirotor (quadcopter) UAV with an attached GoPro camera was used. Once a dolphin group was located, the UAV was flown at a starting height of 50 m directly above the group, subsequently descending 5 m every 30 s until reaching 5 m. We assessed three behavioural responses to a VTOL UAV at different heights: (i) direction changes, (ii) swimming speed and (iii) diving. Responses by D. delphis (n = 15) and T. truncatus (n = 10) groups were analysed separately. There were no significant responses of T. truncatus to any of the studied variables. For D. delphis, however, there were statistically significant changes in direction when the UAV was flown at a height of 5 m. Our results indicate that UAVs do not induce immediate behavioural responses in common or bottlenose dolphins when flown at heights > 5 m, demonstrating that the use of VTOL UAVs to study dolphins has minimal impact on the animals. However, we advise the use of the precautionary principle when interpreting these results as characteristics of this study site (e.g., high whale-watching activity) may have habituated dolphins to anthropogenic disturbance.

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.

Operational Protocols for the Use of Drones in Marine Animal Research

The use of drones to study marine animals shows promise for the examination of numerous aspects of their ecology, behaviour, health and movement patterns. However, the responses of some marine phyla to the presence of drones varies broadly, as do the general operational protocols used to study them. Inconsistent methodological approaches could lead to difficulties comparing studies and can call into question the repeatability of research. This review draws on current literature and researchers with a wealth of practical experience to outline the idiosyncrasies of studying various marine taxa with drones. We also outline current best practice for drone operation in marine environments based on the literature and our practical experience in the field. The protocols outlined herein will be of use to researchers interested in incorporating drones as a tool into their research on marine animals and will help form consistent approaches for drone-based studies in the future.

Life history and social structure as drivers of persistent organic pollutant levels and stable isotopes in Hawaiian false killer whales (Pseudorca crassidens)

False killer whales are long-lived, slow to mature, apex predators, and therefore susceptible to bioaccumulation of persistent organic pollutants (POPs). Hawaiian waters are home to three distinct populations: pelagic; Northwestern Hawaiian Islands (NWHI) insular; and main Hawaiian Islands (MHI) insular. Following a precipitous decline over recent decades, the MHI population was listed as "endangered" under the Endangered Species Act in 2012. This study assesses the risk of POP exposure to these populations by examining pollutant concentrations and ratios from blubber samples (n = 56) related to life history characteristics and MHI social clusters. Samples were analyzed for PCBs, DDTs, PBDEs, and some organochlorine pesticides. Skin samples (n = 52) were analyzed for stable isotopes δ¹³C and δ¹⁵N to gain insight into MHI false killer whale foraging ecology. Pollutant levels were similar among populations, although MHI whales had a significantly higher mean ratio of DDTs/PCBs than NWHI whales. The ∑PCB concentrations of 28 MHI individuals (68%) sampled were equal to or greater than suggested thresholds for deleterious health effects in marine mammals. The highest POP values among our samples were found in four stranded MHI animals. Eight of 24 MHI adult females have not been documented to have given birth; whether they have yet to reproduce, are reproductive senescent, or are experiencing reproductive dysfunction related to high POP exposure is unknown. Juvenile/sub-adults had significantly higher concentrations of certain contaminants than those measured in adults, and may be at greater risk of negative health effects during development. Multivariate analyses, POP ratios, and stable isotope ratios indicate varying risk of POP exposure, foraging locations and potentially prey items among MHI social clusters. Our findings provide invaluable insight into the ongoing risk POPs pose to the MHI population's viability, as well as consideration of risk for the NWHI and pelagic stocks.

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.

