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

Title data

Schmalenberger, Achim ; Tebbe, Christoph C. ; Kertesz, Michael A. ; Drake, Harold L. ; Küsel, Kirsten:
Two-dimensional single strand conformation polymorphism (SSCP) of 16S rRNA gene fragments reveals highly dissimilar bacterial communities in an acidic fen.
In: European Journal of Soil Biology. Vol. 44 (2008) Issue 5-6 . - pp. 495-500.
ISSN 1164-5563
DOI: https://doi.org/10.1016/j.ejsobi.2008.07.002

Abstract in another language

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.

Further data

Item Type: Article in a journal
Refereed: Yes
Additional notes: BAYCEER62656
Institutions of the University: Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Biology > Chair Ecological Microbiology
Research Institutions > Research Centres > Bayreuth Center of Ecology and Environmental Research- BayCEER
Faculties
Faculties > Faculty of Biology, Chemistry and Earth Sciences
Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Biology
Research Institutions
Research Institutions > Research Centres
Result of work at the UBT: Yes
DDC Subjects: 500 Science
Date Deposited: 29 Jul 2015 05:53
Last Modified: 29 Jul 2015 05:53
URI: https://eref.uni-bayreuth.de/id/eprint/17389