Difference between revisions of "Archaea" - New World Encyclopedia

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Archaea

Scientific classification

Domain:

Archaea
Woese, Kandler & Wheelis, 1990

Phyla / Classes

Phylum Crenarchaeota
Phylum Euryarchaeota
    Halobacteria
    Methanobacteria
    Methanococci
    Methanopyri
    Archaeoglobi
    Thermoplasmata
    Thermococci
Phylum Korarchaeota
Phylum Nanoarchaeota

Archaea (AmE [ɑɹˈkiə], BrE [ɑːˈkiːə]; from Greek αρχαία, "ancient ones"; singular Archaeum, Archaean, or Archaeon), also called Archaebacteria (AmE [ɑɹkɪbækˈtɪɹɪə], BrE [ɑːkɪbækˈtɪəɹɪə]), is a major division of living organisms. Although there is still uncertainty in the approximate phylogeny of the groups, Archaea, Eukaryota and Bacteria are the fundamental classifications in what is called the three-domain system. Like bacteria, Archaea are single-celled organisms lacking nuclei and are therefore prokaryotes, classified as belonging to kingdom Monera in the traditional six-kingdom taxonomy. They were originally described in extreme environments, but have since been found in all types of habitat.

A single organism from this domain has been called an "archaean." Furthermore, this biologic term is also used as an adjective.

History

Archaea were identified in 1977 by Carl Woese and George E. Fox as being a separate branch based on their separation from other prokaryotes on 16S rRNA phylogenetic trees.^[1] These two groups were originally named the Archaebacteria and Eubacteria, treated as kingdoms or subkingdoms, which Woese and Fox termed Urkingdoms. Woese argued that they represented fundamentally different branches of living things. He later renamed the groups Archaea and Bacteria to emphasize this, and argued that together with Eukarya they compose three Domains of living organisms.^[2]

The biological term, Archaea, should not be confused with the geologic phrase Archean eon, also known as the Archeozoic era. This latter term refers to the primordial period of earth history when Archaea and Bacteria were the only cellular organisms living on the planet. Probable fossils of these microbes have been dated to almost 3.8 billion years ago. Their remains have been found in sediment from western Greenland, the oldest sediment to be discovered. (3800 mya).^[3]^[4]

A phylogenetic tree based on rRNA data, showing the separation of bacteria, archaea, and eukaryote.

Archaea, Bacteria and Eukaryotes

Archaea are similar to other prokaryotes in most aspects of cell structure and metabolism. However, their genetic transcription and translation — the two central processes in molecular biology — do not show many typical bacterial features, and are in many aspects similar to those of eukaryotes. For instance, archaean translation uses eukaryotic-like initiation and elongation factors, and their transcription involves TATA-binding proteins and TFIIB as in eukaryotes. Many archaeal tRNA and rRNA genes harbor unique archaeal introns which are neither like eukaryotic introns, nor like bacterial (type I and type II etc which can "home") introns.

Several other characteristics also set the Archaea apart. Like bacteria and eukaryotes, archaea possess glycerol-based phospholipids. However, three features of the archaeal lipids are unusual:

The archaeal lipids are unique because the stereochemistry of the glycerol is the reverse of that found in bacteria and eukaryotes. This is strong evidence for a different biosynthetic pathway.

Most bacteria and eukaryotes have membranes composed mainly of glycerol-ester lipids, whereas archaea have membranes composed of glycerol-ether lipids. Even when bacteria have ether-linked lipids, the stereochemistry of the glycerol is the bacterial form. These differences may be an adaptation on the part of Archaea to hyperthermophily. However, it is worth noting that even mesophilic archaea have ether-linked lipids.

Archaeal lipids are based upon the isoprenoid sidechain. This is a five-carbon unit that is also common in rubber and as a component of some vitamins common in bacteria and eukaryotes. However, only the archaea incorporate these compounds into their cellular lipids, frequently as C-20 (four monomers) or C-40 (eight monomers) side-chains. In some archaea, the C-40 isoprenoid side-chain is actually long enough to span the membrane, forming a monolayer for a cell membrane with glycerol phosphate moieties on both ends. Although dramatic, this adaptation is most common in the extremely thermophilic archaea.

