Comparison of two molecular methods to assess soil microbial diversity

Our knowledge of microbial soil biodiversity depends on the ability to combine different observation levels, ranging from the phenotypic to the molecular one, including direct visualization of microorganisms by using an epifluorescence microscope. Soil microbial communities, although still largely undiscovered, represent one of the biggest part of present biodiversity and play a key role in all soil processes. For example, microbial abundance, activity and composition largely determine the sustainable productivity of agricultural land or the degradation of organic pollutants. The diversity of microbial communities associated with plant roots is enormous, in the order of thousands of species. The simultaneous use of different molecular methods makes it possible to have a more holistic knowledge of the soil microbial community and to assess changes in it under different conditions. In this chapter we report the application to the same soil samples of two different phylogenetic molecular techniques, i.e. DGGE (Denaturing Gradient Gel Electrophoresis) and FISH (Fluorescence In Situ Hybridization). DGGE is a useful fingerprint technique of the overall microbial community based on amplification of 16S rRNA. The FISH technique identify, without extracting nucleic acids, active microbial cells at different phylogenetic levels (from domains to species) under an epifluorescence microscope. An example of the application of both methodologies to assessing the microbial community composition of soil samples from a phyto-assisted bioremediation experiment of a contaminated soil by polychlorinated biphenyls (PCBs) is reported.