The use of Unmanned Aerial Vehicles (UAVs) to sample the blow microbiome of small cetaceans

Recent studies describe the use of UAVs in collecting blow samples from large whales to analyze the microbial and viral community in exhaled air. Unfortunately, attempts to collect blow from small cetaceans have not been successful due to their swimming and diving behavior. In order to overcome these limitations, in this study we investigated the application of a specific sampling tool attached to a UAV to analyze the blow from small cetaceans and their respiratory microbiome. Preliminary trials to set up the sampling tool were conducted on a group of 6 bottlenose dolphins (Tursiops truncatus) under human care, housed at Acquario di Genova, with approximately 1 meter distance between the blowing animal and the tool to obtain suitable samples. The same sampling kit, suspended via a 2 meter rope assembled on a waterproof UAV, flying 3 meters above the animals, was used to sample the blows of 5 wild bottlenose dolphins in the Gulf of Ambracia (Greece) and a sperm whale (Physeter macrocephalus) in the southern Tyrrhenian Sea (Italy), to investigate whether this experimental assembly also works for large whale sampling. In order to distinguish between blow-associated microbes and seawater microbes, we pooled 5 seawater samples from the same area where blow samples’ collection were carried out. The the respiratory microbiota was assessed by using the V3-V4 region of the 16S rRNA gene via Illumina Amplicon Sequencing. The pooled water samples contained more bacterial taxa than the blow samples of both wild animals and the sequenced dolphin maintained under human care. The composition of the bacterial community differed between the water samples and between the blow samples of wild cetaceans and that under human care, but these differences may have been mediated by different microbial communities between seawater and aquarium water. The sperm whale’s respiratory microbiome was more similar to the results obtained from wild bottlenose dolphins. Although the number of samples used in this study was limited and sampling and analyses were impaired by several limitations, the results are rather encouraging, as shown by the evident microbial differences between seawater and blow samples, confirmed also by the meta-analysis carried out comparing our results with those obtained in previous studies. Collecting exhaled air from small cetaceans using drones is a challenging process, both logistically and technically. The success in obtaining samples from small cetacean blow in this study in comparison to previous studies is likely due to the distance the sampling kit is suspended from the drone, which reduced the likelihood that the turbulence of the drone propeller interfered with successfully sampling blow, suggested as a factor leading to poor success in previous studies.

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.

Does sociality drive diversity and composition of airway microbiota in cetaceans?

The number of social contacts of mammals is positively correlated with the diversity of their gut microbes. There is some evidence that sociality also affects microbes in the respiratory tract. We tested whether the airway microbiota of cetacean species differ depending on the whales' level of sociality. We sampled the blow of blue (Balaenoptera musculus), grey (Eschrichtius robustus), humpback (Megaptera novaeangliae) and long-finned pilot whales (PWs) (Globicephala melas) and analysed the blow microbiota by barcode tag sequencing targeting the V4 region of the bacterial 16S rRNA gene. Humpback whales (HWs) show higher levels of sociality than blue (BW) and grey (GW), while PWs are the most gregarious among the four species. The blow samples of the HWs showed the highest richness and diversity. HWs were also the only species with a species-specific clustering of their microbial community composition and a relatively large number of core taxa. Therefore, we conclude that it cannot be sociality alone shaping the diversity and composition of airway microbiota. We suggest the whale species' lung volume and size of the plume of exhaled air as an additional factor impacting the transmission potential of blow microbiota from one individual whale to another.

Behaviour reactions of bottlenose dolphins (Tursiops truncatus) to multirotor Unmanned Aerial Vehicles (UAVs)

Unmanned aerial vehicles (UAVs) represent a novel and cost effective research tool to investigate cetacean behaviour, as conventional aircraft are expensive, limited in the altitude they can fly at and potentially disturb sensitive wildlife. In addition, the aerial observation from the UAVs allows assessment of cetacean behaviour from an advantageous perspective and can collect high spatial and temporal resolution data, providing the opportunity to gather accurate data about group size, age class and subsurface behaviour. However, concerns have been raised about the potential risks of disturbance to animals caused by the UAV’s visual and acoustic stimuli. Boat-based surveys were conducted to assess the short-term behavioural responses of resting bottlenose dolphins (Tursiops truncatus) to a lightweight Vertical take-off and landing (VTOL) UAV flown at 10, 25, and 40 m altitude. Changes in group swim direction and frequencies of surface and aerial behavioural events were recorded from an anchored research vessel before (control) and during the aerial survey. The number of reorientation and tail slap events increased significantly between controls and flights when the UAV was flown at 10 m over the animals. In contrast, no significant differences were detected when the aircraft was flown at 25 and 40 m altitude. However, a precautionary approach is recommended for research applications requiring lower flight altitudes, with further research recommended to assess how different cetacean species and age class may respond to the UAV presence.

