Exploring Efficient Sampling Methods for Trace Environmental DNA

Background & Purpose: In recent years, due to environmental issues such as invasive species, endangered species, and global warming, biological and resource surveys have become increasingly important. Traditional methods involve directly capturing organisms, which is costly and has a high environmental impact. Therefore, surveys and analyses using environmental DNA (eDNA) have gained attention as they are more cost-effective and environmentally friendly. eDNA refers to DNA fragments derived from organisms in natural environments such as seas and lakes. The main method for eDNA sampling involves collecting several liters of water to ensure species detection, which can be labor-intensive.Methods: This study aims to identify a sampling method with sensitivity comparable to traditional water collection but is easier and more scalable. Samples were filtered, and DNA was extracted and amplified specifically for fish DNA using MiFish primer. Nanopore sequencing was used, followed by species identification through Blast search. Sampling methods included traditional water collection, underwater drone sampling, passive sampling using a fishing rod to submerge filters, and casting sampling where filters were cast into the water.Results: The study found variability in species detection across different sampling methods. Traditional water collection required many samples to detect a comprehensive range of species. Direct filter sampling was practical and allowed for easy increase in sample numbers. Underwater drone sampling had high detection sensitivity but was labor-intensive, while commercial eDNA kits were costly for scaling up. Combining passive and casting sampling methods proved the most effective in terms of detection sensitivity and cost-efficiency.