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The two-domain system is a
biological classification
In biology, taxonomy () is the scientific study of naming, defining ( circumscribing) and classifying groups of biological organisms based on shared characteristics. Organisms are grouped into taxa (singular: taxon) and these groups are given ...
by which all organisms in the
tree of life
The tree of life is a fundamental archetype in many of the world's mythological, religious, and philosophical traditions. It is closely related to the concept of the sacred tree.Giovino, Mariana (2007). ''The Assyrian Sacred Tree: A History ...
are classified into two big
domains,
Bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
and
Archaea
Archaea ( ; singular archaeon ) is 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 (in the Archaebac ...
.
It emerged from development in the knowledge of archaea diversity and challenge over the widely accepted
three-domain system
The three-domain system is a biological classification introduced by Carl Woese, Otto Kandler, and Mark Wheelis in 1990 that divides cellular life forms into three domains, namely Archaea, Bacteria, and Eukaryota or Eukarya. The key difference fr ...
that defines life into Bacteria, Archaea, and
Eukarya
Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...
.
It was predicted by the
eocyte hypothesis
The eocyte hypothesis in evolutionary biology proposes the origin of eukaryotes from a group of prokaryotes called eocytes (later classified as Thermoproteota, a group of archaea). After his team at the University of California, Los Angeles disc ...
of
James A. Lake in the 1980s,
which was largely superseded by the three-domain system due to better compelling evidences at the time.
Better understanding of archaea, especially in their roles in the origin of eukaryotes by
symbiogenesis
Symbiogenesis (endosymbiotic theory, or serial endosymbiotic theory,) is the leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms. The theory holds that mitochondria, plastids such as chloroplasts, and possi ...
with bacteria, led to the revival of the eocyte hypothesis in the 2000s. The two-domain system became widely appreciated after the discovery of a large group (
superphylum) of archaea called
Asgard
In Nordic mythology, Asgard (Old Norse: ''Ásgarðr'' ; "enclosure of the Æsir") is a location associated with the gods. It appears in a multitude of Old Norse sagas and mythological texts. It is described as the fortified home of the Æsir ...
in 2017,
evidences of which suggest to be the evolutionary root of eukaryotes – implying that eukaryotes are members of the domain Archaea.
While the features of Asgard archaea do not directly rule out the three-domain system,
the notion that eukaryotes originated from archaea and thus belong to Archaea has been strengthened by genetic and proteomic studies.
Under the three-domain system, Eukarya is mainly distinguished by the presence of "eukaryotic signature proteins" that are not found in archaea and bacteria. However, Asgards are found to contain genes that codes for several of such unique proteins, indicating that the proteins originated in archaea.
Background
Classification of life into two main divisions is not new and the first was by a French biologist
Édouard Chatton
Édouard Chatton (; 11 October 1883 – 23 April 1947) was a French biologist who first characterized the distinction between the prokaryotic and eukaryotic cellular types. Chatton coined the terms and published them first in his 1937 paper
' ...
. In 1938, Chatton gave a broad distinction of organisms:
# Procaryotes (that include bacteria)
# Eucaryotes (that include protozoans)
These were later named empires, and Chatton's classification as the
two-empire system
The two-empire system (two-superkingdom 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 ...
. Chatton used the name Eucaryotes only for protozoans, excluded other eukaryotes, and published in limited circulation so that his work was not recognised. His classification was rediscovered by Canadian bacteriologist
Roger Yates Stanier of the
University of California in Berkeley
The University of California, Berkeley (UC Berkeley, Berkeley, Cal, or California) is a public land-grant research university in Berkeley, California. Established in 1868 as the University of California, it is the state's first land-grant univ ...
in 1961 while staying at the
Pasteur Institute
The Pasteur Institute (french: Institut Pasteur) is a French non-profit private foundation dedicated to the study of biology, micro-organisms, diseases, and vaccines. It is named after Louis Pasteur, who invented pasteurization and vaccines f ...
in Paris.
