Data from: Optimizing techniques to capture and extract environmental DNA for detection and quantification of fish

Few studies have examined capture and extraction methods for environmental
DNA (eDNA) to identify techniques optimal for detection and
quantification. In this study, precipitation, centrifugation and
filtration eDNA capture methods and six commercially available DNA
extraction kits were evaluated for their ability to detect and quantify
common carp (Cyprinus carpio) mitochondrial DNA using quantitative PCR in
a series of laboratory experiments. Filtration methods yielded the most
carp eDNA, and a glass fibre (GF) filter performed better than a similar
pore size polycarbonate (PC) filter. Smaller pore sized filters had higher
regression slopes of biomass to eDNA, indicating that they were
potentially more sensitive to changes in biomass. Comparison of DNA
extraction kits showed that the MP Biomedicals FastDNA SPIN Kit yielded
the most carp eDNA and was the most sensitive for detection purposes,
despite minor inhibition. The MoBio PowerSoil DNA Isolation Kit had the
lowest coefficient of variation in extraction efficiency between lake and
well water and had no detectable inhibition, making it most suitable for
comparisons across aquatic environments. Of the methods tested, we
recommend using a 1.5 μm GF filter, followed by extraction with the MP
Biomedicals FastDNA SPIN Kit for detection. For quantification of eDNA,
filtration through a 0.2–0.6 μm pore size PC filter, followed by
extraction with MoBio PowerSoil DNA Isolation Kit was optimal. These
results are broadly applicable for laboratory studies on carps and
potentially other cyprinids. The recommendations can also be used to
inform choice of methodology for field studies.