Genetic and genomic monitoring with minimally invasive sampling methods

The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high-quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low-quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next-generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.

Quantifying hormones in exhaled breath for physiological assessment of large whales at sea

Exhaled breath analysis is a non-invasive assessment tool that has shown promise in human diagnostics, and could greatly benefit research, management, and conservation of large whales. However, hormone assessment of whale respiratory vapor (blow) has been challenged by variable water content and unknown total volume of collected samples. To advance this technique, we investigated urea (a compound present in narrow range in circulation) as a normalizing factor to correct for blow sample concentration. Normalized progesterone, testosterone, and cortisol concentrations of 100 blow samples from 46 photo-identified North Atlantic right whales (Eubalaena glacialis) were more biologically relevant compared to absolute estimates, varying by sex, age class, or individual. Progesterone was elevated in adult females compared with other cohorts and highest in one independently confirmed pregnant female. For both sexes, testosterone was two-fold higher in reproductively mature whales but studied adult females showed the widest variation. Cortisol was present in relatively low concentrations in blow and demonstrated variation between individual whales, suggesting potential for studies of individual differences in adrenal activity. Incorporation of methodologies that normalize sample concentration are essential for blow hormone analysis of free-swimming whales, and measurement of urea could be used to optimize non-invasive physiological assessment of whales.

Fecal steroid hormones reveal reproductive state in female blue whales sampled in the Gulf of California, Mexico

Steroid hormone assessment using non-invasive sample collection techniques can reveal the reproductive status of aquatic mammals and the physiological mechanisms by which they respond to changes in their environment. A portion of the eastern North Pacific blue whale (Balaenoptera musculus) population that seasonally visits the Gulf of California, Mexico has been monitored using photo-identified individuals for over 30 years. The whales use the area in winter-early spring for nursing their calves and feeding and it therefore is well suited for fecal sample collection. Using radioimmunoassays in 25 fecal samples collected between 2009 and 2012 to determine reproductive state and stress, we validated three steroid hormones (progesterone, corticosterone and cortisol) in adult female blue whales. Females that were categorized as pregnant had higher mean fecal progesterone metabolite concentrations (1292.6 ± 415.6 ng·g^-1) than resting and lactating females (14.0 ± 3.7 ng·g^-1; 23.0 ± 5.4 ng·g^-1, respectively). Females classified as pregnant also had higher concentrations of corticosterone metabolites (37.5 ± 9.9 ng·g^-1) than resting and lactating females (17.4 ± 2.0 ng·g^-1; 16.8 ± 2.8 ng·g^-1, respectively). In contrast, cortisol metabolite concentrations showed high variability between groups and no significant relationship to reproductive state. We successfully determined preliminary baseline parameters of key steroid hormones by reproductive state in adult female blue whales. The presence of pregnant or with luteal activity and known lactating females confirms that the Gulf of California is an important winter-spring area for the reproductive phase of these blue whales. The baseline corticosterone levels we are developing will be useful for assessing the impact of the increasing coastal development and whale-watching activities on the whales in the Gulf of California.

