Environmental DNA metabarcoding provides enhanced detection of the European eelAnguilla anguillaand fish community structure in pumped river catchments

Abstract

The European eel Anguilla anguilla (eel hereafter) is critically endangered and has a catadromous lifecycle, which means adult eels that live in pumped catchments must pass through pumps during their downstream spawning migration. We are currently lacking detailed site-by-site eel distribution information in order to estimate the overall impact of individual pumping stations on eel escapement, and as such lack the data to enable informed prioritisation of pumping station management and targeted mitigation. In this study, we investigated whether environmental DNA (eDNA) metabarcoding can provide increased detection sensitivity for eel and fish community structure in highly regulated pumped catchments, when compared directly to current standard practice fish survey protocols (seine netting/electric fishing). Eels were detected in 14/17 sites (82.4%) using eDNA metabarcoding in contrast to 3/17 (17.6%) using traditional catch methods. Additionally, when using eDNA monitoring species richness was higher in 16/17 sites (94.1%) and site occupancy ≥ traditional methods for 23/26 of the fish species detected (88.5%). While eDNA methods presented significantly higher average species richness and species site occupancy overall, eDNA and Catch methods were positively correlated in terms of species richness and site occupancy. We therefore found that eDNA metabarcoding was a high sensitivity method for detecting eels in pumped catchments, while also increasing the detection of overall fish community structure compared to traditional catch methods. In addition, we highlight how eDNA monitoring is especially suited to increased detection of particular species, with traditional methods sufficient for others. This high sensitivity, coupled with the ability to sample multiple sites in a short time frame suggests eDNA metabarcoding could be an invaluable tool when prioritising pumping station management.

Using DNA metabarcoding to investigate diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison)

“…More detailed quantitative data on fish abundance in the environment are required to distinguish prey selection from density-dependent predation. Indeed, small and benthic species are often underreported in conventional fish surveys, but recent eDNA metabarcoding studies have shown that these species might be much more abundant than previously thought (Hänfling et al 2016; Li et al 2019; Griffiths et al 2020).…”

Integrating environmental DNA monitoring to inform eel (Anguilla anguilla) status in freshwaters at their easternmost range - A case study in Cyprus

“…All downstream analyses were carried out using R version 3.6.3 (R Core Team, 2019). A low-frequency read threshold of 0.001 was applied to eDNA data, removing any reads which make up less than 0.1% of total reads assigned to any given sample as previously applied in other studies using this 12S marker (Griffiths et al, 2020; Handley et al, 2019; Hänfling et al, 2016). All maps were visualised, and associated metadata extracted using QGIS (QGIS Development Team, 2022).…”

“…To assess the eel distribution in Cyprus, and therefore inform current status, a wide range of catchments must be monitored in a short time frame. Environmental DNA (eDNA) metabarcoding of water samples has already proven to be effective for monitoring A. anguilla in heavily modified river systems in the UK (Griffiths et al, 2020). Therefore, this case study builds upon current knowledge by applying eDNA metabarcoding of water samples taken in 2020, alongside data from electrofishing/netting surveys carried out over a ten-year period (2009 - 2019) as part of the national WFD monitoring programme.…”

Strategies for sample labelling and library preparation in DNA metabarcoding studies

“…In the primary reaction the metabarcoding primers carry 5′ sequence overhangs of c. 33–34 nucleotides in length. These can be with (Clarke et al, 2017; Griffiths et al, 2020; Kitson et al, 2018; Li et al, 2019; Vesterinen et al, 2018) or without (Bista et al, 2017; de Vere et al, 2017; Galan et al, 2017; Miya et al, 2015; Swift et al, 2018; Vesterinen et al, 2018) nucleotide tags (Figure 2c,d). The sequence overhangs allow the resulting amplicons to be targeted by the second round of primers, which carry sequencing adapters and indices.…”