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 : 000218 ( Main/Merge ); précédent : 000217; suivant : 000219Discovery 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
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000562
- to stream Pmc, to step Curation: 000562
- to stream Pmc, to step Checkpoint: 000206
- to stream Ncbi, to step Merge: 000562
- to stream Ncbi, to step Curation: 000562
- to stream Ncbi, to step Checkpoint: 000562
Links to Exploration step
PMC:4234266Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">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</title>
<author><name sortKey="Kahn, Peter" sort="Kahn, Peter" uniqKey="Kahn P" first="Peter" last="Kahn">Peter Kahn</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Herfort, Lydie" sort="Herfort, Lydie" uniqKey="Herfort L" first="Lydie" last="Herfort">Lydie Herfort</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Peterson, Tawnya D" sort="Peterson, Tawnya D" uniqKey="Peterson T" first="Tawnya D" last="Peterson">Tawnya D. Peterson</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Zuber, Peter" sort="Zuber, Peter" uniqKey="Zuber P" first="Peter" last="Zuber">Peter Zuber</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">25168204</idno>
<idno type="pmc">4234266</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4234266</idno>
<idno type="RBID">PMC:4234266</idno>
<idno type="doi">10.1002/mbo3.206</idno>
<date when="2014">2014</date>
<idno type="wicri:Area/Pmc/Corpus">000562</idno>
<idno type="wicri:Area/Pmc/Curation">000562</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000206</idno>
<idno type="wicri:Area/Ncbi/Merge">000562</idno>
<idno type="wicri:Area/Ncbi/Curation">000562</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">000562</idno>
<idno type="wicri:doubleKey">2045-8827:2014:Kahn P:discovery:of:a</idno>
<idno type="wicri:Area/Main/Merge">000218</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">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</title>
<author><name sortKey="Kahn, Peter" sort="Kahn, Peter" uniqKey="Kahn P" first="Peter" last="Kahn">Peter Kahn</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Herfort, Lydie" sort="Herfort, Lydie" uniqKey="Herfort L" first="Lydie" last="Herfort">Lydie Herfort</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Peterson, Tawnya D" sort="Peterson, Tawnya D" uniqKey="Peterson T" first="Tawnya D" last="Peterson">Tawnya D. Peterson</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Zuber, Peter" sort="Zuber, Peter" uniqKey="Zuber P" first="Peter" last="Zuber">Peter Zuber</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
</analytic>
<series><title level="j">MicrobiologyOpen</title>
<idno type="ISSN">2045-8827</idno>
<idno type="eISSN">2045-8827</idno>
<imprint><date when="2014">2014</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<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>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Andersson, Jo" uniqKey="Andersson J">JO Andersson</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Arndt, H" uniqKey="Arndt H">H Arndt</name>
</author>
<author><name sortKey="Dietrich, D" uniqKey="Dietrich D">D Dietrich</name>
</author>
<author><name sortKey="Auer, B" uniqKey="Auer B">B Auer</name>
</author>
<author><name sortKey="Cleven, Ej" uniqKey="Cleven E">EJ Cleven</name>
</author>
<author><name sortKey="Gr Fenhan, T" uniqKey="Gr Fenhan T">T Gräfenhan</name>
</author>
<author><name sortKey="Weitere, M" uniqKey="Weitere M">M Weitere</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Azam, L" uniqKey="Azam L">L Azam</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Baptista, A" uniqKey="Baptista A">A Baptista</name>
</author>
<author><name sortKey="Howe, B" uniqKey="Howe B">B Howe</name>
</author>
<author><name sortKey="Freire, J" uniqKey="Freire J">J Freire</name>
</author>
<author><name sortKey="Maier, D" uniqKey="Maier D">D Maier</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Barnes, Ca" uniqKey="Barnes C">CA Barnes</name>
</author>
<author><name sortKey="Duxbury, Ac" uniqKey="Duxbury A">AC Duxbury</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bass, D" uniqKey="Bass D">D Bass</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Caron, Da" uniqKey="Caron D">DA Caron</name>
