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40-471: Archaea ( / ɑːr ˈ k iː ə / ar- KEE -ə ) is a domain of organisms . Traditionally, Archaea only included its prokaryotic members, but this sense has been found to be paraphyletic , as eukaryotes are now known to have evolved from archaea. Even though the domain Archaea includes eukaryotes, the term "archaea" ( sg. : archaeon / ɑːr ˈ k iː ɒ n / ar- KEE -on , from

80-462: A five-dominion system in 2012, adding Prionobiota (acellular and without nucleic acid) and Virusobiota (acellular but with nucleic acid) to the traditional three domains. Alternative classifications of life include: Syntrophy In biology , syntrophy , syntrophism , or cross-feeding (from Greek syn meaning together, trophe meaning nourishment) is the cooperative interaction between at least two microbial species to degrade

120-455: A large number of microbial processes especially in oxygen limited environments, methanogenic environments and anaerobic systems. In anoxic or methanogenic environments such as wetlands, swamps, paddy fields, landfills, digestive tract of ruminants , and anerobic digesters syntrophy is employed to overcome the energy constraints as the reactions in these environments proceed close to thermodynamic equilibrium . The main mechanism of syntrophy

160-570: A long time, archaea were seen as extremophiles that exist only in extreme habitats such as hot springs and salt lakes , 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 (PCR) to detect prokaryotes from environmental samples (such as water or soil) by multiplying their ribosomal genes. This allows

200-1055: A monophyletic group, and that the apparent grouping is caused by long branch attraction (LBA), suggesting that all these lineages belong to "Euryarchaeota". According to Tom A. Williams et al. 2017, Castelle & Banfield (2018) and GTDB release 09-RS220 (24 April 2024): " Altarchaeales " " Diapherotrites " " Micrarchaeota " " Aenigmarchaeota " " Nanohaloarchaeota " " Nanoarchaeota " " Pavarchaeota " " Mamarchaeota " " Woesarchaeota " " Pacearchaeota " Thermococci Pyrococci Methanococci Methanobacteria Methanopyri Archaeoglobi Methanocellales Methanosarcinales Methanomicrobiales Halobacteria Thermoplasmatales Methanomassiliicoccales Aciduliprofundum boonei Thermoplasma volcanium " Korarchaeota " Thermoproteota " Aigarchaeota " " Geoarchaeota " Nitrososphaerota " Bathyarchaeota " " Odinarchaeota " " Thorarchaeota " " Lokiarchaeota " " Helarchaeota " " Heimdallarchaeota " Eukaryota Domain (biology) According to

240-412: A single substrate. This type of biological interaction typically involves the transfer of one or more metabolic intermediates between two or more metabolically diverse microbial species living in close proximity to each other. Thus, syntrophy can be considered an obligatory interdependency and a mutualistic metabolism between different microbial species, wherein the growth of one partner depends on

280-407: A synonym for the category of dominion (Lat. dominium ), introduced by Moore in 1974. Carl Linnaeus made the classification "domain" popular in the famous taxonomy system he created in the middle of the eighteenth century. This system was further improved by the studies of Charles Darwin later on but could not classify bacteria easily, as they have very few observable features to compare to

320-470: Is a stomach called a rumen . The rumen contains billions of microbes, many of which are syntrophic. Some anaerobic fermenting microbes in the rumen (and other gastrointestinal tracts) are capable of degrading organic matter to short chain fatty acids , and hydrogen. The accumulating hydrogen inhibits the microbe's ability to continue degrading organic matter, but the presence of syntrophic hydrogen-consuming microbes allows continued growth by metabolizing

360-554: Is difficult because most have not been isolated in a laboratory and have been detected only by their gene sequences in environmental samples. It is unknown if they are able to produce endospores . Archaea and bacteria are generally similar in size and shape, although a few archaea have very different shapes, such as the flat, square cells of Haloquadratum walsbyi . Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for

400-462: Is essential for acetogenic reactions to be thermodynamically favorable (ΔG < 0). Syntrophic microbial food webs play an integral role in bioremediation especially in environments contaminated with crude oil and petrol. Environmental contamination with oil is of high ecological importance and can be effectively mediated through syntrophic degradation by complete mineralization of alkane , aliphatic and hydrocarbon chains. The hydrocarbons of

