Open AccessAdvantages and limitations of quantitative PCR (Q‐PCR)‐based approaches in microbial ecology
Author(s) -
Smith Cindy J.,
Osborn A. Mark
Publication year - 2009
Publication title -
fems microbiology ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.377
H-Index - 155
eISSN - 1574-6941
pISSN - 0168-6496
DOI - 10.1111/j.1574-6941.2008.00629.x
Subject(s) - biology , amplicon , microbial ecology , computational biology , real time polymerase chain reaction , ecology , amplicon sequencing , molecular ecology , gene , polymerase chain reaction , genetics , bacteria , 16s ribosomal rna , population , demography , sociology
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.