Measuring behavioral responses of sea turtles, saltwater crocodiles, and crested terns to drone disturbance to define ethical operating thresholds

Drones are being increasingly used in innovative ways to enhance environmental research and conservation. Despite their widespread use for wildlife studies, there are few scientifically justified guidelines that provide minimum distances at which wildlife can be approached to minimize visual and auditory disturbance. These distances are essential to ensure that behavioral and survey data have no observer bias and form the basis of requirements for animal ethics and scientific permit approvals. In the present study, we documented the behaviors of three species of sea turtle (green turtles, Chelonia mydas, flatback turtles, Natator depressus, hawksbill turtles, Eretmochelys imbricata), saltwater crocodiles (Crocodylus porosus), and crested terns (Thalasseus bergii) in response to a small commercially available (1.4 kg) multirotor drone flown in Northern Territory and Western Australia. Sea turtles in nearshore waters off nesting beaches or in foraging habitats exhibited no evasive behaviors (e.g. rapid diving) in response to the drone at or above 20-30 m altitude, and at or above 10 m altitude for juvenile green and hawksbill turtles foraging on shallow, algae-covered reefs. Adult female flatback sea turtles were not deterred by drones flying forward or stationary at 10 m altitude when crawling up the beach to nest or digging a body pit or egg chamber. In contrast, flyovers elicited a range of behaviors from crocodiles, including minor, lateral head movements, fleeing, or complete submergence when a drone was present below 50 m altitude. Similarly, a colony of crested terns resting on a sand-bank displayed disturbance behaviors (e.g. flight response) when a drone was flown below 60 m altitude. The current study demonstrates a variety of behavioral disturbance thresholds for diverse species and should be considered when establishing operating conditions for drones in behavioral and conservation studies.

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.

Chirosurveillance: The use of native bats to detect invasive agricultural pests

Invasive insect pests cost the agricultural industry billions of dollars annually in crop losses. Timely detection of pests is critical for management efficiency. Innovative pest detection strategies, such as environmental DNA (eDNA) techniques, combined with efficient predators, maximize sampling resolution across space and time and may improve surveillance. We tested the hypothesis that temperate insectivorous bats can be important sentinels of agricultural insect pest surveillance. Specifically, we used a new high-sensitivity molecular assay for invasive brown marmorated stink bugs (Halyomorpha halys) to examine the extent to which big brown bats (Eptesicus fuscus) detect agricultural pests in the landscape. We documented consistent seasonal predation of stink bugs by big brown bats. Importantly, bats detected brown marmorated stink bugs 3–4 weeks earlier than the current standard monitoring tool, blacklight traps, across all sites. We highlight here the previously unrecognized potential ecosystem service of bats as agents of pest surveillance (or chirosurveillance). Additional studies examining interactions between other bat and insect pest species, coupled with comparisons of detectability among various conventional monitoring methods, are needed to verify the patterns extracted from this study. Ultimately, robust economic analyses will be needed to assess the cost-effectiveness of chirosurveillance as a standard strategy for integrated pest management.

Enhanced non-invasive respiratory sampling from bottlenose dolphins for breath metabolomics measurements

Chemical analysis of exhaled breath metabolites is an emerging alternative to traditional clinical testing for many physiological conditions. The main advantage of breath analysis is its inherent non-invasive nature and ease of sample collection. Therefore, there exists a great interest in further development of this method for both humans and animals. The physiology of cetaceans is exceptionally well suited for breath analysis due to their explosive breathing behavior and respiratory tract morphology. At the present time, breath analysis in cetaceans has very limited practical applications, in large part due to lack of widely adopted sampling device(s) and methodologies that are well-standardized. Here, we present an optimized design and the operating principles of a portable apparatus for reproducible collection of exhaled breath condensate from small cetaceans, such as bottlenose dolphins (Tursiops truncatus). The device design is optimized to meet two criteria: standardized collection and preservation of information-rich metabolomic content of the biological sample, and animal comfort and ease of breath sample collection. The intent is to furnish a fully-benchmarked technology that can be widely adopted by researchers and conservationists to spur further developments of breath analysis applications for marine mammal health assessments.

