Soil microorganisms, such as bacteria and fungi, play important roles in promoting soil quality and improving plant health and nutrition, thus influencing terrestrial ecosystems. Increasing anthropogenic activities, such as sprawling urbanization, agricultural development, pesticides utilization, and pollutions from all sources, can potentially affect soil microbial community composition and diversity, leading to deterioration of soil quality and fertility. However, it is yet to be determined how these changes in microbial diversity can influence surface and ground ecosystems. To that end, there is an acute need for reliable and accurate methods to study the community structure and taxonomy of soil microorganisms. Without the development of effective methods for studying the microbial diversity, distribution, and behavior in polluted soil, a thorough understanding of microbial diversity, as well as its impact on soil health, cannot be achieved.
The determination of species diversity depends on several factors including the intensity of each species, the total number of species present, species evenness, and the spatial distribution of species. Methods to measure microbial community structure and functional diversity in polluted soils can be classified into two groups, i.e., biochemical-based techniques and molecular biological-based techniques. Typically, diversity studies include the relative comparisons of communities across a gradient of stress and disturbance. With current techniques, it is difficult to study true diversity due to lack of knowledge on composition and the techniques to determine the accuracy of the extraction or detection methods. Traditionally, the analysis of soil microbial communities has always depended on culturing techniques using a variety of culture media designed to maximize the recovery of diverse microbial populations. However, only a small fraction (<1%) of the soil microbial community has been accessed with this approach. To overcome these problems, other methods such as the community-level physiological profiling and analysis of phospholipid fatty acids have been used in an attempt to measure a greater proportion of the soil microbial community. In recent years, molecular-based approaches for assessing soil microbial community have provided a new understanding of the phylogenetic diversity of microbial communities in polluted soils. Among all the available techniques, the PCR-based methods are most useful including denaturing/temperature gradient gel electrophoresis (DGGE/TGGE), amplified ribosomal DNA restriction analysis (ARDRA), ribosomal intergenic spacer analysis (RISA), automated ribosomal intergenic spacer analysis (ARISA), etc. The use of these techniques might provide new ways of measuring soil microbial diversity, ultimately leading to a more complete understanding of the potential impacts of pollution on soil microorganisms. Information obtained from such studies will also provide insight on the role of microbial processes in soil health. However, although the PCR-based molecular techniques have been used to overcome the limitations of culture-based methods, they have their own limitations such as the lysis efficiency of cells or fungal structures variation between and within microbial groups. Since each group of methods (biochemical-based versus molecular biological-based) can only provide a partial picture of one aspect of soil microbial diversity, a combined use of techniques from the two groups will certainly help to develop a broader, more complete profile of soil microbial diversity in polluted soils, which will eventually enhance our knowledge on the changes in microbial community function caused by the changes in microbial community structure.