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Applied and Environmental Microbiology, November 1998, p. 4581-4587, Vol. 64, No. 11
0099-2240/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.

Quantification of 16S rRNAs in Complex Bacterial Communities by Multiple Competitive Reverse Transcription-PCR in Temperature Gradient Gel Electrophoresis Fingerprints

Andreas Felske,* Antoon D. L. Akkermans, and Willem M. De Vos

Laboratory of Microbiology, Department of Biomolecular Sciences, Wageningen Agricultural University, 6703 CT Wageningen, The Netherlands

Received 20 April 1998/Accepted 7 July 1998

A novel approach was developed to quantify rRNA sequences in complex bacterial communities. The main bacterial 16S rRNAs in Drentse A grassland soils (The Netherlands) were amplified by reverse transcription (RT)-PCR with bacterium-specific primers and were separated by temperature gradient gel electrophoresis (TGGE). The primer pair used (primers U968-GC and L1401) was found to amplify with the same efficiency 16S rRNAs from bacterial cultures containing different taxa and cloned 16S ribosomal DNA amplicons from uncultured soil bacteria. The sequence-specific efficiency of amplification was determined by monitoring the amplification kinetics by kinetic PCR. The primer-specific amplification efficiency was assessed by competitive PCR and RT-PCR, and identical input amounts of different 16S rRNAs resulted in identical amplicon yields. The sequence-specific detection system used for competitive amplifications was TGGE, which also has been found to be suitable for simultaneous quantification of more than one sequence. We demonstrate that this approach can be applied to TGGE fingerprints of soil bacteria to estimate the ratios of the bacterial 16S rRNAs.

* Corresponding author. Present address: Instituto de Recursos Naturales y Agrobiologia, C.S.I.C., Apartado 1052, 41080 Seville, Spain. Phone: 34 5 4624711, ext. 131. Fax: 34 5 4624002. E-mail: Andreas{at}cica.es.

Applied and Environmental Microbiology, November 1998, p. 4581-4587, Vol. 64, No. 11
0099-2240/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.


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