Get the most out of blow hormones: validation of sampling materials, field storage and extraction techniques for whale respiratory vapour samples

Studies are progressively showing that vital physiological data may be contained in the respiratory vapour (blow) of cetaceans. Nonetheless, fundamental methodological issues need to be addressed before hormone analysis of blow can become a reliable technique. In this study, we performed controlled experiments in a laboratory setting, using known doses of pure parent hormones, to validate several technical factors that may play a crucial role in hormone analyses. We evaluated the following factors: (i) practical field storage of samples on small boats during daylong trips; (ii) efficiency of hormone extraction methods; and (iii) assay interference of different sampler types (i.e. veil nylon, nitex nylon mesh and polystyrene dish). Sampling materials were dosed with mock blow samples of known mixed hormone concentrations (progesterone, 17β-estradiol, testosterone, cortisol, aldosterone and triiodothyronine), designed to mimic endocrine profiles characteristic of pregnant females, adult males, an adrenal glucocorticoid response or a zero-hormone control (distilled H2O). Results showed that storage of samples in a cooler on ice preserved hormone integrity for at least 6 h (P = 0.18). All sampling materials and extraction methods yielded the correct relative patterns for all six hormones. However, veil and nitex mesh produced detectable assay interference (mean 0.22 ± 0.04 and 0.18 ± 0.03 ng/ml, respectively), possibly caused by some nylon-based component affecting antibody binding. Polystyrene dishes were the most efficacious sampler for accuracy and precision (P < 0.001), but required an ethanol rinse for improved progesterone recovery (increased 81%; P < 0.001). Awareness of assay interference from exogenous materials is crucial to future studies. This study establishes critical groundwork to help ensure that hormones can be measured accurately in samples obtained from field collections of whale blow.

Stress physiology in marine mammals: how well do they fit the terrestrial model?

Stressors are commonly accepted as the causal factors, either internal or external, that evoke physiological responses to mediate the impact of the stressor. The majority of research on the physiological stress response, and costs incurred to an animal, has focused on terrestrial species. This review presents current knowledge on the physiology of the stress response in a lesser studied group of mammals, the marine mammals. Marine mammals are an artificial or pseudo grouping from a taxonomical perspective, as this group represents several distinct and diverse orders of mammals. However, they all are fully or semi-aquatic animals and have experienced selective pressures that have shaped their physiology in a manner that differs from terrestrial relatives. What these differences are and how they relate to the stress response is an efflorescent topic of study. The identification of the many facets of the stress response is critical to marine mammal management and conservation efforts. Anthropogenic stressors in marine ecosystems, including ocean noise, pollution, and fisheries interactions, are increasing and the dramatic responses of some marine mammals to these stressors have elevated concerns over the impact of human-related activities on a diverse group of animals that are difficult to monitor. This review covers the physiology of the stress response in marine mammals and places it in context of what is known from research on terrestrial mammals, particularly with respect to mediator activity that diverges from generalized terrestrial models. Challenges in conducting research on stress physiology in marine mammals are discussed and ways to overcome these challenges in the future are suggested.

Blow collection as a non-invasive method for measuring cortisol in the beluga (Delphinapterus leucas)

Non-invasive sampling techniques are increasingly being used to monitor glucocorticoids, such as cortisol, as indicators of stressor load and fitness in zoo and wildlife conservation, research and medicine. For cetaceans, exhaled breath condensate (blow) provides a unique sampling matrix for such purposes. The purpose of this work was to develop an appropriate collection methodology and validate the use of a commercially available EIA for measuring cortisol in blow samples collected from belugas (Delphinapterus leucas). Nitex membrane stretched over a petri dish provided the optimal method for collecting blow. A commercially available cortisol EIA for measuring human cortisol (detection limit 35 pg ml-1) was adapted and validated for beluga cortisol using tests of parallelism, accuracy and recovery. Blow samples were collected from aquarium belugas during monthly health checks and during out of water examination, as well as from wild belugas. Two aquarium belugas showed increased blow cortisol between baseline samples and 30 minutes out of water (Baseline, 0.21 and 0.04 µg dl-1; 30 minutes, 0.95 and 0.14 µg dl-1). Six wild belugas also showed increases in blow cortisol between pre and post 1.5 hour examination (Pre 0.03, 0.23, 0.13, 0.19, 0.13, 0.04 µg dl-1, Post 0.60, 0.31, 0.36, 0.24, 0.14, 0.16 µg dl-1). Though this methodology needs further investigation, this study suggests that blow sampling is a good candidate for non-invasive monitoring of cortisol in belugas. It can be collected from both wild and aquarium animals efficiently for the purposes of health monitoring and research, and may ultimately be useful in obtaining data on wild populations, including endangered species, which are difficult to handle directly.