The next year, Stanier and his colleague
Cornelis Bernardus van Niel
Cornelis Bernardus van Niel (also known as Kees van Niel) (November 4, 1897 – March 10, 1985) was a Dutch-American microbiologist. He introduced the study of general microbiology to the United States and made key discoveries explaining t ...
published in ''Archiv für Mikrobiologie'' (now ''
Archives of Microbiology'') Chatton's classification with Eucaryotes eloborated to include higher algae, protozoans, fungi, plants and animals. It became a popular system of classification, as John O. Corliss wrote in 1986: "
heChatton-Stanier concept of a
kingdom
Kingdom commonly refers to:
* A monarchy ruled by a king or queen
* Kingdom (biology), a category in biological taxonomy
Kingdom may also refer to:
Arts and media Television
* ''Kingdom'' (British TV series), a 2007 British television drama s ...
(better, superkingdom) Prokaryota for bacteria (in the broadest sense) and a second superkingdom Eukaryota for all other organisms has been widely accepted with enthusiasm."
In 1977,
Carl Woese
Carl Richard Woese (; July 15, 1928 – December 30, 2012) was an American microbiologist and biophysicist. Woese is famous for defining the Archaea (a new domain of life) in 1977 through a pioneering phylogenetic taxonomy of 16S ribosomal RNA, ...
and
George E. Fox
George Edward Fox (born December 17, 1945) is an astrobiologist, a Professor Emeritus and researcher at the University of Houston. He is an elected fellow of the American Academy of Microbiology, the American Association for the Advancement of Sc ...
classified prokaryotes into two groups (kingdoms), Archaebacteria (for
methanogens
Methanogens are microorganisms that produce methane as a metabolic byproduct in hypoxic conditions. They are prokaryotic and belong to the domain Archaea. All known methanogens are members of the archaeal phylum Euryarchaeota. Methanogens are comm ...
, the first known archaea) and Eubacteria, based on their
16S ribosomal RNA
16 S 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 rRNA ...
(16S rRNA) genes.
In 1984,
James A. Lake, Michael W. Clark,
Eric Henderson
Eric Charles Henderson (born January 8, 1983) is an American football coach who is the defensive line coach and run game coordinator for the Los Angeles Rams of the National Football League (NFL). He previously served as an assistant coach for ...
, and Melanie Oakes of the
University of California, Los Angeles
The University of California, Los Angeles (UCLA) is a public land-grant research university in Los Angeles, California. UCLA's academic roots were established in 1881 as a teachers college then known as the southern branch of the California St ...
described what was known as "a group of sulfur-dependent bacteria" as new group of organisms called eocytes (for "dawn cells") and created a new kingdom Eocyta. With it they proposed the existence of four kingdoms, based on the structure and composition of the ribosomal subunits, namely Archaebacteria, Eubacteria, Eukaryote and Eocyta
Lake further analyses the rRNA sequences of the four groups and noted that eukaryotes originated from eocytes and not archaebacteria, as was generally assumed. This was the basis of the
eocyte hypothesis
The eocyte hypothesis in evolutionary biology proposes the origin of eukaryotes from a group of prokaryotes called eocytes (later classified as Thermoproteota, a group of archaea). After his team at the University of California, Los Angeles disc ...
.
In 1988, he proposed the division of all life forms into two taxonomic groups:
# Karyotes (that include eukaryotes and proto-eukaryotic organisms such as eocytes)
# Parkaryotes (that consist of eubacteria and archaea such as
halobacteria
Haloarchaea (halophilic archaea, halophilic archaebacteria, halobacteria) are a class of the Euryarchaeota, found in water saturated or nearly saturated with salt. Halobacteria are now recognized as archaea rather than bacteria and are one of th ...
and methanogens)
In 1990, Woese,
Otto Kandler
Otto Kandler (23 October 1920 in Deggendorf – 29 August 2017 in Munich, Bavaria)
was a German botanist and microbiologist. Until his retirement in 1986 he was professor of botany at the Ludwig Maximilian University of Munich.
