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

Comparison between Sampling Techniques for Virological Molecular Analyses: Dolphin Morbillivirus and Herpesvirus Detection from FTA® Card and Frozen Tissue

Stranded animals offer valuable information on marine mammal physiology and pathology; however, the decomposition state of the carcasses and lack of a rigorous cold chain for sample preservation can sometimes discourage diagnostic analyses based on nucleic acid detection. The present paper aims at evaluating the reliability of FTA® card tissue imprints as an alternative matrix to frozen tissues for virological analyses based on biomolecular methods. Given the contribution of Cetacean morbillivirus (CeMV) to strandings and the increase of herpesvirus detection in cetaceans, these two pathogens were selected as representative of RNA and DNA viruses. Dolphin morbillivirus (DMV) and herpesvirus presence was investigated in parallel on tissue imprints on FTA® cards and frozen tissues collected during necropsy of dolphins stranded in Italy. Samples were analysed by nested RT-PCR for DMV and nested-PCR for herpesvirus. Only one animal was positive for herpesvirus, hampering further considerations on this virus. DMV was detected in all animals, both in FTA® card imprints and tissue samples, with differences possibly related to the decomposition condition category of the carcasses. Tissue sampling on FTA® cards seems a promising alternative to frozen tissues for biomolecular analyses, especially when ensuring adequate storage and shipment conditions for frozen tissues is difficult.

Gut bacterial communities in Atlantic bottlenose dolphins (Tursiops truncatus) throughout a disease-driven (Morbillivirus) unusual mortality event

Gut microbiomes are important determinants of animal health. In sentinel marine mammals where animal and ocean health are connected, microbiome impacts can scale to ecosystem-level importance. Mass mortality events affect cetacean populations worldwide, yet little is known about the contributory role of their gut bacterial communities to disease susceptibility and progression. Here, we characterized bacterial communities from fecal samples of common bottlenose dolphins, Tursiops truncatus, across an unusual mortality event (UME) caused by dolphin Morbillivirus (DMV). 16S rRNA gene sequence analysis revealed similar diversity and structure of bacterial communities in individuals stranding before, during, and after the 2013-2015 Mid-Atlantic Bottlenose Dolphin UME and these trends held in a subset of dolphins tested by PCR for DMV infection. Fine-scale shifts related to the UME were not common (10 of 968 bacterial taxa) though potential biomarkers for health monitoring were identified within the complex bacterial communities. Accordingly, acute DMV infection was not associated with a distinct gut bacterial community signature in T. truncatus. However, temporal stratification of DMV-positive dolphins did reveal changes in bacterial community composition between early and late outbreak periods, suggesting that gut community disruptions may be amplified by the indirect effects of accumulating health burdens associated with chronic morbidity.

The bacteria of Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) are site-specific and distinct from freshwater environment

Bacteria play an essential role in the health of marine mammals, and the bacteria of marine mammals are widely concerned, but less is known about freshwater mammals. In this study, we investigated the bacteria of various body sites of Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) and analyzed their association with freshwater environmental bacteria. The bacterial community and function of Yangtze finless porpoise showed apparent site-specificity. Various body sites have distinct differences in bacteria and have their dominant bacteria. Romboutsia, Plesiomonas, Actinobacillus, Candidatus Arthromitus dominated in the intestine (fecal and rectal samples). Fusobacterium, Streptococcus, and Acinetobacter dominated in the oral. The dominant genera in the blowhole include Suttonella, Psychrobacter, and two uncultured genera. Psychrobacter, Flavobacterium, and Acinetobacter were dominant in the skin. The alpha diversity of intestinal (fecal and rectal) bacteria was the lowest, while that of skin was the highest. The oral and skin bacteria of Yangtze finless porpoise significantly differed between the natural and semi-natural conditions, but no sex difference was observed. A clear boundary was found between the animal and the freshwater environmental bacteria. Even the skin bacteria, which are more affected by the environment, are significantly different from the environmental bacteria and harbor indigenous bacteria. Our results provide a comprehensive preliminary exploration of the bacteria of Yangtze finless porpoise and its association with bacteria in the freshwater environment.