Although not unique, the archaeal cell walls are also unusual. For instance, the cell walls of most archaea are formed by surface-layer proteins or an S-layer. S-layers are common in bacteria, where they serve as the sole cell-wall component in some organisms (like the Planctomyces) or an outer layer in many organisms with peptidoglycan. With the exception of one group of methanogens, archaea lack a peptidoglycan wall (and in the case of the exception, the peptidoglycan is very different from the type found in bacteria). Archaeans also have flagella that are notably different in composition and development from the superficially similar flagella of bacteria. Bacterial flagella is a modified type III secretion system, while archeal flagella resemble type IV pilli which use a sec dependent secretion system somewhat similar to but different from type II secretion system. Archea are single celled. They are prokaryotic, have no nucleus, and have one circular chromosome.

Habitats

Archeans live in Yellowstone geysers

Many archaeans are extremophiles. They can survive and thrive at even relatively high temperatures, often above 100°C, as found in geysers,black smokers,and oil wells. Others are found in very cold habitats or in highly-saline, acidic, or alkaline water. However, other archaeans are mesophiles, and have been found in environments like marshland, sewage, sea water and soil. Many methanogenic archaea are found in the digestive tracts of animals such as ruminants, termites, and humans. As of 2007, no clear examples of archaean pathogens are known,^[5]^[6] although a relationship has been proposed between the presence of some methanogens and human periodontal disease.^[7]

Archaea are usually placed into three groups based on preferred habitat. These are the halophiles, methanogens, and thermophiles. Halophiles, sometimes known as Halobacterium live in extremely saline environments. Methanogens live in anaerobic environments and produce methane. These can be found in sediments or in the intestines of animals. Thermophiles live in places that have high temperatures, such as hot springs. These groups do not necessarily agree with molecular phylogenies, are not necessarily complete, nor are they mutually exclusive. Nonetheless, they are a useful starting point for more detailed studies.

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. It is increasingly becoming recognised that methanogens are commonly present in low-temperature environments such as cold sediments. Some studies have even suggested that at these temperatures the pathway by which methanogenesis occurs may change due to the thermodynamic constraints imposed by low temperatures. Perhaps even more significant are the large numbers of archaea found throughout most of the world's oceans, a predominantly cold environment (Giovannoni and Stingl, 2005). These archaea, which belong to several deeply branching lineages unrelated to those previously known, can be present in extremely high numbers (up to 40% of the microbial biomass) although almost none have been isolated in pure culture.^[8] Currently we have almost no information regarding the physiology of these organisms meaning that their effects on global biogeochemical cycles remain unknown. One recent study has shown, however, that one group of marine crenarchaeota are capable of nitrification, a trait previously unknown among the archaea.^[9]

Form

File:Relative scale.png

The sizes of prokaryotes relative to other organisms and biomolecules.

Individual archaeans range from 0.1 μm to over 15 μm in diameter, and some form aggregates or filaments up to 200 μm in length. They occur in various shapes, such as spherical, rod-shape, spiral, lobed, or rectangular. Archaea have no murein in their cell walls. Recently, a species of flat, square archaean that lives in hypersaline pools has been discovered.^[10] They also exhibit a variety of different types of metabolism. Of note, the halobacteria can use light to produce ATP, although no Archaea conduct photosynthesis with an electron transport chain, as occurs in other groups. Rather light-activated ion pumps like bacteriorhodopsin and halorhodopsin play a role in generating ion gradients, whose energy then leads to production of ATP. Archaea can reproduce using binary and multiple fission, fragmentation, and budding.

Evolution and classification

Archaea are divided into two main groups based on rRNA trees, the Euryarchaeota and Crenarchaeota. Two other groups have been tentatively created for certain environmental samples and the peculiar species Nanoarchaeum equitans, discovered in 2002 by Karl Stetter, but their affinities are uncertain.^[11]

Woese argued that the bacteria, archaea, and eukaryotes each represent a primary line of descent that diverged early on from an ancestral progenote with poorly-developed genetic machinery. This hypothesis is reflected in the name Archaea, from the Greek archae or ancient. Later he treated these groups formally as domains, each comprising several kingdoms. This division has become very popular, although the idea of the progenote itself is not generally supported. Some biologists, however, have argued that the archaebacteria and eukaryotes arose from specialized eubacteria.

The relationship between Archaea and Eukarya remains an important problem. Aside from the similarities noted above, many genetic trees group the two together. Some place eukaryotes closer to Eurarchaeota than Crenarchaeota are, although the membrane chemistry suggests otherwise. However, the discovery of archaean-like genes in certain bacteria, such as Thermotoga, makes their relationship difficult to determine, as horizontal gene transfer may have occurred^[12]. Some have suggested that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and cytoplasm, which accounts for various genetic similarities but runs into difficulties explaining cell structure.^[13]

Single gene sequencing for systematics has led to whole genome sequencing; by January, 2007, 31 archaeal genomes have been completed with 29 partially completed ^[14].

