eProbe: Sampling of Environmental DNA within Tree Canopies with Drones

Abstract

Environmental DNA (eDNA) analysis is a powerful tool for studying biodiversity in forests and tree canopies. However, collecting representative eDNA samples from these high and complex environments remains challenging. Traditional methods like surface swabbing or tree rolling are labor-intensive and require significant effort to achieve adequate coverage. This study proposes a novel approach for unmanned aerial vehicles (UAVs) to collect eDNA within tree canopies using a surface swabbing technique. The method involves lowering a probe from a hovering UAV into the canopy, collecting eDNA as it descends and ascends through branches and leaves. To achieve this, a custom-designed robotic system was developed, featuring a winch and a probe for eDNA collection. The design of the probe was optimized and a control logic for the winch developed to reduce the risk of entanglement while ensuring sufficient interaction force to facilitate transfer of eDNA onto the probe. The effectiveness of this method was demonstrated during the XPRIZE Rainforest Semi-Finals as ten eDNA samples were collected from the rainforest canopy and a total of 152 molecular operational taxonomic units (MOTUs) were identified using eDNA metabarcoding. We further investigate how the number of probe interactions with vegetation, the penetration depth, and the sampling duration influence the DNA concentration and community composition of the samples.