Diatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co, Tibet: The effect of sample-size and bioinformatics on the identified communities
文献类型：期刊论文
| 作者 | Kang, Wengang6; Anslan, Sten5; Boerner, Nicole6; Schwarz, Anja6; Schmidt, Robin5; Kuenzel, Sven1; Rioual, Patrick2,4; Echeverria-Galindo, Paula6; Vences, Miguel5; Wang, Junbo3 |
| 刊名 | ECOLOGICAL INDICATORS
 |
| 出版日期 | 2021-02-01 |
| 卷号 | 121页码:13 |
| 关键词 | Diatoms Metabarcoding Tibetan Plateau sedDNA Bioinformatics |
| ISSN号 | 1470-160X |
| DOI | 10.1016/j.ecolind.2020.107070 |
| 英文摘要 | Diatoms (Bacillariophyceae) are characterized by silicified cell walls that favor their long-term preservation in sediments, therefore widely used as bioindicators of present and past water conditions. Alongside with traditional morphological analyses, metabarcoding has become a valuable tool to study the community structures of various organisms, including diatoms. Here, we test whether the quantity of sediment sample used for DNA extraction affects the results obtained from high-throughput sequencing (metabarcoding) of the diatom rbcL region by isolating DNA from 10 g and 0.5 g (wet weight) of lake surface sediment samples. Because bioinformatics processing of metabarcoding data may affect the outcome, we also tested the consistency of the results from three different pipelines: 1) ESVs (exact sequence variants) pipeline; 2) clustering sequences at 95% sequence identity to form OTUs (operational taxonomic units; 95% OTUs); and 3) 97% OTUs pipeline. Additionally, the agreement between metabarcoding data and morphological inventories of corresponding samples were compared. Our results demonstrate highly uniform patterns between the diatom rbcL amplicons from 10 g and 0.5 g of sedimentary DNA (sedDNA) extracts (HTS 10 and HTS 0.5, respectively). Furthermore, after the careful curation of the sequencing data, metabarcoding results were highly consistent among the data sets produced by different bioinformatics pipelines. Comparing results from metabarcoding and microscopy, we identified some taxonomic mismatches: morphological analyses identified 59 diatom genera, whereas metabarcoding 49 to 54 genera. These mismatches are related to incompleteness of the sequence databases, but also to inconsistencies in diatom taxonomy in general and potential dissolution effects of diatom valves caused by high alkalinity of the investigated lake waters. Nevertheless, multivariate community analysis revealed consistent results between data sets identified by microscopy and metabarcoding - water depth and conductivity as the most significant variables in driving diatom communities in Lake Nam Co - further confirming that metabarcoding is a viable method for identifying diatom-environment relationships. |
| WOS关键词 | THROUGHPUT SEQUENCING HTS ; DNA EXTRACTION METHODS ; DIVERSITY ; WATER ; PLATEAU ; CHINA |
| 资助项目 | Deutsche Forschungsgemeinschaft (DFG) via the International Research Training Group GRK 2309 "Geoecosystems in transition on the Tibetan Plateau (TransTiP)" |
| WOS研究方向 | Biodiversity & Conservation ; Environmental Sciences & Ecology |
| 语种 | 英语 |
| WOS记录号 | WOS:000604896100007 |
| 出版者 | ELSEVIER |
| 资助机构 | Deutsche Forschungsgemeinschaft (DFG) via the International Research Training Group GRK 2309 "Geoecosystems in transition on the Tibetan Plateau (TransTiP)" ; Deutsche Forschungsgemeinschaft (DFG) via the International Research Training Group GRK 2309 "Geoecosystems in transition on the Tibetan Plateau (TransTiP)" ; Deutsche Forschungsgemeinschaft (DFG) via the International Research Training Group GRK 2309 "Geoecosystems in transition on the Tibetan Plateau (TransTiP)" ; Deutsche Forschungsgemeinschaft (DFG) via the International Research Training Group GRK 2309 "Geoecosystems in transition on the Tibetan Plateau (TransTiP)" ; Deutsche Forschungsgemeinschaft (DFG) via the International Research Training Group GRK 2309 "Geoecosystems in transition on the Tibetan Plateau (TransTiP)" ; Deutsche Forschungsgemeinschaft (DFG) via the International Research Training Group GRK 2309 "Geoecosystems in transition on the Tibetan Plateau (TransTiP)" ; Deutsche Forschungsgemeinschaft (DFG) via the International Research Training Group GRK 2309 "Geoecosystems in transition on the Tibetan Plateau (TransTiP)" ; Deutsche Forschungsgemeinschaft (DFG) via the International Research Training Group GRK 2309 "Geoecosystems in transition on the Tibetan Plateau (TransTiP)" |
| 源URL | [http://ir.iggcas.ac.cn/handle/132A11/99978]  |
| 专题 | 地质与地球物理研究所_中国科学院新生代地质与环境重点实验室 |
| 通讯作者 | Anslan, Sten |
| 作者单位 | 1.Max Planck Inst Evolutionary Biol, Dept Evolutionary Genet, Plon, Germany 2.CAS Ctr Excellence Life & Paleoenvironm, Beijing, Peoples R China 3.Chinese Acad Sci, Inst Tibetan Plateau Res, Key Lab Tibetan Environm Changes & Land Surface P, Nam Co Observat & Res Stn NAMORS, Beijing 100101, Peoples R China 4.Chinese Acad Sci, Inst Geol & Geophys, Key Lab Cenozo Geol & Environm, Beijing, Peoples R China 5.Tech Univ Carolo Wilhelmina Braunschweig, Zool Inst, Braunschweig, Germany 6.Tech Univ Carolo Wilhelmina Braunschweig, Inst Geosyst & Bioindicat, Braunschweig, Germany |
| 推荐引用方式 GB/T 7714 | Kang, Wengang,Anslan, Sten,Boerner, Nicole,et al. Diatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co, Tibet: The effect of sample-size and bioinformatics on the identified communities[J]. ECOLOGICAL INDICATORS,2021,121:13. |
| APA | Kang, Wengang.,Anslan, Sten.,Boerner, Nicole.,Schwarz, Anja.,Schmidt, Robin.,...&Schwalb, Antje.(2021).Diatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co, Tibet: The effect of sample-size and bioinformatics on the identified communities.ECOLOGICAL INDICATORS,121,13. |
| MLA | Kang, Wengang,et al."Diatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co, Tibet: The effect of sample-size and bioinformatics on the identified communities".ECOLOGICAL INDICATORS 121(2021):13. |
入库方式： OAI收割
来源：地质与地球物理研究所
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