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、提取并识别释放入环境中的DNA，来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巨大。这类方案不统一的情况可能会为检测结果引入偏倚，严重阻碍eDNA在生物多样性检测中的可靠应用。本研究旨在探究eDNA捕获与提取方案的选择，是否会显著影响水生系统中的生物多样性检测结果。我们采集了湖泊与河流水样，通过6种不同方案组合（设置生物学重复）完成eDNA的捕获与提取，并针对4种大型无脊椎动物物种的检测进行了验证。此外，我们利用同一湖水样本的技术重复样本，对比了不同捕获与提取方案对生物多样性宏条形码检测的影响：针对真细菌采用16S引物，针对真核生物则采用细胞色素c氧化酶亚基I（COI）引物。研究结果表明，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。我们发现物种检测率存在显著差异，区间为0%至33%。本研究还发现，能实现最高宏条形码生物多样性检测效果的方案组合各不相同，这表明针对不同的生物多样性检测目标，需要采用适配的实验方案。本研究结果凸显了从水体中捕获和提取eDNA时所选用的分子实验方案，会对生物多样性检测产生强烈影响。在实验中重视方案选择所引入的偏倚，有助于构建更一致、可靠的分子实验流程，从而在水生群落中实现可重复且更高精度的生物多样性检测。