Domain (biology)
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In biological
taxonomy image:Hierarchical clustering diagram.png, 280px, Generalized scheme of taxonomy Taxonomy is a practice and science concerned with classification or categorization. Typically, there are two parts to it: the development of an underlying scheme o ...
, a domain ( or ) (
Latin Latin ( or ) is a classical language belonging to the Italic languages, Italic branch of the Indo-European languages. Latin was originally spoken by the Latins (Italic tribe), Latins in Latium (now known as Lazio), the lower Tiber area aroun ...
: ''regio''), also dominion, superkingdom, realm, or empire, is the highest
taxonomic rank In biology, taxonomic rank (which some authors prefer to call nomenclatural rank because ranking is part of nomenclature rather than taxonomy proper, according to some definitions of these terms) is the relative or absolute level of a group of or ...
of all
organism An organism is any life, living thing that functions as an individual. Such a definition raises more problems than it solves, not least because the concept of an individual is also difficult. Many criteria, few of them widely accepted, have be ...
s taken together. It was introduced in the three-domain system of taxonomy devised by Carl Woese, Otto Kandler and Mark Wheelis in 1990. According to the domain system, the
tree of life The tree of life is a fundamental archetype in many of the world's mythology, mythological, religion, religious, and philosophy, philosophical traditions. It is closely related to the concept of the sacred tree.Giovino, Mariana (2007). ''The ...
consists of either three domains,
Archaea Archaea ( ) is a Domain (biology), domain of organisms. Traditionally, Archaea only included its Prokaryote, prokaryotic members, but this has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even thou ...
,
Bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
, and Eukarya, or two domains, Archaea and Bacteria, with Eukarya included in Archaea. In the three-domain
model A model is an informative representation of an object, person, or system. The term originally denoted the plans of a building in late 16th-century English, and derived via French and Italian ultimately from Latin , . Models can be divided in ...
, the first two are
prokaryote A prokaryote (; less commonly spelled procaryote) is a unicellular organism, single-celled organism whose cell (biology), cell lacks a cell nucleus, nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Ancient Gree ...
s, single-celled
microorganism A microorganism, or microbe, is an organism of microscopic scale, microscopic size, which may exist in its unicellular organism, single-celled form or as a Colony (biology)#Microbial colonies, colony of cells. The possible existence of unseen ...
s without a membrane-bound nucleus. All
organism An organism is any life, living thing that functions as an individual. Such a definition raises more problems than it solves, not least because the concept of an individual is also difficult. Many criteria, few of them widely accepted, have be ...
s that have a cell nucleus and other membrane-bound organelles are included in Eukarya and called eukaryotes.
Non-cellular life Non-cellular life, also known as acellular life, is life that exists without a cellular structure for at least part of its life cycle. Historically, most definitions of life postulated that an organism must be composed of one or more cells, ...
, most notably the
virus A virus is a submicroscopic infectious agent that replicates only inside the living Cell (biology), cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Viruses are ...
es, is not included in this system. Alternatives to the three-domain system include the earlier two-empire system (with the empires Prokaryota and Eukaryota), and the eocyte hypothesis (with two domains of Bacteria and Archaea, with Eukarya included as a branch of Archaea).


Terminology

The term ''domain'' was proposed by Carl Woese, Otto Kandler, and Mark Wheelis (1990) in a three-domain system. This term represents a synonym for the category of dominion (Lat. ''dominium''), introduced by Moore in 1974.


Development of the domain system

Carl Linnaeus Carl Linnaeus (23 May 1707 – 10 January 1778), also known after ennoblement in 1761 as Carl von Linné,#Blunt, Blunt (2004), p. 171. was a Swedish biologist and physician who formalised binomial nomenclature, the modern system of naming o ...
made the classification "domain" popular in the famous
taxonomy image:Hierarchical clustering diagram.png, 280px, Generalized scheme of taxonomy Taxonomy is a practice and science concerned with classification or categorization. Typically, there are two parts to it: the development of an underlying scheme o ...
system he created in the middle of the eighteenth century. This system was further improved by the studies of
Charles Darwin Charles Robert Darwin ( ; 12 February 1809 – 19 April 1882) was an English Natural history#Before 1900, naturalist, geologist, and biologist, widely known for his contributions to evolutionary biology. His proposition that all speci ...
later on but could not classify
bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
easily, as they have very few observable features to compare to the other domains. Carl Woese made a revolutionary breakthrough when, in 1977, he compared the
nucleotide Nucleotides are Organic compound, organic molecules composed of a nitrogenous base, a pentose sugar and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both o ...
sequences of the
16s ribosomal RNA 16S ribosomal RNA (or 16 S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome ( SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure. The genes coding for it are referred to as 16S ...
and discovered that the rank "domain" contained three branches, not two as scientists had previously thought. Initially, due to their physical similarities,
Archaea Archaea ( ) is a Domain (biology), domain of organisms. Traditionally, Archaea only included its Prokaryote, prokaryotic members, but this has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even thou ...
and
Bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
were classified together and called "archaebacteria". 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 Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal ...
. This forms the basis of the three-domain system. While the presence of a nuclear membrane differentiates the Eukarya from the
Archaea Archaea ( ) is a Domain (biology), domain of organisms. Traditionally, Archaea only included its Prokaryote, prokaryotic members, but this has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even thou ...
and
Bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
, both of which lack a nuclear envelope, the Archaea and Bacteria are distinct from each other due to differences in the
biochemistry Biochemistry, or biological chemistry, is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry and biology, biochemistry may be divided into three fields: structural biology, enzymology, a ...
of their
cell membrane The cell membrane (also known as the plasma membrane or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of a cell from the outside environment (the extr ...
s and
RNA Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyrib ...
markers.


