Domain (biology)

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The hierarchy of biological classification's eight major taxonomic ranks. Life is divided into domains, which are subdivided into further groups. Intermediate minor rankings are not shown. Biological classification L Pengo vflip.svg DomainKingdomClassOrderFamily
The hierarchy of biological classification's eight major taxonomic ranks. Life is divided into domains, which are subdivided into further groups. Intermediate minor rankings are not shown.

In biological taxonomy, a domain ( /dəˈmn/ or /dˈmn/ ) (Latin: regio [1] ), also dominion, [2] superkingdom, realm, or empire, [3] is the highest taxonomic rank of organisms in the three-domain system of taxonomy devised by Carl Woese et al. in 1990. [1]

Contents

According to this system, the tree of life consists of three domains: Archaea, Bacteria, and Eukarya. [1] The first two are all prokaryotic microorganisms, or mostly single-celled organisms whose cells have a distorted or non-membrane bound nucleus. All life that has a cell nucleus and eukaryotic membrane-bound organelles is included in Eukarya.

Non-cellular life 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, and Eukarya included within 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. [2]

Characteristics of the three domains

A speculatively rooted tree for RNA genes, showing major branches Bacteria, Archaea, and Eukaryota Phylogenetic tree.svgAquifexThermotogaPlanctomycesGreen filantous bacteriaPyrodicticumThermococcus celerMethanobacteriumHalophiles
A speculatively rooted tree for RNA genes, showing major branches Bacteria, Archaea, and Eukaryota
The three-domains tree and the Eocyte hypothesis (Two domains tree), 2008. Two domain tree.png
The three-domains tree and the Eocyte hypothesis (Two domains tree), 2008.
Phylogenetic tree showing the relationship between the eukaryotes and other forms of life, 2006 Eukaryotes are colored red, archaea green, and bacteria blue. Collapsed tree labels simplified.png
Phylogenetic tree showing the relationship between the eukaryotes and other forms of life, 2006 Eukaryotes are colored red, archaea green, and bacteria blue.

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 membrane, distinct biochemical and RNA markers differentiate the Archaea and Bacteria from each other. [1]

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 ability 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. [1]

Archaea evolved many cell sizes, but all are relatively small. Their size ranges from 0.1 μm to 15 μm diameter and up to 200 μm long. They are about the size of bacteria, or similar in size to the mitochondria found in eukaryotic cells. Members of the genus Thermoplasma are the smallest of the Archaea. [1]

Bacteria

Even though bacteria are prokaryotic cells just like Archaea, their membranes are made of phospholipid bilayers. Cyanobacteria and mycoplasmas are two examples of bacteria. They characteristically do not have ether linkages like Archaea, and they are grouped into a different category—and hence a different domain. There is a great deal of diversity in this domain. Confounded by that diversity and horizontal gene transfer, it is next to impossible to determine how many species of bacteria exist on the planet, or to organize them in a tree-structure, without cross-connections between branches. [1]

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, Chromista, and Fungi. [1]

Exclusion of viruses and prions

The three-domain system does not include any form of non-cellular life. Stefan Luketa proposed a five-domain system in 2012, adding Prionobiota (acellular and without nucleic acid) and Virusobiota (acellular but with nucleic acid) to the traditional three domains. [6]

Alternative classifications

Taxonomical root nodeTwo superdomains (controversial) Two empires Three domains Five Dominiums [7] Five kingdoms Six kingdoms Eocyte hypothesis
Biota / Vitae / Life Acytota / Aphanobionta - Non-cellular life Virusobiota (Viruses, Viroids)
Prionobiota (Prions)
Cytota
cellular life
Prokaryota / Procarya
(Monera)
Bacteria Bacteria Monera Eubacteria Bacteria
Archaea Archaea Archaebacteria Archaea including eukaryotes
Eukaryota / Eukarya Protista
Fungi
Plantae
Animalia

See also: Virus classification
Alternative classifications of life include:

See also

Related Research Articles

Microorganism Microscopic living organism

A microorganism, or microbe, is an organism of microscopic size, which may exist in its single-celled form or as a colony of cells.

