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Applied and Environmental Microbiology, January 2008, p. 300-304, Vol. 74, No. 1
0099-2240/08/$08.00+0     doi:10.1128/AEM.01600-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Single-Nucleotide Primer Extension Assay for Detection and Sequence Typing of "Dehalococcoides" spp.{triangledown} ,{dagger}

Marcell Nikolausz,1* Antonis Chatzinotas,2 Márton Palatinszky,3 Gwenaël Imfeld,4 Paula Martinez,1 and Matthias Kästner1

Department of Bioremediation,1 Department of Environmental Microbiology,2 Department of Isotope Biogeochemistry, UFZ Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany,4 Department of Microbiology, Eötvös Loránd University of Science, Pázmány Péter sétány 1/c, 1117 Budapest, Hungary3

Received 13 July 2007/ Accepted 30 October 2007

A single-nucleotide primer extension (SNuPE) assay in combination with taxon-specific 16S rRNA gene PCR analysis was developed for the detection and typing of populations of the genus "Dehalococcoides". The specificity of the assay was evaluated with 16S rRNA gene sequences obtained from an isolate and an environmental sample representing two Dehalococcoides subgroups, i.e., the Cornell and the Pinellas subgroups. Only one sequence type, belonging to the Pinellas subgroup, was detected in a Bitterfeld-Wolfen region aquifer containing chlorinated ethenes as the main contaminants. The three-primer hybridization assay thus provided a fast and easy-to-implement method for confirming the specificity of taxon-specific PCR and allowed rapid additional taxonomic classification into subgroups. This study demonstrates the great potential of SNuPE as a novel approach for rapid parallel detection of microorganisms and typing of different nucleic acid signature sequences from environmental samples.

* Corresponding author. Mailing address: Department of Bioremediation, UFZ Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig, Germany. Phone: 49 341 235 2053. Fax: 49 341 235 2492. E-mail: marcell.nikolausz{at}ufz.de

{triangledown} Published ahead of print on 9 November 2007.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, January 2008, p. 300-304, Vol. 74, No. 1
0099-2240/08/$08.00+0     doi:10.1128/AEM.01600-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.





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