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New Insights into the Diversity of Marine Picoeukaryotes

Over the last decade, culture-independent surveys of marine picoeukaryotic diversity based on 18S ribosomal DNA clone libraries have unveiled numerous sequences of novel high-rank taxa. This newfound diversity has significantly altered our understanding of marine microbial food webs and the evolutio...

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Detalles Bibliográficos
Autores principales: Not, Fabrice, del Campo, Javier, Balagué, Vanessa, de Vargas, Colomban, Massana, Ramon
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747013/
https://www.ncbi.nlm.nih.gov/pubmed/19787059
http://dx.doi.org/10.1371/journal.pone.0007143
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author Not, Fabrice
del Campo, Javier
Balagué, Vanessa
de Vargas, Colomban
Massana, Ramon
author_facet Not, Fabrice
del Campo, Javier
Balagué, Vanessa
de Vargas, Colomban
Massana, Ramon
author_sort Not, Fabrice
collection PubMed
description Over the last decade, culture-independent surveys of marine picoeukaryotic diversity based on 18S ribosomal DNA clone libraries have unveiled numerous sequences of novel high-rank taxa. This newfound diversity has significantly altered our understanding of marine microbial food webs and the evolution of eukaryotes. However, the current picture of marine eukaryotic biodiversity may be significantly skewed by PCR amplification biases, occurrence of rDNA genes in multiple copies within a single cell, and the capacity of DNA to persist as extracellular material. In this study we performed an analysis of the metagenomic dataset from the Global Ocean Survey (GOS) expedition, seeking eukaryotic ribosomal signatures. This PCR-free approach revealed similar phylogenetic patterns to clone library surveys, suggesting that PCR steps do not impose major biases in the exploration of environmental DNA. The different cell size fractions within the GOS dataset, however, displayed a distinct picture. High protistan diversity in the <0.8 µm size fraction, in particular sequences from radiolarians and ciliates (and their absence in the 0.8–3 µm fraction), suggest that most of the DNA in this fraction comes from extracellular material from larger cells. In addition, we compared the phylogenetic patterns from rDNA and reverse transcribed rRNA 18S clone libraries from the same sample harvested in the Mediterranean Sea. The libraries revealed major differences, with taxa such as pelagophytes or picobiliphytes only detected in the 18S rRNA library. MAST (Marine Stramenopiles) appeared as potentially prominent grazers and we observed a significant decrease in the contribution of alveolate and radiolarian sequences, which overwhelmingly dominated rDNA libraries. The rRNA approach appears to be less affected by taxon-specific rDNA copy number and likely better depicts the biogeochemical significance of marine protists.
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spelling pubmed-27470132009-09-29 New Insights into the Diversity of Marine Picoeukaryotes Not, Fabrice del Campo, Javier Balagué, Vanessa de Vargas, Colomban Massana, Ramon PLoS One Research Article Over the last decade, culture-independent surveys of marine picoeukaryotic diversity based on 18S ribosomal DNA clone libraries have unveiled numerous sequences of novel high-rank taxa. This newfound diversity has significantly altered our understanding of marine microbial food webs and the evolution of eukaryotes. However, the current picture of marine eukaryotic biodiversity may be significantly skewed by PCR amplification biases, occurrence of rDNA genes in multiple copies within a single cell, and the capacity of DNA to persist as extracellular material. In this study we performed an analysis of the metagenomic dataset from the Global Ocean Survey (GOS) expedition, seeking eukaryotic ribosomal signatures. This PCR-free approach revealed similar phylogenetic patterns to clone library surveys, suggesting that PCR steps do not impose major biases in the exploration of environmental DNA. The different cell size fractions within the GOS dataset, however, displayed a distinct picture. High protistan diversity in the <0.8 µm size fraction, in particular sequences from radiolarians and ciliates (and their absence in the 0.8–3 µm fraction), suggest that most of the DNA in this fraction comes from extracellular material from larger cells. In addition, we compared the phylogenetic patterns from rDNA and reverse transcribed rRNA 18S clone libraries from the same sample harvested in the Mediterranean Sea. The libraries revealed major differences, with taxa such as pelagophytes or picobiliphytes only detected in the 18S rRNA library. MAST (Marine Stramenopiles) appeared as potentially prominent grazers and we observed a significant decrease in the contribution of alveolate and radiolarian sequences, which overwhelmingly dominated rDNA libraries. The rRNA approach appears to be less affected by taxon-specific rDNA copy number and likely better depicts the biogeochemical significance of marine protists. Public Library of Science 2009-09-29 /pmc/articles/PMC2747013/ /pubmed/19787059 http://dx.doi.org/10.1371/journal.pone.0007143 Text en Not et al. http://creativecommons.org/licenses/by/4.0/ 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 properly credited.
spellingShingle Research Article
Not, Fabrice
del Campo, Javier
Balagué, Vanessa
de Vargas, Colomban
Massana, Ramon
New Insights into the Diversity of Marine Picoeukaryotes
title New Insights into the Diversity of Marine Picoeukaryotes
title_full New Insights into the Diversity of Marine Picoeukaryotes
title_fullStr New Insights into the Diversity of Marine Picoeukaryotes
title_full_unstemmed New Insights into the Diversity of Marine Picoeukaryotes
title_short New Insights into the Diversity of Marine Picoeukaryotes
title_sort new insights into the diversity of marine picoeukaryotes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747013/
https://www.ncbi.nlm.nih.gov/pubmed/19787059
http://dx.doi.org/10.1371/journal.pone.0007143
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