His most importa ...
and
Mark Wheelis Mark L. Wheelis is an American microbiologist. Wheelis is currently a professor in the College of Biological Sciences, University of California, Davis. Carl Woese and Otto Kandler with Wheelis wrote the important paper '' Towards a natural system o ...
showed that archaea are distinct group of organisms and that eocytes (which was renamed Crenarchaeota as a phylum of Archaea
but corrected as
Thermoproteota
The Thermoproteota (also known as crenarchaea) are archaea that have been classified as a phylum of the Archaea domain. Initially, the Thermoproteota were thought to be sulfur-dependent extremophiles but recent studies have identified characteris ...
in 2021) are one of them. They introduced the major division of life as domains and introduced the
three-domain system
The three-domain system is a biological classification introduced by Carl Woese, Otto Kandler, and Mark Wheelis in 1990 that divides cellular life forms into three domains, namely Archaea, Bacteria, and Eukaryota or Eukarya. The key difference fr ...
that comprises domain Eucarya, domain Bacteria and domain Archaea.
With a number of revisions in the details and discoveries of several new archaea, Woese's classification gradually gained acceptance as "arguably the best-developed and most widely-accepted scientific hypotheses
ith the five-kingdom classificationregarding the evolutionary history of life."
But the three-domain concept did not resolve the issues with the relationship between archaea and eukaryotes.
As
Ford Doolittle
W. Ford Doolittle (born February 21, 1942, in Urbana, Illinois) is an evolutionary and molecular biologist. He is a member of the US National Academy of Sciences and a Fellow of the Royal Society of Canada and the Norwegian Academy of Science a ...
, then at the Dalhousie University, put it in 2020: "
hethree-domain tree wrongly represents evolutionary relationships, presenting a misleading view about how eukaryotes evolved from prokaryotes. The three-domain tree ''does'' recognize a specific archaeal–eukaryotic affinity, but it would have the latter arising independently, not from within, the former."
Concept
The two-domain systems relies mainly on two key concepts that define eukaryotes as members of the domain Archaea and not as a separate domain: eukaryotes originated within Archaea, and Asgards represent the origin of eukaryotes.
Eukaryotes evolved from archaea
The three-domain system presumes that eukaryotes are more closely related to archaea than to bacteria and are sister group to archaea, thus, it treats them as separate domain. As more new archaea were discovered in the early 2000s, this distinction became doubtful as eukaryotes became deeper linked to archaea. The origin of eukaryotes from archaea, meaning the two are of the same group, came to be supported by studies based on ribosome protein sequencing and phylogenetic analyses in 2004.
Phylogenomic
Phylogenomics is the intersection of the fields of evolution and genomics. The term has been used in multiple ways to refer to analysis that involves genome data and evolutionary reconstructions. It is a group of techniques within the larger fields ...
analysis of about 6000 gene sets from 185 bacterial, archaeal and eukaryotic genomes in 2007 also suggested origin of eukaryotes from
Euryarchaeota
Euryarchaeota (from Ancient Greek ''εὐρύς'' eurús, "broad, wide") is a phylum of archaea. Euryarchaeota are highly diverse and include methanogens, which produce methane and are often found in intestines, halobacteria, which survive extre ...
(specifically the
Thermoplasmatales
In alpha taxonomy, taxonomy, the Thermoplasmatales are an order (biology), order of the Thermoplasmata. All are acidophiles, growing optimally at pH below 2. ''Picrophilus'' is currently the most acidophile, acidophilic of all known organisms, b ...
).
