Two-dimensional single strand conformation polymorphism (SSCP) of 16S rRNA gene fragments reveals highly dissimilar bacterial communities in an acidic fen

Achim Schmalenberger, Christoph C. Tebbe, Michael A. Kertesz, Harold L. Drake, Kirsten Küsel

    Research output: Contribution to journalArticlepeer-review

    Abstract

    Genetic fingerprinting methods such as denaturing gradient gel electrophoresis (DGGE) and single strand conformation polymorphism (SSCP) are only able to separate about 20-40 well-distinguishable bands (signals) within each sample. As a result, the diversity of 16S rRNA genes within biological samples may be underestimated, because multiple sequences can migrate at the same rate to form a single band. This study reports a two-dimensional SSCP fingerprinting method that has the capability to resolve hundreds of signals in a single fingerprint by using different gel temperatures in the two dimensions of the separation (20 °C and 30 °C, respectively). Unlike previous two-dimensional approaches, the method presented in this study does not rely on DNA products of variable lengths but is able to separate 16S rRNA gene fragments of the same length. To demonstrate the effectiveness of this new method, DNA samples from oxic and anoxic zones of an acidic fen were examined. Whereas one-dimensional SSCP fingerprints indicated high similarity (>93%) between 16S rRNA gene fragments from oxic and anoxic zones of the fen, the two-dimensional SSCP approach virtually found no similarities. © 2008 Elsevier Masson SAS. All rights reserved.
    Original languageEnglish
    Pages (from-to)495-500
    Number of pages5
    JournalEuropean Journal of Soil Biology
    Volume44
    Issue number5-6
    DOIs
    Publication statusPublished - Sept 2008

    Keywords

    • Bacterial diversity
    • Fen
    • Two-dimensional SSCP

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