Biologists who have studied Archaea

Aled Edwards, Ph.D., University of Toronto
Carl Woese, Ph.D., University of Illinois at Urbana-Champaign
Karl Stetter, Ph.D.,University of Regensburg, Germany
John N. Reeve, Ph.D., Ohio State University
Rolf Bernander, Ph.D., Uppsala University, Sweden
Michael W. Adams, Ph.D., University of Georgia

References
ISBN links support NWE through referral fees

↑ Woese C, Fox G (1977). Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A 74 (11): 5088–90.
↑ Woese, Carl R., Kandler, Otto, Wheelis, Mark L (1990). Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences 87 (12): 4576–4579.
↑ Hahn J, Haug P (1986). Traces of Archaebacteria in ancient sediments. System Appl Microbiol 7: 178-183..
↑ Chappe, B. and Albrecht, P. and Michaelis, W. ({1982). Polar Lipids of Archaebacteria in Sediments and Petroleums. Science 217: 65-66.
↑ Eckburg P, Lepp P, Relman D (2003). Archaea and their potential role in human disease. Infect Immun 71 (2): 591-6. PMID 12540534.
↑ Cavicchioli R, Curmi P, Saunders N, Thomas T (2003). Pathogenic archaea: do they exist?. Bioessays 25 (11): 1119-28. PMID 14579252.
↑ Lepp P, Brinig M, Ouverney C, Palm K, Armitage G, Relman D (2004). Methanogenic Archaea and human periodontal disease. Proc Natl Acad Sci U S A 101 (16): 6176-81. PMID 15067114.
↑ Giovannoni SJ, Stingl U. (2005). Molecular diversity and ecology of microbial plankton. Nature 427 (7057): 343-8.
↑ Konneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA. (2005). Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437 (7057): 543-6.
↑ Burns DG, Camakaris HM, Janssen PH, Dyall-Smith ML. (2004). Cultivation of Walsby's square haloarchaeon.. FEMS Microbiol Lett. 238 (2): 469-73.
↑ Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO. (2002). A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont.. Nature 417 (6884): 27–8.
↑ Nelson KE. et al. (1999). Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399 (6734): 323-9.
↑ Lake JA. (1988). Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences. Nature 331 (6152): 184-6.
↑ http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi

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[1] Woese C, Fox G (1977). Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A 74 (11): 5088–90.

[2] Woese, Carl R., Kandler, Otto, Wheelis, Mark L (1990). Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences 87 (12): 4576–4579.

[3] Hahn J, Haug P (1986). Traces of Archaebacteria in ancient sediments. System Appl Microbiol 7: 178-183..

[4] Chappe, B. and Albrecht, P. and Michaelis, W. ({1982). Polar Lipids of Archaebacteria in Sediments and Petroleums. Science 217: 65-66.

[5] Eckburg P, Lepp P, Relman D (2003). Archaea and their potential role in human disease. Infect Immun 71 (2): 591-6. PMID 12540534.

[6] Cavicchioli R, Curmi P, Saunders N, Thomas T (2003). Pathogenic archaea: do they exist?. Bioessays 25 (11): 1119-28. PMID 14579252.

[7] Lepp P, Brinig M, Ouverney C, Palm K, Armitage G, Relman D (2004). Methanogenic Archaea and human periodontal disease. Proc Natl Acad Sci U S A 101 (16): 6176-81. PMID 15067114.

[8] Giovannoni SJ, Stingl U. (2005). Molecular diversity and ecology of microbial plankton. Nature 427 (7057): 343-8.

[9] Konneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA. (2005). Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437 (7057): 543-6.

[10] Burns DG, Camakaris HM, Janssen PH, Dyall-Smith ML. (2004). Cultivation of Walsby's square haloarchaeon.. FEMS Microbiol Lett. 238 (2): 469-73.

[11] Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO. (2002). A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont.. Nature 417 (6884): 27–8.

[12] Nelson KE. et al. (1999). Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399 (6734): 323-9.

[13] Lake JA. (1988). Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences. Nature 331 (6152): 184-6.

