Molecular versus morphological data for benthic diatoms biomonitoring in Northern Europe freshwater and consequences for ecological status
Diatoms are known to be efficient bioindicators for water quality assessment because of their rapid response to environmental pressures and their omnipresence in water bodies. The identification of benthic diatoms communities in the biofilm, coupled with quality indices such as the Indice de polluos...
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ftdoajarticles:oai:doaj.org/article:f0c8c11214704a7cb9e021ddfff53f97 2023-05-15T16:12:16+02:00 Molecular versus morphological data for benthic diatoms biomonitoring in Northern Europe freshwater and consequences for ecological status Bonnie Bailet Agnes Bouchez Alain Franc Jean-Marc Frigerio François Keck Satu-Maaria Karjalainen Frederic Rimet Susanne Schneider Maria Kahler 2019-06-01T00:00:00Z https://doi.org/10.3897/mbmg.3.34002 https://doaj.org/article/f0c8c11214704a7cb9e021ddfff53f97 EN eng Pensoft Publishers https://mbmg.pensoft.net/article/34002/download/pdf/ https://mbmg.pensoft.net/article/34002/download/xml/ https://mbmg.pensoft.net/article/34002/ https://doaj.org/toc/2534-9708 doi:10.3897/mbmg.3.34002 2534-9708 https://doaj.org/article/f0c8c11214704a7cb9e021ddfff53f97 Metabarcoding and Metagenomics, Vol 3, Iss , Pp 21-35 (2019) Ecology QH540-549.5 article 2019 ftdoajarticles https://doi.org/10.3897/mbmg.3.34002 2022-12-31T04:37:11Z Diatoms are known to be efficient bioindicators for water quality assessment because of their rapid response to environmental pressures and their omnipresence in water bodies. The identification of benthic diatoms communities in the biofilm, coupled with quality indices such as the Indice de polluosensibilité spécifique (IPS) can be used for biomonitoring purposes in freshwater. However, the morphological identification and counting of diatoms species under the microscope is time-consuming and requires extensive expertise to deal with a constantly evolving taxonomy. In response, a molecular-based and potentially more cost-effective method has been developed, coupling high-throughput sequencing and DNA metabarcoding. The method has already been tested for water quality assessment with diatoms in Central Europe. In this study, we applied both the traditional and molecular methods on 180 biofilms samples from Northern Europe (rivers and lakes of Fennoscandia and Iceland). The DNA metabarcoding data were obtained on two different DNA markers, the 18S-V4 and rbcL barcodes, with the NucleoSpin Soil kit for DNA extraction and sequenced on an Ion Torrent PGM platform. We assessed the ability of the molecular method to produce species inventories, IPS scores and ecological status class comparable to the ones generated by the traditional morphology-based approach. The two methods generated correlated but significantly different IPS scores and ecological status assessment. The observed deviations are explained by presence/absence and abundance discrepancies in the species inventories, mainly due to the incompleteness of the barcodes reference databases, primer bias and strictness of the bioinformatic pipeline. Abundance discrepancies are less common than presence/absence discrepancies but have a greater effect on the ecological assessment. Missing species in the reference databases are mostly acidophilic benthic diatoms species, typical of the low pH waters of Northern Europe. The two different DNA markers also generated ... Article in Journal/Newspaper Fennoscandia Iceland Directory of Open Access Journals: DOAJ Articles Metabarcoding and Metagenomics 3 |
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Directory of Open Access Journals: DOAJ Articles |
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topic |
Ecology QH540-549.5 |
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Ecology QH540-549.5 Bonnie Bailet Agnes Bouchez Alain Franc Jean-Marc Frigerio François Keck Satu-Maaria Karjalainen Frederic Rimet Susanne Schneider Maria Kahler Molecular versus morphological data for benthic diatoms biomonitoring in Northern Europe freshwater and consequences for ecological status |
topic_facet |
