Using eDNA for monitoring fish and invertebrate biodiversity in freshwater ecosystems

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. In terms
of  practical implications, this study demonstrates the need for
bespoke sampling protocols when collecting eDNA samples. This study
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.