Polygenic analysis of ammonia-oxidizing bacteria using 16S rDNA, amoA, and amoB genes

Authors

  • Laia Calvó Laboratory of Molecular Microbiology, Institute of Aquatic Ecology, University of Girona, Spain
  • Martí Cortey Unit of Genetics, Department of Biology, University of Girona, Spain
  • José-Luis García-Marín Unit of Genetics, Department of Biology, University of Girona, Spain
  • L. Jesús Garcia-Gil Laboratory of Molecular Microbiology, Institute of Aquatic Ecology, University of Girona, Spain

Keywords:

ammonia-oxidizing bacteria, 16S rDNA, amoA, amoB, polygenic analysis

Abstract

Finding a unique molecular marker capable of quickly providing rigorous and useful phylogenetic information would facilitate assessing the diversity of ammonia-oxidizing bacteria in environmental samples. Since only one of several available markers can be used at a time in these kinds of studies, the 16S rDNA, amoA and amoB genes were evaluated individually and then compared in order to identify the one that best fits the information provided by the composite dataset. Distance-based neighbor-joining and maximum parsimony trees generated using the sequences of the three mentioned genes were analyzed with respect to the combined polygenic trees. Maximum parsimony trees were found to be more accurate than distance-based ones, and the polygenic topology was shown to best fit the information contained in the sequences. However, the taxonomic and phylogenetic information provided by the three markers separately was also valid. Therefore, either of the functional markers (amoA or amoB ) can be used to trace ammonia oxidizers in environmental studies in which only one gene can be targeted. [Int Microbiol 2005; 8(2):103-110]

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Published

2010-02-27

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Section

Research Articles