Traditionally, the classification, or taxonomy, of higher organisms has been based on their morphology: their form and visible structure. However, this has been difficult for microorganisms because of their small size. Typically, prokaryotes were classified based mainly on their biochemical activities (including usable carbon substrates, nitrogen and other nutrient sources, electron acceptors, metabolic products, and resistance to inhibitory compounds), and on staining, which gave an indication of some aspects of their composition, in addition to such morphological features as size, shape, pigmentation, sporulation, intra-cellular inclusions (including those visible after staining), and the presence and location of flagella or the presence of another form of motility. Together, the observable characteristics of an organism can be referred to as its phenotype.
Habitat (and niche) might also be used for classification, including preferences with regard to such environmental factors as temperature and pH. Gross DNA composition (%G + C content) and immunological properties (e.g., serotyping) have also been used for many years. More recently, detailed analysis of the composition of the cell wall and of other cell constituents (e.g., fatty acid analysis) have been added as other useful tools in distinguishing among microorganisms.
Precise characterization of DNA and RNA sequences is now being used extensively to determine relationships among organisms. Such analysis of an organism's genetic makeup reveals its genotype. Genotype obviously affects phenotype, but not all genetic capabilities are necessarily expressed in an organism at a particular time. As might be expected, knowledge of genotypes has greatly increased and modified our understanding of the relationships among microorganisms. In fact, the separate domain of Archaea was not recognized until these newer tools were applied; previously, they were simply considered types of (and may still often be referred to out of habit as) bacteria.
One aspect of taxonomy is the grouping of organisms in progressively higher taxa (singular, taxon), such as families, orders, classes, and phyla. Modern taxonomists base these groupings on phylogeny, or natural evolutionary lines inferred from genetic similarities.
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