Discovery of a Katablepharis sp. in the Columbia River estuary that is abundant during the spring and bears a unique large ribosomal subunit sequence element
Identifieur interne : 000562 ( Ncbi/Merge ); précédent : 000561; suivant : 000563Discovery of a Katablepharis sp. in the Columbia River estuary that is abundant during the spring and bears a unique large ribosomal subunit sequence element
Auteurs : Peter Kahn ; Lydie Herfort ; Tawnya D. Peterson ; Peter ZuberSource :
- MicrobiologyOpen [ 2045-8827 ] ; 2014.
Abstract
Heterotrophic protists play significant roles in pelagic food webs as bacterivorous and herbivorous consumers. However, heterotrophic protists—unlike autotrophic ones—are often difficult to track since they tend to lack features such as photosynthetic pigments that allow for remote sensing or for bulk characterization. Difficulty in the identification of heterotrophic protists has often resulted in lumping them into broad groups, but there is a strong need to develop methods that increase the spatial and temporal resolution of observations applied to particular organisms in order to discover the drivers of population structure and ecological function. In surveys of small subunit rRNA, gene (SSU) sequences of microbial eukaryotes from the Columbia River to the Pacific Ocean, the heterotrophic flagellate
Url:
DOI: 10.1002/mbo3.206
PubMed: 25168204
PubMed Central: 4234266
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PMC:4234266Le document en format XML
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Discovery of a <italic>Katablepharis</italic>
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<author><name sortKey="Kahn, Peter" sort="Kahn, Peter" uniqKey="Kahn P" first="Peter" last="Kahn">Peter Kahn</name>
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<front><div type="abstract" xml:lang="en"><p>Heterotrophic protists play significant roles in pelagic food webs as bacterivorous and herbivorous consumers. However, heterotrophic protists—unlike autotrophic ones—are often difficult to track since they tend to lack features such as photosynthetic pigments that allow for remote sensing or for bulk characterization. Difficulty in the identification of heterotrophic protists has often resulted in lumping them into broad groups, but there is a strong need to develop methods that increase the spatial and temporal resolution of observations applied to particular organisms in order to discover the drivers of population structure and ecological function. In surveys of small subunit rRNA, gene (SSU) sequences of microbial eukaryotes from the Columbia River to the Pacific Ocean, the heterotrophic flagellate <italic>Katablepharis</italic>
sp. were found to dominate protist assemblages (including autotrophic and heterotrophic fractions) in the spring, prior to the freshet. We discovered a 332 base pair unique sequence element (USE) insertion in the large subunit rRNA gene (28S) that is not present in other katablepharids or in any other eukaryote. Using this USE, we were able to detect <italic>Katablepharis</italic>
within mixed assemblages in river, estuarine, and oceanic samples and determine spatial and temporal patterns in absolute abundance through quantitative PCR and fluorescence in situ hybridization. Given their high abundance and repeatable temporal patterns of occurrence, we hypothesize that the Columbia River Estuary <italic>Katablepharis</italic>
(<italic>Katablepharis</italic>
CRE) plays an important role in estuarine biogeochemical and ecosystem function.</p>
</div>
</front>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Microbiologyopen</journal-id>
<journal-id journal-id-type="iso-abbrev">Microbiologyopen</journal-id>
<journal-id journal-id-type="publisher-id">mbo3</journal-id>
<journal-title-group><journal-title>MicrobiologyOpen</journal-title>
</journal-title-group>
<issn pub-type="ppub">2045-8827</issn>
<issn pub-type="epub">2045-8827</issn>
<publisher><publisher-name>BlackWell Publishing Ltd</publisher-name>
<publisher-loc>Oxford, UK</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">25168204</article-id>
<article-id pub-id-type="pmc">4234266</article-id>
<article-id pub-id-type="doi">10.1002/mbo3.206</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Original Research</subject>
</subj-group>
</article-categories>
<title-group><article-title>Discovery of a <italic>Katablepharis</italic>
sp. in the Columbia River estuary that is abundant during the spring and bears a unique large ribosomal subunit sequence element</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Kahn</surname>
<given-names>Peter</given-names>
</name>
<xref ref-type="aff" rid="au1"></xref>
