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Title

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

AuthorsSánchez, Olga ; Gasol, Josep M. ; Balagué, Vanessa ; Massana, Ramon ; Mas, Jordi; Pedrós-Alió, Carlos
KeywordsDGGE
SAR11
Microdiversity
Primers
Methodology
SAR
Issue Date18-Feb-2009
PublisherInter Research
CitationAquatic Microbial Ecology 54(2): 211-216 (2009)
AbstractAlthough 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 gels
Description6 pages, 2 figures, 2 tables
Publisher version (URL)https://doi.org/10.3354/ame01267
URI10261/13201
DOI10.3354/ame01267
ISSN0948-3055
Appears in Collections:(ICM) Artículos
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