Domain (taxonomy)

Development of the domain system

Carl Linnaeus made the classification "domain" popular in the famous taxonomy system he created in the middle of the eighteenth century. This system was further improved by the studies of Charles Darwin later on but could not classify bacteria easily, as they have very few observable features to compare to the other domains.

The mycologist Royall T. Moore proposed the similar term dominion (Latin: dominium) in 1974, but this was not widely adopted. His proposed system had three dominions: Virus, Prokaryota, and Eukaryota.

Carl Woese made a revolutionary breakthrough when, in 1977, he compared the nucleotide sequences of the 16s ribosomal RNA and discovered that the rank "domain" contained three branches, not two as scientists had previously thought. Initially, due to their physical similarities, Archaea (earlier "archaebacteria") was not separated from Bacteria (earlier "eubacteria"). However, scientists now know that these two domains are hardly similar and are internally distinctly different.

Characteristics of the three domains

Each of these three domains contains unique ribosomal RNA. This forms the basis of the three-domain system. While the presence of a nuclear membrane differentiates the Eukarya from the Archaea and Bacteria, both of which lack a nuclear envelope, the Archaea and Bacteria are distinct from each other due to differences in the biochemistry of their cell membranes and RNA markers.

Archaea

Archaea are prokaryotic cells, typically characterized by membrane lipids that are branched hydrocarbon chains attached to glycerol by ether linkages. The presence of these ether linkages in Archaea adds to their capability to withstand extreme temperatures and highly acidic conditions, but many archaea live in mild environments. Halophiles (organisms that thrive in highly salty environments) and hyperthermophiles (organisms that thrive in extremely hot environments) are examples of Archaea.

Archaea are relatively small. They range from 0.1 μm to 15 μm diameter and up to 200 μm long, about the size of bacteria and the mitochondria found in eukaryotic cells. Members of the genus Thermoplasma are the smallest Archaea.

Bacteria

Cyanobacteria and mycoplasmas are two examples of bacteria. Even though bacteria are prokaryotic cells like Archaea, their cell membranes are instead made of phospholipid bilayers, with none of the ether linkages that Archaea have. Internally, bacteria have different RNA structures in their ribosomes, hence they are grouped into a different category. In the two- and three-domain systems, this puts them into a separate domain.

There is a great deal of diversity in the domain Bacteria. That diversity is further confounded by the exchange of genes between different bacterial lineages. The occurrence of duplicate genes between otherwise distantly-related bacteria makes it nearly impossible to distinguish bacterial species, count the bacterial species on the Earth, or organize them into a tree-like structure (unless the structure includes cross-connections between branches, making it a "network" instead of a "tree").

Eukarya

Members of the domain Eukarya—called eukaryotes—have membrane-bound organelles (including a nucleus containing genetic material) and are represented by four kingdoms: Plantae, Protista, Animalia, and Fungi. It's believed to have evolved from Archaea, according to the Eocyte hypothesis.

Exclusion of viruses and prions

The three-domain system includes no form of non-cellular life. Stefan Luketa proposed a five-dominion system in 2012, adding Prionobiota (acellular and without nucleic acid) and Virusobiota (acellular but with nucleic acid) to the traditional three domains.

Alternative classifications

Alternative classifications of life include:

• The two-empire system, proposed by Mayr (1998), with top-level groupings of Prokaryota (or Monera) and Eukaryota.
• The eocyte hypothesis, proposed by Lake et al. (1984), which posits two domains, Bacteria and Archaea, with Eukaryota included as a subordinate clade branching from Archaea.
• The five-dominium system, proposed by Stefan Luketa (2012), The listed Eukarya, Archaea, Bacteria, Virusobiota, Prionobiota.