UAV remote sensing applications in marine monitoring: Knowledge visualization and review

With the booming development of information technology and the growing demand for remote sensing data, unmanned aerial vehicle (UAV) remote sensing technology has emerged. In recent years, UAV remote sensing technology has developed rapidly and has been widely used in the fields of military defense, agricultural monitoring, surveying and mapping management, and disaster and emergency response and management. Currently, increasingly serious marine biological and environmental problems are raising the need for effective and timely monitoring. Compared with traditional marine monitoring technologies, UAV remote sensing is becoming an important means for marine monitoring thanks to its flexibility, efficiency and low cost, while still producing systematic data with high spatial and temporal resolutions. This study visualizes the knowledge domain of the application and research advances of UAV remote sensing in marine monitoring by analyzing 1130 articles (from 1993 to early 2022) using a bibliometric approach and provides a review of the application of UAVs in marine management mapping, marine disaster and environmental monitoring, and marine wildlife monitoring. It aims to promote the extensive application of UAV remote sensing in the field of marine research.

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.

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.

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.

Big Data in Conservation Genomics: Boosting Skills, Hedging Bets, and Staying Current in the Field

A current challenge in the fields of evolutionary, ecological, and conservation genomics is balancing production of large-scale datasets with additional training often required to handle such datasets. Thus, there is an increasing need for conservation geneticists to continually learn and train to stay up-to-date through avenues such as symposia, meetings, and workshops. The ConGen meeting is a near-annual workshop that strives to guide participants in understanding population genetics principles, study design, data processing, analysis, interpretation, and applications to real-world conservation issues. Each year of ConGen gathers a diverse set of instructors, students, and resulting lectures, hands-on sessions, and discussions. Here, we summarize key lessons learned from the 2019 meeting and more recent updates to the field with a focus on big data in conservation genomics. First, we highlight classical and contemporary issues in study design that are especially relevant to working with big datasets, including the intricacies of data filtering. We next emphasize the importance of building analytical skills and simulating data, and how these skills have applications within and outside of conservation genetics careers. We also highlight recent technological advances and novel applications to conservation of wild populations. Finally, we provide data and recommendations to support ongoing efforts by ConGen organizers and instructors-and beyond-to increase participation of underrepresented minorities in conservation and eco-evolutionary sciences. The future success of conservation genetics requires both continual training in handling big data and a diverse group of people and approaches to tackle key issues, including the global biodiversity-loss crisis.

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.

Remotely Piloted Aircraft System (RPAS)-Based Wildlife Detection: A Review and Case Studies in Maritime Antarctica

Simple Summary

Remotely piloted aircraft systems (RPAS) have been successfully applied in wildlife monitoring with imaging sensors to improve or to supplement conventional field observations. To effectively utilize this technique, we reviewed previous studies related to wildlife detection with RPAS. First, this study provides an overview of the applications of RPAS for wild animal studies from the perspective of individual detection and population surveys as well as behavioral studies. In terms of the RPAS payload, applying thermal-imaging sensors was determined to be advantageous in detecting homeothermic animals due to the thermal contrast with background habitat using case studies detecting southern elephant seal (Mirounga leonina) using RGB and thermal imaging sensors in King George Island, maritime Antarctica.

Abstract

In wildlife biology, it is important to conduct efficient observations and quantitative monitoring of wild animals. Conventional wildlife monitoring mainly relies on direct field observations by the naked eyes or through binoculars, on-site image acquisition at fixed spots, and sampling or capturing under severe areal constraints. Recently, remotely piloted aircraft systems (RPAS), also called drones or unmanned aerial vehicles (UAV), were successfully applied to detect wildlife with imaging sensors, such as RGB and thermal-imaging sensors, with superior detection capabilities to those of human observation. Here, we review studies with RPAS which has been increasingly used in wildlife detection and explain how an RPAS-based high-resolution RGB image can be applied to wild animal studies from the perspective of individual detection and population surveys as well as behavioral studies. The applicability of thermal-imaging sensors was also assessed with further information extractable from image analyses. In addition, RPAS-based case studies of acquisition of high-resolution RGB images for the purpose of detecting southern elephant seals (Mirounga leonina) and shape property extraction using thermal-imaging sensor in King George Island, maritime Antarctica is presented as applications in an extreme environment. The case studies suggest that currently available cost-effective small-sized RPAS, which are capable of flexible operation and mounting miniaturized imaging sensors, and are easily maneuverable even from an inflatable boat, can be an effective and supportive technique for both the visual interpretation and quantitative analysis of wild animals in low-accessible extreme or maritime environments.

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.