Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach
Background: Continuous efforts to estimate actual diversity and to trace the species distribution and ranges in the natural environments have gone in equal pace with advancements of the technologies in the study of microbial species diversity from microscopic observations to DNA-based barcoding. DNA...
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ftarchimer:oai:archimer.ifremer.fr:48494 |
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Open Polar |
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Archimer (Archive Institutionnelle de l'Ifremer - Institut français de recherche pour l'exploitation de la mer) |
op_collection_id |
ftarchimer |
language |
English |
description |
Background: Continuous efforts to estimate actual diversity and to trace the species distribution and ranges in the natural environments have gone in equal pace with advancements of the technologies in the study of microbial species diversity from microscopic observations to DNA-based barcoding. DNA metabarcoding based on Next Generation Sequencing (NGS) constitutes the latest advancement in these efforts. Here we use NGS data from different sites to investigate the geographic range of six species of the diatom family Leptocylindraceae and to identify possible new taxa within the family. Methodology/Principal Findings: We analysed the V4 and V9 regions of the nuclear-encoded SSU rDNA gene region in the NGS database of the European ERA-Biodiversa project BioMarKs, collected in plankton and sediments at six coastal sites in European coastal waters, as well as environmental sequences from the NCBI database. All species known in the family Leptocylindraceae were detected in both datasets, but the much larger Illumina V9 dataset showed a higher species coverage at the various sites than the 454 V4 dataset. Sequences identical or similar to the references of Leptocylindrus aporus, L. convexus, L. danicus/hargravesii and Tenuicylindrus belgicus were found in the Mediterranean Sea, North Atlantic Ocean and Black Sea as well as at locations outside Europe. Instead, sequences identical or close to that of L. minimus were found in the North Atlantic Ocean and the Black Sea but not in the Mediterranean Sea, while sequences belonging to a yet undescribed taxon were encountered only in Oslo Fjord and Baffin Bay. Conclusions/Significance: Identification of Leptocylindraceae species in NGS datasets has expanded our knowledge of the species biogeographic distribution and of the overall diversity of this diatom family. Individual species appear to be widespread, but not all of them are found everywhere. Despite the sequencing depth allowed by NGS and the wide geographic area covered by this study, the diversity of this ancient diatom family appears to be low, at least at the level of the marker used in this study. |
format |
Article in Journal/Newspaper |
author |
Nanjappa, Deepak Audic, Stephane Romac, Sarah Kooistra, Wiebe H. C. F. Zingone, Adriana |
spellingShingle |
Nanjappa, Deepak Audic, Stephane Romac, Sarah Kooistra, Wiebe H. C. F. Zingone, Adriana Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach |
author_facet |
Nanjappa, Deepak Audic, Stephane Romac, Sarah Kooistra, Wiebe H. C. F. Zingone, Adriana |
author_sort |
Nanjappa, Deepak |
title |
Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach |
title_short |
Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach |
title_full |
Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach |
title_fullStr |
Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach |
title_full_unstemmed |
Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach |
title_sort |
assessment of species diversity and distribution of an ancient diatom lineage using a dna metabarcoding approach |
publisher |
Public Library Science |
publishDate |
2014 |
url |
https://archimer.ifremer.fr/doc/00374/48494/48846.pdf https://archimer.ifremer.fr/doc/00374/48494/48847.eps https://archimer.ifremer.fr/doc/00374/48494/48848.eps https://archimer.ifremer.fr/doc/00374/48494/48849.eps https://archimer.ifremer.fr/doc/00374/48494/48850.eps https://archimer.ifremer.fr/doc/00374/48494/48851.eps https://archimer.ifremer.fr/doc/00374/48494/48852.eps https://archimer.ifremer.fr/doc/00374/48494/48853.eps https://archimer.ifremer.fr/doc/00374/48494/48854.eps https://archimer.ifremer.fr/doc/00374/48494/48855.xlsx https://archimer.ifremer.fr/doc/00374/48494/48856.pdf https://doi.org/10.1371/journal.pone.0103810 https://archimer.ifremer.fr/doc/00374/48494/ |
geographic |
Baffin Bay |
geographic_facet |
Baffin Bay |
genre |
Baffin Bay Baffin Bay Baffin North Atlantic |
genre_facet |
Baffin Bay Baffin Bay Baffin North Atlantic |
op_source |
Plos One (1932-6203) (Public Library Science), 2014-08 , Vol. 9 , N. 8 , P. e103810 (1-15) |
op_relation |
