Design of Shewanella-specific 16S rRNA primers and application to analysis of Shewanella in a minerotrophic wetland

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Abstract

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.

Original languageEnglish (US)
Pages (from-to)426-432
Number of pages7
JournalEnvironmental Microbiology
Volume8
Issue number3
DOIs
StatePublished - Mar 2006

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Shewanella
Wetlands
wetlands
Iron
wetland
ribosomal RNA
iron
polymerase chain reaction
Polymerase Chain Reaction
probes (equipment)
clone
Clone Cells
Shewanella oneidensis
probe
clones
rRNA Genes
Restriction Fragment Length Polymorphisms
peat
restriction fragment length polymorphism
polymorphism

ASJC Scopus subject areas

  • Environmental Science(all)
  • Applied Microbiology and Biotechnology
  • Microbiology

Cite this

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abstract = "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.",
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