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Microbial communities can exhibit an enormous range of complexity, from those with a mere handful of populations to those with thousands of species derived from all three domains of life. For community analysis, genetic fingerprinting techniques allow the comparative profiling of many environmental samples and thus facilitate the spatial and temporal analysis of microbial communities in ecosystems. Two of these approaches, denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP), are described herein. In reality, complex microbial communities with population richness exceeding several hundred species are beyond single-primer pair PCR analysis. Many would consider the current analytical methods more exploratory in nature, just the beginning to quantitatively address the complex relationships between microbial communities. The marker should be composed of DGGE PCR products, and under no circumstances should size markers be used. T-RFLP has been used as an effective tool in the dissection of microbial communities. The digestions were carried out assuming that PCR products were generated with a labeled 63F bacterial domain-specific primer. Hence, all fragments are derived from the 5'- terminus of bacterial rRNA genes.

Microbial source tracking (MST), the determination of a source of microorganisms into an environment, is a phrase that has been used by various microbiology disciplines. This chapter discusses some of the research and development efforts in bio-forensic technologies underway in the Department of Homeland Security (DHS) Science and Technology Directorate. The chapter provides examples of some outbreaks that occurred and the responses by various relevant groups. A number of natural disease outbreaks have tested the readiness of the health care and political communities to respond and quickly and effectively manage them. A few recent outbreaks that can serve as examples are those of Sin Nombre hantavirus pulmonary syndrome, West Nile disease, severe acute respiratory syndrome (SARS), United Kingdom foot-and-mouth disease, Asian soybean rust, and avian influenza. Anthrax is caused by the gram-positive endospore-forming bacterium Bacillus anthracis. It has a long history as a human pathogen, and several authorities speculate that it was the cause of the sixth Egyptian plague recorded in the book of Genesis. There is opportunity for all those interested ultimately in human health safety, whether they are directly involved in issues related to human disease, plant disease, animal disease, water quality, air quality, soil quality, or food safety, to join their resources. It is the combined knowledge of these fields that will allow the most efficient approach for national security.