ABSTRACT
Antarctica .....................................................................................................366 16.7 Potential Advancements in Real Time PCR ................................................. 367 16.8 Summary ...................................................................................................... 368 References .............................................................................................................. 369
Real-time PCR is a powerful tool for exploring microbial community structure and function. It allows the quantitative measurement of speci c genes from DNA or RNA extracted from cultures or environmental samples. It is possible to target groups of bacteria on a phylogenetic basis using the 16S rRNA gene, or genes for particular functions, such as sulfate reduction or hydrocarbon degradation. The target of the assay is determined by the primer and/or probe pair. The speci city can be broad
(genus or group level), or narrow (a particular species, strain, or genotype) allowing insight into microbial community structure and function in much greater detail than before. Rather than only being able to detect the presence or absence of a particular species or gene, as is possible with standard PCR, we are now able to follow changes in the abundance of a gene in response to outside factors. For example, Ben-Dov et al. (2007) followed the community dynamics of sulfate-reducing bacteria in wastewater using the dissimilatory sulfate reductase (dsrA) and adenosine-5′-phosphosulfate reductase (aspA) genes. Another example is the use of the ammonium monooxygenase gene (amoA) to follow the effect of fertilization with ammonium sulfate in both microcosms and a eld trial (Okano et al., 2004). In bioremediation studies, the concentration of catabolic genes such as naphthalene dioxygenase (ndoB) or alkane monooxygenase (alkB) has been correlated with the soil hydrocarbon concentration (Powell et al., 2006a; Baldwin et al., 2008), providing a link between the microbial process and its effect on its environment.
