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A Natural System
Difficulties in
Classifying Microbes

Molecular Phylogeny
Molecular Ecology

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The Difficulty of Classifying Microorganisms

©2000 Gary Olsen, University of Illinois

Determinative Microbiology

The prokaryotes and eukaryotic protists were more difficult to classify. They are much simpler, and there are few obvious features that are sufficiently widespread to permit meaningful measurements of similarity between distantly related organisms. Some of the features that have been used to classify prokaryotes include:

Gram stain (cell wall structure)
Mole percent G+C in the genome
Growth temperature
Ability to form heat stable spores
Electron acceptors for respiration (if any)
Photosynthetic ability
Cell shape
Ability to use various carbon and nitrogen sources
Special nutritional requirements (e.g., vitamins)

Leading microbiologists in the 20th century (e.g., Stanier and van Niel) realized and acknowledged that classifications based upon features such as these were not natural systems, but they also realized that no satisfactory alternatives were available. Consequently, the resulting classification of bacteria (excluding cyanobacteria, which were classified with the eukaryotic algae) was codified in a volume called Bergey's Manual of Determinative Bacteriology.l3 In doing so, it was recognized that the classification could be used to accurately identify organisms that had already been characterized. However, given a new isolate with the following properties:

32% G+C genome
thermophilic (85 C optimum)
rod-shaped prokaryote
grows on H2, CO2 and N2
no special growth factors required

microbiologists were unable to predict its phylogeny or additional properties. That is, it was not possible to say much about a new organism other than what was directly measured.

Determinative Classification Is Adequate for Some Questions, But Not Others

From the standpoint of many areas of microbiology, a determinative classification is sufficient. For example, in clinical microbiology the identification of organisms permits the physician to assess pathogenicity, and to select a treatment. In this context, the purely determinative nature of a classification was not crucial. If the organism has previously been described, and hence is already in the classification, then it can be identified and treated.14

However, from a biological point of view, the lack of a natural system was an unsatisfactory state of affairs. It does not permit the projection of properties of previously described organisms onto new ones that might be closely related, but not identical, to those known before. In addition, it does not help us understand an organism that we have been unable to cultivate in the laboratory. Finally, it does not permit studies of the origin and evolution of cellular functions (e.g., drug resistance, aerobiosis or photosynthesis), because there is no evolutionary (historical) framework.

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