Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies
Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies
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DOI：
10.1111/1755-0998.12336
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发表时间：
2015-05-01
影响因子：
7.7
通讯作者：
Gemeinholzer, Birgit
中科院分区：
文献类型：
--
作者：
Zimmermann, Jonas;Gloeckner, Gernot;Gemeinholzer, Birgit
硅藻经常用于水质评估；然而，物种水平的鉴定是困难的、耗时的，并且需要对所研究的生物体有深入的了解，因为非同质物种特异性的形态特征很少。我们在此研究基于 DNA 的识别方法（使用 NGS 平台的元条形码）与形态硅藻识别相比的表现，并提出优化硅藻淡水质量评估的工作流程。采用DNA和形态学方法对奥德拉河和卢萨蒂安尼斯河系统从源头到河口沿线七个不同地点的硅藻多样性进行了分析，并进行了比较。 NGS 技术几乎总是能识别出更多数量的分类单元（NGS 为 270 个，而光学显微镜 LM 为 103 个），这些分类单元的存在随后可以通过 LM 进行验证。基于序列的方法可以更深入地了解环境样本的分类多样性。整个河流系统的分类单元检索差异很大，具体取决于物种的出现和参考数据库的分类深度。来自河流系统贫营养部分的大多数稀有类群在所使用的参考数据库中没有得到很好的体现。提出了基于 DNA 的 NGS 硅藻鉴定工作流程。评估了 28000 个硅藻序列。我们的研究结果证明，通过 V4 区域 (18S) 的 NGS 测序对硅藻进行元条形码在水质评估方面具有巨大潜力，并且可以补充甚至可能改进光学显微镜的识别。
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. 28000 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.