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Applied and Environmental Microbiology, February 2009, p. 956-964, Vol. 75, No. 4
0099-2240/09/$08.00+0     doi:10.1128/AEM.01411-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Application of Denaturing High-Performance Liquid Chromatography in Microbial Ecology: Fermentor Sludge, Compost, and Soil Community Profiling{triangledown}

Andreas Otto Wagner,* Cornelia Malin, and Paul Illmer

University of Innsbruck, Institute of Microbiology, Technikerstrasse 25, A-6020 Innsbruck, Austria

Received 24 June 2008/ Accepted 9 December 2008

Genetic fingerprinting methods, such as denaturing gradient gel electrophoresis (DGGE), are used in microbial ecology for the analysis of mixed microbial communities but are associated with various problems. In the present study we used a new alternative method: denaturing high-performance liquid chromatography (dHPLC). This method was previously shown to work with samples from water and gut flora but had not yet been applied to complex environmental samples. In contrast to other publications dealing with dHPLC, we used a commonly available HPLC system. Samples from different origins (fermentor sludge, compost, and soil), all ecologically significant, were tested, and the 16S rRNA gene was amplified via PCR. After optimization of the HPLC elution conditions, amplicons of pure cultures and mixed microbial populations could be separated successfully. Systematic differentiation was carried out by a cloning approach, since fraction collection of the peaks did not result in satisfactory fragment separation. dHPLC was evaluated as a tool for microbial community analysis on a genetic level and demonstrated major improvements compared to gel-based fingerprinting methods, such as DGGE, that are commonly used in microbial ecology.

* Corresponding author. Mailing address: Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria. Phone: 43/(0)512/507/6006. Fax: 43/(0)512/507/2928. E-mail: andreas.wagner{at}uibk.ac.at

{triangledown} Published ahead of print on 16 December 2008.

Applied and Environmental Microbiology, February 2009, p. 956-964, Vol. 75, No. 4
0099-2240/09/$08.00+0     doi:10.1128/AEM.01411-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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