Many prokaryotes are able to convert any given carbon source into biosynthetic building blocks—e.g., amino acids, purines, pyrimidines, lipids, sugars, and enzyme cofactors. The amount and activity of each enzyme in these biosynthetic pathways are carefully regulated so that the cell produces only as much of any compound as is needed at any time.

During the process of evolution, some bacteria have lost genes that encode certain biosynthetic reactions and are hence likely to require nutritional supplements. For example, Mycoplasma, whose DNA content is about one-quarter the size of that of E. coli, has many nutritional requirements and has even lost the ability to make a cell wall.

Taxonomic rankings

The classification of bacteria has long presented unique challenges in biological systematics. In the 17th century, when bacteria were first observed under a microscope, only two categories of life were recognized in biological systematics: plants and animals. Lacking any obvious relation to animals, bacteria initially were classified in the plant kingdom. In the latter part of the 19th century, however, German zoologist Ernst Haeckel, recognizing the basic morphological characteristics of single-celled life—particularly the lack of a clearly defined nucleus among many of those organisms—proposed a third kingdom of “lower” life, Protista, and within it the class Monera, which would contain the structureless (nuclei-lacking) microorganisms. About the same time, German naturalist and botanist Ferdinand Cohn began to systematically organize bacteria into genera and species. Although Cohn’s arrangement of the bacteria was based on morphology, he recognized that bacteria could not be adequately classified by morphology alone. In 1938, seeking to further distinguish the bacteria from other forms of life, American biologist Herbert F. Copeland elevated Monera to the level of kingdom.

Although kingdom Monera was readily adopted and later accepted as part of a five-kingdom system (whereby American biologist Robert H. Whittaker separated the fungi into their own kingdom), in the purview of some researchers, Monera remained an unsatisfactory division. The differences between prokaryotic organisms, namely between bacteria and archaea, are great; those groups of organisms are as different from one another as they are from plants and animals. Hence, in 1990 Carl R. Woese and colleagues proposed the three-domain system, dividing life into the Bacteria, the Archaea, and the Eukarya. Still other researchers disagreed with the domain system, however, and in 1998 British zoologist Thomas Cavalier-Smith presented yet another classification scheme, the six-kingdom system, which contained kingdom Bacteria with two subdivisions, Eubacteria and Archaebacteria. In 2015 Cavalier-Smith and others revised the system to include seven kingdoms, whereby kingdom Bacteria was split into two separate kingdoms—Bacteria (containing the eubacteria) and Archaea (containing the archaebacteria).

According to the rules of nomenclature under the International Code of Nomenclature of Bacteria—the body that governs the naming of prokaryotes—valid taxa for bacteria extend from subspecies to class; taxonomic categories above class (e.g., phylum) are not considered valid.

The bacterial species problem

As with the general taxonomy of bacteria, the basic concept of species in bacterial systematics is problematic. Unlike in higher organisms, in which a species is defined by the ability of organisms with common characteristics to interbreed and give rise to fertile offspring, bacteria generally reproduce asexually. When genetic material is exchanged between bacterial cells, it can occur between individuals of different species through the process of horizontal gene transfer, thereby confusing the limits of interbreeding.

Speciation among bacteria is suspected of occurring at the level of subspecies, or ecotype, whereby genetically distinct populations survive within the same ecological niche until, through adaptation and natural selection, one type outcompetes the others, clearing the niche of its diversity. The process of divergence within the niche then begins anew. Hence, a single named species of bacteria can have numerous ecotypes. For that reason, some researchers consider the species level in bacterial classification to be nearly comparable to the genus level in the classification systems of other organisms.

Genetic approaches

Genetic approaches to the classification of bacteria are aimed at identifying a degree of relatedness between organisms to obtain a more-fundamental measure of the time elapsed since two organisms diverged from a common ancestor.