Environmental DNA for freshwater fish monitoring: insights for conservation within a protected area

Abstract

BackgroundMany fish species have been introduced in wild ecosystems around the world to provide food or leisure, deliberately or from farm escapes. Some of those introductions have had large ecological effects. The north American native rainbow trout (Oncorhynchus mykiss Walbaum, 1792) is one of the most widely farmed fish species in the world. It was first introduced in Spain in the late 19th century for sport fishing (Elvira 1995) and nowadays is used there for both fishing and aquaculture. On the other hand, the European native brown trout (Salmo trutta L.) is catalogued as vulnerable in Spain. Detecting native and invasive fish populations in ecosystem monitoring is crucial, but it may be difficult from conventional sampling methods such as electrofishing. These techniques encompass some mortality, thus are not adequate for some ecosystems as the case of protected areas. Environmental DNA (eDNA) analysis is a sensitive and non-invasive method that can be especially useful for rare and low-density species detection and inventory in water bodies.MethodsIn this study we employed two eDNA based methods (qPCR and nested PCR-RFLP) to detect salmonid species from mountain streams within a protected area, The Biosphere Reserve and Natural Park of Redes (Upper Nalón Basin, Asturias, Northern Spain), where brown trout is the only native salmonid. We also measured some habitat variables to see how appropriate for salmonids the area is. The sampling area is located upstream impassable dams and contains one rainbow trout fish farm.ResultsEmploying qPCR methodology, brown trout eDNA was detected in all the nine sampling sites surveyed, while nested PCR-RFLP method failed to detect it in two sampling points. Rainbow trout eDNA was detected with both techniques at all sites in the Nalón River’ (n1, n2 and n3). Salmonid habitat units and water quality were high from the area studied.DiscussionIn this study, a high quantity of rainbow trout eDNA was found upstream and downstream of a fish farm located inside a Biosphere Reserve. Unreported escapes from the fish farm are a likely explanation of these results. Since salmonid habitat is abundant and the water quality high, the establishment of rainbow trout populations would be favored should escapes occur. Environmental DNA has here proved to be a valuable tool for species detection in freshwater environments, and the probe-based qPCR highly sensitive technique for detection of scarce species. We would recommend this method for routine monitoring and early detection of introduced species within natural reserves.

How can eDNA contribute in riverine macroinvertebrate assessment? A metabarcoding approach in the Nalón River (Asturias, Northern Spain)

“…COI gene reference database was constructed from NCBI COI sequences using the workflow developed by Baker (2017) using all COI sequences except the ones from environmental samples contained in the NCBI database. Then, BLAST alignment was done against this database with the settings described by Fernandez et al (2018) as optimal for this gene and taxonomic groups (maximum E-value = 10 -50 ; minimum percent identity = 90.0 and 97 to assign at family and species level, respectively; and minimum percent query coverage = 0.9), employing "assign_taxonomy. py" python script without clustering or dereplication, taking into account all the sequences and haplotypes obtained.…”

Analysis of a coastal North Sea fish community: Comparison of aquatic environmental DNA concentrations to fish catches

“…The methodology was tested on an artificial (mock) community with 30 bony fish species, two cartilaginous fish species, and eight marine invertebrate species. Quantitative PCR, in many studies used for eDNA quantification of single species (e.g., Doi et al, 2015;Fernandez et al, 2018;Harper et al, 2018;Knudsen et al, 2019;Nevers et al, 2018;Weltz et al, 2017), was here used to determine the in situ eDNA concentration (copies/L seawater) of the entire vertebrate community (Ushio et al, 2018). Species-specific eDNA concentrations of 39 fishes were inferred from the total eDNA concentration and the relative read abundance.…”

Assessment of fish biodiversity in four Korean rivers using environmental DNA metabarcoding

“…Although the methodology in each research group may be slightly different, similar conclusions have been reached in other studies (Bista et al, 2017;Deiner et al, 2016). eDNA metabarcoding analysis is also adequate for surveying aquatic species in protected areas, as it minimizes disturbance of vulnerable communities (Fernandez et al, 2018).…”