eProbe: Sampling of Environmental DNA within Tree Canopies with Drones

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, such as 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 by using a surface
swabbing technique. The method involves lowering a probe from a hovering
UAV into the canopy and 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 was 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 10 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.