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The impact of OTU sequence similarity threshold on diatom‐based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean)

Extensive studies on the taxonomic resolution required for bioassessment purposes have determined that resolution above species level (genus, family) is sufficient for their use as indicators of relevant environmental pressures. The high‐throughput sequencing (HTS) and meta‐barcoding methods now use...

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Autores principales: Tapolczai, Kálmán, Vasselon, Valentin, Bouchez, Agnès, Stenger‐Kovács, Csilla, Padisák, Judit, Rimet, Frédéric
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6342121/
https://www.ncbi.nlm.nih.gov/pubmed/30680104
http://dx.doi.org/10.1002/ece3.4701
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author Tapolczai, Kálmán
Vasselon, Valentin
Bouchez, Agnès
Stenger‐Kovács, Csilla
Padisák, Judit
Rimet, Frédéric
author_facet Tapolczai, Kálmán
Vasselon, Valentin
Bouchez, Agnès
Stenger‐Kovács, Csilla
Padisák, Judit
Rimet, Frédéric
author_sort Tapolczai, Kálmán
collection PubMed
description Extensive studies on the taxonomic resolution required for bioassessment purposes have determined that resolution above species level (genus, family) is sufficient for their use as indicators of relevant environmental pressures. The high‐throughput sequencing (HTS) and meta‐barcoding methods now used for bioassessment traditionally employ an arbitrary sequence similarity threshold (SST) around 95% or 97% to cluster sequences into operational taxonomic units, which is considered descriptive of species‐level resolution. In this study, we analyzed the effect of the SST on the resulting diatom‐based ecological quality index, which is based on OTU abundance distribution along a defined environmental gradient, ideally avoiding taxonomic assignments that could result in high rates of unclassified OTUs and biased final values. A total of 90 biofilm samples were collected in 2014 and 2015 from 51 stream sites on Mayotte Island in parallel with measures of relevant physical and chemical parameters. HTS sequencing was performed on the biofilms using the rbcL region as the genetic marker and diatom‐specific primers. Hierarchical clustering was used to group sequences into OTUs using 20 experimental SST levels (80%–99%). An OTU‐based quality index (Idx(OTU)) was developed based on a weighted average equation using the abundance profiles of the OTUs. The developed Idx(OTU) revealed significant correlations between the Idx(OTU) values and the reference pressure gradient, which reached maximal performance using an SST of 90% (well above species level delimitation). We observed an interesting and important trade‐off with the power to discriminate between sampling sites and index stability that will greatly inform future applications of the index. Taken together, the results from this study detail a thoroughly optimized and validated approach to generating robust, reproducible, and complete indexes that will greatly facilitate effective and efficient environmental monitoring.
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spelling pubmed-63421212019-01-24 The impact of OTU sequence similarity threshold on diatom‐based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean) Tapolczai, Kálmán Vasselon, Valentin Bouchez, Agnès Stenger‐Kovács, Csilla Padisák, Judit Rimet, Frédéric Ecol Evol Original Research Extensive studies on the taxonomic resolution required for bioassessment purposes have determined that resolution above species level (genus, family) is sufficient for their use as indicators of relevant environmental pressures. The high‐throughput sequencing (HTS) and meta‐barcoding methods now used for bioassessment traditionally employ an arbitrary sequence similarity threshold (SST) around 95% or 97% to cluster sequences into operational taxonomic units, which is considered descriptive of species‐level resolution. In this study, we analyzed the effect of the SST on the resulting diatom‐based ecological quality index, which is based on OTU abundance distribution along a defined environmental gradient, ideally avoiding taxonomic assignments that could result in high rates of unclassified OTUs and biased final values. A total of 90 biofilm samples were collected in 2014 and 2015 from 51 stream sites on Mayotte Island in parallel with measures of relevant physical and chemical parameters. HTS sequencing was performed on the biofilms using the rbcL region as the genetic marker and diatom‐specific primers. Hierarchical clustering was used to group sequences into OTUs using 20 experimental SST levels (80%–99%). An OTU‐based quality index (Idx(OTU)) was developed based on a weighted average equation using the abundance profiles of the OTUs. The developed Idx(OTU) revealed significant correlations between the Idx(OTU) values and the reference pressure gradient, which reached maximal performance using an SST of 90% (well above species level delimitation). We observed an interesting and important trade‐off with the power to discriminate between sampling sites and index stability that will greatly inform future applications of the index. Taken together, the results from this study detail a thoroughly optimized and validated approach to generating robust, reproducible, and complete indexes that will greatly facilitate effective and efficient environmental monitoring. John Wiley and Sons Inc. 2018-12-18 /pmc/articles/PMC6342121/ /pubmed/30680104 http://dx.doi.org/10.1002/ece3.4701 Text en © 2018 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Research
Tapolczai, Kálmán
Vasselon, Valentin
Bouchez, Agnès
Stenger‐Kovács, Csilla
Padisák, Judit
Rimet, Frédéric
The impact of OTU sequence similarity threshold on diatom‐based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean)
title The impact of OTU sequence similarity threshold on diatom‐based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean)
title_full The impact of OTU sequence similarity threshold on diatom‐based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean)
title_fullStr The impact of OTU sequence similarity threshold on diatom‐based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean)
title_full_unstemmed The impact of OTU sequence similarity threshold on diatom‐based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean)
title_short The impact of OTU sequence similarity threshold on diatom‐based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean)
title_sort impact of otu sequence similarity threshold on diatom‐based bioassessment: a case study of the rivers of mayotte (france, indian ocean)
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6342121/
https://www.ncbi.nlm.nih.gov/pubmed/30680104
http://dx.doi.org/10.1002/ece3.4701
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