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During the past two decades, the extensive research efforts in biotechnology, especially in the area of molecular biology, have resulted in important discoveries, some of which carry the potential for valuable contributions to the health and welfare of man. Techniques of genetic engineering are now being applied to the development of drugs, improvements in the quality and quantity of agricultural products, pollution control, and basic research in biology and medicine.

The recent incorporation of molecular biological approaches into studies in microbial ecology promises a new level of information concerning the structure and function of microbial communities as they mediate degradation of organic compounds, cycle nutrients and trace elements, and interact with other plant and animal communities. Traditional methods of environmental analysis, which are mainly based on cultural, physiological, and biochemical techniques, are readily complemented by qualitatively and quantitatively specific molecular techniques. For instance, nucleic acid hybridization technology can be used to identify and quantitate individual bacterial species within a natural microbial community. Such enumeration can be achieved with specificity and speed to aid in the isolation and characterization of desirable microorganisms. The focus of this chapter is to provide an overview of the use of molecular techniques in the analysis of the structure and activity of microbial community in soils. A major emphasis is placed on