Carl Woese Scientist who correctly proposed the existence of Archaea and horizontal gene transfer

Carl Richard Woese was an American microbiologist and biophysicist. Woese is famous for defining the Archaea in 1977 by phylogenetic taxonomy of 16S ribosomal RNA, a technique he pioneered that revolutionized microbiology. He also originated the RNA world hypothesis in 1967, although not by that name. Woese held the Stanley O. Ikenberry Chair and was professor of microbiology at the University of Illinois at Urbana–Champaign.

In biology, a kingdom is the second highest taxonomic rank, just below domain. Kingdoms are divided into smaller groups called phyla. Traditionally, some textbooks from the United States and Canada used a system of six kingdoms while textbooks in Great Britain, India, Greece, Brazil and other countries use five kingdoms only. Some recent classifications based on modern cladistics have explicitly abandoned the term kingdom, noting that some traditional kingdoms are not monophyletic, meaning that they do not consist of all the descendants of a common ancestor. The terms flora, fauna, and, in the 21st century, funga are also used for life present in a particular region or time.

Three-domain system Hypothesis for classification of life

The three-domain system is a biological classification introduced by Carl Woese et al. in 1990 that divides cellular life forms into archaea, bacteria, and eukaryote domains. The key difference from earlier classifications is the splitting of archaea from bacteria.

Last universal common ancestor Last recent common ancestor of all current life

The last universal common ancestor or last universal cellular ancestor (LUCA), also called the last universal ancestor (LUA), is the most recent population of organisms from which all organisms now living on Earth have a common descent—the most recent common ancestor of all current life on Earth. A related concept is that of progenote. LUCA is not thought to be the first life on Earth, but rather the latest that is ancestral to all current existing life.

Two-empire system

The two-empire system was the top-level biological classification system in general use before the establishment of the three-domain system. It classified cellular life into Prokaryota and Eukaryota as either "empires" or "superkingdoms". When the three-domain system was introduced, some biologists preferred the two-superkingdom system, claiming that the three-domain system overemphasized the division between Archaea and Bacteria. However, given the current state of knowledge and the rapid progress in biological scientific advancement, especially due to genetic analyses, that view has all but vanished.

In taxonomy, the Thermoplasmata are a class of the Euryarchaeota.

Tree of life (biology) Metaphor for the relationship between species of organisms

The tree of life or universal tree of life is a metaphor, model and research tool used to explore the evolution of life and describe the relationships between organisms, both living and extinct, as described in a famous passage in Charles Darwin's On the Origin of Species (1859).

The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth.

Neomura

Neomura is a possible clade composed of the two domains of life of Archaea and Eukaryota. The group was named by Thomas Cavalier-Smith in 2002. Its name means "new walls", reflecting his hypothesis that it evolved from Bacteria, and one of the major changes was the replacement of peptidoglycan cell walls with other glycoproteins. As of August 2017, the neomuran hypothesis is not accepted by most workers; molecular phylogenies suggest that eukaryotes are most closely related to one group of archaeans and evolved from them, rather than forming a clade with all archaeans.

Monera Biological kingdom that contains unicellular organisms with a prokaryotic cell organization

Monera (/məˈnɪərə/) is a biological kingdom that is made up of prokaryotes. As such, it is composed of single-celled organisms that lack a true nucleus.

Prokaryote Unicellular organism that lacks a membrane-bound nucleus

A prokaryote is a single-celled organism that lacks a nucleus, and other membrane-bound organelles. The word prokaryote comes from the Greek πρό and κάρυον. In the two-empire system arising from the work of Édouard Chatton, prokaryotes were classified within the empire Prokaryota. But in the three-domain system, based upon molecular analysis, prokaryotes are divided into two domains: Bacteria and Archaea. Organisms with nuclei are placed in a third domain, Eukaryota. In the study of the origins of life, prokaryotes are thought to have arisen before eukaryotes.

Archaea Domain of single-celled organisms

Archaea constitute a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this term has fallen out of use.