[14] ttp://www.ncbi.nlm.nih.gov/genomes/lproks.cgi

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@@ Line 19: / Line 19: @@
 Phylum [[Nanoarchaeum|Nanoarchaeota]]
 }}
-'''Archaea''' ({{IPA|AmE [ɑɹˈkiə], BrE [ɑːˈkiːə]}};  from [[Greek language|Greek]] αρχαία, "ancient ones";  singular '''Archaeum''', '''Archaean''', or '''Archaeon'''), also called '''Archaebacteria''' ({{IPA|AmE [ɑɹkɪbækˈtɪɹɪə], BrE [ɑːkɪbækˈtɪəɹɪə]}}), is a major division of [[life|living]] [[organism]]s.  Although there is still uncertainty in the exact [[phylogeny]] of the groups, Archaea, [[Eukaryotes|Eukaryota]] and [[Eubacteria|Bacteria]] are the fundamental classifications in what is called the [[taxonomy#Domain and Kingdom systems|three-domain system]].  Like bacteria, Archaea are single-celled organisms lacking [[cell nucleus|nuclei]] and are therefore [[prokaryote]]s, classified as [[Monera]] in the alternative six-[[kingdom (biology)|kingdom]] [[Linnaean taxonomy|taxonomy]].  They were originally described in [[extremophile|extreme]] environments, but have since been found in all types of [[Habitat (ecology)|habitat]].
+'''Archaea''' ({{IPA|AmE [ɑɹˈkiə], BrE [ɑːˈkiːə]}};  from [[Greek language|Greek]] αρχαία, "ancient ones";  singular '''Archaeum''', '''Archaean''', or '''Archaeon'''), also called '''Archaebacteria''' ({{IPA|AmE [ɑɹkɪbækˈtɪɹɪə], BrE [ɑːkɪbækˈtɪəɹɪə]}}), is a major division of [[life|living]] [[organism]]s.  Although there is still uncertainty in the approximate [[phylogeny]] of the groups, Archaea, [[Eukaryotes|Eukaryota]] and [[Eubacteria|Bacteria]] are the fundamental classifications in what is called the [[three-domain system]].  Like bacteria, Archaea are single-celled organisms lacking [[cell nucleus|nuclei]] and are therefore [[prokaryote]]s, classified as belonging to kingdom [[Monera]] in the traditional six-[[kingdom (biology)|kingdom]] [[Linnaean taxonomy|taxonomy]].  They were originally described in [[extremophile|extreme]] environments, but have since been found in all types of [[Habitat (ecology)|habitat]].
 A ''single'' organism from this domain has been called an "'''archaean'''."  Furthermore, this biologic term is also used as an adjective.
 ==History==
-Archaea were identified in 1977 by [[Carl Woese]] and [[George E. Fox]] as being a separate branch based on their separation from other prokaryotes on 16S [[rRNA]] [[phylogenetic tree]]s.<ref>{{cite journal | author = Woese C, Fox G | title = Phylogenetic structure of the prokaryotic domain: the primary kingdoms | journal = Proc Natl Acad Sci U S A | volume = 74 | issue = 11 | pages = 5088–90 | year = 1977 | id = PMID 270744}}</ref> These two groups were originally named the Archaebacteria and Eubacteria, treated as [[kingdom (biology)|kingdom]]s or subkingdoms, which Woese and Fox termed Urkingdoms. Woese argued that they represented fundamentally different branches of living things. He later renamed the groups Archaea and [[Bacteria]] to emphasize this, and argued that together with [[Eukaryota|Eukarya]] they compose [[three-domain system|three Domains]] of living organisms.<ref>{{cite journal |quotes=no | author = Woese, Carl R., Kandler, Otto, Wheelis, Mark L | title = Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya | journal = Proceedings of the National Academy of Sciences | year = 1990 | issue = 12 | volume = 87 | pages = 4576–4579}}</ref>
+Archaea were identified in 1977 by [[Carl Woese]] and [[George E. Fox]] as being a separate branch based on their separation from other prokaryotes on 16S [[rRNA]] [[phylogenetic tree]]s.<ref>{{cite journal | author = Woese C, Fox G | title = Phylogenetic structure of the prokaryotic domain: the primary kingdoms | journal = Proc Natl Acad Sci U S A | volume = 74 | issue = 11 | pages = 5088–90 | year = 1977 | pmid =  270744}}</ref> These two groups were originally named the Archaebacteria and Eubacteria, treated as [[kingdom (biology)|kingdom]]s or subkingdoms, which Woese and Fox termed Urkingdoms. Woese argued that they represented fundamentally different branches of living things. He later renamed the groups Archaea and [[Bacteria]] to emphasize this, and argued that together with [[Eukaryota|Eukarya]] they compose [[three-domain system|three Domains]] of living organisms.<ref>{{cite journal |quotes=no | author = Woese, Carl R., Kandler, Otto, Wheelis, Mark L | title = Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya | journal = Proceedings of the National Academy of Sciences | year = 1990 | issue = 12 | volume = 87 | pages = 4576–4579}}</ref>
