Abstract
Classical methods for estimating the abundance of fish populations are often both expensive, time-consuming and destructive. Analyses of the environmental DNA (eDNA) present in water samples could alleviate such constraints. Here, we developed protocols to detect and quantify brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) populations by applying the droplet digital PCR (ddPCR) method to eDNA molecules extracted from water samples collected in 28 Swedish mountain lakes. Overall, contemporary fish CPUE (catch per unit effort) estimates from standardized survey gill nettings were not correlated to eDNA concentrations for either of the species. In addition, the measured environmental variables (e.g. dissolved organic carbon concentrations, temperature, and pH) appear to not influence water eDNA concentrations of the studied fish species. Detection probabilities via eDNA analysis showed moderate success (less than 70% for both species) while the presence of eDNA from Arctic char (in six lakes) and brown trout (in one lake) was also indicated in lakes where the species were not detected with the gillnetting method. Such findings highlight the limits of one or both methods to reliably detect fish species presence in natural systems. Additional analysis showed that the filtration of water samples through 1.2 μm glass fiber filters and 0.45 μm mixed cellulose ester filters was more efficient in recovering DNA than using 0.22 μm enclosed polyethersulfone filters, probably due to differential efficiencies of DNA extraction. Altogether, this work showed the potentials and limits of the approach for the detection and the quantification of fish abundance in natural systems while providing new insights in the application of the ddPCR method applied to environmental DNA.
Highlights
Environmental DNA is often considered as a powerful tool to investigate the spatial and temporal distributions of many terrestrial and aquatic organisms, primarily for microbial organisms but with an increasing interest for macro-organisms over the past decade [1,2,3,4]
The specific goal of this project was to test for statistical relationships between CPUE-based fish population abundance estimates from the gillnetting method and Environmental DNA (eDNA) concentrations estimates from the droplet digital PCR (ddPCR) method
We aimed to evaluate the use of the ddPCR approach for the quantification of species-specific DNA molecules retrieved from lake water sample with the goal to estimate the abundance of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) populations
Summary
Environmental DNA (eDNA) is often considered as a powerful tool to investigate the spatial and temporal distributions of many terrestrial and aquatic organisms, primarily for microbial organisms but with an increasing interest for macro-organisms over the past decade [1,2,3,4]. Numerous studies applied molecular methods to natural water samples with the aim to quantify the abundance of fish populations—via molecular quantitative methods—or to assess the diversity and composition of fish communities—via DNA metabarcoding approach— with examples of potentials and limits of this approach [5,6,7]. Methodological biases may affect the quality of the recovered eDNA signal from water samples (e.g. sampling volume, sampling representativeness, filtration methods, DNA extraction’s efficiency, PCR inhibitions or low detection rate using quantitative molecular method). If these challenges could be overcome, eDNA analysis would offer an efficient and powerful tool for population monitoring. Meaningful outcomes from such approaches have already been provided for ecological studies tracking invasion fronts [15,16] or establishing community structures [1, 17]
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