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（Environmental DNA, eDNA）通过捕获、提取并鉴定释放至环境中的DNA片段，实现生物多样性的检测。然而，不同研究中eDNA的捕获与提取实验方案差异显著。这类方案的不统一可能为检测结果引入偏倚，严重制约eDNA在生物多样性可靠检测中的应用。本研究针对水生生态系统中，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探究。我们采集了湖水与河水样本，采用6种不同的实验方案组合完成eDNA的捕获与提取并设置重复，随后针对4种大型无脊椎动物物种进行检测。此外，利用同一湖水样本的技术重复样本，我们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：其中以16S作为真细菌的检测靶标，以细胞色素c氧化酶亚基I（COI）作为真核生物的检测靶标。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获得的序列数量。我们观测到物种检出率存在显著差异，区间为0%至33%。研究还发现，能实现最高元条形码生物多样性检测的方案组合因靶标不同而存在差异，这说明针对不同的生物多样性检测靶标，需采用适配的实验方案。本研究结果凸显了水体eDNA捕获与提取所用分子实验方案的选择，会对生物多样性检测产生强烈影响。若能充分考量方案选择带来的偏倚，将有助于构建一致性与可靠性更强的分子工作流程，从而实现水生群落生物多样性检测的可重复性提升与检出率优化。