Data from: Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies

Diatoms are frequently used for water quality assessments; however, identification to species level is difficult, time-consuming and needs in-depth knowledge of the organisms under investigation, as nonhomoplastic species-specific morphological characters are scarce. We here investigate how identification methods based on DNA (metabarcoding using NGS platforms) perform in comparison to morphological diatom identification and propose a workflow to optimize diatom fresh water quality assessments. Diatom diversity at seven different sites along the course of the river system Odra and Lusatian Neisse from the source to the mouth is analysed with DNA and morphological methods, which are compared. The NGS technology almost always leads to a higher number of identified taxa (270 via NGS vs. 103 by light microscopy LM), whose presence could subsequently be verified by LM. The sequence-based approach allows for a much more graduated insight into the taxonomic diversity of the environmental samples. Taxa retrieval varies considerably throughout the river system, depending on species occurrences and the taxonomic depth of the reference databases. Mostly rare taxa from oligotrophic parts of the river systems are less well represented in the reference database used. A workflow for DNA-based NGS diatom identification is presented. 28 000 diatom sequences were evaluated. Our findings provide evidence that metabarcoding of diatoms via NGS sequencing of the V4 region (18S) has a great potential for water quality assessments and could complement and maybe even improve the identification via light microscopy.硅藻（Diatoms）常被用于水质评估，但其物种水平的鉴定工作难度高、耗时长，且需要对研究对象具备深入的专业认知——这是因为物种特异性且非同源同塑的形态特征极为稀缺。本研究探讨基于DNA的鉴定方法（即利用下一代测序（Next Generation Sequencing, NGS）平台的元条形码（metabarcoding）技术）相较于硅藻形态鉴定的实际效果，并提出一套可优化淡水硅藻水质评估的工作流程。本研究针对奥得河（Odra）与卢萨蒂亚内塞河（Lusatian Neisse）流域从源头至入海口沿线的7个采样点，分别采用DNA检测与形态学方法分析硅藻多样性，并对两种方法的结果进行对比。NGS技术几乎总能鉴定出更多的分类单元（NGS法鉴定出270个分类单元，光学显微镜（light microscopy, LM）法仅为103个），且经LM法可验证这些分类单元的存在。基于序列的鉴定方法可对环境样本的分类多样性实现更为精细化的解析。流域内不同区域的分类单元检出率差异显著，这取决于物种的分布情况以及参考数据库的分类学覆盖深度。来自流域寡营养区域的稀有分类单元，在所使用的参考数据库中收录情况普遍较差。本研究提出了一套基于NGS的硅藻DNA鉴定工作流程，并对28000条硅藻序列进行了分析评估。本研究结果证实，通过对18S rRNA基因V4区进行NGS测序开展硅藻元条形码分析，在水质评估中具备极大应用潜力，可作为光学显微镜鉴定方法的有效补充，甚至有望实现鉴定效果的优化升级。