Reticulamoeba Is a Long-Branched Granofilosean (Cercozoa) That Is Missing from Sequence Databases
Identifieur interne : 000453 ( Pmc/Checkpoint ); précédent : 000452; suivant : 000454Reticulamoeba Is a Long-Branched Granofilosean (Cercozoa) That Is Missing from Sequence Databases
Auteurs : David Bass [Royaume-Uni] ; Akinori Yabuki [Royaume-Uni] ; Sébastien Santini [France] ; Sarah Romac [France] ; Cédric Berney [Royaume-Uni]Source :
- PLoS ONE [ 1932-6203 ] ; 2012.
Abstract
We sequenced the 18S ribosomal RNA gene of seven isolates of the enigmatic marine amoeboflagellate
Url:
DOI: 10.1371/journal.pone.0049090
PubMed: 23226495
PubMed Central: 3514243
Affiliations:
- France, Royaume-Uni
- Angleterre, Grand Londres, Oxfordshire
- Londres, Marseille, Oxford
- Université d'Oxford
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PMC:3514243Le document en format XML
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main"><italic>Reticulamoeba</italic>
Is a Long-Branched Granofilosean (Cercozoa) That Is Missing from Sequence Databases</title>
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<front><div type="abstract" xml:lang="en"><p>We sequenced the 18S ribosomal RNA gene of seven isolates of the enigmatic marine amoeboflagellate <italic>Reticulamoeba</italic>
Grell, which resolved into four genetically distinct <italic>Reticulamoeba</italic>
lineages, two of which correspond to <italic>R. gemmipara</italic>
Grell and <italic>R. minor</italic>
Grell, another with a relatively large cell body forming lacunae, and another that has similarities to both <italic>R. minor</italic>
and <italic>R. gemmipara</italic>
but with a greater propensity to form cell clusters. These lineages together form a long-branched clade that branches within the cercozoan class Granofilosea (phylum Cercozoa), showing phylogenetic affinities with the genus <italic>Mesofila</italic>
. The basic morphology of <italic>Reticulamoeba</italic>
is a roundish or ovoid cell with a more or less irregular outline. Long and branched reticulopodia radiate from the cell. The reticulopodia bear granules that are bidirectionally motile. There is also a biflagellate dispersal stage. <italic>Reticulamoeba</italic>
is frequently observed in coastal marine environmental samples. PCR primers specific to the <italic>Reticulamoeba</italic>
clade confirm that it is a frequent member of benthic marine microbial communities, and is also found in brackish water sediments and freshwater biofilm. However, so far it has not been found in large molecular datasets such as the nucleotide database in NCBI GenBank, metagenomic datasets in Camera, and the marine microbial eukaryote sampling and sequencing consortium BioMarKs, although closely related lineages can be found in some of these datasets using a highly targeted approach. Therefore, although such datasets are very powerful tools in microbial ecology, they may, for several methodological reasons, fail to detect ecologically and evolutionary key lineages.</p>
</div>
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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id>
<journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id>
<journal-id journal-id-type="publisher-id">plos</journal-id>
<journal-id journal-id-type="pmc">plosone</journal-id>
<journal-title-group><journal-title>PLoS ONE</journal-title>
</journal-title-group>
<issn pub-type="epub">1932-6203</issn>
<publisher><publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, USA</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">23226495</article-id>
<article-id pub-id-type="pmc">3514243</article-id>
<article-id pub-id-type="publisher-id">PONE-D-12-21384</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0049090</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
<subj-group subj-group-type="Discipline-v2"><subject>Biology</subject>
<subj-group><subject>Computational Biology</subject>
<subj-group><subject>Genomics</subject>
<subj-group><subject>Genome Databases</subject>
</subj-group>
</subj-group>
</subj-group>
<subj-group><subject>Ecology</subject>
<subj-group><subject>Biodiversity</subject>
<subject>Coastal Ecology</subject>
<subject>Marine Ecology</subject>
<subject>Microbial Ecology</subject>
</subj-group>
</subj-group>
<subj-group><subject>Evolutionary Biology</subject>
<subj-group><subject>Organismal Evolution</subject>
<subj-group><subject>Eukaryotic Evolution</subject>
<subject>Microbial Evolution</subject>
</subj-group>
</subj-group>
</subj-group>
<subj-group><subject>Genomics</subject>
<subj-group><subject>Genome Databases</subject>
</subj-group>
</subj-group>
<subj-group><subject>Marine Biology</subject>
<subj-group><subject>Coastal Ecology</subject>
<subject>Marine Ecology</subject>
</subj-group>
</subj-group>
<subj-group><subject>Microbiology</subject>
<subj-group><subject>Microbial Ecology</subject>
<subject>Microbial Evolution</subject>
<subject>Protozoology</subject>
</subj-group>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title><italic>Reticulamoeba</italic>
Is a Long-Branched Granofilosean (Cercozoa) That Is Missing from Sequence Databases</article-title>
<alt-title alt-title-type="running-head"><italic>Reticulamoeba</italic>
Diversity and Ecology</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Bass</surname>
<given-names>David</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="corresp" rid="cor1"><sup>*</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Yabuki</surname>
<given-names>Akinori</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
<xref ref-type="author-notes" rid="fn1"><sup>¤</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Santini</surname>
<given-names>Sébastien</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Romac</surname>