</author>
<author><name sortKey="Goldman, Jc" uniqKey="Goldman J">JC Goldman</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Crump, Bc" uniqKey="Crump B">BC Crump</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Crump, Bc" uniqKey="Crump B">BC Crump</name>
</author>
<author><name sortKey="Baross, Ja" uniqKey="Baross J">JA Baross</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Crump, Bc" uniqKey="Crump B">BC Crump</name>
</author>
<author><name sortKey="Peterson, Bj" uniqKey="Peterson B">BJ Peterson</name>
</author>
<author><name sortKey="Raymond, Pa" uniqKey="Raymond P">PA Raymond</name>
</author>
<author><name sortKey="Amon, Rm" uniqKey="Amon R">RM Amon</name>
</author>
<author><name sortKey="Rinehart, A" uniqKey="Rinehart A">A Rinehart</name>
</author>
<author><name sortKey="Mcclelland, Jw" uniqKey="Mcclelland J">JW McClelland</name>
</author>
<author><name sortKey="Holmes, Rm" uniqKey="Holmes R">RM Holmes</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Diez, B" uniqKey="Diez B">B Diez</name>
</author>
<author><name sortKey="Pedros Alio, C" uniqKey="Pedros Alio C">C Pedros-Alio</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Domaizon, I" uniqKey="Domaizon I">I Domaizon</name>
</author>
<author><name sortKey="Viboud, S" uniqKey="Viboud S">S Viboud</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Drummond, Aj" uniqKey="Drummond A">AJ Drummond</name>
</author>
<author><name sortKey="Ashton, B" uniqKey="Ashton B">B Ashton</name>
</author>
<author><name sortKey="Buxton, S" uniqKey="Buxton S">S Buxton</name>
</author>
<author><name sortKey="Cheung, M" uniqKey="Cheung M">M Cheung</name>
</author>
<author><name sortKey="Cooper, A" uniqKey="Cooper A">A Cooper</name>
</author>
<author><name sortKey="Duran, C" uniqKey="Duran C">C Duran</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Elwood, Hj" uniqKey="Elwood H">HJ Elwood</name>
</author>
<author><name sortKey="Olsen, Gj" uniqKey="Olsen G">GJ Olsen</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Frey, Be" uniqKey="Frey B">BE Frey</name>
</author>
<author><name sortKey="Lara Lara, R" uniqKey="Lara Lara R">R Lara-Lara</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gifford, Dj" uniqKey="Gifford D">DJ Gifford</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Haertel, L" uniqKey="Haertel L">L Haertel</name>
</author>
<author><name sortKey="Osterberg, Cl" uniqKey="Osterberg C">Cl Osterberg</name>
</author>
<author><name sortKey="Curl, H" uniqKey="Curl H">H Curl</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hassouna, N" uniqKey="Hassouna N">N Hassouna</name>
</author>
<author><name sortKey="Mithot, B" uniqKey="Mithot B">B Mithot</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Koch, T" uniqKey="Koch T">T Koch</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lara Lara, Jr" uniqKey="Lara Lara J">JR Lara-Lara</name>
</author>
<author><name sortKey="Frey, Be" uniqKey="Frey B">BE Frey</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lim, El" uniqKey="Lim E">EL Lim</name>
</author>
<author><name sortKey="Dennett, Mr" uniqKey="Dennett M">MR Dennett</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lopez Garcia, P" uniqKey="Lopez Garcia P">P Lopez-Garcia</name>
</author>
<author><name sortKey="Rodriguez Valera, C" uniqKey="Rodriguez Valera C">C Rodriguez-Valera</name>
</author>
<author><name sortKey="Pedros Alio, C" uniqKey="Pedros Alio C">C Pedros-Alio</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Massana, R" uniqKey="Massana R">R Massana</name>
</author>
<author><name sortKey="Terrado, R" uniqKey="Terrado R">R Terrado</name>
</author>
<author><name sortKey="Forn, I" uniqKey="Forn I">I Forn</name>
</author>
<author><name sortKey="Lovejoy, C" uniqKey="Lovejoy C">C Lovejoy</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Moon Van Der Staay, Sy" uniqKey="Moon Van Der Staay S">SY Moon-van der Staay</name>
</author>
<author><name sortKey="De Wachter, R" uniqKey="De Wachter R">R De Wachter</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Okamoto, N" uniqKey="Okamoto N">N Okamoto</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Pernthaler, J" uniqKey="Pernthaler J">J Pernthaler</name>
</author>
