The classification, nomenclature, and identification of bacteria; sometimes used as a term to indicate the theory of classification. The bacteria are members of the kingdom Prokaryotae, which is defined in terms of the unique structural and biochemical properties of their cells; more specifically, the organization of the deoxyribonucleic acid (DNA) in the nucleus, the lack of a nuclear membrane, the lack of independent membrane-bounded cytoplasmic organelles, the lack of endocytosis and exocytosis, and the chemical nature of some components of plasma membrane and cell walls.
Classification involves the recognition of similarities and relationships as a basis for the arrangement of the bacteria into taxonomic groups or taxa. The basic taxon is the species. Identification involves the recognition of a bacterium as a member of one of the established taxa, appropriately named, by the comparison of a number of characters with those in the description. See Bacteria, Taxonomic categories
A bacterial species is a conceptual entity that is hard to define, despite its role as the basic taxonomic grouping. Bacteriologists accept the imprecision and recognize that a species represents a cluster of clones exhibiting some variations in minor properties. They have developed a formal approach to the description of the taxon while trying to solve the problems encountered in the process of recognizing and naming species. The description is an assembly of such structural, chemical, physiologic, genetic, and ecologic characteristics as can be determined for the available strains that closely resemble each other. A strain is any pure culture of an organism isolated from nature, and the collected strains may then be conserved as cultures in the laboratory for study and comparison. In addition to the description, one strain must be designated by the author and preserved in a culture collection as a type strain, or permanent example, of the species and available to all who study bacteria. If that type strain is lost or succumbs, a formal proposal of a substitute strain (neotype) must be published. In general, bacterial taxonomy is built around the living type specimen: a species consists of the type strain and, whenever available, all other strains sufficiently similar to the type strain to be considered as included in the species. There is a provision for the description and naming of a distinctive species that is not yet cultivable, with the requirement for a suitably preserved type specimen.
A new species, validly described, must be assigned to a genus in order to accord with the binomial system of nomenclature initiated by C. Linnaeus. Thus, a species assigned to the genus Bacillus would be referred to as, for example, Bacillus subtilis. Such formal names of taxa are italicized to indicate that they are considered to accord with the formal description. If there is no appropriate genus available, a new genus must be named in accord with the International Code of Nomenclature of Bacteria and provided with a description that circumscribes the included species, and a type species must be designated as the exemplary representative of the genus.
The lowest nomenclatural rank that is recognized by the Code is subspecies, which is a subdivision of the species recognizing consistent variations in otherwise stable characters in the species description, for example, Bacillus cereus ssp. mycoides. There are times, however, when even finer but unofficial subdivisions of the species are useful and contribute to science, for example, for the epidemiology of pathogenic species. Then, groups of strains may be recognized by some special character as a variety of the species. These may be based on a biological property (biovar), antigenic variation (serovar), pathogenicity (pathovar), or susceptibility to particular bacterial viruses (phagovar). These characters have no formal standing in nomenclature.
Several new techniques are presently used in modern approaches to taxonomy. Numerical taxonomy (taxometrics) is a first approach for the analysis of phenotype. It implies the existence of programs for computer-assisted identification, either as recognizable phenons or by relation into a computer-stored classification and key program. Either of these methods has found considerable application in dealing with masses of isolates (for example, in studies of pollution or of sediments), or in dealing with results of automated systems for identification of pathogens in clinical bacteriology. See Numerical taxonomy
Chemotaxonomy applies systematic data on the molecular architecture of components of the bacterial cell to the solution of taxonomic problems. This has been a powerful tool since the 1950s, and a number of chemotaxonomic markers have been identified, ranging from molecules unique to the Prokaryotae or specific groups of bacteria to mechanisms or products of metabolism that characterize genera or species. The availability, and relative simplicity of techniques for amino acid analysis, for sequential analysis of polymers, for gas and thin-layer chromatography, for fermentation products and lipids, and so on, have made the systematic studies possible. These have led to a more effective definition of taxonomic groups based on biochemical assessment of cell wall composition, lipid composition of membranes, the types of isoprenoid quinones, the amino acid sequences of select proteins, and the characterization of proteins, such as the cytochromes and many other macromolecules. See Chemotaxonomy
Nucleic acid studies have been by far the most potent generators and arbiters of data on relatedness, with distinct capability for applications to the phylogenetic assessment of taxonomic arrangements. See Deoxyribonucleic acid (dna), Ribonucleic acid (rna)