<given-names>Sarah</given-names>
</name>
<xref ref-type="aff" rid="aff4"><sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Berney</surname>
<given-names>Cédric</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
</contrib-group>
<aff id="aff1"><label>1</label>
<addr-line>Department of Life Sciences, The Natural History Museum, London, United Kingdom</addr-line>
</aff>
<aff id="aff2"><label>2</label>
<addr-line>Department of Zoology, University of Oxford, Oxford, United Kingdom</addr-line>
</aff>
<aff id="aff3"><label>3</label>
<addr-line>Structural and Genomic Information Laboratory, CNRS, UMR 7256, Mediterranean Institute of Microbiology, Aix-Marseille University, Marseille, France</addr-line>
</aff>
<aff id="aff4"><label>4</label>
<addr-line>CNRS, UMR 7144, Equipe Evolution du Plancton et Paleo-Oceans, Roscoff, France</addr-line>
</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>López-García</surname>
<given-names>Purificación</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1"><addr-line>Université Paris Sud, France</addr-line>
</aff>
<author-notes><corresp id="cor1">* E-mail: <email>d.bass@nhm.ac.uk</email>
</corresp>
<fn fn-type="conflict"><p><bold>Competing Interests: </bold>
The authors have declared that no competing interests exist.</p>
</fn>
<fn fn-type="con"><p>Conceived and designed the experiments: DB CB. Performed the experiments: DB AY CB. Analyzed the data: CB DB. Contributed reagents/materials/analysis tools: DB. Wrote the paper: DB CB. Contributed to preparation and analysis of Biomarks total database: SS. Coordinated overall Biomarks sampling and sequence generation: SR.</p>
</fn>
<fn id="fn1" fn-type="current-aff"><label>¤</label>
<p>Current address: Marine Biodiversity Research Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan</p>
</fn>
</author-notes>
<pub-date pub-type="collection"><year>2012</year>
</pub-date>
<pub-date pub-type="epub"><day>4</day>
<month>12</month>
<year>2012</year>
</pub-date>
<volume>7</volume>
<issue>12</issue>
<elocation-id>e49090</elocation-id>
<history><date date-type="received"><day>19</day>
<month>7</month>
<year>2012</year>
</date>
<date date-type="accepted"><day>8</day>
<month>10</month>
<year>2012</year>
</date>
</history>
<permissions><copyright-year>2012</copyright-year>
<copyright-holder>Bass et al</copyright-holder>
<license><license-p>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.</license-p>
</license>
</permissions>
<abstract><p>We sequenced the 18S ribosomal RNA gene of seven isolates of the enigmatic marine amoeboflagellate <italic>Reticulamoeba</italic>
Grell, which resolved into four genetically distinct <italic>Reticulamoeba</italic>
lineages, two of which correspond to <italic>R. gemmipara</italic>
Grell and <italic>R. minor</italic>
Grell, another with a relatively large cell body forming lacunae, and another that has similarities to both <italic>R. minor</italic>
and <italic>R. gemmipara</italic>
but with a greater propensity to form cell clusters. These lineages together form a long-branched clade that branches within the cercozoan class Granofilosea (phylum Cercozoa), showing phylogenetic affinities with the genus <italic>Mesofila</italic>
. The basic morphology of <italic>Reticulamoeba</italic>
is a roundish or ovoid cell with a more or less irregular outline. Long and branched reticulopodia radiate from the cell. The reticulopodia bear granules that are bidirectionally motile. There is also a biflagellate dispersal stage. <italic>Reticulamoeba</italic>
is frequently observed in coastal marine environmental samples. PCR primers specific to the <italic>Reticulamoeba</italic>
clade confirm that it is a frequent member of benthic marine microbial communities, and is also found in brackish water sediments and freshwater biofilm. However, so far it has not been found in large molecular datasets such as the nucleotide database in NCBI GenBank, metagenomic datasets in Camera, and the marine microbial eukaryote sampling and sequencing consortium BioMarKs, although closely related lineages can be found in some of these datasets using a highly targeted approach. Therefore, although such datasets are very powerful tools in microbial ecology, they may, for several methodological reasons, fail to detect ecologically and evolutionary key lineages.</p>
</abstract>
<funding-group><funding-statement>DB and CB are funded by NERC (<ext-link ext-link-type="uri" xlink:href="http://www.nerc.ac.uk">www.nerc.ac.uk</ext-link>
) research grants NE/H009426/1 and NE/H000887/1. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement>
</funding-group>
<counts><page-count count="11"></page-count>
</counts>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>France</li>
<li>Royaume-Uni</li>
</country>
<region><li>Angleterre</li>
<li>Grand Londres</li>
<li>Oxfordshire</li>
</region>
<settlement><li>Londres</li>
<li>Marseille</li>
<li>Oxford</li>
</settlement>
<orgName><li>Université d'Oxford</li>
</orgName>
</list>
<tree><country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Bass, David" sort="Bass, David" uniqKey="Bass D" first="David" last="Bass">David Bass</name>
</region>
<name sortKey="Berney, Cedric" sort="Berney, Cedric" uniqKey="Berney C" first="Cédric" last="Berney">Cédric Berney</name>
<name sortKey="Yabuki, Akinori" sort="Yabuki, Akinori" uniqKey="Yabuki A" first="Akinori" last="Yabuki">Akinori Yabuki</name>
</country>
<country name="France"><noRegion><name sortKey="Santini, Sebastien" sort="Santini, Sebastien" uniqKey="Santini S" first="Sébastien" last="Santini">Sébastien Santini</name>
</noRegion>
<name sortKey="Romac, Sarah" sort="Romac, Sarah" uniqKey="Romac S" first="Sarah" last="Romac">Sarah Romac</name>
</country>
</tree>
</affiliations>
</record>
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