Influence of primer mismatch and microdiversity on DGGE results: a case study with SAR 11

6 pages, 2 figures, 2 tables

Detalles Bibliográficos
Autores: Sánchez, Olga, Gasol, Josep M., Balagué, Vanessa, Massana, Ramon, Mas, Jordi, Pedrós-Alió, Carlos
Tipo de recurso: artículo
Fecha de publicación:2009
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/13201
Acceso en línea:http://hdl.handle.net/10261/13201
Access Level:acceso abierto
Palabra clave:DGGE
SAR11
Microdiversity
Primers
Methodology
SAR
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spelling Influence of primer mismatch and microdiversity on DGGE results: a case study with SAR 11Sánchez, OlgaGasol, Josep M.Balagué, VanessaMassana, RamonMas, JordiPedrós-Alió, CarlosDGGESAR11MicrodiversityPrimersMethodologySAR6 pages, 2 figures, 2 tablesAlthough SAR 11 is usually the dominant bacterial group in most marine ecosystems when analyzed with clone libraries and fluorescence in situ hybridization, it is often not retrieved in studies where denaturing gradient gel electrophoresis (DGGE) has bee used. We analyzed the microdiversity of SAR11 in Blanes Bay (NW Mediterranean) and we suggest that the high evenness of multiple microdiverse phylotypes, none of which being particularly dominant, is the probable reason for this methodological discrepancy. We used seeding experiments in which different amounts of 2 SAR11-affiliated clones were mixed with DNA from an environmental sample obtained from the Blanes Bay Microbial Observatory. Two primer sets differing at 2 base positions produced DGGE images that varied in their SAR11 detection threshold concentration. Our results show that primer mismatches and/or the presence of faint bands due to microdiversity could explain why SAR11 is frequently not retrieved from DGGE gelsThis work was supported by the Spanish projects ESTRAMAR (CTM2004-12631/MAR), GENMμMAR (CTM2004-02586/MAR), TRAGUA (CSD2006-00044), TEC2006-13109-C03-02/MIC, PET2008-0165-02, MODIVUS (CTM2005-04975/ MAR), and EU NoEs MARBEF and Marine Genomics EuropeInter ResearchConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2009info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501http://hdl.handle.net/10261/13201reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttps://doi.org/10.3354/ame01267Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/132012026-05-22T06:33:51Z
dc.title.none.fl_str_mv Influence of primer mismatch and microdiversity on DGGE results: a case study with SAR 11
title Influence of primer mismatch and microdiversity on DGGE results: a case study with SAR 11
spellingShingle Influence of primer mismatch and microdiversity on DGGE results: a case study with SAR 11
Sánchez, Olga
DGGE
SAR11
Microdiversity
Primers
Methodology
SAR
title_short Influence of primer mismatch and microdiversity on DGGE results: a case study with SAR 11
title_full Influence of primer mismatch and microdiversity on DGGE results: a case study with SAR 11
title_fullStr Influence of primer mismatch and microdiversity on DGGE results: a case study with SAR 11
title_full_unstemmed Influence of primer mismatch and microdiversity on DGGE results: a case study with SAR 11
title_sort Influence of primer mismatch and microdiversity on DGGE results: a case study with SAR 11
dc.creator.none.fl_str_mv Sánchez, Olga
Gasol, Josep M.
Balagué, Vanessa
Massana, Ramon
Mas, Jordi
Pedrós-Alió, Carlos
author Sánchez, Olga
author_facet Sánchez, Olga
Gasol, Josep M.
Balagué, Vanessa
Massana, Ramon
Mas, Jordi
Pedrós-Alió, Carlos
author_role author
author2 Gasol, Josep M.
Balagué, Vanessa
Massana, Ramon
Mas, Jordi
Pedrós-Alió, Carlos
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv DGGE
SAR11
Microdiversity
Primers
Methodology
SAR
topic DGGE
SAR11
Microdiversity
Primers
Methodology
SAR
description 6 pages, 2 figures, 2 tables
publishDate 2009
dc.date.none.fl_str_mv 2009
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/13201
url http://hdl.handle.net/10261/13201
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv https://doi.org/10.3354/ame01267
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Inter Research
publisher.none.fl_str_mv Inter Research
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,812429

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