In 2008, researchers from
Natural History Museum, London
The Natural History Museum in London is a museum that exhibits a vast range of specimens from various segments of natural history. It is one of three major museums on Exhibition Road in South Kensington, the others being the Science Museum an ...
and
Newcastle University
Newcastle University (legally the University of Newcastle upon Tyne) is a UK public university, public research university based in Newcastle upon Tyne, North East England. It has overseas campuses in Singapore and Malaysia. The university is ...
reported a comprehensive analysis of 53 genes from archaea, bacteria and eukaryotes that included essential components of the nucleic acid replication, transcription, and translation machineries. The conclusion was that eukaryotes evolved from archaea, specifically Crenarchaeota (eocytes) and the results "favor a topology that supports the eocyte hypothesis rather than archaebacterial monophyly and the 3-domains tree of life."
A study around the same time also found several genes that are common to eukaryotes and archaea within the Crenarchaeota. These accumulating evidences support the two-domain system.
One of the distinctions of the domain Eukarya in the three-domain system is that eukaryotes have unique proteins such as
actin
Actin is a family of globular multi-functional proteins that form microfilaments in the cytoskeleton, and the thin filaments in muscle fibrils. It is found in essentially all eukaryotic cells, where it may be present at a concentration of over ...
(
cytoskeletal
The cytoskeleton is a complex, dynamic network of interlinking protein filaments present in the cytoplasm of all cells, including those of bacteria and archaea. In eukaryotes, it extends from the cell nucleus to the cell membrane and is compo ...
microfilament
Microfilaments, also called actin filaments, are protein filaments in the cytoplasm of eukaryotic cells that form part of the cytoskeleton. They are primarily composed of polymers of actin, but are modified by and interact with numerous other pr ...
involved in cell motility),
tubulin
Tubulin in molecular biology can refer either to the tubulin protein superfamily of globular proteins, or one of the member proteins of that superfamily. α- and β-tubulins polymerize into microtubules, a major component of the eukaryotic cytoske ...
(component of the large cytoskeleton,
microtubule
Microtubules are polymers of tubulin that form part of the cytoskeleton and provide structure and shape to eukaryotic cells. Microtubules can be as long as 50 micrometres, as wide as 23 to 27 nm and have an inner diameter between 11 an ...
) and the
ubiquitin
Ubiquitin is a small (8.6 kDa) regulatory protein found in most tissues of eukaryotic organisms, i.e., it is found ''ubiquitously''. It was discovered in 1975 by Gideon Goldstein and further characterized throughout the late 1970s and 1980s. Fo ...
system (protein degradation and recycling) that are not found in prokaryotes. However, these so-called "eukaryotic signature proteins"
are present in TACK (comprising the phyla
Thaumarchaeota
The Nitrososphaerota (syn. Thaumarchaeota) are a phylum of the Archaea proposed in 2008 after the genome of ''Cenarchaeum symbiosum'' was sequenced and found to differ significantly from other members of the hyperthermophilic phylum Thermoproteo ...
,
Aigarchaeota
The "Aigarchaeota" are a proposed archaeal phylum of which the main representative is '' Caldiarchaeum subterraneum''.. It is not yet clear if this represents a new phylum or a and order of the Nitrososphaerota, since the genome of ''Caldiarchaeu ...
, Crenarchaeota and
Korarchaeota
In taxonomy, the Korarchaeota are a phylum of the Archaea. The name is derived from the Greek noun koros or kore, meaning ''young man'' or ''young woman,'' and the Greek adjective archaios which means ''ancient.'' They are also known as Xenarchae ...
) archaea but not in other archaea as indicated by genes that codes for such proteins.
The first eukaryotic protein identified was actin and actin-related proteins (Arp) 2 and 3 in Crenarchaeota. The implication is that that it explains the possible process of
phagocytosis
Phagocytosis () is the process by which a cell uses its plasma membrane to engulf a large particle (≥ 0.5 μm), giving rise to an internal compartment called the phagosome. It is one type of endocytosis. A cell that performs phagocytosis is ...
by which an ancient archaeal host eats other cells like bacteria to give rise to the first eukaryote by symbiogenesis.