Ecology QH540-549.5 |
description |
Diatoms are known to be efficient bioindicators for water quality assessment because of their rapid response to environmental pressures and their omnipresence in water bodies. The identification of benthic diatoms communities in the biofilm, coupled with quality indices such as the Indice de polluosensibilité spécifique (IPS) can be used for biomonitoring purposes in freshwater. However, the morphological identification and counting of diatoms species under the microscope is time-consuming and requires extensive expertise to deal with a constantly evolving taxonomy. In response, a molecular-based and potentially more cost-effective method has been developed, coupling high-throughput sequencing and DNA metabarcoding. The method has already been tested for water quality assessment with diatoms in Central Europe. In this study, we applied both the traditional and molecular methods on 180 biofilms samples from Northern Europe (rivers and lakes of Fennoscandia and Iceland). The DNA metabarcoding data were obtained on two different DNA markers, the 18S-V4 and rbcL barcodes, with the NucleoSpin Soil kit for DNA extraction and sequenced on an Ion Torrent PGM platform. We assessed the ability of the molecular method to produce species inventories, IPS scores and ecological status class comparable to the ones generated by the traditional morphology-based approach. The two methods generated correlated but significantly different IPS scores and ecological status assessment. The observed deviations are explained by presence/absence and abundance discrepancies in the species inventories, mainly due to the incompleteness of the barcodes reference databases, primer bias and strictness of the bioinformatic pipeline. Abundance discrepancies are less common than presence/absence discrepancies but have a greater effect on the ecological assessment. Missing species in the reference databases are mostly acidophilic benthic diatoms species, typical of the low pH waters of Northern Europe. The two different DNA markers also generated ... |
format |
Article in Journal/Newspaper |
author |
Bonnie Bailet Agnes Bouchez Alain Franc Jean-Marc Frigerio François Keck Satu-Maaria Karjalainen Frederic Rimet Susanne Schneider Maria Kahler |
author_facet |
Bonnie Bailet Agnes Bouchez Alain Franc Jean-Marc Frigerio François Keck Satu-Maaria Karjalainen Frederic Rimet Susanne Schneider Maria Kahler |
author_sort |
Bonnie Bailet |
title |
Molecular versus morphological data for benthic diatoms biomonitoring in Northern Europe freshwater and consequences for ecological status |
title_short |
Molecular versus morphological data for benthic diatoms biomonitoring in Northern Europe freshwater and consequences for ecological status |
title_full |
Molecular versus morphological data for benthic diatoms biomonitoring in Northern Europe freshwater and consequences for ecological status |
title_fullStr |
Molecular versus morphological data for benthic diatoms biomonitoring in Northern Europe freshwater and consequences for ecological status |
title_full_unstemmed |
Molecular versus morphological data for benthic diatoms biomonitoring in Northern Europe freshwater and consequences for ecological status |
title_sort |
molecular versus morphological data for benthic diatoms biomonitoring in northern europe freshwater and consequences for ecological status |
publisher |
Pensoft Publishers |
publishDate |
2019 |
url |
https://doi.org/10.3897/mbmg.3.34002 https://doaj.org/article/f0c8c11214704a7cb9e021ddfff53f97 |
genre |
Fennoscandia Iceland |
genre_facet |
Fennoscandia Iceland |
op_source |
Metabarcoding and Metagenomics, Vol 3, Iss , Pp 21-35 (2019) |
op_relation |
https://mbmg.pensoft.net/article/34002/download/pdf/ https://mbmg.pensoft.net/article/34002/download/xml/ https://mbmg.pensoft.net/article/34002/ https://doaj.org/toc/2534-9708 doi:10.3897/mbmg.3.34002 2534-9708 https://doaj.org/article/f0c8c11214704a7cb9e021ddfff53f97 |
op_doi |
https://doi.org/10.3897/mbmg.3.34002 |
container_title |
Metabarcoding and Metagenomics |
container_volume |
3 |
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1765997523556630528 |