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Abstract
Environmental DNA is increasingly being used for assessing the presence and relative abundance of fish in freshwater, but existing protocols typically rely on filtering large volumes of water which is not always practical. We compared the effects of water volume, filtration type and eDNA extraction procedures in the detection of fish in three freshwater bodies (pond, lake and river) using a short fragment of the 12s rRNA mtDNA gene. Quantification of eDNA capture efficiency after DNA extraction, as well as amplification efficiency, were evaluated by conventional PCR and quantitative PCR. No significant differences on eDNA capture yield were found among freshwater bodies, but increasing water volume had a positive effect on eDNA capture and amplification efficiency. Although highest eDNA capture rates were obtained using 2 L of filtered water, 100 mL syringe filtration in combination with ethanol- sodium acetate precipitation proved to be more practical and increased quantitative PCR amplification efficiency by 6.4%. Our results indicate that such method may be optimal to detect fish species effectively across both lotic and lentic freshwater environments.
Highlights
Environmental DNA is increasingly being used in freshwater environments to detect the presence of target invertebrate and vertebrate species, based on the detection of short extracellular DNA fragments released into the environment [1,2,3]. eDNA detection can be used for management purposes, such as monitoring of species’ presence/absence [1], invasive species detection [4], relative abundance estimates [5] and use of space [6]
Significant interactions were identified between water body and volume (F (8, 40) = 3.781, p = 0.003), with 2000 mL of water resulting in higher capture efficiency in the pond compared to all lower filtering volumes in the Tawe (Tukey’s Post-hoc test, p < 0.001), and between filter type and water body (F (4, 25) = 3.667, p = 0.024), with much higher efficiency of syringe filtration combined with ethanol precipitation compared to cellulose nitrate filtering in the pond (Tukey’s Post-hoc test, p < 0.001) (Table 1)
The results from three different comparisons testing the effects of filtration volume, filtration type and extraction procedure, evaluated by DNA capture yield and amplification efficiencies highlight the importance of selecting the appropriate sampling method due to their variable efficiencies
Summary
Environmental DNA (eDNA) is increasingly being used in freshwater environments to detect the presence of target invertebrate and vertebrate species, based on the detection of short extracellular DNA fragments released into the environment [1,2,3]. eDNA detection can be used for management purposes, such as monitoring of species’ presence/absence [1], invasive species detection [4], relative abundance estimates [5] and use of space [6]. EDNA detection can be used for management purposes, such as monitoring of species’ presence/absence [1], invasive species detection [4], relative abundance estimates [5] and use of space [6]. In some cases it can offer more efficient estimations of relative abundance than conventional sampling techniques [7] as it can provide higher detection sensitivity [8].
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