<xref ref-type="corresp" rid="cor1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Herfort</surname>
<given-names>Lydie</given-names>
</name>
<xref ref-type="aff" rid="au1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Peterson</surname>
<given-names>Tawnya D</given-names>
</name>
<xref ref-type="aff" rid="au1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Zuber</surname>
<given-names>Peter</given-names>
</name>
<xref ref-type="aff" rid="au1"></xref>
</contrib>
<aff id="au1"><label>1</label>
<institution>Center for Coastal Margin Observation & Prediction and Institute of Environmental Health, Oregon Health & Science University</institution>
<addr-line>3181 SW Sam Jackson Park Road, Mail code HRC3, Portland, Oregon, 97239</addr-line>
</aff>
</contrib-group>
<author-notes><corresp id="cor1"><bold>Correspondence</bold>
Peter Kahn, Institute of Environmental Health and Center for Coastal Margin Observation & Prediction and, Oregon Health & Science University, Portland, OR 97239. Tel: (001) 503 748 1643; Fax: (001) 503 748 1464; E-mail: <email>kahnp@ohsu.edu</email>
</corresp>
<fn><p><bold>Funding Information</bold>
This study was carried out within the context of the Science and Technology Center for Coastal Margin Observation & Prediction (CMOP) supported by the National Science Foundation (grant number OCE-0424602).</p>
</fn>
</author-notes>
<pub-date pub-type="ppub"><month>10</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="epub"><day>28</day>
<month>8</month>
<year>2014</year>
</pub-date>
<volume>3</volume>
<issue>5</issue>
<fpage>764</fpage>
<lpage>776</lpage>
<history><date date-type="received"><day>07</day>
<month>4</month>
<year>2014</year>
</date>
<date date-type="rev-recd"><day>16</day>
<month>6</month>
<year>2014</year>
</date>
<date date-type="accepted"><day>11</day>
<month>7</month>
<year>2014</year>
</date>
</history>
<permissions><copyright-statement>© 2014 The Authors. <italic>MicrobiologyOpen</italic>
published by John Wiley & Sons Ltd.</copyright-statement>
<copyright-year>2014</copyright-year>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/3.0/"><license-p>This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<abstract><p>Heterotrophic protists play significant roles in pelagic food webs as bacterivorous and herbivorous consumers. However, heterotrophic protists—unlike autotrophic ones—are often difficult to track since they tend to lack features such as photosynthetic pigments that allow for remote sensing or for bulk characterization. Difficulty in the identification of heterotrophic protists has often resulted in lumping them into broad groups, but there is a strong need to develop methods that increase the spatial and temporal resolution of observations applied to particular organisms in order to discover the drivers of population structure and ecological function. In surveys of small subunit rRNA, gene (SSU) sequences of microbial eukaryotes from the Columbia River to the Pacific Ocean, the heterotrophic flagellate <italic>Katablepharis</italic>
sp. were found to dominate protist assemblages (including autotrophic and heterotrophic fractions) in the spring, prior to the freshet. We discovered a 332 base pair unique sequence element (USE) insertion in the large subunit rRNA gene (28S) that is not present in other katablepharids or in any other eukaryote. Using this USE, we were able to detect <italic>Katablepharis</italic>
within mixed assemblages in river, estuarine, and oceanic samples and determine spatial and temporal patterns in absolute abundance through quantitative PCR and fluorescence in situ hybridization. Given their high abundance and repeatable temporal patterns of occurrence, we hypothesize that the Columbia River Estuary <italic>Katablepharis</italic>
(<italic>Katablepharis</italic>
CRE) plays an important role in estuarine biogeochemical and ecosystem function.</p>
</abstract>
<kwd-group><kwd>Columbia River coastal margin</kwd>
<kwd>heterotrophic protist diversity</kwd>
<kwd><italic>Katablepharis</italic>
CRE</kwd>
<kwd>unique sequence element</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
<affiliations><list></list>
<tree><noCountry><name sortKey="Herfort, Lydie" sort="Herfort, Lydie" uniqKey="Herfort L" first="Lydie" last="Herfort">Lydie Herfort</name>
<name sortKey="Kahn, Peter" sort="Kahn, Peter" uniqKey="Kahn P" first="Peter" last="Kahn">Peter Kahn</name>
<name sortKey="Peterson, Tawnya D" sort="Peterson, Tawnya D" uniqKey="Peterson T" first="Tawnya D" last="Peterson">Tawnya D. Peterson</name>
<name sortKey="Zuber, Peter" sort="Zuber, Peter" uniqKey="Zuber P" first="Peter" last="Zuber">Peter Zuber</name>
</noCountry>
</tree>
</affiliations>
</record>
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