Direct fishing and eDNA metabarcoding for biomonitoring during a 3-year survey significantly improves number of fish detected around a South East Asian reservoir

Abstract

Biodiversity has to be accurately evaluated to assess more precisely possible dam effects on fish populations, in particular on the most biodiverse rivers such as the Mekong River. To improve tools for fish biodiversity assessment, a methodological survey was performed in the surroundings of a recent hydropower dam in the Mekong basin, the Nam Theun 2 project. Results of two different approaches, experimental surface gillnets capture and environmental DNA metabarcoding assays based on 12S ribosomal RNA and cytochrome b, were compared during 3 years (2014–2016). Pitfalls and benefits were identified for each method but the combined use of both approaches indisputably allows describing more accurately fish diversity around the reservoir. Importantly, striking convergent results were observed for biodiversity reports. 75% of the fish species caught by gillnets (62/82) were shown by the metabarcoding study performed on DNA extracted from water samples. eDNA approach also revealed to be sensitive by detecting 30 supplementary species known as present before the dam construction but never caught by gillnets during 3 years. Furthermore, potential of the marker-genes study might be underestimated since it was not possible to assign some sequences at lower taxonomic levels. Although 121 sequences were generated for this study, a third of species in the area, that exhibits high endemism, are still unknown in DNA databases. Efforts to complete local reference libraries must continue to improve the taxonomic assignment quality when using the non-invasive and promising eDNA approach. These results are of broader interest because of increasing number of hydropower projects in the Mekong Basin. They reveal the crucial importance to sample tissues/DNA of species before dam projects, i.e. before the species could become endangered and difficult to catch, to obtain more precise biomonitoring in the future as we believe eDNA metabarcoding will rapidly be integrated as a standard tool in such studies.

Composition and distribution of fish environmental DNA in an Adirondack watershed

“…Several studies have compared eDNA detections with traditional fish survey methods and show convergence toward very similar sets of taxa identified in aggregate, that is, for significant survey efforts spanning space and time ( Thomsen et al, 2016 ; Hänfling et al, 2016 ; Pont et al, 2018 ; Gillet et al, 2018 ; Goutte et al, 2020 ). In the St. Regis, few expected taxa were recalcitrant to eDNA ( Table 1 ), but four missing taxa were noted for which primer-site divergence could be excluded as a cause.…”

“…In the study, we exclusively examined the 12S locus, which has been the most productive locus in several multilocus comparisons ( Shaw et al, 2016 ; Hänfling et al, 2016 ; Gillet et al, 2018 ) but not all ( Li et al, 2018 ). A large majority of expected taxa were detected with 12S reads in aggregate in this environment ( Table 1 ), to the limit of marker resolution, with only modest levels of off-target amplification ( Supplemental File S13 ).…”

“…Routine eDNA monitoring could also be more economical and standardized than traditional active-capture approaches. Several studies have shown eDNA detections to be accurate relative to capture methods, in aggregate ( Shaw et al, 2016 ; Hänfling et al, 2016 ; Evans et al, 2017 ; Gillet et al, 2018 ; Pont et al, 2018 ; Goutte et al, 2020 ), although agreement is often less on a site-by-site basis ( Shaw et al, 2016 ; Li et al, 2018 ). On the other hand, eDNA methods have biases and complications of their own.…”

“…eDNA can be transported far from its source population ( Pont et al, 2018 ) and can derive from anthropogenic and natural secondary sources ( Merkes et al, 2014 ; Stoeckle, Soboleva & Charlop-Powers 2017 ; Cornman et al, 2018 ; Song, Small & Casman, 2017 ), complicating interpretation. Amplification biases can strongly skew sequence compositions recovered at ‘barcode’ loci ( Kelly, Andrew & Ramón, 2019 ; Kelly et al, 2014 ), and multiple loci may be needed to detect most taxa of interest ( Shaw et al, 2016 ; Gillet et al, 2018 ; Li et al, 2018 ). How well compositions derived from barcode loci can discriminate ecological signals from environmental and methodological noise therefore remains an area of active investigation, and conclusions may vary across loci, environments, and management objectives ( Emilson et al, 2017 ; Laroche et al, 2017 ; Berry et al, 2019 ).…”

Macroinvertebrate community diversity and habitat quality relationships along a large river from targeted eDNA metabarcode assays

“…Targeted META has shown great promise in resolving fish diversity from eDNA water samples, often correlating well with traditional fish sampling counts (Civade et al, 2016;Gillet et al, 2018;Hänfling et al, 2016;Shaw et al, 2016;Thomsen et al, 2016). Further development of sequence reference libraries (e.g., NCBI GenBank and Barcode of Life Data System (BOLD)) is needed alongside META assay design, to propel this methodology into a practical biomonitoring tool for macroinvertebrates (Cordier et al, 2017;Ekrem et al, 2007;Zimmermann et al, 2014).…”