The use of environmental DNA for biodiversity monitoring in lentic and lotic ecosystems

Abstract Global biodiversity is facing an extinction crisis leading to increasing pressure on industries to monitor their potential environmental impact. Relatedly, there is demand for more efficient biodiversity monitoring methods, resulting in growing interest in the use of environmental DNA (eDNA). Many questions, however, regarding the reliability of this relatively novel method remain, particularly for non‐specialist end‐users of the technology. Here, the use of commercially available (in the UK) eDNA assays for monitoring freshwater fish and invertebrate biodiversity was compared to conventional surveillance techniques. Samples were collected from different habitats, on varying spatial scales and using multiple sampling regimes to assess how eDNA results were affected. For aquatic macroinvertebrates and fish, more taxa were detected by eDNA than conventional surveys conducted in parallel, and for fish, all taxa detected by conventional monitoring were confirmed by eDNA. For aquatic macroinvertebrates, several species were only detected through conventional methods, and the number of families detected by eDNA was lower than for conventional monitoring at all sites. eDNA results varied significantly between sampling locations within lentic sites and, for lotic sites, with the number of subsamples collected. Practical implication. This study demonstrates the need for bespoke sampling protocols when collecting eDNA samples. It also improves understanding of using eDNA for detecting aquatic taxa that could inform species surveillance protocols. These are essential if eDNA is to be used by practitioners as a regulatory monitoring tool.