Explore the vast range of titles available.

Accurate, cost‐effective monitoring of fish is required to assess the quality of lakes under the European Water Framework Directive. Recent studies have shown that environmental DNA (eDNA) metabarcoding is an effective and non‐invasive method, which can provide semi‐quantitative information about fish communities in large lakes. This study further investigated the potential of fish‐based eDNA metabarcoding as a tool for lake assessment by collecting and analysing water samples from eight Welsh lakes and six meres in Cheshire, England, with well‐described fish faunas. Water samples (N = 252) were assayed using two mitochondrial DNA regions (Cytb and 12S rRNA). eDNA sampling indicated the presence of very similar species in the lakes compared to those expected on the basis of existing and historical information. Firstly, 24 species were detected, with a total of 111 species occurrences in the lakes studied using eDNA. Secondly, there was a significant positive correlation between expected faunas and eDNA data in terms of confidence of species occurrence (Spearman's r = 0.74, df = 109, p < 0.001). Thirdly, eDNA data can estimate relative abundance with the standard five‐level classification scale (‘DAFOR’). Lastly, four ecological fish communities were characterized using eDNA data which agree with the predefined lake types according to environmental characteristics. Synthesis and applications. There are some limitations when using conventional captured‐based methods for surveying species richness and relative abundance, such as morphological identification bias, difficulties in recording small‐bodied, rare and/or elusive species and destructive impacts on the environment. This study provides further evidence that environmental DNA metabarcoding outperforms other captured‐based survey techniques in a wide range of lake types for community‐level analysis whether in species detection, relative abundance estimate using the standard five‐level classification scale or characterization ecological fish communities. Therefore, the fish‐based environmental DNA metabarcoding, a non‐invasive genetic method, has great potential as an assessment tool for lake quality under the European Water Framework Directive. There are some limitations when using conventional captured‐based methods for surveying species richness and relative abundance, such as morphological identification bias, difficulties in recording small‐bodied, rare and/or elusive species and destructive impacts on the environment. This study provides further evidence that environmental DNA metabarcoding outperforms other captured‐based survey techniques in a wide range of lake types for community‐level analysis whether in species detection, relative abundance estimate using the standard five‐level classification scale or characterization ecological fish communities. Therefore, the fish‐based environmental DNA metabarcoding, a non‐invasive genetic method, has great potential as an assessment tool for lake quality under the European Water Framework Directive.

Environmental DNA (eDNA) metabarcoding is transforming biodiversity monitoring in aquatic environments. Such an approach has been developed and deployed for monitoring lake fish communities in Great Britain, where the method has repeatedly shown a comparable or better performance than conventional approaches. Previous analyses indicated that 20 water samples per lake are sufficient to reliably estimate fish species richness, but it is unclear how reduced eDNA sampling effort affects richness, or other biodiversity estimates and metrics. As the number of samples strongly influences the cost of monitoring programmes, it is essential that sampling effort is optimised for a specific monitoring objective. The aim of this project was to explore the effect of reduced eDNA sampling effort on biodiversity metrics (namely species richness and community composition) using algorithmic and statistical resampling techniques of a data set from 101 lakes, covering a wide spectrum of lake types and ecological quality. The results showed that reliable estimation of lake fish species richness could, in fact, usually be achieved with a much lower number of samples. For example, in almost 90% of lakes, 95% of complete fish richness could be detected with only 10 water samples, regardless of lake area. Similarly, other measures of alpha and beta-diversity were not greatly affected by a reduction in sample size from 20 to 10 samples. We also found that there is no significant difference in detected species richness between shoreline and offshore sampling transects, allowing for simplified field logistics. This could potentially allow the effective sampling of a larger number of lakes within a given monitoring budget. However, rare species were more often missed with fewer samples, with potential implications for monitoring of invasive or endangered species. These results should inform the design of eDNA sampling strategies, so that these can be optimised to achieve specific monitoring goals.

1. Accurate, cost-effective monitoring of fish is required to assess the quality of lakes under the European Water Framework Directive (WFD). Recent studies have shown that environmental DNA (eDNA) metabarcoding is an effective and non-invasive method, which can provide semi-quantitative information on fish communities in large lakes. 2. This study further investigated the potential of eDNA metabarcoding as a tool for WFD status assessment by collecting and analysing water samples from eight Welsh lakes and six meres in Cheshire, England, with well described fish faunas. Water samples (N = 252) were assayed using two mitochondrial DNA regions (Cytb and 12S rRNA). 3. eDNA sampling indicated the presence of very similar species in the lakes compared to those expected on the basis of existing and historical information. In total, 24 species were detected with a total of 111 species occurrences in the lakes studied using eDNA. Secondly, there was a significant positive correlation between expected faunas and eDNA data in terms of confidence of species occurrence (Spearman's r = 0.74, df = 109, p < 0.001). Thirdly, eDNA data can estimate relative abundance with the standard five-level classification scale (DAFOR). Lastly, four ecological fish communities were characterised using eDNA data which agrees with the pre-defined lake types according to environmental characteristics. 4. Synthesis and applications. This study provides further evidence that eDNA metabarcoding could be a powerful and non-invasive monitoring tool for WFD purpose in a wide range of lake types, considerably outperforming other methods for community level analysis. Footnotes * Figure 4 and Table 5 revised. Supplemental files updated.