Primers containing universal bases reduce multiple amoA gene specific DGGE band patterns when analysing the diversity of beta-ammonia oxidizers in the environment

Romana Hornek*, Andreas Pommerening-Röser, Hans Peter Koops, Andreas H. Farnleitner, Norbert Kreuzinger, Alexander Kirschner, Robert L. Mach

*Corresponding author for this work

Research output: Journal article (peer-reviewed)Journal article

73 Citations (Scopus)

Abstract

The gene encoding the active site of the ammonia monooxygenase (amoA) has been exploited as molecular marker for studying ammonia-oxidizing bacteria (AOB) diversity in the environment. Primers amplifying functional genes are often degenerated and therefore produce multiple band patterns, when analysed with the Denaturing gradient gel electrophoresis (DGGE) approach. To improve the DGGE band patterns we have designed new primer sets which contain inosine residues and are specific for the amoA gene. Primers were evaluated analysing pure AOB cultures and two habitats (wastewater treatment plant, soda pools). We found that the application of inosine primers helped to reduce the apparent complexity of the DGGE band pattern. Comparison of sequences from environmental samples using either degenerated or inosine containing amoA primers retrieved both identical and additional sequences. Both primer sets seem to be limited in their ability to detect the presence of all AOB by DGGE analyses.

Original languageEnglish
Pages (from-to)147-155
Number of pages9
JournalJournal of Microbiological Methods
Volume66
Issue number1
DOIs
Publication statusPublished - Jul 2006
Externally publishedYes

Keywords

  • Ammonia oxidizing bacteria
  • amoA
  • DGGE
  • Inosine
  • Soda pool
  • Wastewater treatment plant

ASJC Scopus subject areas

  • Microbiology
  • Molecular Biology
  • Microbiology (medical)

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