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.

Drones or Unmanned Aerial Vehicles (UAVs) have huge potential to improve the safety and efficiency of sample collection from wild animals under logistically challenging circumstances. Here we present a method for surveying population health that uses UAVs to sample respiratory vapor, 'whale blow,' exhaled by free-swimming humpback whales (Megaptera novaeangliae), and coupled this with amplification and sequencing of respiratory tract microbiota. We developed a low-cost multirotor UAV incorporating a sterile petri dish with a remotely operated 'blow' to sample whale blow with minimal disturbance to the whales. This design addressed several sampling challenges: accessibility; safety; cost, and critically, minimized the collection of atmospheric and seawater microbiota and other potential sources of sample contamination. We collected 59 samples of blow from northward migrating humpback whales off Sydney, Australia and used high throughput sequencing of bacterial ribosomal gene markers to identify putative respiratory tract microbiota. Model-based comparisons with seawater and dronecaptured air demonstrated that our system minimized external sources of contamination and successfully captured sufficient material to identify whale blow-specific microbial taxa. Whale-specific taxa included species and genera previously associated with the respiratory tracts or oral cavities of mammals (e.g., Pseudomonas, Clostridia, Cardiobacterium), as well as species previously isolated from dolphin or killer whale blowholes (Corynebacteria, others). Many examples of exogenous marine species were identified, including Tenacibaculum and Psychrobacter spp. that have been associated with the skin microbiota of marine mammals and fish and may include pathogens. This information provides a baseline of respiratory tract microbiota profiles of contemporary whale health. Customized UAVs are a promising new tool for marine megafauna research and may have broad application in cost-effective monitoring and management of whale populations worldwide.

Shipping routes in the ocean are analogous to terrestrial roads, in that they are regularly used thoroughfares that concentrate the movement of vessels between multiple locations. We applied a terrestrial road ecology framework to examine the ecological impacts of increased global shipping on “marine giants” (ie great whales, basking sharks [Cetorhinus maximus], and whale sharks [Rhincodon typus]). This framework aided in identifying where such “marine roads” and marine giants are likely to interact and the consequences of those interactions. We also reviewed known impacts of shipping routes on these species, and then applied the road ecology framework to detect unknown and potentially threatening processes. In the marine environment, such a framework can be used to incorporate knowledge of existing shipping impacts into management practices, thereby reducing the detrimental effects of future expansion of shipping routes on marine giants.

There is growing interest in characterizing the viromes of diverse mammalian species, particularly in the context of disease emergence. However, little is known about virome diversity in aquatic mammals, in part due to difficulties in sampling. We characterized the virome of the exhaled breath (or blow) of the Eastern Australian humpback whale (Megaptera novaeangliae). To achieve an unbiased survey of virome diversity, a meta-transcriptomic analysis was performed on 19 pooled whale blow samples collected via a purpose-built Unmanned Aerial Vehicle (UAV, or drone) approximately 3 km off the coast of Sydney, Australia during the 2017 winter annual northward migration from Antarctica to northern Australia. To our knowledge, this is the first time that UAVs have been used to sample viruses. Despite the relatively small number of animals surveyed in this initial study, we identified six novel virus species from five viral families. This work demonstrates the potential of UAVs in studies of virus disease, diversity, and evolution.

Migratory Group V (Stock E1) humpback whales Megaptera novaeangliae are at risk of entanglement with fishing gear as they migrate north and south along the east coast of Australia. This study investigated the effectiveness of 2 distinct tones for use as an alarm to acoustically alert whales to fishing gear presence and therefore reduce the chance of entanglement. We compared how whales responded in terms of changes of surface behaviour and changes in direction of travel in response to 2 acoustic tones and when there was no alarm. These 2 acoustic tones were a 5 kHz tone (5 s emission interval and 400 ms emission duration, similar to but higher frequency than the signal from a Future Oceans F3 TM 3 kHz Whale Pinger®) and a 2−2.1 kHz swept tone (8 s emission interval and 1.5 s emission duration). A total of 108 tracks (focal follows) were collected using a theodolite at Cape Solander, Sydney, Australia, during the whales' 2013 northern migration. Linear mixed effects models were used to determine the effect of the different acoustic tones on whale direction (heading), and behaviour (dive duration and speed). Whales showed no detectable response to either alarm. Whale direction and surfacing behaviour did not differ whether the alarm was 'on' or 'off'. Although the response may have been different if the alarms were attached to fishing gear, the lack of measurable response suggests that the types of tones used are not likely to be effective in alarms intended to reduce entanglement of northward migrating Australian humpback whales.