Design of Shewanella-specific 16S rRNA primers and application to analysis of Shewanella in a minerotrophic wetland.
In this study, an existing probe was used as a polymerase chain reaction (PCR) primer to study iron-reducing members of the genus Shewanella in a minerotrophic wetland where iron reduction had previously been implicated. The probe was found to be non-specific and a new set of PCR primers were developed that were specific for Shewanella. These primers were used to analyse the wetland iron-reducing communities by characterizing 16S rRNA genes amplified from DNA extracted from peat. Polymerase chain reaction clone libraries were screened using restriction fragment length polymorphism and diagnostic operational taxonomic units for Shewanella species were identified. A statistical method was used to determine the coverage of the clone libraries, which was found to be between 83% and 97%. The dominant species in the wetland samples at two geochemically distinct zones were phylogenetically related to the iron-reducing microorganism Shewanella oneidensis.
Todorova
Svetoslava G
SG
Department of Civil and Environmental Engineering, 151 Link Hall, Syracuse University, Syracuse, NY, USA.
Costello
Andria M
AM
D016172:DNA Fingerprinting; D017931:DNA Primers; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D017753:Ecosystem; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods*; D012150:Polymorphism, Restriction Fragment Length; D012329:RNA, Bacterial / Q000032:analysis / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000032:analysis* / Q000235:genetics; D017422:Sequence Analysis, DNA; D020592:Shewanella / Q000235:genetics / Q000302:isolation & purification*
D017931:DNA Primers; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S