Molecular fingrprinting of microbial populations

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Molecular phylogenetic surveys give a much larger picture of the diversity of an environment than the older cultivation-dependent methods, but a real drawback is the time, expense, and energy required.This might not be the case much longer, as sequence-based methods continue to evolve - particularly 454 sequencing and related methods.Nevertheless, at least for now these molecular surveys are almost always performed one at a time; a single snapshot of a point in the environment. But microbial ecologists know that a lot of the interesting microbiology is the variation in the populations from one place to the next (measured in micrometers to thousands of kilometers) or from one time to another (measured in minutes to thousands of years). How, for example, do you survey the dynamics of the microbial population in each layer of a Yellowstone microbial mat, from it's source pool to it's drainage into a cold stream, during the diurnal and seasonal cycles? Or follow the changes in microbial population in the subsurface as a gasoline plume forms from a leaky storage tank?

The answer is to use "fingerprinting" methods that provide patterns that can be used to distinguish populations without necessarily sequencing anything (although it is useful to be able to go in and get sequences, or identifications of organisms, from the bands that make up the patterns in some cases). A relatively old-fashioned approach is DGGE; denaturing gradient gel electrophoresis. The emerging alternative is terminal-RFLP. We'll talk about these technologies and examples of how they can be used.

We'll also talk about real-time PCR, not because it's a fingerprinting method, but because it is often used in conjuction with these methods to look at the numbers of specific kinds of organisms in a population.