440-588: Is made possible thanks to the methanogen M.o.H, which consumes the hydrogen produced by organism S, by turning the positive Gibbs free energy into negative Gibbs free energy. This situation favors growth of organism S and also provides energy for methanogens by consuming hydrogen. Down the line, acetate accumulation is also prevented by similar syntrophic relationship. Syntrophic degradation of substrates like butyrate and benzoate can also happen without hydrogen consumption. An example of propionate and butyrate degradation with interspecies formate transfer carried out by

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480-435: Is prominent in syntrophic metabolism. The metabolic reactions and the energy involved for syntrophic degradation with H 2 consumption: A classical syntrophic relationship can be illustrated by the activity of ‘ Methanobacillus omelianskii ’. It was isolated several times from anaerobic sediments and sewage sludge and was regarded as a pure culture of an anaerobe converting ethanol to acetate and methane. In fact, however,

520-428: Is removing the metabolic end products of one species so as to create an energetically favorable environment for another species. This obligate metabolic cooperation is required to facilitate the degradation of complex organic substrates under anaerobic conditions. Complex organic compounds such as ethanol, propionate , butyrate , and lactate cannot be directly used as substrates for methanogenesis by methanogens. On

560-893: The enzymes involved in transcription and translation . Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes , including archaeols . Archaea use more diverse energy sources than eukaryotes, ranging from organic compounds such as sugars, to ammonia , metal ions or even hydrogen gas . The salt-tolerant Haloarchaea use sunlight as an energy source, and other species of archaea fix carbon (autotrophy), but unlike plants and cyanobacteria , no known species of archaea does both. Archaea reproduce asexually by binary fission , fragmentation , or budding ; unlike bacteria, no known species of Archaea form endospores . The first observed archaea were extremophiles , living in extreme environments such as hot springs and salt lakes with no other organisms. Improved molecular detection tools led to

600-525: The gastrointestinal tract in humans and ruminants , where their vast numbers facilitate digestion . Methanogens are also used in biogas production and sewage treatment , and biotechnology exploits enzymes from extremophile archaea that can endure high temperatures and organic solvents . For much of the 20th century, prokaryotes were regarded as a single group of organisms and classified based on their biochemistry , morphology and metabolism . Microbiologists tried to classify microorganisms based on

640-595: The methanogens were known). 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 in their cell walls, 2. two unusual coenzymes, 3. results of 16S ribosomal RNA gene sequencing. To emphasize this difference, Woese, Otto Kandler and Mark Wheelis later proposed reclassifying organisms into three natural domains known as

680-453: The nutrients , growth factors , or substrates provided by the other(s). Syntrophy is often used synonymously for mutualistic symbiosis especially between at least two different bacterial species. Syntrophy differs from symbiosis in a way that syntrophic relationship is primarily based on closely linked metabolic interactions to maintain thermodynamically favorable lifestyle in a given environment. Syntrophy plays an important role in

720-788: The three-domain system : the Eukarya , the Bacteria and the Archaea, in what is now known as the Woesian Revolution . The word archaea comes from the Ancient Greek ἀρχαῖα , meaning "ancient things", as the first representatives of the domain Archaea were methanogens 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 halophilic and hyperthermophilic microbes were also included in Archaea. For

760-430: The viruses , is not included in this system. Alternatives to the three-domain system include the earlier two-empire system (with the empires Prokaryota and Eukaryota), and the eocyte hypothesis (with two domains of Bacteria and Archaea, with Eukarya included as a branch of Archaea). The term domain was proposed by Carl Woese , Otto Kandler , and Mark Wheelis (1990) in a three-domain system . This term represents

800-667: The Greek "αρχαίον", which means ancient) in English still generally refers specifically to prokaryotic members of Archaea. Archaea were initially classified as bacteria , receiving the name archaebacteria ( / ˌ ɑːr k i b æ k ˈ t ɪər i ə / , in the Archaebacteria kingdom ), but this term has fallen out of use. Archaeal cells have unique properties separating them from Bacteria and Eukaryota . Archaea are further divided into multiple recognized phyla . Classification

840-437: The H 2 waste produced during amino acid breakdown, preventing a toxic build-up. Another way to improve amino acid breakdown is through interspecies electron transfer mediated by formate. Species like Desulfovibrio employ this method. Amino acid fermenting anaerobes such as Clostridium species, Peptostreptococcus asacchaarolyticus , Acidaminococcus fermentans were known to breakdown amino acids like glutamate with

