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 influence...