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.

Original languageEnglish
Pages (from-to)495-500
Number of pages6
JournalEuropean Journal of Soil Biology
Volume44
Issue number5-6
DOIs
Publication statusPublished - Sep 2008
Externally publishedYes

Keywords

  • Bacterial diversity
  • Fen
  • Two-dimensional SSCP

Fingerprint

Dive into the research topics of 'Two-dimensional single strand conformation polymorphism (SSCP) of 16S rRNA gene fragments reveals highly dissimilar bacterial communities in an acidic fen'. Together they form a unique fingerprint.

Cite this