Diatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co, Tibet: The effect of sample-size and bioinformatics on the identified communities

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 stu...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Wengang Kang, Sten Anslan, Nicole Börner, Anja Schwarz, Robin Schmidt, Sven Künzel, Patrick Rioual, Paula Echeverría-Galindo, Miguel Vences, Junbo Wang, Antje Schwalb
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Diatoms Metabarcoding Tibetan Plateau sedDNA Bioinformatics Ecology QH540-549.5
Acceso en línea:	https://doaj.org/article/2c0e716828c3457d88dd9e635421a871
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:2c0e716828c3457d88dd9e635421a871
record_format	dspace
spelling	oai:doaj.org-article:2c0e716828c3457d88dd9e635421a8712021-12-01T04:34:11ZDiatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co, Tibet: The effect of sample-size and bioinformatics on the identified communities1470-160X10.1016/j.ecolind.2020.107070https://doaj.org/article/2c0e716828c3457d88dd9e635421a8712021-02-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S1470160X20310098https://doaj.org/toc/1470-160XDiatoms (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.Wengang KangSten AnslanNicole BörnerAnja SchwarzRobin SchmidtSven KünzelPatrick RioualPaula Echeverría-GalindoMiguel VencesJunbo WangAntje SchwalbElsevierarticleDiatomsMetabarcodingTibetan PlateausedDNABioinformaticsEcologyQH540-549.5ENEcological Indicators, Vol 121, Iss , Pp 107070- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Diatoms Metabarcoding Tibetan Plateau sedDNA Bioinformatics Ecology QH540-549.5
spellingShingle	Diatoms Metabarcoding Tibetan Plateau sedDNA Bioinformatics Ecology QH540-549.5 Wengang Kang Sten Anslan Nicole Börner Anja Schwarz Robin Schmidt Sven Künzel Patrick Rioual Paula Echeverría-Galindo Miguel Vences Junbo Wang Antje Schwalb Diatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co, Tibet: The effect of sample-size and bioinformatics on the identified communities
description	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.
format	article
author	Wengang Kang Sten Anslan Nicole Börner Anja Schwarz Robin Schmidt Sven Künzel Patrick Rioual Paula Echeverría-Galindo Miguel Vences Junbo Wang Antje Schwalb
author_facet	Wengang Kang Sten Anslan Nicole Börner Anja Schwarz Robin Schmidt Sven Künzel Patrick Rioual Paula Echeverría-Galindo Miguel Vences Junbo Wang Antje Schwalb
author_sort	Wengang Kang
title	Diatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co, Tibet: The effect of sample-size and bioinformatics on the identified communities
title_short	Diatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co, Tibet: The effect of sample-size and bioinformatics on the identified communities
title_full	Diatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co, Tibet: The effect of sample-size and bioinformatics on the identified communities
title_fullStr	Diatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co, Tibet: The effect of sample-size and bioinformatics on the identified communities
title_full_unstemmed	Diatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co, Tibet: The effect of sample-size and bioinformatics on the identified communities
title_sort	diatom metabarcoding and microscopic analyses from sediment samples at lake nam co, tibet: the effect of sample-size and bioinformatics on the identified communities
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/2c0e716828c3457d88dd9e635421a871
work_keys_str_mv	AT wengangkang diatommetabarcodingandmicroscopicanalysesfromsedimentsamplesatlakenamcotibettheeffectofsamplesizeandbioinformaticsontheidentifiedcommunities AT stenanslan diatommetabarcodingandmicroscopicanalysesfromsedimentsamplesatlakenamcotibettheeffectofsamplesizeandbioinformaticsontheidentifiedcommunities AT nicoleborner diatommetabarcodingandmicroscopicanalysesfromsedimentsamplesatlakenamcotibettheeffectofsamplesizeandbioinformaticsontheidentifiedcommunities AT anjaschwarz diatommetabarcodingandmicroscopicanalysesfromsedimentsamplesatlakenamcotibettheeffectofsamplesizeandbioinformaticsontheidentifiedcommunities AT robinschmidt diatommetabarcodingandmicroscopicanalysesfromsedimentsamplesatlakenamcotibettheeffectofsamplesizeandbioinformaticsontheidentifiedcommunities AT svenkunzel diatommetabarcodingandmicroscopicanalysesfromsedimentsamplesatlakenamcotibettheeffectofsamplesizeandbioinformaticsontheidentifiedcommunities AT patrickrioual diatommetabarcodingandmicroscopicanalysesfromsedimentsamplesatlakenamcotibettheeffectofsamplesizeandbioinformaticsontheidentifiedcommunities AT paulaecheverriagalindo diatommetabarcodingandmicroscopicanalysesfromsedimentsamplesatlakenamcotibettheeffectofsamplesizeandbioinformaticsontheidentifiedcommunities AT miguelvences diatommetabarcodingandmicroscopicanalysesfromsedimentsamplesatlakenamcotibettheeffectofsamplesizeandbioinformaticsontheidentifiedcommunities AT junbowang diatommetabarcodingandmicroscopicanalysesfromsedimentsamplesatlakenamcotibettheeffectofsamplesizeandbioinformaticsontheidentifiedcommunities AT antjeschwalb diatommetabarcodingandmicroscopicanalysesfromsedimentsamplesatlakenamcotibettheeffectofsamplesizeandbioinformaticsontheidentifiedcommunities
_version_	1718405833605251072

Diatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co, Tibet: The effect of sample-size and bioinformatics on the identified communities

Ejemplares similares