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880-627: The bacterial species on the Earth, or organize them into a tree-like structure (unless the structure includes cross-connections between branches, making it a "network" instead of a "tree"). Members of the domain Eukarya – called eukaryotes – have membrane-bound organelles (including a nucleus containing genetic material) and are represented by five kingdoms : Plantae , Protozoa , Animalia , Chromista , and Fungi . The three-domain system includes no form of non-cellular life . Stefan Luketa proposed

920-1052: The basis of the three-domain system. While the presence of a nuclear membrane differentiates the Eukarya from the Archaea and Bacteria , both of which lack a nuclear envelope , the Archaea and Bacteria are distinct from each other due to differences in the biochemistry of their cell membranes and RNA markers. Archaea are prokaryotic cells, typically characterized by membrane lipids that are branched hydrocarbon chains attached to glycerol by ether linkages. The presence of these ether linkages in Archaea adds to their ability to withstand extreme temperatures and highly acidic conditions, but many archaea live in mild environments. Halophiles , organisms that thrive in highly salty environments, and hyperthermophiles , organisms that thrive in extremely hot environments, are examples of Archaea. Archaea evolved many cell sizes, but all are relatively small. Their size ranges from 0.1 μm to 15 μm diameter and up to 200 μm long. They are about

960-532: The culturable and well-investigated species of archaea are members of two main phyla , the " Euryarchaeota " and the Thermoproteota (formerly Crenarchaeota). Other groups have been tentatively created, such as the peculiar species Nanoarchaeum equitans — discovered in 2003 and assigned its own phylum, the " Nanoarchaeota ". A new phylum " Korarchaeota " has also been proposed, containing a small group of unusual thermophilic species sharing features of both

1000-759: The culture turned out to consist of a methanogenic archaeon "organism M.o.H" and a Gram-negative Bacterium "Organism S" which involves the oxidization of ethanol into acetate and methane mediated by interspecies hydrogen transfer . Individuals of organism S are observed as obligate anaerobic bacteria that use ethanol as an electron donor , whereas M.o.H are methanogens that oxidize hydrogen gas to produce methane. Organism S: 2 Ethanol + 2 H 2 O → 2 Acetate + 2 H + 4 H 2 (ΔG°' = +9.6 kJ per reaction) Strain M.o.H.: 4 H 2 + CO 2 → Methane + 2 H 2 O (ΔG°' = -131 kJ per reaction) Co-culture: 2 Ethanol + CO 2 → 2 Acetate + 2 H + Methane (ΔG°' = -113 kJ per reaction) The oxidization of ethanol by organism S

1040-465: The degradation process thermodynamically favorable Studies have shown that bacterial degradation of amino acids can be significantly enhanced through the process of syntrophy. Microbes growing poorly on amino acid substrates alanine , aspartate , serine , leucine , valine , and glycine can have their rate of growth dramatically increased by syntrophic H 2 scavengers. These scavengers, like Methanospirillum and Acetobacterium , metabolize

1080-498: The detection and identification of organisms that have not been cultured in the laboratory. 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 genes to reveal relationships among organisms ( molecular phylogenetics ). Most of

1120-411: The discovery of archaea in almost every habitat , including soil, oceans, and marshlands . Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet. Archaea are a major part of Earth's life . They are part of the microbiota of all organisms. In the human microbiome , they are important in the gut , mouth, and on

1160-489: The domain system, the tree of life consists of either three domains, Archaea , Bacteria , and Eukarya , or two domains , Archaea and Bacteria , with Eukarya included in Archaea. In the three-domain model , the first two are prokaryotes , single-celled microorganisms without a membrane-bound nucleus . All organisms that have a cell nucleus and other membrane-bound organelles are included in Eukarya and called eukaryotes . Non-cellular life , most notably

1200-548: The ether linkages that Archaea have. Internally, bacteria have different RNA structures in their ribosomes , hence they are grouped into a different category. In the two- and three-domain systems, this puts them into a separate domain. There is a great deal of diversity in the domain Bacteria . That diversity is further confounded by the exchange of genes between different bacterial lineages. The occurrence of duplicate genes between otherwise distantly-related bacteria makes it nearly impossible to distinguish bacterial species, count

1240-706: The main phyla, but most closely related to the Thermoproteota. Other detected species of archaea are only distantly related to any of these groups, such as the Archaeal Richmond Mine acidophilic nanoorganisms (ARMAN, comprising Micrarchaeota and Parvarchaeota), which were discovered in 2006 and are some of the smallest organisms known. A superphylum – TACK – which includes the Thaumarchaeota (now Nitrososphaerota ), " Aigarchaeota ", Crenarchaeota (now Thermoproteota ), and " Korarchaeota "

