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Chapter 5 : Approaches to Identification
The classification can be a general-purpose classification designed to provide a comprehensive catalog of all bacteria, or it can be a special-purpose classification covering a restricted range of organisms that are found in a particular environment or possess particular properties. This chapter summarizes various approaches to identification of microorganisms with emphasis on prokaryotes. However, virtually all the methods can be adapted to microbial eukaryotes. Microorganisms can be analyzed at various levels to gain information suitable for constructing databases and effecting identification. Nucleic acid hybridization also offers identification possibilities; indeed, chromosomal DNA hybridization forms the basis of the generally accepted species definition in bacterial systematics. The genetic information is expressed as proteins. Electrophoretic analysis of whole-cell proteins has been an effective approach to classification and identification. Other cell components can be analyzed by a range of techniques applied to either whole cells or particular cell extracts. For example, cellular and membrane lipids can be profiled using gas chromatography (GC), or whole cells can be volatilized and the products detected by mass spectrometry (MS). Morphology and physiology are the classical levels at which most conventional identification is done. The presence or absence of particular enzymes or metabolic pathways are typically characterized using commercial kits, and, again, computerized databases can be developed to enable rapid identification. The chapter reviews the application of these various methods and the practicalities of using them in the context of environmental microbiology.