Editor: Michael Wagner
Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology
Article first published online: 9 DEC 2008
© 2008 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved
FEMS Microbiology Ecology
Volume 67, Issue 1, pages 6–20, January 2009
How to Cite
Smith, C. J. and Osborn, A. M. (2009), Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology. FEMS Microbiology Ecology, 67: 6–20. doi: 10.1111/j.1574-6941.2008.00629.x
- Issue published online: 9 DEC 2008
- Article first published online: 9 DEC 2008
- Received 20 June 2008; revised 10 October 2008; accepted 24 October 2008.First published online December 2008.
- 16S rRNA gene;
Quantitative PCR (Q-PCR or real-time PCR) approaches are now widely applied in microbial ecology to quantify the abundance and expression of taxonomic and functional gene markers within the environment. Q-PCR-based analyses combine ‘traditional’ end-point detection PCR with fluorescent detection technologies to record the accumulation of amplicons in ‘real time’ during each cycle of the PCR amplification. By detection of amplicons during the early exponential phase of the PCR, this enables the quantification of gene (or transcript) numbers when these are proportional to the starting template concentration. When Q-PCR is coupled with a preceding reverse transcription reaction, it can be used to quantify gene expression (RT-Q-PCR). This review firstly addresses the theoretical and practical implementation of Q-PCR and RT-Q-PCR protocols in microbial ecology, highlighting key experimental considerations. Secondly, we review the applications of (RT)-Q-PCR analyses in environmental microbiology and evaluate the contribution and advances gained from such approaches. Finally, we conclude by offering future perspectives on the application of (RT)-Q-PCR in furthering understanding in microbial ecology, in particular, when coupled with other molecular approaches and more traditional investigations of environmental systems.