-The biological term, Archaea, should not be confused with the [[geologic]] phrase '''[[Archean]]''' eon, also known as the '''Archeozoic''' era. This latter term refers to the primordial period of [[earth]] history when Archaea and Bacteria were the only [[cellular]] organisms living on the planet.  Probable [[fossils]] of these [[microbes]] have been dated to almost 3.8 billion years ago (3800 [[Mya (unit)|mya]]).<ref>{{cite journal | author = Hahn J, Haug P | title = Traces of Archaebacteria in ancient sediments | journal = System Appl Microbiol | volume = 7 | pages = 178-183. | year = 1986}}</ref><ref>{{cite journal | author = Chappe, B. and Albrecht, P. and Michaelis, W. | title = Polar Lipids of Archaebacteria in Sediments and Petroleums | journal = Science | volume = 217 |  number = 4554 | pages = 65-66 | doi = 10.1126/science.217.4554.65 | year = {1982}}</ref>
+The biological term, Archaea, should not be confused with the [[geologic]] phrase '''[[Archean]]''' eon, also known as the '''Archeozoic''' era. This latter term refers to the primordial period of [[earth]] history when Archaea and Bacteria were the only [[cellular]] organisms living on the planet.  Probable [[fossils]] of these [[microbes]] have been dated to almost 3.8 billion years ago. Their remains have been found in sediment from western Greenland, the oldest sediment to be discovered.  (3800 [[Mya (unit)|mya]]).<ref>{{cite journal | author = Hahn J, Haug P | title = Traces of Archaebacteria in ancient sediments | journal = System Appl Microbiol | volume = 7 | pages = 178-183. | year = 1986}}</ref><ref>{{cite journal | author = Chappe, B. and Albrecht, P. and Michaelis, W. | title = Polar Lipids of Archaebacteria in Sediments and Petroleums | journal = Science | volume = 217 |  number = 4554 | pages = 65-66 | doi = 10.1126/science.217.4554.65 | year = {1982}}</ref>
 [[image:Phylogenetic_tree.svg|thumb|right|320px|A phylogenetic tree based on [[rRNA]] data, showing the separation of bacteria, archaea, and eukaryote.]]
@@ Line 45: / Line 45: @@
 ==Habitats==
 [[Image:Colourful Thermophilic Archaebacteria Stain in Midway Geyser Basin.jpg|thumb|right|200px|Archeans live in Yellowstone geysers]]
-They can survive and thrive at even relatively high temperatures, often above 100°C, as found in [[geyser]]s and [[black smoker]]s.  Others are found in very cold habitats or in highly-[[salt|saline]], [[acid]]ic, or [[alkaline]] water.  However, other archaeans are [[mesophile]]s, and have been found in environments like [[marsh]]land, [[sewage]], sea water and [[soil]].  Many [[methanogen]]ic archaea are found in the digestive tracts of animals such as [[ruminant]]s, [[termite]]s, and humans.  As of 2007, no clear examples of archaean pathogens are known,<ref>{{cite journal |author=Eckburg P, Lepp P, Relman D |title=Archaea and their potential role in human disease |journal=Infect Immun |volume=71 |issue=2 |pages=591-6 |year=2003 |id=PMID 12540534}}</ref><ref>{{cite journal |author=Cavicchioli R, Curmi P, Saunders N, Thomas T |title=Pathogenic archaea: do they exist? |journal=Bioessays |volume=25 |issue=11 |pages=1119-28 |year=2003 |id=PMID 14579252}}</ref> although a relationship has been proposed between the presence of some methanogens and human [[periodontal disease]].<ref>{{cite journal |author=Lepp P, Brinig M, Ouverney C, Palm K, Armitage G, Relman D |title=Methanogenic Archaea and human periodontal disease |journal=Proc Natl Acad Sci U S A |volume=101 |issue=16 |pages=6176-81 |year=2004 |id=PMID 15067114}}</ref>
-Archaea are usually placed into three groups based on preferred habitat. These are the [[halophile]]s, [[methanogen]]s, and [[thermophile]]s. Halophiles live in extremely saline environments. Methanogens live in [[anaerobic environment]]s and produce methane. These can be found in sediments or in the intestines of animals. Thermophiles live in places that have high temperatures, such as hot springs. These groups do not necessarily agree with molecular phylogenies, are not necessarily complete, nor are they mutually exclusive. Nonetheless, they are a useful starting point for more detailed studies.