Horizontal gene transfer in evolution Evolutionary consequences of transfer of genetic material between organisms of different taxa

Scientists trying to reconstruct evolutionary history have been challenged by the fact that genes can sometimes transfer between distant branches on the tree of life. This movement of genes can occur through horizontal gene transfer (HGT), scrambling the information on which biologists relied to reconstruct the phylogeny of organisms. Conversely, HGT can also help scientists to reconstruct and date the tree of life. Indeed, a gene transfer can be used as a phylogenetic marker, or as the proof of contemporaneity of the donor and recipient organisms, and as a trace of extinct biodiversity.

Eukaryote Domain of life having cells with nuclei

Eukaryotes are organisms whose cells have a nucleus enclosed within a nuclear envelope. Eukaryotes belong to the domain Eukaryota or Eukarya; their name comes from the Greek εὖ and κάρυον. The domain Eukaryota makes up one of the three domains of life; bacteria and archaea make up the other two domains. The eukaryotes are usually now regarded as having emerged in the Archaea or as a sister of the now cultivated Asgard archaea. Eukaryotes represent a small minority of the number of organisms; however, due to their generally much larger size, their collective global biomass is estimated to be about equal to that of prokaryotes. Eukaryotes emerged approximately 2.1–1.7 billion years ago, during the Proterozoic eon, likely as flagellated phagotrophs.

Evolution of cells Evolutionary origin and subsequent development of cells

Evolution of cells refers to the evolutionary origin and subsequent evolutionary development of cells. Cells first emerged at least 3.8 billion years ago, approximately 750 million years after Earth was formed.

Eocyte hypothesis Hypothesis in evolutionary biology

The eocyte hypothesis is a biological classification that indicates eukaryotes emerged within the prokaryotic Crenarchaeota, a phylum within the archaea. This hypothesis was originally proposed by James A. Lake and colleagues in 1984 based on the discovery that the shapes of ribosomes in the Crenarchaeota and eukaryotes are more similar to each other than to either bacteria or the second major phylum of archaea, the Euryarchaeota.

The Woeseian revolution was the progression of the phylogenetic tree of life concept from two main divisions, known as the Prokarya and Eukarya, into three domains now classified as Bacteria, Archaea, and Eukaryotes. The discovery of the new domain stemmed from the work of biophysicist Carl Woese in 1977 from a principle of evolutionary biology designated as Woese's dogma. It states that the evolution of ribosomal RNA (rRNA) was a necessary precursor to the evolution of modern life forms. Although the three-domain system has been widely accepted, the initial introduction of Woese’s discovery received criticism from the scientific community.

Lokiarchaeota is a proposed phylum of the Archaea. The phylum includes all members of the group previously named Deep Sea Archaeal Group (DSAG), also known as Marine Benthic Group B (MBG-B). A phylogenetic analysis disclosed a monophyletic grouping of the Lokiarchaeota with the eukaryotes. The analysis revealed several genes with cell membrane-related functions. The presence of such genes support the hypothesis of an archaeal host for the emergence of the eukaryotes; the eocyte-like scenarios.

The biological classification system of life introduced by British zoologist Thomas Cavalier-Smith involves systematic arrangements of all life forms on earth. Following and improving the classification systems introduced by Carl Linnaeus, Ernst Haeckel, Robert Whittaker, and Carl Woese, Cavalier-Smith's classification attempts to incorporate the latest developments in taxonomy. His classification has been a major foundation in modern taxonomy, particularly with revisions and reorganisations of kingdoms and phyla.

Darwinian threshold Period during the evolution of the first cells

Darwinian threshold or Darwinian transition is a term introduced by Carl Woese to describe a transition period during the evolution of the first cells when genetic transmission moves from a predominantly horizontal mode to a vertical mode. The process starts when the ancestors of the Last Universal Common Ancestor become refractory to horizontal gene transfer (HGT) and become individual entities with vertical heredity upon which natural selection is effective. After this transition, life is characterized by genealogies that have a modern tree-like phylogeny.

References

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