SRA

Metabarcoding of environmental DNA has emerged as a powerful tool for species detection and has the potential to overcome many of the limitations of traditional amphibian surveys. Turbid water can harbour a large diversity of amphibian species, but sampling of such systems is very challenging, in some cases prohibitively so. We compared three eDNA field sampling methodologies (precipitation, standard 47mm filters and high-capacity filtering capsules) in detecting amphibian species and characterising amphibian communities in ponds in Portugal with varying turbidity levels. On average, capsules filtered c. 7 times more water than standard filters (mean = 7.89 L and 1.1 L respectively; precipitation was always limited to 0.015 L). Capsules also captured more total DNA (mean = 367 ng) than either standard filters (mean = 194 ng) or precipitation (mean = 70 ng). However, there was no significant difference between capsules and standard filters either for the detection of single target species or for overall amphibian community characterisation. Capsules and standard filters both outperformed precipitation, but none of the eDNA methods consistently outperformed traditional sampling, in these relatively small ponds. The study highlights a number of causes of substantial variation in eDNA sampling and provides recommendations for optimising metabarcoding of amphibian communities