<author><name sortKey="Glockner, Fo" uniqKey="Glockner F">FO Glockner</name>
</author>
<author><name sortKey="Schonhuber, W" uniqKey="Schonhuber W">W Schonhuber</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ploug, H" uniqKey="Ploug H">H Ploug</name>
</author>
<author><name sortKey="Zimmermann Timm, H" uniqKey="Zimmermann Timm H">H Zimmermann-Timm</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Pomeroy, Lr" uniqKey="Pomeroy L">LR Pomeroy</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Roegner, Gc" uniqKey="Roegner G">GC Roegner</name>
</author>
<author><name sortKey="Needoba, Ja" uniqKey="Needoba J">JA Needoba</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rodriguez Martinez, R" uniqKey="Rodriguez Martinez R">R Rodríguez-Martínez</name>
</author>
<author><name sortKey="Labrenz, M" uniqKey="Labrenz M">M Labrenz</name>
</author>
<author><name sortKey="Del Campo, J" uniqKey="Del Campo J">J del Campo</name>
</author>
<author><name sortKey="Forn, I" uniqKey="Forn I">I Forn</name>
</author>
<author><name sortKey="Jurgens, K" uniqKey="Jurgens K">K Jürgens</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Scholin, Ca" uniqKey="Scholin C">CA Scholin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sherr, Eb" uniqKey="Sherr E">EB Sherr</name>
</author>
<author><name sortKey="Caron, Da" uniqKey="Caron D">DA Caron</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sherr, Eb" uniqKey="Sherr E">EB Sherr</name>
</author>
<author><name sortKey="Sherr, Bf" uniqKey="Sherr B">BF Sherr</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Simenstad, Ca" uniqKey="Simenstad C">CA Simenstad</name>
</author>
<author><name sortKey="Small, Lf" uniqKey="Small L">LF Small</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Slapeta, J" uniqKey="Slapeta J">J Slapeta</name>
</author>
<author><name sortKey="Lopez Garcia, P" uniqKey="Lopez Garcia P">P Lopez-Garcia</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Small, Lf" uniqKey="Small L">LF Small</name>
</author>
<author><name sortKey="Mcintire, Cd" uniqKey="Mcintire C">CD McIntire</name>
</author>
<author><name sortKey="Macdonald, Kb" uniqKey="Macdonald K">KB MacDonald</name>
</author>
<author><name sortKey="Lara Lara, Jr" uniqKey="Lara Lara J">JR Lara-Lara</name>
</author>
<author><name sortKey="Frey, Be" uniqKey="Frey B">BE Frey</name>
</author>
<author><name sortKey="Amspoker, Mc" uniqKey="Amspoker M">MC Amspoker</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Stoeck, T" uniqKey="Stoeck T">T Stoeck</name>
</author>
<author><name sortKey="Taylor, Gt" uniqKey="Taylor G">GT Taylor</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sullivan, Be" uniqKey="Sullivan B">BE Sullivan</name>
</author>
<author><name sortKey="Prahl, Fg" uniqKey="Prahl F">FG Prahl</name>
</author>
<author><name sortKey="Small, Lf" uniqKey="Small L">LF Small</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sverdrup, H" uniqKey="Sverdrup H">H Sverdrup</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Weber, F" uniqKey="Weber F">F Weber</name>
</author>
<author><name sortKey="Del Campo, J" uniqKey="Del Campo J">J del Campo</name>
</author>
<author><name sortKey="Wylezich, C" uniqKey="Wylezich C">C Wylezich</name>
</author>
<author><name sortKey="Massana, R" uniqKey="Massana R">R Massana</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhu, F" uniqKey="Zhu F">F Zhu</name>
</author>
<author><name sortKey="Massana, R" uniqKey="Massana R">R Massana</name>
</author>
<author><name sortKey="Not, F" uniqKey="Not F">F Not</name>
</author>
<author><name sortKey="Marie, D" uniqKey="Marie D">D Marie</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Main/Merge
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000218 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Merge/biblio.hfd -nk 000218 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Ticri/CIDE |area= CyberinfraV1 |flux= Main |étape= Merge |type= RBID |clé= PMC:4234266 |texte= 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 }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Merge/RBID.i -Sk "pubmed:25168204" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Merge/biblio.hfd \ | NlmPubMed2Wicri -a CyberinfraV1
![]() | This area was generated with Dilib version V0.6.25. | ![]() |