Three-domain system

A phylogenetic tree based on rRNA data, showing the separation of bacteria, archaea, and eukaryotes

The three-domain system is a biological classification introduced by Carl Woese in 1977^[1][2] that divides cellular life forms into archaea, bacteria, and eukaryote domains. In particular, it emphasizes the separation of prokaryotes into two groups, originally called Eubacteria (now Bacteria) and Archaebacteria (now Archaea). Woese argued that, on the basis of differences in 16S rRNA genes, these two groups and the eukaryotes each arose separately from an ancestor with poorly developed genetic machinery, often called a progenote. To reflect these primary lines of descent, he treated each as a domain, divided into several different kingdoms. Woese initially used the term "kingdom" to refer to the three primary phylogenic groupings now referred to as "domains," until the latter term was coined in 1990.^[2]

Classification

The three-domain system adds a level of classification (the domains) "above" the kingdoms present in the five-or-six-kingdom systems. This classification system recognizes the fundamental divide between the two prokaryotic groups, insofar as archaea appear to be more closely related to eukaryotes than they are to their fellow prokaryotic bacteria. The current system has the following kingdoms in the three domains:

Archaea Domain – prokaryotic, no nuclear membrane, distinct biochemistry and RNA markers from bacteria, possess unique ancient evolutionary history for which they are considered some of the oldest species of organisms on Earth; traditionally classified as archaebacteria; often characterized by living in extreme environments

• Kingdom Archaebacteria
  Examples:

• Methanogens – metabolize hydrogen and carbon dioxide into methane
• Halophiles – thrive in salt
• Thermoacidophiles – thrive in acid and high temperatures (up to 110 degrees Celsius)

Bacteria Domain – prokaryotic, consists of prokaryotic cells possessing primarily diacyl glycerol diester lipids in their membranes and bacterial rRNA, no nuclear membrane, traditionally classified as bacteria, contain most known pathogenic prokaryotic organisms (see ^[3] for exceptions), studied far more extensively than Archaea

• Kingdom Eubacteria
  Examples:

• Cyanobacteria – photosynthesizing bacteria
• Spirochaete – Gram-negative bacteria that include those causing syphilis and Lyme disease
• Firmicutes – Gram-positive bacteria including Bifidobacterium animalis which is present in the human large intestine

Eukarya Domain – eukaryotes, nuclear membrane

• Kingdom Fungi or fungi
  Examples:

• Saccharomycotina – includes true yeasts
• Basidiomycota – includes blue oyster mushrooms

• Kingdom Plantae or plants
  Examples:

• Bryophyta – mosses
• Magnoliophyta – flowering plants

• Kingdom Animalia or animals
  Examples:

• Arthropoda – includes insects, arachnids, and crustaceans
• Chordata – includes vertebrates and, as such, human beings

• Kingdom Protista or protists (recognized to be paraphyletic, and thus subject to dissolution and/or redefinition)
  Examples:

• Rhodophyta – red algae
• Chromalveolata – includes dinoflagellates

Niches

Each of the three cell types tends to fit into recurring specialties or roles. Bacteria tend to be the most prolific reproducers, at least in moderate environments. Archaeans tend to adapt quickly to extreme environments, such as high temperatures, high acids, high sulfur, etc. This includes adapting to use a wide variety of food sources. Eukaryotes are the most flexible with regard to forming cooperative colonies, such as in multi-cellular organisms, including humans. In fact, the structure of a Eukaryote is likely to have derived from a joining of different cell types, forming organelles.

Criticism

Parts of the three-domain theory have been challenged by some scientists, including Ernst Mayr, Thomas Cavalier-Smith, Radhey Gupta, and Steven Voutier.^[4][5][6] In particular, Gupta argues that the primary division within prokaryotes should be among those surrounded by a single membrane (monoderm), including gram-positive bacteria and archaebacteria, and those with an inner and outer cell membrane (diderm), including gram-negative bacteria. He claims that sequence features and phylogenies from some highly-conserved proteins are inconsistent with the three-domain theory, and that it should be abandoned despite its widespread acceptance.

See also

• Bacterial phyla
• Five-kingdom system
• Monera
• Phylogenetic tree
• Taxonomy
• Two-empire system
• Archaea

References