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Plastid 16S rRNA gene diversity among eukaryotic picophytoplankton sorted by flow cytometry from the South Pacific Ocean
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Shi, Xiao Li, Lepère, Cécile, Scanlan, David J. and Vaulot, Daniel (2011) Plastid 16S rRNA gene diversity among eukaryotic picophytoplankton sorted by flow cytometry from the South Pacific Ocean. PL o S One, Vol.6 (No.4). e18979 . doi:10.1371/journal.pone.0018979 ISSN 1932-6203.
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Official URL: http://dx.doi.org/10.1371/journal.pone.0018979
Abstract
The genetic diversity of photosynthetic picoeukaryotes was investigated in the South East Pacific Ocean. Genetic libraries of
the plastid 16S rRNA gene were constructed on picoeukaryote populations sorted by flow cytometry, using two different
primer sets, OXY107F/OXY1313R commonly used to amplify oxygenic organisms, and PLA491F/OXY1313R, biased towards
plastids of marine algae. Surprisingly, the two sets revealed quite different photosynthetic picoeukaryote diversity patterns,
which were moreover different from what we previously reported using the 18S rRNA nuclear gene as a marker. The first
16S primer set revealed many sequences related to Pelagophyceae and Dictyochophyceae, the second 16S primer set was
heavily biased toward Prymnesiophyceae, while 18S sequences were dominated by Prasinophyceae, Chrysophyceae and
Haptophyta. Primer mismatches with major algal lineages is probably one reason behind this discrepancy. However, other
reasons, such as DNA accessibility or gene copy numbers, may be also critical. Based on plastid 16S rRNA gene sequences,
the structure of photosynthetic picoeukaryotes varied along the BIOSOPE transect vertically and horizontally. In oligotrophic
regions, Pelagophyceae, Chrysophyceae, and Prymnesiophyceae dominated. Pelagophyceae were prevalent at the DCM
depth and Chrysophyceae at the surface. In mesotrophic regions Pelagophyceae were still important but Chlorophyta
contribution increased. Phylogenetic analysis revealed a new clade of Prasinophyceae (clade 16S-IX), which seems to be
restricted to hyper-oligotrophic stations. Our data suggest that a single gene marker, even as widely used as 18S rRNA,
provides a biased view of eukaryotic communities and that the use of several markers is necessary to obtain a complete
image.
Item Type: | Journal Article | ||||
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Subjects: | Q Science > QK Botany | ||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||
Library of Congress Subject Headings (LCSH): | Phytoplankton -- Genetics, Plastids, Flow cytometry | ||||
Journal or Publication Title: | PL o S One | ||||
Publisher: | Public Library of Science | ||||
ISSN: | 1932-6203 | ||||
Official Date: | 28 April 2011 | ||||
Dates: |
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Volume: | Vol.6 | ||||
Number: | No.4 | ||||
Page Range: | e18979 | ||||
DOI: | 10.1371/journal.pone.0018979 | ||||
Status: | Peer Reviewed | ||||
Publication Status: | Published | ||||
Access rights to Published version: | Restricted or Subscription Access | ||||
Funder: | Natural Environment Research Council (Great Britain) (NERC), Centre national de la recherche scientifique (France) (CNRS), France. Agence nationale de la recherche (ANR), China Scholarship Council (CSC), Université Pierre et Marie Curie (UPMC), Fondation Franco-Chinoise pour la Science et ses Applications (FFCSA) | ||||
Grant number: | 06-BDIV-013 (ANR), NE/C003160/1 (NERC) |
Data sourced from Thomson Reuters' Web of Knowledge
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