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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

Titelangaben

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. Bd. 44 (2008) Heft 5-6 . - S. 495-500.
ISSN 1164-5563
DOI: https://doi.org/10.1016/j.ejsobi.2008.07.002

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.

Weitere Angaben

Publikationsform: Artikel in einer Zeitschrift
Begutachteter Beitrag: Ja
Zusätzliche Informationen: BAYCEER62656
Institutionen der Universität: Fakultäten > Fakultät für Biologie, Chemie und Geowissenschaften > Fachgruppe Biologie > Lehrstuhl Ökologische Mikrobiologie
Forschungseinrichtungen > Forschungszentren > Bayreuther Zentrum für Ökologie und Umweltforschung - BayCEER
Fakultäten
Fakultäten > Fakultät für Biologie, Chemie und Geowissenschaften
Fakultäten > Fakultät für Biologie, Chemie und Geowissenschaften > Fachgruppe Biologie
Forschungseinrichtungen
Forschungseinrichtungen > Forschungszentren
Titel an der UBT entstanden: Ja
Themengebiete aus DDC: 500 Naturwissenschaften und Mathematik
Eingestellt am: 29 Jul 2015 05:53
Letzte Änderung: 29 Jul 2015 05:53
URI: https://eref.uni-bayreuth.de/id/eprint/17389