An overview of real-time quantitative PCR: Principles and formats for environmental microbiology studies

A fluorescence-based real-time quantitative polymerase chain reaction (qPCR) is a powerful and commonly used molecular technique for quantifying the rRNA or DNA of targeted organisms in environmental samples. qPCR assays are easy to perform, making them capable of high throughput and can combine high sensitivity with reliable specificity. qPCR analysis is the combination of the traditional endpoint PCR attached with fluorescents to record the accumulation of the amplicons in real time during each cycle of the PCR. Detection of amplicons during the early exponential phase enables quantification of the gene numbers because they are proportional to the starting template. This review is focussed on currently used qPCR platforms, the chemistries involved in real-time PCR systems mainly applied for the environmental microbiology studies. The various factors affecting quantification of environmental microbial communities using qPCR have also been discussed.