title: Quantitative PCR targeting 16S rRNA and reductive dehalogenase genes simultaneously monitors multiple Dehalococcoides strains.
abstract: The 16S rRNA gene provides insufficient information to infer the range of chloroorganic electron acceptors used by different Dehalococcoides organisms. To overcome this limitation and provide enhanced diagnostic tools for growth measurements, site assessment, and bioremediation monitoring, a quantitative real-time PCR (qPCR) approach targeting 16S rRNA genes and three Dehalococcoides reductive dehalogenase (RDase) genes with assigned function (i.e., tceA, bvcA, and vcrA) was designed and evaluated. qPCR standard curves generated for the RDase genes by use of genomic DNA from Dehalococcoides pure cultures correlated with standard curves obtained for both Bacteria- and Dehalococcoides-targeted 16S rRNA genes, suggesting that the RDase genes are useful targets for quantitative assessment of Dehalococcoides organisms. RDase gene probe/primer pairs were specific for the Dehalococcoides strains known to carry the diagnostic RDase gene sequences, and the qPCR method allowed the detection of as few as 1 to 20 and quantification of as few as 50 to 100 tceA, bvcA, or vcrA gene targets per PCR volume. The qPCR approach was applied to dechlorinating enrichment cultures, microcosms, and samples from a contaminated site. In characterized enrichment cultures where known Dehalococcoides strains were enumerated, the sum of the three RDase genes equaled the total Dehalococcoides cell numbers. In site samples and chloroethane-dechlorinating microcosms, the sum of the three RDase genes was much less than that predicted by Dehalococcoides-targeted qPCR, totaling 10 to 30% of the total Dehalococcoides cell numbers. Hence, a large number of Dehalococcoides spp. contain as-yet-unidentified RDase genes, indicating that our current understanding of the dechlorinating Dehalococcoides community is incomplete.
authors.affiliation: Georgia Institute of Technology, School of Civil and Environmental Engineering, 311 Ferst Drive, 3230 ES&T Building, Atlanta, GA 30332-0512, USA. krita@ce.gatech.edu
authors.forename: Kirsti M
authors.initials: KM
authors.lastname: Ritalahti
authors.forename: Benjamin K
authors.initials: BK
authors.lastname: Amos
authors.forename: Youlboong
authors.initials: Y
authors.lastname: Sung
authors.forename: Qingzhong
authors.initials: Q
authors.lastname: Wu
authors.forename: Stephen S
authors.initials: SS
authors.lastname: Koenigsberg
authors.forename: Frank E
authors.initials: FE
authors.lastname: Löffler
mesh_terms: D015373:Bacterial Typing Techniques; D041862:Chloroflexi / Q000145:classification* / Q000201:enzymology / Q000235:genetics / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000032:analysis; D004275:DNA, Ribosomal / Q000032:analysis; D005618:Fresh Water / Q000382:microbiology; D010088:Oxidoreductases / Q000235:genetics* / Q000378:metabolism; D016133:Polymerase Chain Reaction / Q000379:methods*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D013045:Species Specificity; D014877:Water Pollution, Chemical
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D010088:Oxidoreductases; C112990:tetrachloroethene dehalogenase