info:eu-repo/grantAgreement/EC/FP7/517836/EU//BIODIVERSA https://archimer.ifremer.fr/doc/00374/48494/48846.pdf https://archimer.ifremer.fr/doc/00374/48494/48847.eps https://archimer.ifremer.fr/doc/00374/48494/48848.eps https://archimer.ifremer.fr/doc/00374/48494/48849.eps https://archimer.ifremer.fr/doc/00374/48494/48850.eps https://archimer.ifremer.fr/doc/00374/48494/48851.eps https://archimer.ifremer.fr/doc/00374/48494/48852.eps https://archimer.ifremer.fr/doc/00374/48494/48853.eps https://archimer.ifremer.fr/doc/00374/48494/48854.eps https://archimer.ifremer.fr/doc/00374/48494/48855.xlsx https://archimer.ifremer.fr/doc/00374/48494/48856.pdf doi:10.1371/journal.pone.0103810 https://archimer.ifremer.fr/doc/00374/48494/ |
op_rights |
2014 Nanjappa et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. info:eu-repo/semantics/openAccess restricted use |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1371/journal.pone.0103810 |
container_title |
PLoS ONE |
container_volume |
9 |
container_issue |
8 |
container_start_page |
e103810 |
_version_ |
1766365423023947776 |
spelling |
ftarchimer:oai:archimer.ifremer.fr:48494 2023-05-15T15:35:08+02:00 Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach Nanjappa, Deepak Audic, Stephane Romac, Sarah Kooistra, Wiebe H. C. F. Zingone, Adriana 2014-08 application/pdf https://archimer.ifremer.fr/doc/00374/48494/48846.pdf https://archimer.ifremer.fr/doc/00374/48494/48847.eps https://archimer.ifremer.fr/doc/00374/48494/48848.eps https://archimer.ifremer.fr/doc/00374/48494/48849.eps https://archimer.ifremer.fr/doc/00374/48494/48850.eps https://archimer.ifremer.fr/doc/00374/48494/48851.eps https://archimer.ifremer.fr/doc/00374/48494/48852.eps https://archimer.ifremer.fr/doc/00374/48494/48853.eps https://archimer.ifremer.fr/doc/00374/48494/48854.eps https://archimer.ifremer.fr/doc/00374/48494/48855.xlsx https://archimer.ifremer.fr/doc/00374/48494/48856.pdf https://doi.org/10.1371/journal.pone.0103810 https://archimer.ifremer.fr/doc/00374/48494/ eng eng Public Library Science info:eu-repo/grantAgreement/EC/FP7/517836/EU//BIODIVERSA https://archimer.ifremer.fr/doc/00374/48494/48846.pdf https://archimer.ifremer.fr/doc/00374/48494/48847.eps https://archimer.ifremer.fr/doc/00374/48494/48848.eps https://archimer.ifremer.fr/doc/00374/48494/48849.eps https://archimer.ifremer.fr/doc/00374/48494/48850.eps https://archimer.ifremer.fr/doc/00374/48494/48851.eps https://archimer.ifremer.fr/doc/00374/48494/48852.eps https://archimer.ifremer.fr/doc/00374/48494/48853.eps https://archimer.ifremer.fr/doc/00374/48494/48854.eps https://archimer.ifremer.fr/doc/00374/48494/48855.xlsx https://archimer.ifremer.fr/doc/00374/48494/48856.pdf doi:10.1371/journal.pone.0103810 https://archimer.ifremer.fr/doc/00374/48494/ 2014 Nanjappa et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. info:eu-repo/semantics/openAccess restricted use CC-BY Plos One (1932-6203) (Public Library Science), 2014-08 , Vol. 9 , N. 8 , P. e103810 (1-15) text Publication info:eu-repo/semantics/article 2014 ftarchimer https://doi.org/10.1371/journal.pone.0103810 2021-09-23T20:29:18Z Background: Continuous efforts to estimate actual diversity and to trace the species distribution and ranges in the natural environments have gone in equal pace with advancements of the technologies in the study of microbial species diversity from microscopic observations to DNA-based barcoding. DNA metabarcoding based on Next Generation Sequencing (NGS) constitutes the latest advancement in these efforts. Here we use NGS data from different sites to investigate the geographic range of six species of the diatom family Leptocylindraceae and to identify possible new taxa within the family. Methodology/Principal Findings: We analysed the V4 and V9 regions of the nuclear-encoded SSU rDNA gene region in the NGS database of the European ERA-Biodiversa project BioMarKs, collected in plankton and sediments at six coastal sites in European coastal waters, as well as environmental sequences from the NCBI database. All species known in the family Leptocylindraceae were detected in both datasets, but the much larger Illumina V9 dataset showed a higher species coverage at the various sites than the 454 V4 dataset. Sequences identical or similar to the references of Leptocylindrus aporus, L. convexus, L. danicus/hargravesii and Tenuicylindrus belgicus were found in the Mediterranean Sea, North Atlantic Ocean and Black Sea as well as at locations outside Europe. Instead, sequences identical or close to that of L. minimus were found in the North Atlantic Ocean and the Black Sea but not in the Mediterranean Sea, while sequences belonging to a yet undescribed taxon were encountered only in Oslo Fjord and Baffin Bay. Conclusions/Significance: Identification of Leptocylindraceae species in NGS datasets has expanded our knowledge of the species biogeographic distribution and of the overall diversity of this diatom family. Individual species appear to be widespread, but not all of them are found everywhere. Despite the sequencing depth allowed by NGS and the wide geographic area covered by this study, the diversity of this ancient diatom family appears to be low, at least at the level of the marker used in this study. Article in Journal/Newspaper Baffin Bay Baffin Bay Baffin North Atlantic Archimer (Archive Institutionnelle de l'Ifremer - Institut français de recherche pour l'exploitation de la mer) Baffin Bay PLoS ONE 9 8 e103810 |