Metabolite content profiling of bottlenose dolphin exhaled breath

Changing ocean health and the potential impact on marine mammal health are gaining global attention. Direct health assessments of wild marine mammals, however, is inherently difficult. Breath analysis metabolomics is a very attractive assessment tool due to its noninvasive nature, but it is analytically challenging. It has never been attempted in cetaceans for comprehensive metabolite profiling. We have developed a method to reproducibly sample breath from small cetaceans, specifically Atlantic bottlenose dolphins (Tursiops truncatus). We describe the analysis workflow to profile exhaled breath metabolites and provide here a first library of volatile and nonvolatile compounds in cetacean exhaled breath. The described analytical methodology enabled us to document baseline compounds in exhaled breath of healthy animals and to study changes in metabolic content of dolphin breath with regard to a variety of factors. The method of breath analysis may provide a very valuable tool in future wildlife conservation efforts as well as deepen our understanding of marine mammals biology and physiology.

Chemical analysis of whale breath volatiles: a case study for non-invasive field health diagnostics of marine mammals

We explored the feasibility of collecting exhaled breath from a moribund gray whale (Eschrichtius robustus) for potential non-invasive health monitoring of marine mammals. Biogenic volatile organic compound (VOC) profiling is a relatively new field of research, in which the chemical composition of breath is used to non-invasively assess the health and physiological processes on-going within an animal or human. In this study, two telescopic sampling poles were designed and tested with the primary aim of collecting whale breath exhalations (WBEs). Once the WBEs were successfully collected, they were immediately transferred onto a stable matrix sorbent through a custom manifold system. A total of two large volume WBEs were successfully captured and pre-concentrated onto two Tenax^®-TA traps (one exhalation per trap). The samples were then returned to the laboratory where they were analyzed using solid phase micro extraction (SPME) and gas chromatography/mass spectrometry (GC/MS). A total of 70 chemicals were identified (58 positively identified) in the whale breath samples. These chemicals were also matched against a database of VOCs found in humans, and 44% of chemicals found in the whale breath are also released by healthy humans. The exhaled gray whale breath showed a rich diversity of chemicals, indicating the analysis of whale breath exhalations is a promising new field of research.

Methods to examine reproductive biology in free-ranging, fully-marine mammals

Historical overexploitation of marine mammals, combined with present-day pressures, has resulted in severely depleted populations, with many species listed as threatened or endangered. Understanding breeding patterns of threatened marine mammals is crucial to assessing population viability, potential recovery and conservation actions. However, determining reproductive parameters of wild fully-marine mammals (cetaceans and sirenians) is challenging due to their wide distributions, high mobility, inaccessible habitats, cryptic lifestyles and in many cases, large body size and intractability. Consequently, reproductive biologists employ an innovative suite of methods to collect useful information from these species. This chapter reviews historic, recent and state-of-the-art methods to examine diverse aspects of reproduction in fully-aquatic mammals.

Clonally related methicillin-resistant Staphylococcus aureus isolated from short-finned pilot whales (Globicephala macrorhynchus), human volunteers, and a bayfront cetacean rehabilitation facility

