A targeted real-time PCR assay for studying naphthalene degradation in the environment

Mari Nyyssönen (Corresponding Author), Reetta Piskonen, Merja Itävaara

    Research output: Contribution to journalArticleScientificpeer-review

    27 Citations (Scopus)


    A quantitative real-time polymerase chain reaction (PCR) assay was developed for monitoring naphthalene degradation during bioremediation processes. The phylogenetic affiliations of known naphthalene-hydroxylating dioxygenase genes were determined to target functionally related bacteria, and degenerate primers were designed on the basis of the close relationships among dioxygenase genes identified from naphthalene-degrading Proteobacteria. Evaluation of the amplification specificity demonstrated that the developed real-time PCR assay represents a rapid, precise means for the group-specific enumeration of naphthalene-degrading bacteria. According to validation with bacterial pure cultures, the assay discriminated between the targeted group of naphthalene dioxygenase sequences and genes in other naphthalene or aromatic hydrocarbon-degrading bacterial strains. Specific amplification of gene fragments sharing a high sequence similarity with the genes included in the assay design was also observed in soil samples recovered from large-scale remediation processes. The target genes could be quantified reproducibly at over five orders of magnitude down to 3 × 102 gene copies. To investigate the suitability of the assay in monitoring naphthalene biodegradation, the assay was applied in enumerating the naphthalene dioxygenase genes in a soil slurry microcosm. The results were in good agreement with contaminant mineralization and dot blot quantification of nahAc gene copies. Furthermore, the real-time PCR assay was found to be more sensitive than hybridization-based analysis.
    Original languageEnglish
    Pages (from-to)533-543
    Number of pages11
    JournalMicrobial Ecology
    Issue number3
    Publication statusPublished - 2006
    MoE publication typeA1 Journal article-refereed


    • bioremediation
    • process monitoring
    • napthalene dioxygenase
    • real-time PCR


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