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.

环境DNA（eDNA）通过捕获、提取并识别释放至环境中的DNA片段，实现生物多样性的检测。然而，不同研究中eDNA的捕获与提取方案差异显著。这种方案的不统一可能会对检测结果引入偏倚，严重阻碍eDNA在生物多样性检测中的可靠应用。我们针对水生系统中eDNA捕获与提取方案的选择是否会显著影响生物多样性检测展开了实验验证。我们采集了湖泊与河流水样，采用六种不同的方案组合对eDNA进行捕获与提取并设置重复，同时针对四种大型无脊椎动物物种的检出情况进行了检测。此外，利用同一湖泊水样的技术重复样本，我们还对比了捕获与提取方案对生物多样性元条形码检测的影响：针对真细菌采用16S引物，针对真核生物则采用细胞色素c氧化酶I（cytochrome c oxidase I, COI）引物。实验结果表明，eDNA捕获与提取的方案组合会显著影响DNA得率以及下一代测序得到的序列数量。我们观测到物种检出率存在显著差异，检出范围从0%至33%不等。不同方案组合所实现的元条形码生物多样性检出峰值存在差异，这说明针对不同的生物多样性靶标，需采用适配的实验方案。本研究结果凸显出：从水体中捕获与提取eDNA所选用的分子实验方案，会对生物多样性检测结果产生极强的影响。若能充分考量方案选择所引发的偏倚，将有助于构建更具一致性与可靠性的分子实验流程，从而提升水生群落生物多样性检测的可重复性与检出率。