In May of 2011, a live mass stranding of 26 short-finned pilot whales (Globicephala macrorhynchus) occurred in the lower Florida Keys. Five surviving whales were transferred from the original stranding site to a nearby marine mammal rehabilitation facility where they were constantly attended to by a team of volunteers. Bacteria cultured during the routine clinical care of the whales and necropsy of a deceased whale included methicillin-sensitive and methicillin-resistant Staphylococcus aureus (MSSA and MRSA). In order to investigate potential sources or reservoirs of MSSA and MRSA, samples were obtained from human volunteers, whales, seawater, and sand from multiple sites at the facility, nearby recreational beaches, and a canal. Samples were collected on 3 days. The second collection day was 2 weeks after the first, and the third collection day was 2 months after the last animal was removed from the facility. MRSA and MSSA were isolated on each day from the facility when animals and volunteers were present. MSSA was found at an adjacent beach on all three collection days. Isolates were characterized by utilizing a combination of quantitative real-time PCR to determine the presence of mecA and genes associated with virulence, staphylococcal protein A typing, staphylococcal cassette chromosome mec typing, multilocus sequence typing, and pulsed field gel electrophoresis (PFGE). Using these methods, clonally related MRSA were isolated from multiple environmental locations as well as from humans and animals. Non-identical but genetically similar MSSA and MRSA were also identified from distinct sources within this sample pool. PFGE indicated that the majority of MRSA isolates were clonally related to the prototype human strain USA300. These studies support the notion that S. aureus may be shed into an environment by humans or pilot whales and subsequently colonize or infect exposed new hosts.

Overcoming the challenges of studying conservation physiology in large whales: a review of available methods

Large whales are subjected to a variety of conservation pressures that could be better monitored and managed if physiological information could be gathered readily from free-swimming whales. However, traditional approaches to studying physiology have been impractical for large whales, because there is no routine method for capture of the largest species and there is presently no practical method of obtaining blood samples from free-swimming whales. We review the currently available techniques for gathering physiological information on large whales using a variety of non-lethal and minimally invasive (or non-invasive) sample matrices. We focus on methods that should produce information relevant to conservation physiology, e.g. measures relevant to stress physiology, reproductive status, nutritional status, immune response, health, and disease. The following four types of samples are discussed: faecal samples, respiratory samples ('blow'), skin/blubber samples, and photographs. Faecal samples have historically been used for diet analysis but increasingly are also used for hormonal analyses, as well as for assessment of exposure to toxins, pollutants, and parasites. Blow samples contain many hormones as well as respiratory microbes, a diverse array of metabolites, and a variety of immune-related substances. Biopsy dart samples are widely used for genetic, contaminant, and fatty-acid analyses and are now being used for endocrine studies along with proteomic and transcriptomic approaches. Photographic analyses have benefited from recently developed quantitative techniques allowing assessment of skin condition, ectoparasite load, and nutritional status, along with wounds and scars from ship strikes and fishing gear entanglement. Field application of these techniques has the potential to improve our understanding of the physiology of large whales greatly, better enabling assessment of the relative impacts of many anthropogenic and ecological pressures.

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.

Thar she blows! A novel method for DNA collection from cetacean blow

Background

Molecular tools are now widely used to address crucial management and conservation questions. To date, dart biopsying has been the most commonly used method for collecting genetic data from cetaceans; however, this method has some drawbacks. Dart biopsying is considered inappropriate for young animals and has recently come under scrutiny from ethical boards, conservationists, and the general public. Thus, identifying alternative genetic collection techniques for cetaceans remains a priority, especially for internationally protected species.

Methodology/Principal Findings

In this study, we investigated whether blow-sampling, which involves collecting exhalations from the blowholes of cetaceans, could be developed as a new less invasive method for DNA collection. Our current methodology was developed using six bottlenose dolphins, Tursiops truncatus, housed at the National Aquarium, Baltimore (USA), from which we were able to collect both blow and blood samples. For all six individuals, we found that their mitochondrial and microsatellite DNA profile taken from blow, matched their corresponding mitochondrial and microsatellite DNA profile collected from blood. This indicates that blow-sampling is a viable alternative method for DNA collection.

Conclusion/Significance

In this study, we show that blow-sampling provides a viable and less invasive method for collection of genetic data, even for small cetaceans. In contrast to dart biopsying, the advantage of this method is that it capitalizes on the natural breathing behaviour of dolphins and can be applied to even very young dolphins. Both biopsy and blow-sampling require close proximity of the boat, but blow-sampling can be achieved when dolphins voluntarily bow-ride and involves no harmful contact.