Water sampling for environmental DNA surveys by using an unmanned aerial vehicle

Abstract

Environmental DNA (eDNA) techniques utilizing DNA fragments from water have recently been developed to investigate the distribution and abundance/biomass of aquatic organisms. The eDNA technique is based on the analysis of DNA fragments in sampled water; thus, an unmanned aerial vehicle (UAV; drone) would be a useful way of collecting water for eDNA sampling, and may consequently allow us to extend eDNA surveys both spatially and temporally. Here, we developed a new method of water collection by using UAV with bleachable equipment, to avoid DNA contamination. To test the performance and contamination risk of UAV water sampling in eDNA surveys, we sampled water from a dam reservoir, detected eDNA from two fish species, and compared the water samples obtained by UAV with those obtained by boat. Additionally, we investigated contamination using blank samples. The results revealed that our UAV water sampling method performed similar to the boat sampling method. No positive signals were detected in the blank samples, including those used for UAV sampling, transportation, filtering, and PCR blanks. Our UAV method can be used to investigate species distributions using eDNA. Combinations of UAV technologies, including remote and thermal sensing, will enable efficient environmental monitoring in various waterbodies.

In situ Autonomous Acquisition and Preservation of Marine Environmental DNA Using an Autonomous Underwater Vehicle

“…Coupling the use of eDNA analyses to advances in marine robotics will usher in a new era for studying ecosystem processes and perhaps provide new ways of collecting biological data that is akin to the physical and chemical sensor data already being collected in the ocean. For example, utilization of drones for eDNA sample collection has been previously reported using an unmanned aerial vehicle (UAV) in a freshwater reservoir (Doi et al, 2017). Hoffmann et al (2016) provides a concept of utilizing a hydroplane drone for improved sample collection with less effort.…”

Effects of species traits and ecosystem characteristics on species detection by eDNA metabarcoding in lake fish communities

“…In this regard, the lakeshore water sampling conducted in the present study revealed the presence of numerous benthopelagic species based on eDNA metabarcoding, but relatively few pelagic species. Accordingly, in order to detect a larger number of pelagic species, we would need to perform offshore sampling, for example, using drone-assisted water collection for eDNA surveys 36 . The lateral body shape traits of species may also be associated with their micro-habitat use; for example, species with eel-like and short and/or deep body shapes appear to prefer sheltered micro-habitats (i.e., beneath stones) and pelagic zones.…”

Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects

“…Because of the sensitivity of the technique, this is a serious issue in eDNA surveys and may result in false positive detections and subsequent misinterpretation of results (Goldberg et al 2016;Wilson et al 2016). eDNA analysis requires multiple steps of sample handling and manipulation in the field (collection, storage and transportation) and in the lab (storage, DNA extraction, amplification, library preparation and sequencing), so contamination may occur at various stages of the research (Goldberg et al 2016;Doi et al 2017). In the field, contamination may occur when DNA from one or multiple samples is unintentionally transferred into another sample, either from another site in the same study or from an unknown locality.…”