Archaea

Archaea are prokaryotic cells, typically characterized by membrane lipids that are branched
hydrocarbon In organic chemistry, a hydrocarbon is an organic compound consisting entirely of hydrogen and carbon. Hydrocarbons are examples of group 14 hydrides. Hydrocarbons are generally colourless and Hydrophobe, hydrophobic; their odor is usually fain ...
chains attached to glycerol by ether linkages. The presence of these ether linkages in Archaea adds to their ability to withstand extreme temperatures and highly
acid An acid is a molecule or ion capable of either donating a proton (i.e. Hydron, hydrogen cation, H+), known as a Brønsted–Lowry acid–base theory, Brønsted–Lowry acid, or forming a covalent bond with an electron pair, known as a Lewis ...
ic conditions, but many archaea live in mild environments.
Halophile A halophile (from the Greek word for 'salt-loving') is an extremophile that thrives in high salt In common usage, salt is a mineral composed primarily of sodium chloride (NaCl). When used in food, especially in granulated form, it is more ...
s (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 Cyanobacteria ( ) are a group of autotrophic gram-negative bacteria that can obtain biological energy via oxygenic photosynthesis. The name "cyanobacteria" () refers to their bluish green (cyan) color, which forms the basis of cyanobacteri ...
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 Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
. 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 five kingdoms: Plantae, Protozoa,
Animalia Animals are multicellular, eukaryotic organisms in the Biology, biological Kingdom (biology), kingdom Animalia (). With few exceptions, animals heterotroph, consume organic material, Cellular respiration#Aerobic respiration, breathe oxygen, ...
, Chromista, and
Fungi A fungus (: fungi , , , or ; or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and mold (fungus), molds, as well as the more familiar mushrooms. These organisms are classified as one ...
.


Exclusion of viruses and prions

The three-domain system includes no form of non-cellular
life Life, also known as biota, refers to matter that has biological processes, such as Cell signaling, signaling and self-sustaining processes. It is defined descriptively by the capacity for homeostasis, Structure#Biological, organisation, met ...
. Stefan Luketa proposed a five-dominion system in 2012, adding
Prion A prion () is a Proteinopathy, misfolded protein that induces misfolding in normal variants of the same protein, leading to cellular death. Prions are responsible for prion diseases, known as transmissible spongiform encephalopathy (TSEs), w ...
obiota (acellular and without nucleic acid) and
Virus A virus is a submicroscopic infectious agent that replicates only inside the living Cell (biology), cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Viruses are ...
obiota (acellular but with nucleic acid) to the traditional three domains.


Alternative classifications

Alternative classifications of life include: * The two-empire system or superdomain system, proposed by Mayr (1998), with top-level groupings of Prokaryota (or Monera) and Eukaryota. * The eocyte hypothesis, proposed by
Lake A lake is often a naturally occurring, relatively large and fixed body of water on or near the Earth's surface. It is localized in a basin or interconnected basins surrounded by dry land. Lakes lie completely on land and are separate from ...
''et al''. (1984), which posits two domains, Bacteria and Archaea, with Eukaryota included as a subordinate clade branching from Archaea.


See also

* Biological dark matter * Neomura, which is the two domains of life of Archaea and Eukaryota *
Phylogenetics In biology, phylogenetics () is the study of the evolutionary history of life using observable characteristics of organisms (or genes), which is known as phylogenetic inference. It infers the relationship among organisms based on empirical dat ...
* Protein structure *
Realm (virology) In virology, realm is the highest taxonomic rank established for viruses by the International Committee on Taxonomy of Viruses (ICTV), which oversees virus taxonomy. Six virus realms are recognized and united by specific Conserved sequence, highl ...
, an equivalent rank for non-cellular life *
Systematics Systematics is the study of the diversification of living forms, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees (synonyms: phylogenetic trees, phylogenies). Phy ...


References


External links

* {{Portal bar, Biology, Evolutionary biology, Science