Data from: Detection of the endangered European weather loach (Misgurnus fossilis) via water and sediment samples: testing multiple eDNA workflows.

The European weather loach (Misgurnus fossilis) is classified as highly
endangered in several countries of Central Europe. Populations of M.
fossilis are predominantly found in ditches with low water levels and
thick sludge layers and are thus hard to detect using conventional fishing
methods. Therefore, environmental DNA (eDNA) monitoring appears
particularly relevant for this species. In previous studies, M. fossilis
was surveyed following eDNA water sampling protocols, which were not
optimized for this species. Therefore, we created two full factorial study
designs to test six different eDNA workflows for sediment samples and
twelve different workflows for water samples. We used qPCR to compare the
Threshold cycle (Ct) values of the different workflows, which indicate the
target DNA amount in the sample, and spectrophotometry to quantify and
compare the total DNA amount inside the samples. We analyzed 96 water
samples and 48 sediment samples from a pond with a known population of M.
fossilis. We tested several method combinations for long-term sample
preservation, DNA capture and DNA extraction. Additionally, we analyzed
the DNA yield of samples from a ditch with a natural M. fossilis
population monthly over one year to determine the optimal sampling period.
Our results showed that the long-term water preservation method commonly
used for eDNA surveys of M. fossilis did not lead to optimal DNA yields,
and we present a valid long-term sample preservation alternative. A
cost-efficient high salt DNA extraction led to the highest target DNA
yields and can be used for sediment and water samples. Furthermore, we
were able to show that in a natural habitat of M. fossilis, total and
target eDNA were higher between June and September, which implies that
this period is favorable for eDNA sampling. Our results will help to
improve the reliability of future eDNA surveys of M. fossilis.

欧洲泥鳅（Misgurnus fossilis）在中欧多个国家被列为极度濒危物种。该物种种群主要栖息于水位偏低、淤泥层较厚的沟渠中，因此传统捕捞手段难以对其进行有效探测。鉴于此，环境DNA（environmental DNA, eDNA）监测对该物种而言显得尤为关键。既往针对欧洲泥鳅的调查均采用eDNA水体采样方案，但此类方案并未针对该物种进行优化。为此，本研究设计了两套全因子试验设计，分别针对沉积物样本测试6种不同的eDNA实验流程，针对水体样本测试12种不同的实验流程。我们采用实时荧光定量PCR（quantitative Polymerase Chain Reaction, qPCR）对比不同实验流程的循环阈值（Threshold cycle, Ct）值——该数值可反映样本中的靶标DNA含量；同时通过分光光度法定量并对比样本中的总DNA含量。我们从一处已知存在欧洲泥鳅种群的池塘中采集了96份水体样本与48份沉积物样本，并针对这些样本测试了多种用于长期保存、DNA捕获与DNA提取的方法组合。此外，我们还对一处拥有天然欧洲泥鳅种群的沟渠中的样本开展了为期1年的月度采样与分析，以确定该物种eDNA监测的最佳采样时段。研究结果表明，此前常用于欧洲泥鳅eDNA调查的水体样本长期保存方法并未实现最优DNA得率，本研究提出了一种有效的长期样本保存替代方案。采用高盐法的DNA提取流程具备最优成本效益比，可获得最高的靶标DNA得率，且适用于沉积物与水体两类样本。此外，我们证实，在欧洲泥鳅的天然栖息地中，总DNA与靶标eDNA的含量在6月至9月间处于较高水平，这表明该时段为开展eDNA采样的适宜时期。本研究结果将有助于提升未来欧洲泥鳅eDNA调查的可靠性。