title: Single-nucleotide primer extension assay for detection and sequence typing of "Dehalococcoides" spp.
abstract: 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.
authors.affiliation: Department of Bioremediation, UFZ Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig, Germany. marcell.nikolausz@ufz.de
authors.forename: Marcell
authors.initials: M
authors.lastname: Nikolausz
authors.forename: Antonis
authors.initials: A
authors.lastname: Chatzinotas
authors.forename: Márton
authors.initials: M
authors.lastname: Palatinszky
authors.forename: Gwenaël
authors.initials: G
authors.lastname: Imfeld
authors.forename: Paula
authors.initials: P
authors.lastname: Martinez
authors.forename: Matthias
authors.initials: M
authors.lastname: Kästner
mesh_terms: D015373:Bacterial Typing Techniques / Q000379:methods*; D041862:Chloroflexi / Q000145:classification* / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D005838:Genotype; D009693:Nucleic Acid Hybridization / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods*; D012680:Sensitivity and Specificity
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal