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Archaea ( ; singular archaeon ) constitute a
domain Domain may refer to: Mathematics *Domain of a function, the set of input values for which the (total) function is defined **Domain of definition of a partial function **Natural domain of a partial function **Domain of holomorphy of a function *Doma ...
of single-celled organisms. These
microorganism A microorganism, or microbe,, ''mikros'', "small") and ''organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes ...
s lack
cell nuclei In cell biology Cell biology (also cellular biology or cytology) is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical process ...
and are therefore
prokaryotes A prokaryote () is a single-celled organism A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contig ...

prokaryotes
. Archaea were initially classified as
bacteria Bacteria (; common noun bacteria, singular bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typ ...

bacteria
, receiving the name archaebacteria (in the Archaebacteria
kingdom Kingdom may refer to: Monarchy * A type of monarchy * A realm ruled by: **A king, during the reign of a male monarch **A queen regnant, during the reign of a female monarch Taxonomy * Kingdom (biology), a category in biological taxonomy Arts an ...
), but this term has fallen out of use. Archaeal cells have unique properties separating them from the other two domains,
Bacteria Bacteria (; common noun bacteria, singular bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typ ...

Bacteria
and
Eukaryota Eukaryotes () are organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interact ...

Eukaryota
. Archaea are further divided into multiple recognized phyla. Classification is difficult because most have not been isolated in a laboratory and have been detected only by their
gene sequences
gene sequences
in environmental samples. Archaea and bacteria are generally similar in size and shape, although a few archaea have very different shapes, such as the flat and square cells of ''
Haloquadratum walsbyi ''Haloquadratum walsbyi'' is a species of archaea which was discovered in a brine pool in the Sinai peninsula of Egypt. It is noted for both its flat, square-shaped cells, and its unusual ability to survive in aqueous environments with high conc ...
''. Despite this morphological similarity to bacteria, archaea possess
gene In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mecha ...

gene
s and several
metabolic pathway In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell (biology), cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence ...
s that are more closely related to those of eukaryotes, notably for the
enzyme Enzymes () are proteins that act as biological catalysts (biocatalysts). Catalysts accelerate chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates in ...

enzyme
s involved in transcription and
translation Translation is the communication of the meaning Meaning most commonly refers to: * Meaning (linguistics), meaning which is communicated through the use of language * Meaning (philosophy), definition, elements, and types of meaning discusse ...

translation
. Other aspects of archaeal biochemistry are unique, such as their reliance on
ether lipid. Note ether at first and second positions. . Note ether at first position, and ester at second position. Image:Platelet-activating factor.svg, Platelet-activating factor. Note ether at first position, and acetyl group at second position. In an or ...

ether lipid
s in their
cell membrane The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane A biological membrane, biomembrane or cell membrane is a selectively permeable membra ...

cell membrane
s, including
archaeol
archaeol
s. Archaea use more energy sources than eukaryotes: these range from
organic compounds In chemistry Chemistry is the study of the properties and behavior of . It is a that covers the that make up matter to the composed of s, s and s: their composition, structure, properties, behavior and the changes they undergo during ...
, such as sugars, to
ammonia Ammonia is a chemical compound, compound of nitrogen and hydrogen with the chemical formula, formula NH3. A Binary compounds of hydrogen, stable binary hydride, and the simplest pnictogen hydride, ammonia is a colourless gas with a distinct ch ...

ammonia
,
metal ions A metal (from Greek Greek may refer to: Greece Anything of, from, or related to Greece Greece ( el, Ελλάδα, , ), officially the Hellenic Republic, is a country located in Southeast Europe. Its population is approximately 10.7 mil ...
or even
hydrogen gas Hydrogen is the chemical element Image:Simple Periodic Table Chart-blocks.svg, 400px, Periodic table, The periodic table of the chemical elements In chemistry, an element is a pure substance consisting only of atoms that all have the same ...

hydrogen gas
. Salt-tolerant archaea (the
Haloarchaea Haloarchaea (halophilic archaea, halophilic archaebacteria, halobacteria) are a class of the Euryarchaeota, found in water Water is an Inorganic compound, inorganic, Transparency and translucency, transparent, tasteless, odorless, and ...
) use sunlight as an energy source, and other species of archaea fix carbon, but unlike plants and
cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum In biology, a phylum (; plural The plural (sometimes list of glossing abbreviations, abbreviated ), in many languages, is one of the values of the grammatical number, grammatical ...

cyanobacteria
, no known species of archaea does both. Archaea reproduce asexually by
binary fission Binary may refer to: Science and technology Mathematics * Binary number In mathematics and digital electronics Digital electronics is a field of electronics The field of electronics is a branch of physics and electrical engineeri ...

binary fission
, fragmentation, or
budding Budding is a type of asexual reproduction Asexual reproduction is a type of reproduction Reproduction (or procreation or breeding) is the biological process by which new individual organism In biology, an organism (from Ancient Gr ...

budding
; unlike bacteria, no known species of Archaea form
endospore An endospore is a dormant, tough, and non-reproductive structure produced by some bacteria Bacteria (; common noun bacteria, singular bacterium) are a type of Cell (biology), biological cell. They constitute a large domain (biology), dom ...
s. The first observed archaea were
extremophile An extremophile (from Latin ' meaning "extreme" and Greek ' () meaning "love") is an organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contiguous system that embodies the ...
s, living in extreme environments, such as
hot spring A hot spring, hydrothermal spring, or geothermal spring is a spring Spring(s) may refer to: Common uses * Spring (season), a season of the year * Spring (device), a mechanical device that stores energy * Spring (hydrology), a natural source of w ...

hot spring
s and
salt lake A salt lake or saline lake is a landlocked body of water (Lysefjord) in Norway Norway, officially the Kingdom of Norway,Names in the official and recognised languages: Bokmål Bokmål (, ; literally "book tongue") is an official wr ...

salt lake
s with no other organisms. Improved molecular detection tools led to the discovery of archaea in almost every
habitat In ecology Ecology (from el, οἶκος, "house" and el, -λογία, label=none, "study of") is the study of the relationships between living organisms, including humans, and their physical environment. Ecology considers at the ...

habitat
, including soil, oceans, and
marshland A marsh is a that is dominated by rather than species.Keddy, P.A. 2010. Wetland Ecology: Principles and Conservation (2nd edition). Cambridge University Press, Cambridge, UK. 497 p Marshes can often be found at the edges of lakes and stre ...

marshland
s. Archaea are particularly numerous in the oceans, and the archaea in
plankton Plankton are the diverse collection of organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology ...

plankton
may be one of the most abundant groups of organisms on the planet. Archaea are a major part of
Earth's life
Earth's life
. They are part of the
microbiota Microbiota are "ecological communities of commensal, symbiotic and pathogenic microorganisms A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usu ...
of all organisms. In the
human microbiome The human microbiome is the aggregate of all microbiota Microbiota are "ecological communities of commensal, symbiotic and pathogenic microorganisms A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ...
, they are important in the
gut
gut
, mouth, and on the skin. Their morphological, metabolic, and geographical diversity permits them to play multiple ecological roles: carbon fixation; nitrogen cycling; organic compound turnover; and maintaining microbial symbiotic and
syntrophicIn biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanisms, De ...
communities, for example. No clear examples of archaeal
pathogen In biology, a pathogen ( el, πάθος, "suffering", "passion" and , "producer of") in the oldest and broadest sense, is any organism that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a Germ theory ...
s or
parasite Parasitism is a Symbiosis, close relationship between species, where one organism, the parasite, lives on or inside another organism, the Host (biology), host, causing it some harm, and is adaptation (biology), adapted structurally to this w ...
s are known. Instead they are often
mutualists Mutualism describes the ecological Biological interaction, interaction between two or more species where each species has a net benefit. Mutualism is a common type of ecological interaction. Prominent examples include most vascular plants engage ...
or
commensals
commensals
, such as the
methanogen Methanogens are microorganisms that produce 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 n ...
s (methane-producing strains) that inhabit the
gastrointestinal tract The gastrointestinal tract (GI tract, digestive tract, alimentary canal) is the tract or passageway of the digestive system The human digestive system consists of the gastrointestinal tract The gastrointestinal tract, (GI tract, GIT, d ...
in humans and
ruminant Ruminants (suborder Ruminantia) are large ungulate, hoofed herbivorous grazing or browsing mammals that are able to acquire nutrients from plant-based food by Enteric fermentation, fermenting it in a specialized stomach prior to digestion, princi ...
s, where their vast numbers aid
digestion Digestion is the breakdown of large insoluble food Food is any substance consumed to provide Nutrient, nutritional support for an organism. Food is usually of plant, animal or Fungus, fungal origin, and contains essential nutrients, such a ...
. Methanogens are also used in
biogas Biogas is the mixture of gas Gas is one of the four fundamental states of matter In physics Physics is the natural science that studies matter, its Elementary particle, fundamental constituents, its Motion (physics), motion and ...

biogas
production and
sewage treatment Sewage treatment (or domestic wastewater treatment, municipal wastewater treatment) is a type of wastewater treatment Wastewater treatment is a process used to remove contaminants from wastewater or sewage Sewage, or domestic/municip ...
, and
biotechnology Biotechnology is a broad area of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Phy ...

biotechnology
exploits enzymes from extremophile archaea that can endure high temperatures and organic
solvents A solvent (from the Latin Latin (, or , ) is a classical language belonging to the Italic languages, Italic branch of the Indo-European languages. Latin was originally spoken in the area around Rome, known as Latium. Through the power of the ...
.


Classification


Early concept

For much of the 20th century, prokaryotes were regarded as a single group of organisms and classified based on their
biochemistry Biochemistry or biological chemistry, is the study of chemical process In a scientific Science () is a systematic enterprise that Scientific method, builds and organizes knowledge in the form of Testability, testable explanations and pr ...

biochemistry
,
morphology Morphology, from the Greek and meaning "study of shape", may refer to: Disciplines * Morphology (archaeology), study of the shapes or forms of artifacts * Morphology (astronomy), study of the shape of astronomical objects such as nebulae, galaxies ...
and
metabolism Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life Life is a characteristic that distinguishes physical entities A bubble of exhaled gas in water In common usage and classical mechanics, a phys ...

metabolism
. Microbiologists tried to classify microorganisms based on the structures of their
cell wall A cell wall is a structural layer surrounding some types of cells, just outside the cell membrane cell membrane vs. Prokaryotes The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to a ...
s, their shapes, and the substances they consume. In 1965,
Emile Zuckerkandl Émile Zuckerkandl (July 4, 1922 – November 9, 2013) was an Austrian-born French biologist considered one of the founders of the field of molecular evolution Molecular evolution is the process of change in the sequence composition of cellula ...
and
Linus Pauling Linus Carl Pauling (; February 28, 1901 – August 19, 1994) was an American chemist, biochemist, chemical engineer, peace activist, author, and educator. He published more than 1,200 papers and books, of which about 850 dealt with scientific t ...

Linus Pauling
instead proposed using the sequences of the
gene In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mecha ...

gene
s in different prokaryotes to work out how they are related to each other. This
phylogenetic In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanism ...

phylogenetic
approach is the main method used today. Archaea – at that time only the
methanogen Methanogens are microorganisms that produce 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 n ...
s were known – were first classified separately from bacteria in 1977 by
Carl Woese Carl Richard Woese (; July 15, 1928 – December 30, 2012) was an American microbiologist A microbiologist (from Greek ) is a scientist A scientist is a person who conducts Scientific method, scientific research to advance knowledge in an B ...

Carl Woese
and George E. Fox based on their
ribosomal RNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA A non-coding RNA (ncRNA) is an RNA Ribonucleic acid (RNA) is a polymer A polymer (; Greek '' poly-'', "many" + '' -mer'', "part") is a substance or material consis ...
(rRNA) genes. They called these groups the ''Urkingdoms'' of Archaebacteria and Eubacteria, though other researchers treated them as kingdoms or subkingdoms. Woese and Fox gave the first evidence for Archaebacteria as a separate "line of descent": 1. lack of
peptidoglycan Peptidoglycan or murein is a polymer A polymer (; Greek ''poly- Poly, from the Greek :wikt:πολύς, πολύς meaning "many" or "much", may refer to: Businesses * China Poly Group Corporation, a Chinese business group, and its subsidia ...

peptidoglycan
in their cell walls, 2. two unusual coenzymes, 3. results of
16S ribosomal RNA 16 S ribosomal RNA (or 16 S rRNA Ribosomal ribonucleic acid (rRNA) is a type of which is the primary component of s, essential to all cells. rRNA is a which carries out in ribosomes. Ribosomal RNA is transcribed from (rDNA) and then ...
gene sequencing. To emphasize this difference, Woese,
Otto Kandler Otto Kandler (23 October 1920 in Deggendorf - 29 August 2017 in Munich Munich ( ; german: München ; bar, Minga ) is the capital and most populous city of Bavaria. With a population of 1,558,395 inhabitants as of 31 July 2020, it is the ...
and
Mark WheelisMark L. Wheelis is an American microbiologist A microbiologist (from Greek ) is a scientist A scientist is a person who conducts Scientific method, scientific research to advance knowledge in an Branches of science, area of interest. In class ...
later proposed reclassifying organisms into three natural domains known as the
three-domain system The three-domain system is a biological classification In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, ...
: the
Eukarya Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy (biology), tax ...
, the
Bacteria Bacteria (; common noun bacteria, singular bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typ ...

Bacteria
and the Archaea, in what is now known as "The Woesian Revolution". The word ''archaea'' comes from the
Ancient Greek Ancient Greek includes the forms of the Greek language Greek ( el, label=Modern Greek Modern Greek (, , or , ''Kiní Neoellinikí Glóssa''), generally referred to by speakers simply as Greek (, ), refers collectively to the diale ...
, meaning "ancient things", as the first representatives of the domain Archaea were
methanogen Methanogens are microorganisms that produce 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 n ...
s and it was assumed that their metabolism reflected Earth's primitive atmosphere and the organisms' antiquity, but as new habitats were studied, more organisms were discovered. Extreme
halophilicThe 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 Eukaryote, eukaryotic ...
and
hyperthermophilic A hyperthermophile is an organism that thrives in extremely hot environments—from 60 °C (140 °F) upwards. An optimal temperature for the existence of hyperthermophiles is often above 80 °C (176 °F). Hyperthermophiles are often within the domai ...
microbes were also included in Archaea. For a long time, archaea were seen as extremophiles that exist only in extreme habitats such as
hot spring A hot spring, hydrothermal spring, or geothermal spring is a spring Spring(s) may refer to: Common uses * Spring (season), a season of the year * Spring (device), a mechanical device that stores energy * Spring (hydrology), a natural source of w ...

hot spring
s and
salt lake A salt lake or saline lake is a landlocked body of water (Lysefjord) in Norway Norway, officially the Kingdom of Norway,Names in the official and recognised languages: Bokmål Bokmål (, ; literally "book tongue") is an official wr ...

salt lake
s, but by the end of the 20th century, archaea had been identified in non-extreme environments as well. Today, they are known to be a large and diverse group of organisms abundantly distributed throughout nature. This new appreciation of the importance and ubiquity of archaea came from using
polymerase chain reaction Polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies (complete copies or partial copies) of a specific DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM. ...

polymerase chain reaction
(PCR) to detect prokaryotes from environmental samples (such as water or soil) by multiplying their ribosomal genes. This allows the detection and identification of organisms that have not been cultured in the laboratory.


Classification

The classification of archaea, and of prokaryotes in general, is a rapidly moving and contentious field. Current classification systems aim to organize archaea into groups of organisms that share structural features and common ancestors. These classifications rely heavily on the use of the sequence of
ribosomal RNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA A non-coding RNA (ncRNA) is an RNA Ribonucleic acid (RNA) is a polymer A polymer (; Greek '' poly-'', "many" + '' -mer'', "part") is a substance or material consis ...
genes to reveal relationships among organisms (
molecular phylogenetics Molecular phylogenetics () is the branch of phylogeny A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram A diagram is a symb ...
). Most of the culturable and well-investigated species of archaea are members of two main phyla, the
Euryarchaeota Euryarchaeota (Greek for "broad old quality") is a phylum In biology, a phylum (; plural The plural (sometimes list of glossing abbreviations, abbreviated ), in many languages, is one of the values of the grammatical number, grammatical ca ...
and
Crenarchaeota The Crenarchaeota (also known as Crenarchaea or eocytes) are archaea that have been classified as a phylum (biology), phylum of the Archaea domain. Initially, the Crenarchaeota were thought to be sulfur-dependent extremophiles but recent studies ...
. Other groups have been tentatively created, like the peculiar species '' Nanoarchaeum equitans'', which was discovered in 2003 and has been given its own phylum, the
Nanoarchaeota Nanoarchaeota (Greek, "dwarf or tiny ancient one") are a phylum (biology), phylum of the Archaea.See the National Center for Biotechnology Information, NCBI]webpage on Nanoarchaeota Data extracted from the This phylum currently has only one repr ...
. A new phylum
Korarchaeota In alpha taxonomy, taxonomy, the Korarchaeota are a phylum (biology), 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.' ...

Korarchaeota
has also been proposed. It contains a small group of unusual thermophilic species that shares features of both of the main phyla, but is most closely related to the Crenarchaeota. Other recently detected species of archaea are only distantly related to any of these groups, such as the Archaeal Richmond Mine acidophilic nanoorganisms (ARMAN, comprising
Micrarchaeota DPANN is a superphylum of Archaea first proposed in 2013. Many members show novel signs of horizontal gene transfer from other domains of life. They are known as nanoarchaea or ultra-small archaea due to their smaller size (nanometric) compared to ...
and Parvarchaeota), which were discovered in 2006 and are some of the smallest organisms known. A superphylum – TACK – which includes the
Thaumarchaeota The Thaumarchaeota or Thaumarchaea (from the grc, θαῦμα, thaûma, miracle) are a phylum In biology, a phylum (; plural The plural (sometimes list of glossing abbreviations, abbreviated ), in many languages, is one of the values of ...
,
Aigarchaeota The "Aigarchaeota" are a proposed archaea Archaea ( ; singular archaeon ) constitute a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria ...
,
Crenarchaeota The Crenarchaeota (also known as Crenarchaea or eocytes) are archaea that have been classified as a phylum (biology), phylum of the Archaea domain. Initially, the Crenarchaeota were thought to be sulfur-dependent extremophiles but recent studies ...
, and
Korarchaeota In alpha taxonomy, taxonomy, the Korarchaeota are a phylum (biology), 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.' ...

Korarchaeota
was proposed in 2011 to be related to the origin of eukaryotes. In 2017, the newly discovered and newly named
Asgard Asgard (Old Norse Old Norse, Old Nordic, or Old Scandinavian is a stage of development of North Germanic dialects before their final divergence into separate Nordic languages. Old Norse was spoken by inhabitants of Scandinavia S ...
superphylum was proposed to be more closely related to the original eukaryote and a sister group to TACK.


Cladogram

According to Tom A. Williams ''et al.'' (2017) and Castelle & Banfield (2018) (DPANN):


Concept of species

The classification of archaea into species is also controversial. Biology defines a
species In biology, a species is the basic unit of biological classification, classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individu ...

species
as a group of related organisms. The familiar exclusive breeding criterion (organisms that can breed with each other but not with others) is of no help since archaea only reproduce asexually. Archaea show high levels of
horizontal gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism (from Ancient G ...
between lineages. Some researchers suggest that individuals can be grouped into species-like populations given highly similar genomes and infrequent gene transfer to/from cells with less-related genomes, as in the genus '' Ferroplasma''. On the other hand, studies in '' Halorubrum'' found significant genetic transfer to/from less-related populations, limiting the criterion's applicability. Some researchers question whether such species designations have practical meaning. Current knowledge on genetic diversity is fragmentary and the total number of archaeal species cannot be estimated with any accuracy. Estimates of the number of phyla range from 18 to 23, of which only 8 have representatives that have been cultured and studied directly. Many of these hypothesized groups are known from a single rRNA sequence, indicating that the diversity among these organisms remains obscure. The Bacteria also include many uncultured microbes with similar implications for characterization.


Origin and evolution

The
age of the Earth The age of Earth is estimated to be 4.54 ± 0.05 1,000,000,000, billion years This age may represent the age of the Earth's accretion (astrophysics), accretion, or core formation, or of the material from which the Earth formed. This dating is b ...
is about 4.54 billion years. Scientific evidence suggests that life began on Earth at least 3.5  billion years ago. The earliest evidence for is
graphite Graphite (), archaically referred to as plumbago, is a Crystallinity, crystalline form of the element carbon with its atoms arranged in a Hexagonal crystal system, hexagonal structure. It occurs naturally in this form and is the most stable for ...

graphite
found to be
biogenic A biogenic substance is a product made by or of life forms. While the term originally was specific to metabolite compounds that had toxic effects on other organisms, it has developed to encompass any constituents, secretions, and metabolites of pl ...
in 3.7-billion-year-old
metasedimentary rocks In geology, metasedimentary rock is a type of metamorphic rock. Such a rock was first formed through the deposition and solidification of sediment. Then, the rock was buried underneath subsequent rock and was subjected to high pressures and tempera ...
discovered in Western Greenland and
microbial mat The cyanobacterial algal mat, salty lake on the White Sea">algal_mat.html" ;"title="cyanobacterial algal mat">cyanobacterial algal mat, salty lake on the White Sea seaside A microbial mat is a multi-layered sheet of microorganisms, mainly bacteria ...
fossils A fossil (from Classical Latin Classical Latin is the form of Latin language Latin (, or , ) is a classical language belonging to the Italic languages, Italic branch of the Indo-European languages. Latin was originally spoken in the a ...

fossils
found in 3.48-billion-year-old
sandstone Sandstone is a clastic sedimentary rock of a clast (sand grain), derived from a basalt Basalt (, ) is a fine-grained extrusive igneous rock formed from the rapid cooling of low-viscosity lava rich in magnesium and iron ('' mafic ' ...

sandstone
discovered in
Western Australia Western Australia (abbreviated as WA) is a state State may refer to: Arts, entertainment, and media Literature * ''State Magazine'', a monthly magazine published by the U.S. Department of State * The State (newspaper), ''The State'' (newspape ...

Western Australia
. In 2015, possible remains of biotic matter were found in 4.1-billion-year-old rocks in Western Australia. Although probable prokaryotic cell
fossils A fossil (from Classical Latin Classical Latin is the form of Latin language Latin (, or , ) is a classical language belonging to the Italic languages, Italic branch of the Indo-European languages. Latin was originally spoken in the a ...

fossils
date to almost 3.5  billion years ago, most prokaryotes do not have distinctive morphologies, and fossil shapes cannot be used to identify them as archaea. Instead, chemical fossils of unique
lipid In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanis ...
s are more informative because such compounds do not occur in other organisms. Some publications suggest that archaeal or eukaryotic lipid remains are present in shales dating from 2.7 billion years ago, though such data have since been questioned. These lipids have also been detected in even older rocks from west Greenland. The oldest such traces come from the Isua greenstone belt, Isua district, which includes Earth's oldest known sediments, formed 3.8 billion years ago. The archaeal lineage may be the most ancient that exists on Earth. Woese argued that the Bacteria, Archaea, and Eukaryotes represent separate lines of descent that diverged early on from an ancestral colony of organisms. One possibilityKandler O. The early diversification of life and the origin of the three domains: A proposal. In: Wiegel J, Adams WW, editors. Thermophiles: The keys to molecular evolution and the origin of life? Athens: Taylor and Francis, 1998: 19–31. is that this occurred before the evolution of cells, when the lack of a typical cell membrane allowed unrestricted lateral gene transfer, and that the common ancestors of the three domains arose by fixation of specific subsets of genes. It is possible that the last common ancestor of bacteria and archaea was a thermophile, which raises the possibility that lower temperatures are "extreme environments" for archaea, and organisms that live in cooler environments appeared only later. Since archaea and bacteria are no more related to each other than they are to eukaryotes, the term ''prokaryote'' may suggest a false similarity between them. However, structural and functional similarities between lineages often occur because of shared ancestral traits or Convergent evolution, evolutionary convergence. These similarities are known as a ''grade'', and prokaryotes are best thought of as a grade of life, characterized by such features as an absence of membrane-bound organelles.


Comparison with other domains

The following table compares some major characteristics of the three domains, to illustrate their similarities and differences. Archaea were split off as a third domain because of the large differences in their ribosomal RNA structure. The particular molecule 16S rRNA is key to the production of proteins in all organisms. Because this function is so central to life, organisms with mutations in their 16S rRNA are unlikely to survive, leading to great (but not absolute) stability in the structure of this polynucleotide over generations. 16S rRNA is large enough to show organism-specific variations, but still small enough to be compared quickly. In 1977, Carl Woese, a microbiologist studying the genetic sequences of organisms, developed a new comparison method that involved splitting the RNA into fragments that could be sorted and compared with other fragments from other organisms. The more similar the patterns between species, the more closely they are related. Woese used his new rRNA comparison method to categorize and contrast different organisms. He compared a variety of species and happened upon a group of methanogens with rRNA vastly different from any known prokaryotes or eukaryotes. These methanogens were much more similar to each other than to other organisms, leading Woese to propose the new domain of Archaea. His experiments showed that the archaea were genetically more similar to eukaryotes than prokaryotes, even though they were more similar to prokaryotes in structure. This led to the conclusion that Archaea and Eukarya shared a common ancestor more recent than Eukarya and Bacteria. The development of the nucleus occurred after the split between Bacteria and this common ancestor. One property unique to archaea is the abundant use of ether-linked lipids in their cell membranes. Ether linkages are more chemically stable than the ester linkages found in bacteria and eukarya, which may be a contributing factor to the ability of many archaea to survive in extreme environments that place heavy stress on cell membranes, such as extreme heat and salinity. Comparative analysis of archaeal genomes has also identified several molecular conserved signature indels and signature proteins uniquely present in either all archaea or different main groups within archaea. Another unique feature of archaea, found in no other organisms, is methanogenesis (the metabolic production of methane). Methanogenic archaea play a pivotal role in ecosystems with organisms that derive energy from oxidation of methane, many of which are bacteria, as they are often a major source of methane in such environments and can play a role as primary producers. Methanogens also play a critical role in the carbon cycle, breaking down organic carbon into methane, which is also a major greenhouse gas.


Relationship to bacteria

The relationships among the three-domain system, three domains are of central importance for understanding the origin of life. Most of the
metabolic pathway In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell (biology), cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence ...
s, which are the object of the majority of an organism's genes, are common between Archaea and Bacteria, while most genes involved in genome expression are common between Archaea and Eukarya. Within prokaryotes, archaeal cell structure is most similar to that of gram-positive bacteria, largely because both have a single lipid bilayer and usually contain a thick sacculus (exoskeleton) of varying chemical composition. In some phylogenetic trees based upon different gene/protein sequences of prokaryotic homologs, the archaeal homologs are more closely related to those of gram-positive bacteria. Archaea and gram-positive bacteria also share conserved indels in a number of important proteins, such as Hsp70 and glutamine synthetase I; but the phylogeny of these genes was interpreted to reveal interdomain gene transfer, and might not reflect the organismal relationship(s). It has been proposed that the archaea evolved from gram-positive bacteria in response to antibiotic evolutionary pressure, selection pressure. This is suggested by the observation that archaea are resistant to a wide variety of antibiotics that are produced primarily by gram-positive bacteria, and that these antibiotics act primarily on the genes that distinguish archaea from bacteria. The proposal is that the selective pressure towards resistance generated by the gram-positive antibiotics was eventually sufficient to cause extensive changes in many of the antibiotics' target genes, and that these strains represented the common ancestors of present-day Archaea. The evolution of Archaea in response to antibiotic selection, or any other competitive selective pressure, could also explain their adaptation to extreme environments (such as high temperature or acidity) as the result of a search for unoccupied niches to escape from antibiotic-producing organisms; Thomas Cavalier-Smith, Cavalier-Smith has made a similar suggestion. This proposal is also supported by other work investigating protein structural relationships and studies that suggest that gram-positive bacteria may constitute the earliest branching lineages within the prokaryotes.


Relation to eukaryotes

The evolutionary relationship between archaea and eukaryotes remains unclear. Aside from the similarities in cell structure and function that are discussed below, many genetic trees group the two. Complicating factors include claims that the relationship between eukaryotes and the archaeal phylum
Crenarchaeota The Crenarchaeota (also known as Crenarchaea or eocytes) are archaea that have been classified as a phylum (biology), phylum of the Archaea domain. Initially, the Crenarchaeota were thought to be sulfur-dependent extremophiles but recent studies ...
is closer than the relationship between the
Euryarchaeota Euryarchaeota (Greek for "broad old quality") is a phylum In biology, a phylum (; plural The plural (sometimes list of glossing abbreviations, abbreviated ), in many languages, is one of the values of the grammatical number, grammatical ca ...
and the phylum Crenarchaeota and the presence of archaea-like genes in certain bacteria, such as ''Thermotogae, Thermotoga maritima'', from
horizontal gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism (from Ancient G ...
. The standard hypothesis states that the ancestor of the eukaryotes diverged early from the Archaea, and that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and cytoplasm; this hypothesis explains various genetic similarities but runs into difficulties explaining cell structure. An alternative hypothesis, the eocyte hypothesis, posits that Eukaryota emerged relatively late from the Archaea. A lineage of archaea discovered in 2015, ''Lokiarchaeum'' (of proposed new Phylum "Lokiarchaeota"), named for a hydrothermal vent called Loki's Castle in the Arctic Ocean, was found to be the most closely related to eukaryotes known at that time. It has been called a transitional organism between prokaryotes and eukaryotes. Several sister phyla of "Lokiarchaeota" have since been found ("Thorarchaeota", "Odinarchaeota", "Heimdallarchaeota"), all together comprising a newly proposed supergroup
Asgard Asgard (Old Norse Old Norse, Old Nordic, or Old Scandinavian is a stage of development of North Germanic dialects before their final divergence into separate Nordic languages. Old Norse was spoken by inhabitants of Scandinavia S ...
, which may appear as a sister taxon to Proteoarchaeota. Details of the relation of Asgard members and eukaryotes are still under consideration, although, in January 2020, scientists reported that ''Candidatus Prometheoarchaeum syntrophicum'', a type of Asgard archaea, may be a possible link between simple prokaryotic and complex eukaryotic microorganisms about two billion years ago.


Morphology

Individual archaea range from 0.1 Micrometre, micrometers (μm) to over 15 μm in diameter, and occur in various shapes, commonly as spheres, rods, spirals or plates. Other morphologies in the
Crenarchaeota The Crenarchaeota (also known as Crenarchaea or eocytes) are archaea that have been classified as a phylum (biology), phylum of the Archaea domain. Initially, the Crenarchaeota were thought to be sulfur-dependent extremophiles but recent studies ...
include irregularly shaped lobed cells in ''Sulfolobus'', needle-like filaments that are less than half a micrometer in diameter in ''Thermofilum'', and almost perfectly rectangular rods in ''Thermoproteus'' and ''Pyrobaculum''. Archaea in the genus ''Haloquadratum'' such as ''
Haloquadratum walsbyi ''Haloquadratum walsbyi'' is a species of archaea which was discovered in a brine pool in the Sinai peninsula of Egypt. It is noted for both its flat, square-shaped cells, and its unusual ability to survive in aqueous environments with high conc ...
'' are flat, square specimens that live in hypersaline pools. These unusual shapes are probably maintained by both their cell walls and a prokaryotic cytoskeleton. Proteins related to the cytoskeleton components of other organisms exist in archaea, and filaments form within their cells, but in contrast with other organisms, these cellular structures are poorly understood. In ''Thermoplasma'' and '' Ferroplasma'' the lack of a
cell wall A cell wall is a structural layer surrounding some types of cells, just outside the cell membrane cell membrane vs. Prokaryotes The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to a ...
means that the cells have irregular shapes, and can resemble Amoeboid, amoebae. Some species form aggregates or filaments of cells up to 200 μm long. These organisms can be prominent in biofilms. Notably, aggregates of ''Thermococcus coalescens'' cells fuse together in culture, forming single giant cells. Archaea in the genus ''Pyrodictium'' produce an elaborate multicell colony involving arrays of long, thin hollow tubes called ''cannulae'' that stick out from the cells' surfaces and connect them into a dense bush-like agglomeration. The function of these cannulae is not settled, but they may allow communication or nutrient exchange with neighbors. Multi-species colonies exist, such as the "string-of-pearls" community that was discovered in 2001 in a German swamp. Round whitish colonies of a novel Euryarchaeota species are spaced along thin filaments that can range up to long; these filaments are made of a particular bacteria species.


Structure, composition development, and operation

Archaea and bacteria have generally similar Cell (biology), cell structure, but cell composition and organization set the archaea apart. Like bacteria, archaea lack interior membranes and organelles. Like bacteria, the
cell membrane The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane A biological membrane, biomembrane or cell membrane is a selectively permeable membra ...

cell membrane
s of archaea are usually bounded by a
cell wall A cell wall is a structural layer surrounding some types of cells, just outside the cell membrane cell membrane vs. Prokaryotes The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to a ...
and they swim using one or more flagella. Structurally, archaea are most similar to gram-positive bacteria. Most have a single plasma membrane and cell wall, and lack a periplasmic space; the exception to this general rule is ''Ignicoccus'', which possess a particularly large periplasm that contains membrane-bound vesicle (biology), vesicles and is enclosed by an outer membrane.


Cell wall and flagella

Most archaea (but not ''Thermoplasma'' and '' Ferroplasma'') possess a cell wall. In most archaea the wall is assembled from surface-layer proteins, which form an S-layer. An S-layer is a rigid array of protein molecules that cover the outside of the cell (like chain mail). This layer provides both chemical and physical protection, and can prevent macromolecules from contacting the cell membrane. Unlike bacteria, archaea lack
peptidoglycan Peptidoglycan or murein is a polymer A polymer (; Greek ''poly- Poly, from the Greek :wikt:πολύς, πολύς meaning "many" or "much", may refer to: Businesses * China Poly Group Corporation, a Chinese business group, and its subsidia ...

peptidoglycan
in their cell walls. Methanobacteriales do have cell walls containing pseudopeptidoglycan, which resembles eubacterial peptidoglycan in morphology, function, and physical structure, but pseudopeptidoglycan is distinct in chemical structure; it lacks D-amino acids and N-acetylmuramic acid, substituting the latter with N-Acetyltalosaminuronic acid. Archaeal flagella are known as archaellum, archaella, that operate like bacterial flagellum, flagella – their long stalks are driven by rotatory motors at the base. These motors are powered by a electrochemical gradient, proton gradient across the membrane, but archaella are notably different in composition and development. The two types of flagella evolved from different ancestors. The bacterial flagellum shares a common ancestor with the type III secretion system, while archaeal flagella appear to have evolved from bacterial type IV pili. In contrast with the bacterial flagellum, which is hollow and assembled by subunits moving up the central pore to the tip of the flagella, archaeal flagella are synthesized by adding subunits at the base.


Membranes

Archaeal membranes are made of molecules that are distinctly different from those in all other life forms, showing that archaea are related only distantly to bacteria and eukaryotes. In all organisms,
cell membrane The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane A biological membrane, biomembrane or cell membrane is a selectively permeable membra ...

cell membrane
s are made of molecules known as phospholipids. These molecules possess both a chemical polarity, polar part that dissolves in water (the phosphate "head"), and a "greasy" non-polar part that does not (the lipid tail). These dissimilar parts are connected by a glycerol moiety. In water, phospholipids cluster, with the heads facing the water and the tails facing away from it. The major structure in cell membranes is a double layer of these phospholipids, which is called a lipid bilayer. The phospholipids of archaea are unusual in four ways: * They have membranes composed of glycerol-
ether lipid. Note ether at first and second positions. . Note ether at first position, and ester at second position. Image:Platelet-activating factor.svg, Platelet-activating factor. Note ether at first position, and acetyl group at second position. In an or ...

ether lipid
s, whereas bacteria and eukaryotes have membranes composed mainly of glycerol-ester
lipid In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanis ...
s. The difference is the type of bond that joins the lipids to the glycerol moiety; the two types are shown in yellow in the figure at the right. In ester lipids this is an ester, ester bond, whereas in ether lipids this is an ether, ether bond. * The stereochemistry of the archaeal glycerol moiety is the mirror image of that found in other organisms. The glycerol moiety can occur in two forms that are mirror images of one another, called ''enantiomers''. Just as a right hand does not fit easily into a left-handed glove, enantiomers of one type generally cannot be used or made by
enzyme Enzymes () are proteins that act as biological catalysts (biocatalysts). Catalysts accelerate chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates in ...

enzyme
s adapted for the other. The archaeal phospholipids are built on a backbone of ''sn''-glycerol-1-phosphate, which is an enantiomer of ''sn''-glycerol-3-phosphate, the phospholipid backbone found in bacteria and eukaryotes. This suggests that archaea use entirely different enzymes for synthesizing phospholipids as compared to bacteria and eukaryotes. Such enzymes developed very early in life's history, indicating an early split from the other two domains. * Archaeal lipid tails differ from those of other organisms in that they are based upon long isoprene, isoprenoid chains with multiple side-branches, sometimes with cyclopropane or cyclohexane rings. By contrast, the fatty acids in the membranes of other organisms have straight chains without side branches or rings. Although isoprenoids play an important role in the biochemistry of many organisms, only the archaea use them to make phospholipids. These branched chains may help prevent archaeal membranes from leaking at high temperatures. * In some archaea, the lipid bilayer is replaced by a monolayer. In effect, the archaea fuse the tails of two phospholipid molecules into a single molecule with two polar heads (a bolaamphiphile); this fusion may make their membranes more rigid and better able to resist harsh environments. For example, the lipids in '' Ferroplasma'' are of this type, which is thought to aid this organism's survival in its highly acidic habitat.


Metabolism

Archaea exhibit a great variety of chemical reactions in their
metabolism Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life Life is a characteristic that distinguishes physical entities A bubble of exhaled gas in water In common usage and classical mechanics, a phys ...

metabolism
and use many sources of energy. These reactions are classified into primary nutritional groups, nutritional groups, depending on energy and carbon sources. Some archaea obtain energy from inorganic compounds such as sulfur or
ammonia Ammonia is a chemical compound, compound of nitrogen and hydrogen with the chemical formula, formula NH3. A Binary compounds of hydrogen, stable binary hydride, and the simplest pnictogen hydride, ammonia is a colourless gas with a distinct ch ...

ammonia
(they are chemotrophs). These include nitrifying bacteria, nitrifiers,
methanogen Methanogens are microorganisms that produce 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 n ...
s and anaerobic organism, anaerobic methane oxidisers. In these reactions one compound passes electrons to another (in a redox reaction), releasing energy to fuel the cell's activities. One compound acts as an electron donor and one as an electron acceptor. The energy released is used to generate adenosine triphosphate (ATP) through chemiosmosis, the same basic process that happens in the mitochondrion of eukaryotic cells. Other groups of archaea use sunlight as a source of energy (they are phototrophs), but oxygen–generating photosynthesis does not occur in any of these organisms. Many basic
metabolic pathway In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell (biology), cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence ...
s are shared among all forms of life; for example, archaea use a modified form of glycolysis (the Entner–Doudoroff pathway) and either a complete or partial citric acid cycle. These similarities to other organisms probably reflect both early origins in the history of life and their high level of efficiency. Some Euryarchaeota are
methanogen Methanogens are microorganisms that produce 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 n ...
s (archaea that produce methane as a result of metabolism) living in anaerobic environments, such as swamps. This form of metabolism evolved early, and it is even possible that the first free-living organism was a methanogen. A common reaction involves the use of carbon dioxide as an electron acceptor to oxidize hydrogen. Methanogenesis involves a range of coenzymes that are unique to these archaea, such as coenzyme M and methanofuran. Other organic compounds such as alcohols, acetic acid or formic acid are used as alternative electron acceptors by methanogens. These reactions are common in Gut (zoology), gut-dwelling archaea. Acetic acid is also broken down into methane and carbon dioxide directly, by ''acetotrophic'' archaea. These acetotrophs are archaea in the order Methanosarcinales, and are a major part of the communities of microorganisms that produce
biogas Biogas is the mixture of gas Gas is one of the four fundamental states of matter In physics Physics is the natural science that studies matter, its Elementary particle, fundamental constituents, its Motion (physics), motion and ...

biogas
. Other archaea use in the atmosphere as a source of carbon, in a process called carbon fixation (they are autotrophs). This process involves either a highly modified form of the Calvin cycle or another metabolic pathway called the 3-hydroxypropionate/ 4-hydroxybutyrate cycle. The Crenarchaeota also use the reverse Krebs cycle while the Euryarchaeota also use the reductive acetyl-CoA pathway. Carbon fixation is powered by inorganic energy sources. No known archaea carry out photosynthesis (Halobacterium is the only known phototroph archeon but it uses an alternative process to photosynthesis). Archaeal energy sources are extremely diverse, and range from the oxidation of
ammonia Ammonia is a chemical compound, compound of nitrogen and hydrogen with the chemical formula, formula NH3. A Binary compounds of hydrogen, stable binary hydride, and the simplest pnictogen hydride, ammonia is a colourless gas with a distinct ch ...

ammonia
by the Nitrosopumilales to the oxidation of hydrogen sulfide or elemental sulfur by species of ''Sulfolobus'', using either oxygen or metal ions as electron acceptors. Phototrophic archaea use light to produce chemical energy in the form of ATP. In the Halobacteria, light-activated ion pumps like bacteriorhodopsin and halorhodopsin generate ion gradients by pumping ions out of and into the cell across the plasma membrane. The energy stored in these electrochemical gradients is then converted into ATP by ATP synthase. This process is a form of photophosphorylation. The ability of these light-driven pumps to move ions across membranes depends on light-driven changes in the structure of a retinol Cofactor (biochemistry), cofactor buried in the center of the protein.


Genetics

Archaea usually have a single circular chromosome, with as many as 5,751,492 base pairs in ''Methanosarcina acetivorans'', the largest known archaeal genome. The tiny 490,885 base-pair genome of '' Nanoarchaeum equitans'' is one-tenth of this size and the smallest archaeal genome known; it is estimated to contain only 537 protein-encoding genes. Smaller independent pieces of DNA, called ''plasmids'', are also found in archaea. Plasmids may be transferred between cells by physical contact, in a process that may be similar to bacterial conjugation. Archaea are genetically distinct from bacteria and eukaryotes, with up to 15% of the proteins encoded by any one archaeal genome being unique to the domain, although most of these unique genes have no known function. Of the remainder of the unique proteins that have an identified function, most belong to the Euryarchaeota and are involved in methanogenesis. The proteins that archaea, bacteria and eukaryotes share form a common core of cell function, relating mostly to Transcription (genetics), transcription, Translation (biology), translation, and nucleotide, nucleotide metabolism. Other characteristic archaeal features are the organization of genes of related function – such as enzymes that catalyze steps in the same
metabolic pathway In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell (biology), cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence ...
into novel operons, and large differences in tRNA genes and their aminoacyl tRNA synthetases. Transcription in archaea more closely resembles eukaryotic than bacterial transcription, with the archaeal RNA polymerase being very close to its equivalent in eukaryotes, while archaeal translation shows signs of both bacterial and eukaryotic equivalents. Although archaea have only one type of RNA polymerase, its structure and function in transcription seems to be close to that of the eukaryotic RNA polymerase II, with similar protein assemblies (the general transcription factors) directing the binding of the RNA polymerase to a gene's promoter (biology), promoter, but other archaeal transcription factors are closer to those found in bacteria. Post-transcriptional modification is simpler than in eukaryotes, since most archaeal genes lack introns, although there are many introns in their transfer RNA and
ribosomal RNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA A non-coding RNA (ncRNA) is an RNA Ribonucleic acid (RNA) is a polymer A polymer (; Greek '' poly-'', "many" + '' -mer'', "part") is a substance or material consis ...
genes, and introns may occur in a few protein-encoding genes.


Gene transfer and genetic exchange

''Haloferax volcanii'', an extreme halophilic archaeon, forms cytoplasmic bridges between cells that appear to be used for transfer of DNA from one cell to another in either direction. When the hyperthermophilic archaea ''Sulfolobus solfataricus'' and ''Sulfolobus acidocaldarius'' are exposed to DNA-damaging UV irradiation or to the agents bleomycin or mitomycin C, species-specific cellular aggregation is induced. Aggregation in ''S. solfataricus'' could not be induced by other physical stressors, such as pH or temperature shift, suggesting that aggregation is induced specifically by DNA damage. Ajon et al. showed that UV-induced cellular aggregation mediates chromosomal marker exchange with high frequency in ''S. acidocaldarius''. Recombination rates exceeded those of uninduced cultures by up to three orders of magnitude. Frols et al. and Ajon et al. hypothesized that cellular aggregation enhances species-specific DNA transfer between ''Sulfolobus'' cells in order to provide increased repair of damaged DNA by means of homologous recombination. This response may be a primitive form of sexual interaction similar to the more well-studied bacterial transformation systems that are also associated with species-specific DNA transfer between cells leading to homologous recombinational repair of DNA damage.


Archaeal viruses

Archaea are the target of a number of viruses in a diverse virosphere distinct from bacterial and eukaryotic viruses. They have been organized into 15-18 DNA-based families so far, but multiple species remain un-isolated and await classification. These families can be informally divided into two groups: archaea-specific and cosmopolitan. Archaeal-specific viruses target only archaean species and currently include 12 families. Numerous unique, previously unidentified viral structures have been observed in this group, including: bottle-shaped, spindle-shaped, coil-shaped, and droplet-shaped viruses. While the reproductive cycles and genomic mechanisms of archaea-specific species may be similar to other viruses, they bear unique characteristics that were specifically developed due to the morphology of host cells they infect. Their virus release mechanisms differ from that of other phages. Bacteriophages generally undergo either Lytic cycle, lytic pathways, Lysogenic cycle, lysogenic pathways, or (rarely) a mix of the two. Most archaea-specific viral strains maintain a stable, somewhat lysogenic, relationship with their hosts – appearing as a chronic infection. This involves the gradual, and continuous, production and release of Virus, virions without killing the host cell. Prangishyili (2013) noted that it has been hypothesized that tailed archaeal phages originated from bacteriophages capable of infecting haloarchaeal species. If the hypothesis is correct, it can be concluded that other double-stranded DNA viruses that make up the rest of the archaea-specific group are their own unique group in the global viral community. Krupovic et al. (2018) states that the high levels of
horizontal gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism (from Ancient G ...
, rapid mutation rates in viral genomes, and lack of universal gene sequences have led researchers to perceive the evolutionary pathway of archaeal viruses as a network. The lack of similarities among phylogenetic markers in this network and the global virosphere, as well as external linkages to non-viral elements, may suggest that some species of archaea specific viruses evolved from non-viral mobile genetic elements (MGE). These viruses have been studied in most detail in thermophilics, particularly the orders Sulfolobales and Thermoproteales. Two groups of single-stranded DNA viruses that infect archaea have been recently isolated. One group is exemplified by the ''Halorubrum pleomorphic virus 1'' (''Pleolipoviridae'') infecting halophilic archaea, and the other one by the ''Aeropyrum coil-shaped virus'' (''Spiraviridae'') infecting a hyperthermophilic (optimal growth at 90–95 °C) host. Notably, the latter virus has the largest currently reported ssDNA genome. Defenses against these viruses may involve RNA interference from repetitive DNA sequences that are related to the genes of the viruses.


Reproduction

Archaea reproduce asexually by binary or multiple fission (biology), fission, fragmentation, or
budding Budding is a type of asexual reproduction Asexual reproduction is a type of reproduction Reproduction (or procreation or breeding) is the biological process by which new individual organism In biology, an organism (from Ancient Gr ...

budding
; mitosis and meiosis do not occur, so if a species of archaea exists in more than one form, all have the same genetic material. Cell division is controlled in a cell cycle; after the cell's chromosome is replicated and the two daughter chromosomes separate, the cell divides. In the genus ''Sulfolobus'', the cycle has characteristics that are similar to both bacterial and eukaryotic systems. The chromosomes replicate from multiple starting points (origin of replication, origins of replication) using DNA polymerases that resemble the equivalent eukaryotic enzymes. In Euryarchaeota the cell division protein FtsZ, which forms a contracting ring around the cell, and the components of the septum that is constructed across the center of the cell, are similar to their bacterial equivalents. In cren- and thaumarchaea, the cell division machinery Cdv fulfills a similar role. This machinery is related to the eukaryotic ESCRT-III machinery which, while best known for its role in cell sorting, also has been seen to fulfill a role in separation between divided cell, suggesting an ancestral role in cell division. Both bacteria and eukaryotes, but not archaea, make spores. Some species of
Haloarchaea Haloarchaea (halophilic archaea, halophilic archaebacteria, halobacteria) are a class of the Euryarchaeota, found in water Water is an Inorganic compound, inorganic, Transparency and translucency, transparent, tasteless, odorless, and ...
undergo phenotypic switching and grow as several different cell types, including thick-walled structures that are resistant to osmotic shock and allow the archaea to survive in water at low salt concentrations, but these are not reproductive structures and may instead help them reach new habitats.


Behavior


Communication

Quorum sensing was originally thought to not exist in Archaea, but recent studies have shown evidence of some species being able to perform cross-talk through quorum sensing. Other studies have shown syntrophic interactions between archaea and bacteria during biofilm growth. Although research is limited in archaeal quorum sensing, some studies have uncovered LuxR proteins in archaeal species, displaying similarities with bacteria LuxR, and ultimately allowing for the detection of small molecules that are used in high density communication. Similarly to bacteria, Archaea LuxR solos have shown to bind to AHLs (lactones) and non-AHLs ligans, which is a large part in performing intraspecies, interspecies, and interkingdom communication through quorum sensing.


Ecology


Habitats

Archaea exist in a broad range of
habitat In ecology Ecology (from el, οἶκος, "house" and el, -λογία, label=none, "study of") is the study of the relationships between living organisms, including humans, and their physical environment. Ecology considers at the ...

habitat
s, and are now recognized as a major part of global ecosystems, and may represent about 20% of microbial cells in the oceans. However, the first-discovered archaeans were
extremophile An extremophile (from Latin ' meaning "extreme" and Greek ' () meaning "love") is an organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contiguous system that embodies the ...
s. Indeed, some archaea survive high temperatures, often above , as found in geysers, black smokers, and oil wells. Other common habitats include very cold habitats and highly salt, saline, acidic, or alkaline water, but archaea include mesophiles that grow in mild conditions, in swamps and marshland, sewage, the oceans, the intestinal tract of animals, and soils. Extremophile archaea are members of four main physiological groups. These are the halophiles, thermophiles, alkaliphiles, and Acidophile (organisms), acidophiles. These groups are not comprehensive or phylum-specific, nor are they mutually exclusive, since some archaea belong to several groups. Nonetheless, they are a useful starting point for classification. Halophiles, including the genus ''Halobacterium'', live in extremely saline environments such as
salt lake A salt lake or saline lake is a landlocked body of water (Lysefjord) in Norway Norway, officially the Kingdom of Norway,Names in the official and recognised languages: Bokmål Bokmål (, ; literally "book tongue") is an official wr ...

salt lake
s and outnumber their bacterial counterparts at salinities greater than 20–25%. Thermophiles grow best at temperatures above , in places such as hot springs; ''hyperthermophilic'' archaea grow optimally at temperatures greater than . The archaeal ''Methanopyrus kandleri'' Strain 116 can even reproduce at , the highest recorded temperature of any organism. Other archaea exist in very acidic or alkaline conditions. For example, one of the most extreme archaean acidophiles is ''Picrophilus, Picrophilus torridus'', which grows at pH 0, which is equivalent to thriving in 1.2 Molar concentration, molar sulfuric acid. This resistance to extreme environments has made archaea the focus of speculation about the possible properties of extraterrestrial life. Some extremophile habitats are not dissimilar to those on Mars, leading to the suggestion that viable microbes could be transferred between planets in meteorites. Recently, several studies have shown that archaea exist not only in mesophilic and thermophilic environments but are also present, sometimes in high numbers, at low temperatures as well. For example, archaea are common in cold oceanic environments such as polar seas. Even more significant are the large numbers of archaea found throughout the world's oceans in non-extreme habitats among the
plankton Plankton are the diverse collection of organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology ...

plankton
community (as part of the picoplankton). Although these archaea can be present in extremely high numbers (up to 40% of the microbial biomass), almost none of these species have been isolated and studied in pure culture. Consequently, our understanding of the role of archaea in ocean ecology is rudimentary, so their full influence on global biogeochemistry, biogeochemical cycles remains largely unexplored. Some marine Crenarchaeota are capable of nitrification, suggesting these organisms may affect the oceanic nitrogen cycle, although these oceanic Crenarchaeota may also use other sources of energy. Vast numbers of archaea are also found in the sediments that cover the sea floor, with these organisms making up the majority of living cells at depths over 1 meter below the ocean bottom. It has been demonstrated that in all oceanic surface sediments (from 1000- to 10,000-m water depth), the impact of viral infection is higher on archaea than on bacteria and virus-induced lysis of archaea accounts for up to one-third of the total microbial biomass killed, resulting in the release of ~0.3 to 0.5 gigatons of carbon per year globally.


Role in chemical cycling

Archaea recycle elements such as carbon, nitrogen, and sulfur through their various habitats. Archaea carry out many steps in the nitrogen cycle. This includes both reactions that remove nitrogen from ecosystems (such as nitrate-based respiration and denitrification) as well as processes that introduce nitrogen (such as nitrate assimilation and nitrogen fixation). Researchers recently discovered archaeal involvement in
ammonia Ammonia is a chemical compound, compound of nitrogen and hydrogen with the chemical formula, formula NH3. A Binary compounds of hydrogen, stable binary hydride, and the simplest pnictogen hydride, ammonia is a colourless gas with a distinct ch ...

ammonia
oxidation reactions. These reactions are particularly important in the oceans. The archaea also appear crucial for ammonia oxidation in soils. They produce nitrite, which other microbes then oxidize to nitrate. Plants and other organisms consume the latter. In the sulfur cycle, archaea that grow by oxidizing sulfur compounds release this element from rocks, making it available to other organisms, but the archaea that do this, such as ''Sulfolobus'', produce sulfuric acid as a waste product, and the growth of these organisms in abandoned mines can contribute to acid mine drainage and other environmental damage. In the carbon cycle, methanogen archaea remove hydrogen and play an important role in the decay of organic matter by the populations of microorganisms that act as decomposers in anaerobic ecosystems, such as sediments, marshes, and sewage treatment, sewage-treatment works.


Interactions with other organisms

The well-characterized interactions between archaea and other organisms are either Mutualism (biology), mutual or commensalism, commensal. There are no clear examples of known archaeal
pathogen In biology, a pathogen ( el, πάθος, "suffering", "passion" and , "producer of") in the oldest and broadest sense, is any organism that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a Germ theory ...
s or
parasite Parasitism is a Symbiosis, close relationship between species, where one organism, the parasite, lives on or inside another organism, the Host (biology), host, causing it some harm, and is adaptation (biology), adapted structurally to this w ...
s, but some species of methanogens have been suggested to be involved in periodontal disease, infections in the mouth, and '' Nanoarchaeum equitans'' may be a parasite of another species of archaea, since it only survives and reproduces within the cells of the Crenarchaeon ''Ignicoccus, Ignicoccus hospitalis'', and appears to offer no benefit to its host (biology), host.


Mutualism

One well-understood example of mutualism (biology), mutualism is the interaction between protozoa and methanogen, methanogenic archaea in the digestive tracts of animals that digest cellulose, such as
ruminant Ruminants (suborder Ruminantia) are large ungulate, hoofed herbivorous grazing or browsing mammals that are able to acquire nutrients from plant-based food by Enteric fermentation, fermenting it in a specialized stomach prior to digestion, princi ...
s and termites. In these anaerobic environments, protozoa break down plant cellulose to obtain energy. This process releases hydrogen as a waste product, but high levels of hydrogen reduce energy production. When methanogens convert hydrogen to methane, protozoa benefit from more energy. In anaerobic protozoa, such as ''Plagiopyla frontata'', archaea reside inside the protozoa and consume hydrogen produced in their hydrogenosomes. Archaea also associate with larger organisms. For example, the marine archaean ''Cenarchaeum, Cenarchaeum symbiosum'' lives within (is an endosymbiont of) the sponge ''Axinella, Axinella mexicana''.


Commensalism

Archaea can also be commensals, benefiting from an association without helping or harming the other organism. For example, the methanogen ''Methanobrevibacter smithii'' is by far the most common archaean in the human flora, making up about one in ten of all the prokaryotes in the human gut. In termites and in humans, these methanogens may in fact be mutualists, interacting with other microbes in the gut to aid digestion. Archaean communities also associate with a range of other organisms, such as on the surface of corals, and in the region of soil that surrounds plant roots (the Rhizosphere (ecology), rhizosphere).


Significance in technology and industry

Extremophile archaea, particularly those resistant either to heat or to extremes of acidity and alkalinity, are a source of
enzyme Enzymes () are proteins that act as biological catalysts (biocatalysts). Catalysts accelerate chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates in ...

enzyme
s that function under these harsh conditions. These enzymes have found many uses. For example, thermostable DNA polymerases, such as the Pfu DNA polymerase from ''Pyrococcus furiosus'', revolutionized molecular biology by allowing the
polymerase chain reaction Polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies (complete copies or partial copies) of a specific DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM. ...

polymerase chain reaction
to be used in research as a simple and rapid technique for cloning DNA. In industry, amylases, galactosidases and pullulanases in other species of ''Pyrococcus'' that function at over allow food processing at high temperatures, such as the production of low lactose milk and whey. Enzymes from these thermophilic archaea also tend to be very stable in organic solvents, allowing their use in environmentally friendly processes in green chemistry that synthesize organic compounds. This stability makes them easier to use in structural biology. Consequently, the counterparts of bacterial or eukaryotic enzymes from extremophile archaea are often used in structural studies. In contrast with the range of applications of archaean enzymes, the use of the organisms themselves in biotechnology is less developed. Methanogen, Methanogenic archaea are a vital part of
sewage treatment Sewage treatment (or domestic wastewater treatment, municipal wastewater treatment) is a type of wastewater treatment Wastewater treatment is a process used to remove contaminants from wastewater or sewage Sewage, or domestic/municip ...
, since they are part of the community of microorganisms that carry out anaerobic digestion and produce
biogas Biogas is the mixture of gas Gas is one of the four fundamental states of matter In physics Physics is the natural science that studies matter, its Elementary particle, fundamental constituents, its Motion (physics), motion and ...

biogas
. In mineral processing, acidophilic archaea display promise for the extraction of metals from ores, including gold, cobalt and copper. Archaea host a new class of potentially useful antibiotics. A few of these archaeocins have been characterized, but hundreds more are believed to exist, especially within ''
Haloarchaea Haloarchaea (halophilic archaea, halophilic archaebacteria, halobacteria) are a class of the Euryarchaeota, found in water Water is an Inorganic compound, inorganic, Transparency and translucency, transparent, tasteless, odorless, and ...
'' and ''Sulfolobus''. These compounds differ in structure from bacterial antibiotics, so they may have novel modes of action. In addition, they may allow the creation of new selectable markers for use in archaeal molecular biology.


See also

* Aerobic methane production * Earliest known life forms * List of Archaea genera * List of sequenced archaeal genomes * Nuclear localization sequence * ''The Surprising Archaea'' (book) * Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya * Unique properties of hyperthermophilic archaea


References


Further reading

* * * * * * * *


External links


General


Introduction to the Archaea, ecology, systematics and morphology

Oceans of Archaea
nbsp;– E.F. DeLong, ''ASM News'', 2003


Classification


NCBI taxonomy page on Archaea


nbsp;– list of Prokaryotic names with Standing in Nomenclature
Shotgun sequencing finds nanoorganisms
nbsp;– discovery of the ARMAN group of archaea


Genomics


Browse any completed archaeal genome at UCSC

Comparative Analysis of Archaeal Genomes
(at United States Department of Energy, DOE's Integrated Microbial Genomes System, IMG system) {{Portal bar, Biology, Evolutionary biology, Paleontology Archaea, Extremophiles Domains (biology)