Tubulin-like proteins named artubulins are found in the genomes of several ammonium-oxidising Thaumarchaeota. A protein called endosomal sorting complexes required for transport (
ESCRT The endosomal sorting complexes required for transport (ESCRT) machinery is made up of cytosolic protein complexes, known as ESCRT-0, ESCRT-I, ESCRT-II, and ESCRT-III. Together with a number of accessory proteins, these ESCRT complexes enable a un ...
III) that is involved in eukaryotic cell division were found in all TACK groups. The ESCRT-III-like proteins constitute the primary cell division system in these archaea. Genes of the ubiquitin system are known from multiple genomes of Aigarchaeota. Ubiquitin-related protein called Urm1 is also present in Crenarchaeota. DNA replication system (GINS proteins) in Crenarchaeota and Halobacteria are similar to the CMG (CDC45, MCM, GINS) complex of eukaryotes. The presence of these eukaryotic proteins in archaea indicates their direct relationship and that eukaryotes emerged from archaea.
Asgards are the last eukaryotic common ancestor
The discovery of Asgard, described as "eukaryote-like archaea",
in 2012 and the following phylogenetic analyses have strengthened the two-domain view of life.
These archaea called
Lokiarchaeota
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). Lokiarchaeota is part of the superphylum Asgard contai ...
contain more eukaryotic protein-genes than the TACK group. Initial genetic analysis and later reanalysis showed that out of over 31 selected eukaryotic genes in the archaea, 75% of them directly support eukaryote-archaea grouping, meaning a single domain of Archaea; although the findings did not completely rule out the three-domain system.
As more Asgard groups were subsequently discovered including
Thorarchaeota
"''Candidatus'' Thorarchaeota", or simply Thorarchaeota, is a phylum within the superphylum Asgard archaea. The Asgard superphylum represents the closest prokaryotic relatives of eukaryotes. Since there is such a close relation between the two ...
,
Odinarchaeota
Asgard or Asgardarchaeota is a proposed superphylum consisting of a group of archaea that includes Lokiarchaeota, Thorarchaeota, Odinarchaeota, and Heimdallarchaeota. It appears the eukaryotes emerged within the Asgard, in a branch containing th ...
and Heimdallarchaeota, their relationships with eukaryotes became better established. Phylogenetic analyses using ribosomal RNA genes indicated that eukaryotes stemmed from Asgards, and that Heimdallarchaeota are the closest relatives of eukaryotes.
Eukaryotic origin from Heimdallarchaeota is also supported by phylogenomic study in 2020.
A new group of Asgard found in 2021 (provisionally named Wukongarchaeota) also indicated a deep root for eukaryotic origin. A report in 2022 of another Asgard, named Njordarchaeota, indicates that Heimdallarchaeota-Wukongarchaeota branch is possibly the origin group for eukaryotes.
The Asgards contain at least 80 genes for eukaryotic signature proteins. In addition to actin, tubulin, ubiquitin and ESCRT proteins found in TACK archaea, Asgards contain functional genes for several other eukaryotic proteins such as
profilins, unbiquitin system (E1-like, E2-like and small-RING finger (srfp) proteins), membrane-trafficking systems (such as Sec23/24 and TRAPP domains), variety of small
GTPases
GTPases are a large family of hydrolase enzymes that bind to the nucleotide guanosine triphosphate (GTP) and hydrolyze it to guanosine diphosphate (GDP). The GTP binding and hydrolysis takes place in the highly conserved P-loop "G domain", a pro ...
(including Gtr/Rag family GTPase orthologues), and
gelsolins. Although these information do not completely resolve the three-domain and two-domain controversies,
they are generally considered favouring the two-domain system.
Classification
The two-domain system defines classification of all known cellular life forms into two domains: Bacteria and Archaea. It overrides the domain Eukaryota recognised in the three-domain classification as one of the main domains. In contrast to the eocyte hypothesis, which proposed two major groups of life (similar to domains) and posited that archaea could be divided to both bacterial and eukaryotic groups, it merged archaea and eukaryotes into a single domain, bacteria entirely in a separate domain.
