The classical approaches to taxonomy make use of morphological, physiological, biochemical, ecological and genetic characteristics. They are quite useful in routine identification and may provide phylogenetic information as well.
- Morphological Characteristics
Morphological features are important in microbial taxonomy as it is easy to study and analyze, particularly the eukaryotic microorganisms and the more complex prokaryotes. The morphological comparisons are also valuable because the structural features depend on the expression of many genes, are usually genetically stable, and normally (at least in eukaryotes) do not vary greatly with environmental changes.
|Cell shape||All major groups|
|Cell size||All major groups|
|Colonial morphology||All major groups|
|Ultrastructural characteristics||All major groups|
|Staining behavior||Bacteria, some fungi|
|Cilia and flagella||All major groups|
|Mechanism of motility||Gliding bacteria, spirochetes|
|Endospore shape and location||Endospore-forming bacteria|
|Spore morphology and location||Bacteria, protists, fungi|
|Cellular inclusions||All major groups|
|Color||All major groups|
- Physiological and Metabolic Characteristics
Physiological and metabolic characteristics are very useful because they are directly related to the nature and activity of microbial enzymes and transport proteins. Since proteins are gene products, analysis of these characteristics provides an indirect comparison of microbial genomes.
Some of the physiological and metabolic characteristics used in classification and identification are as follows:
|Carbon and nitrogen sources||Cell wall constituents|
|Energy sources||Fermentation products|
|General nutritional type||Growth temperature optimum and range|
|Luminescence||Mechanisms of energy conversion|
|Oxygen relationships||pH optimum and growth range|
|Photosynthetic pigments||Salt requirements and tolerance|
|Secondary metabolites formed||Sensitivity to metabolic inhibitors and antibiotics|
- Ecological Characteristics
The ability of a microorganism to colonize a specific environment is of taxonomic value. Some microbes may be very similar in many other respects but inhabit different ecological niches, suggesting they may not be as closely related as first suspected. Some examples of taxonomically important ecological properties are:
|Life-cycle patterns||Symbiotic relationships|
|Ability to cause disease||Habitat preferences|
- Genetic Characteristics
The species is defined in terms of sexual reproduction wherever possible. Because most eukaryotes are able to reproduce sexually, genetic analysis has been quite useful in the classification of these organisms. Although prokaryotes do not reproduce sexually, the study of chromosomal gene exchange through transformation, conjugation, and transduction is sometimes useful in their classification also.
Transformation can occur between different prokaryotic species but only rarely between genera. The demonstration of transformation between two strains provides evidence of a close relationship since transformation cannot occur unless the genomes are fairly similar.
Conjugation studies also yield taxonomically useful data, particularly with the enteric bacteria. For example, Escherichia can undergo conjugation with the genera Salmonella and Shigella but not with Proteus and Enterobacter. These observations fit with other data showing that the first three of these genera are more closely related to one another than to Proteus and Enterobacter.
Plasmids are important taxonomically because they can confound the analysis of phenotypic traits. Most microbial genera carry plasmids and some plasmids are passed from one microbe to another with relative ease. When such plasmids encode a phenotypic trait (or traits) that is being used to develop a taxonomic scheme, the investigator may assume that the trait is encoded by chromosomal genes. Thus a microbe’s phenetic characteristics are misunderstood and its relative degree of relatedness to another microbe may be overestimated. For example, hydrogen sulfide production and lactose fermentation are very important in the taxonomy of the enteric bacteria, yet genes for both traits can be borne on plasmids as well as bacterial chromosomes.