气候变化领域集成服务门户(CCPortal): Diatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co; Tibet: The effect of sample-size and bioinformatics on the identified communities

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DOI	10.1016/j.ecolind.2020.107070
	Diatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co; Tibet: The effect of sample-size and bioinformatics on the identified communities
	Kang W.; Anslan S.; Börner N.; Schwarz A.; Schmidt R.; Künzel S.; Rioual P.; Echeverría-Galindo P.; Vences M.; Wang J.; Schwalb A.
发表日期	2021
ISSN	1470160X
卷号	121
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. © 2020 The Author(s)
英文关键词	Bioinformatics; Diatoms; Metabarcoding; sedDNA; Tibetan Plateau
语种	英语
scopus关键词	Ecological Indicators
来源机构	中国科学院地质与地球物理研究所
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/158309
作者单位	Institute of Geosystems and Bioindication; Technische Universität Braunschweig; Braunschweig; Germany; Zoological Institute; Technische Universität Braunschweig; Braunschweig; Germany; Department of Evolutionary Genetics; Max Planck Institute for Evolutionary Biology; Plön; Germany; Key Laboratory of Cenozoic Geology & Environment; Institute of Geology and Geophysics; Chinese Academy of Sciences; Beijing; China; Key Laboratory of Tibetan Environment Changes and Land Surface Processes (TEL)/Nam Co Observation and Research Station (NAMORS); Institute of Tibetan Plateau Research; Chinese Academy of Sciences; Beijing; 100101; China; CAS Center for Excellence in Life and Paleoenvironment; Beijing; China
推荐引用方式 GB/T 7714	Kang W.,Anslan S.,Börner N.,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]. 中国科学院地质与地球物理研究所,2021,121.
APA	Kang W..,Anslan S..,Börner N..,Schwarz A..,Schmidt R..,...&Schwalb A..(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.,121.
MLA	Kang W.,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".121(2021).