Domain Bacteria
It consists entirely of all bacteria. All bacteria are prokaryotes (lacking nucleus), thus, the domain is made up of prokaryotic organisms. Some examples are:
*
Cyanobacteria
Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, blu ...
– photosynthesising bacteria that are related to the plastids of eukaryotes.
*
Spirochaetota
A spirochaete () or spirochete is a member of the phylum Spirochaetota (), (synonym Spirochaetes) which contains distinctive diderm (double-membrane) gram-negative bacteria, most of which have long, helically coiled (corkscrew-shaped or ...
–
Gram-negative
Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wall ...
bacteria that are involved in human diseases like syphilis and lyme disease.
*
Actinomycetota
The ''Actinomycetota'' (or ''Actinobacteria'') are a phylum of all gram-positive bacteria. They can be terrestrial or aquatic. They are of great economic importance to humans because agriculture and forests depend on their contributions to soi ...
–
Gram-positive
In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall.
Gram-positive bacte ...
bacteria including ''
Streptomyces
''Streptomyces'' is the largest genus of Actinomycetota and the type genus of the family Streptomycetaceae. Over 500 species of ''Streptomyces'' bacteria have been described. As with the other Actinomycetota, streptomycetes are gram-positive, ...
'' species from which several antibiotics were discovered including
streptomycin
Streptomycin is an antibiotic medication used to treat a number of bacterial infections, including tuberculosis, ''Mycobacterium avium'' complex, endocarditis, brucellosis, ''Burkholderia'' infection, plague, tularemia, and rat bite fever. Fo ...
,
neomycin
Neomycin is an aminoglycoside antibiotic that displays bactericidal activity against gram-negative aerobic bacilli and some anaerobic bacilli where resistance has not yet arisen. It is generally not effective against gram-positive bacilli and ...
,
bottromycin
Bottromycin is a macrocyclic peptide with antibiotic activity. It was first discovered in 1957 as a natural product isolated from '' Streptomyces bottropensis''. It has been shown to inhibit methicillin-resistant ''Staphylococcus aureus'' (MRSA) ...
s and
chloramphenicol
Chloramphenicol is an antibiotic useful for the treatment of a number of bacterial infections. This includes use as an eye ointment to treat conjunctivitis. By mouth or by injection into a vein, it is used to treat meningitis, plague, cholera, a ...
.
Domain Archaea
It comprises both prokaryotic and eukaryotic organisms.
Archaea
Archaea are prokaryotic organisms and some examples are:
* All
methanogens
Methanogens are microorganisms that produce methane as a metabolic byproduct in hypoxic conditions. They are prokaryotic and belong to the domain Archaea. All known methanogens are members of the archaeal phylum Euryarchaeota. Methanogens are comm ...
– which produce the gas
methane
Methane ( , ) is a chemical compound with the chemical formula (one carbon atom bonded to four hydrogen atoms). It is a group-14 hydride, the simplest alkane, and the main constituent of natural gas. The relative abundance of methane on Eart ...
.
* Most
halophiles
The halophiles, named after the Greek word for "salt-loving", are extremophiles that thrive in high salt concentrations. While most halophiles are classified into the domain Archaea, there are also bacterial halophiles and some eukaryotic species, ...
– which live in very salty water.
* Most
thermoacidophiles – which live in acidic high-temperature water.
Eukarya
Eukaryotes are those having nucleus in their cells, and are classified into four groups:
*
Protists
A protist () is any eukaryotic organism (that is, an organism whose cells contain a cell nucleus) that is not an animal, plant, or fungus. While it is likely that protists share a common ancestor (the last eukaryotic common ancestor), the excl ...
– an informal taxon for unicellular eukaryotes that include malarial parasites, amoeba, and diatoms.
* Kingdom Fungi – multicellular eukaryotes such as mushroom, yeast, and mould.
* Kingdom Plantae – all plants.
* Kingdom Animalia – all animals.
References
{{Reflist
Biological classification
High-level systems of taxonomy
Domains (biology)