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1280-545: The mutual system of Syntrophomonas wolfei and Methanobacterium formicicum : Propionate＋2H 2 O＋2CO 2 → Acetate ＋3Formate ＋3H (ΔG°'=＋65.3 kJ/mol) Butyrate＋2H2O＋2CO 2 → 2Acetate- ＋3Formate- ＋3H ΔG°'=＋38.5 kJ/mol) Direct interspecies electron transfer (DIET) which involves electron transfer without any electron carrier such as H 2 or formate was reported in the co-culture system of Geobacter mettalireducens and Methanosaeto or Methanosarcina The defining feature of ruminants , such as cows and goats,

1320-760: The oil are broken down after activation by fumarate , a chemical compound that is regenerated by other microorganisms. Without regeneration, the microbes degrading the oil would eventually run out of fumarate and the process would cease. This breakdown is crucial in the processes of bioremediation and global carbon cycling. Syntrophic microbial communities are key players in the breakdown of aromatic compounds , which are common pollutants. The degradation of aromatic benzoate to methane produces intermediate compounds such as formate , acetate , CO 2 and H 2 . The buildup of these products makes benzoate degradation thermodynamically unfavorable. These intermediates can be metabolized syntrophically by methanogens and makes

1360-573: The other domains. Carl Woese made a revolutionary breakthrough when, in 1977, he compared the nucleotide sequences of the 16s ribosomal RNA and discovered that the rank "domain" contained three branches, not two as scientists had previously thought. Initially, due to their physical similarities, Archaea and Bacteria were classified together and called "archaebacteria". However, scientists now know that these two domains are hardly similar and are internally distinctly different. Each of these three domains contains unique ribosomal RNA . This forms

1400-478: The other hand, fermentation of these organic compounds cannot occur in fermenting microorganisms unless the hydrogen concentration is reduced to a low level by the methanogens. The key mechanism that ensures the success of syntrophy is interspecies electron transfer. The interspecies electron transfer can be carried out via three ways: interspecies hydrogen transfer , interspecies formate transfer and interspecies direct electron transfer. Reverse electron transport

1440-454: The size of bacteria, or similar in size to the mitochondria found in eukaryotic cells. Members of the genus Thermoplasma are the smallest of the Archaea. Cyanobacteria and mycoplasmas are two examples of bacteria. Even though bacteria are prokaryotic cells just like Archaea, their cell membranes are instead made of phospholipid bilayers . Bacteria cell membranes are distinct from Archean membranes: They characteristically have none of

1480-451: 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 syntrophic communities, for example. No clear examples of archaeal pathogens or parasites are known. Instead they are often mutualists or commensals , such as the methanogens (methane-producing strains) that inhabit

1520-484: The structures of their cell walls , their shapes, and the substances they consume. In 1965, Emile Zuckerkandl and Linus Pauling instead proposed using the sequences of the genes in different prokaryotes to work out how they are related to each other. This phylogenetic approach is the main method used today. Archaea were first classified separately from bacteria in 1977 by Carl Woese and George E. Fox , based on their ribosomal RNA (rRNA) genes. (At that time only

1560-675: The waste products. In addition, fermentative bacteria gain maximum energy yield when protons are used as electron acceptor with concurrent H 2 production. Hydrogen-consuming organisms include methanogens , sulfate-reducers, acetogens , and others. Some fermentation products, such as fatty acids longer than two carbon atoms, alcohols longer than one carbon atom, and branched chain and aromatic fatty acids, cannot directly be used in methanogenesis . In acetogenesis processes, these products are oxidized to acetate and H 2 by obligated proton reducing bacteria in syntrophic relationship with methanogenic archaea as low H 2 partial pressure

1600-822: Was proposed in 2011 to be related to the origin of eukaryotes. In 2017, the newly discovered and newly named Asgard superphylum was proposed to be more closely related to the original eukaryote and a sister group to TACK. In 2013, the superphylum DPANN was proposed to group " Nanoarchaeota ", " Nanohaloarchaeota ", Archaeal Richmond Mine acidophilic nanoorganisms (ARMAN, comprising " Micrarchaeota " and " Parvarchaeota "), and other similar archaea. This archaeal superphylum encompasses at least 10 different lineages and includes organisms with extremely small cell and genome sizes and limited metabolic capabilities. Therefore, DPANN may include members obligately dependent on symbiotic interactions, and may even include novel parasites. However, other phylogenetic analyses found that DPANN does not form

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