An Economical Custom-Built Drone for Assessing Whale Health

Abstract

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.

New views of humpback whale flow dynamics and oral morphology during prey engulfment

“…; Pirotta et al . , ; Johnston ), and particularly of humpback whales (Ware et al . , Christiansen et al .…”

Challenges of collecting blow from small cetaceans

“…), Quick‐DNA (Pirotta et al. ); in all cases, a greater volume of starting material would have been available, for example, a greater volume of blow obtained from captive dolphins (Frère et al. ) or from larger animals (Pirotta et al.…”

“…) or from larger animals (Pirotta et al. ). While we anticipate our DNA extraction methodology was suitable to detect dolphin DNA if present in the sample, some improvement to the collection method could be made to enhance the capture of detectable DNA.…”

“…Remotely piloted aircraft (e.g., drones) are increasingly being used as the platform of choice to monitor wildlife in many different circumstances (Linchant et al 2015, Gonzalez et al 2016 and have enabled the collection of data that were previously difficult if not impossible to collect. In studies of marine mammals, drones have been used with thermal imaging to assess populations (Seymour et al 2017), determine body condition and identify individual whales (Dawson et al 2017, Christiansen et al 2018, count dugongs (Hodgson et al 2013) and pinnipeds (McIntosh et al 2018), acquire photographic images to estimate population size (Colefax et al 2018, Hodgson et al 2018, record behavior (Goebel et al 2015, Fiori et al 2017, Torres et al 2018, and collect blow samples from whales (Pirotta et al 2017, Dom ınguez-S anchez et al 2018. The collection of biological samples is of particular interest, as drones are potentially a noninvasive tool with minimal impact on the animals (Christiansen et al 2016).…”

“…Blow samples collected from cetaceans can be analyzed for DNA to investigate population structure (Fr ere et al 2010), analyzed for hormones for stress (Hunt et al 2014, Thompson et al 2014) and health (Apprill et al 2017), and screened for epizootics, microbiota (Pirotta et al 2017), and viruses (Geoghegan et al 2018). Such studies have been successfully executed on large cetaceans such as baleen whales (Dom ınguez-S anchez et al 2018, Harcourt et al 2019) as these animals have proven the most suitable to approach and sample with this emerging technology.…”