Application of eDNA metabarcoding in a fragmented lowland river: Spatial and methodological comparison of fish species composition

Abstract

Assessments of fish communities tend to rely on capture‐based methods that, due to sampling biases, can underestimate actual species richness. Alternatively, environmental DNA (eDNA) based metabarcoding is a noncapture approach that infers species richness and distribution by collecting and sequencing DNA present in the ecosystem. Here, eDNA metabarcoding was applied to the lower River Severn, a highly modified and impounded river, to identify the species present in the fish assemblage. Using a universal primer for fish (12S mtDNA region), comparisons were made between the species identified as present by eDNA metabarcoding versus long‐term data available from fisheries monitoring data based on capture methods. Depending on the stringency of detection thresholds applied, the two methods detected between 15 and 25 fish species present in the river, with the eDNA metabarcoding detecting most species previously reported in the capture surveys, although with differences in the relative abundance of species between the methods. Notably, eDNA metabarcoding detected species of high conservation importance that were never sampled by capture techniques, including native European shads (Alosa spp.). Differences in the similarity indices of species detection were greater between the sampling methods than between sampling sites on each river. These results highlight the high potential of eDNA metabarcoding to provide an effective monitoring tool for biodiversity and conservation in rivers, but also indicate the need for complementary multi‐method sampling for robust estimates of fish species richness.

Biodiversity assessment across a dynamic riverine system: A comparison of eDNA metabarcoding versus traditional fish surveying methods

“…By extrapolation of the detection data for freshwater fishes (Figure 4), we demonstrated the superior ability of eDNA metabarcoding for species richness estimation in this habitat. Our findings add to a growing body of literature supporting the use of eDNA for the analysis of freshwater fish communities in riverine systems (e.gAntognazza et al, 2021; Berger et al, 2020; Cilleros et al, 2019). However, we observed a distinct drop in species detection in the tidal stretches of the river Thames compared with that obtained by traditional survey methods, in which several lower tidal sites failed to produce any sequences.…”

“…The eDNA metabarcoding signal we detected was representative of the pattern of fish communities known to exist within the catchment, from the upper freshwater reaches to the tidal Thames. Our study thus adds to a growing number of examples of eDNA metabarcoding being comparable, or even outperforming, traditional fish survey methods (i.e., electrofishing, visual surveys, acoustic telemetry, poisoning), across diverse aquatic environments including temperate rivers and canals (Pont et al, 2018; McDevitt et al, 2019; Antognazza et al, 2021), temperate and tropical lakes (Doble et al, 2020; Hänfling et al, 2016), and marine settings (Afzali et al, 2020). Although our results show the power and potential for the detection of fish diversity in freshwaters, they also illustrated the need for further refinement of eDNA collection in turbid estuaries.…”

“…Here, we targeted two regions for eDNA amplification: the mitochondrial 12S rRNA gene, and the mitochondrial cytochrome c oxidase subunit 1 (CO1) (Table S2). We used the MiFish 12S primer set (Miya et al, 2015), which has been successfully used in eDNA studies in both freshwater and marine systems (Berger et al, 2020; Doble et al, 2020; Oka et al, 2021), including for a subset of UK fish species (Antognazza et al, 2021; McDevitt et al, 2019) and the Fish_MiniE CO1 primer set designed for fragmented fish DNA (Shokralla et al, 2015), modified to remove the M13 tails.…”

A Review of Environmental DNA Field and Laboratory Protocols Applied in Fish Ecology and Environmental Health

“…ASVs have been used for fish monitoring based on eDNA. Antognazza et al (2020) used ASVs to detect fish species composition in a fragmented lowland river and compared eDNA-based and long-term fishing monitoring results; the results showed that eDNA could detect species such as European shads (Alosa spp.) with high conservation value that were never sampled by capture techniques.…”

Similarities and Differences in Fish Community Composition Accessed by Electrofishing, Gill Netting, Seining, Trawling, and Water eDNA Metabarcoding in Temperate Reservoirs

“…Most comparisons of the wf-eDNA approach with traditional sampling methods to characterize ecological communities have been conducted at the local scale and show how wf-eDNA and traditional sampling methods represent community composition in lakes, reservoirs, and rivers (Murienne et al, 2019;Czeglédi et al, 2021;Gehri et al, 2021). Several studies have also shown that wf-eDNA is a complementary approach to traditional sampling methods to assess fish community composition in lakes and rivers (Shaw et al, 2016;Doi et al, 2019;Sard et al, 2019;Antognazza et al, 2021;Ritterbusch et al, 2022). In general, wf-eDNA may characterize a large number of taxa with less sampling effort than traditional sampling methods for detecting fish in low-diversity freshwater systems (McElroy et al, 2020).…”