Data from: Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA

Environmental DNA (eDNA) is used to detect biodiversity by the capture,
extraction, and identification of DNA shed to the environment. However,
eDNA capture and extraction protocols vary widely across studies. This use
of different protocols potentially biases detection results and could
significantly hinder a reliable use of eDNA to detect biodiversity. We
tested whether choice of eDNA capture and extraction protocols
significantly influenced biodiversity detection in aquatic systems. We
sampled lake and river water, captured and extracted eDNA using six
combinations of different protocols with replication, and tested for the
detection of four macroinvertebrate species. Additionally, using the same
lake water technical replicates, we compared the effect of capture and
extraction protocols on metabarcode detections of biodiversity using 16S
for eubacteria and cytochrome c oxidase I (COI) for eukaryotes. Protocol
combinations for capture and extraction of eDNA significantly influenced
DNA yield and number of sequences obtained from next generation
sequencing. We found significantly different detection rates of species
ranging from zero percent to thirty-three percent. Differences in which
protocol combinations produced the highest metabarcoded biodiversity were
detected and demonstrate that different protocols are required for
different biodiversity targets. Our results highlight that the choice of
molecular protocols used for capture and extraction of eDNA from water can
strongly affect biodiversity detection. Consideration of biases caused by
choice of protocols should lead to a more consistent and reliable
molecular workflow for repeatable and increased detection of biodiversity
in aquatic communities.