+Many archaeans are [[extremophile]]s. They can survive and thrive at even relatively high temperatures, often above 100°C, as found in [[geyser]]s,[[black smoker]]s,and oil wells.  Others are found in very cold habitats or in highly-[[salt|saline]], [[acid]]ic, or [[alkaline]] water.  However, other archaeans are [[mesophile]]s, and have been found in environments like [[marsh]]land, [[sewage]], sea water and [[soil]].  Many [[methanogen]]ic archaea are found in the digestive tracts of animals such as [[ruminant]]s, [[termite]]s, and humans.  As of 2007, no clear examples of archaean pathogens are known,<ref>{{cite journal |author=Eckburg P, Lepp P, Relman D |title=Archaea and their potential role in human disease |journal=Infect Immun |volume=71 |issue=2 |pages=591-6 |year=2003 |id=PMID 12540534}}</ref><ref>{{cite journal |author=Cavicchioli R, Curmi P, Saunders N, Thomas T |title=Pathogenic archaea: do they exist? |journal=Bioessays |volume=25 |issue=11 |pages=1119-28 |year=2003 |id=PMID 14579252}}</ref> although a relationship has been proposed between the presence of some methanogens and human [[periodontal disease]].<ref>{{cite journal |author=Lepp P, Brinig M, Ouverney C, Palm K, Armitage G, Relman D |title=Methanogenic Archaea and human periodontal disease |journal=Proc Natl Acad Sci U S A |volume=101 |issue=16 |pages=6176-81 |year=2004 |id=PMID 15067114}}</ref>
-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. It is increasingly becoming recognised that [[methanogen]]s are commonly present in low-temperature environments such as cold [[sediment]]s. Some studies have even suggested that at these temperatures the pathway by which [[methanogenesis]] occurs may change due to the [[thermodynamic]] constraints imposed by low temperatures. Perhaps even more significant are the large numbers of archaea found throughout most of the world's oceans, a predominantly cold environment (Giovannoni and Stingl, 2005). These archaea, which belong to several deeply branching lineages unrelated to those previously known, can be present in extremely high numbers (up to 40% of the microbial biomass) although almost none have been isolated in [[pure culture]].<ref>{{cite journal | author = Giovannoni SJ, Stingl U. | title = Molecular diversity and ecology of microbial plankton | journal = Nature | volume = 427 | issue = 7057 | pages = 343-8 | year = 2005 | id = PMID 16163344 }}</ref> Currently we have almost no information regarding the physiology of these organisms meaning that their effects on global biogeochemical cycles remain unknown. One recent study has shown, however, that one group of marine [[crenarchaeota]] are capable of [[nitrification]], a trait previously unknown among the archaea.<ref>{{cite journal | author = Konneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA. | title = Isolation of an autotrophic ammonia-oxidizing marine archaeon | journal = Nature | volume = 437 | issue = 7057 | pages = 543-6 | year = 2005 | id = PMID 16177789 }}</ref>
+Archaea are usually placed into three groups based on preferred habitat. These are the [[halophile]]s, [[methanogen]]s, and [[thermophile]]s. Halophiles, sometimes known as ''Halobacterium'' live in extremely saline environments. Methanogens live in [[anaerobic environment]]s and produce methane. These can be found in sediments or in the intestines of animals. Thermophiles live in places that have high temperatures, such as hot springs. These groups do not necessarily agree with molecular phylogenies, are not necessarily complete, nor are they mutually exclusive. Nonetheless, they are a useful starting point for more detailed studies.
+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. It is increasingly becoming recognised that [[methanogen]]s are commonly present in low-temperature environments such as cold [[sediment]]s. Some studies have even suggested that at these temperatures the pathway by which [[methanogenesis]] occurs may change due to the [[thermodynamic]] constraints imposed by low temperatures. Perhaps even more significant are the large numbers of archaea found throughout most of the world's oceans, a predominantly cold environment (Giovannoni and Stingl, 2005). These archaea, which belong to several deeply branching lineages unrelated to those previously known, can be present in extremely high numbers (up to 40% of the microbial biomass) although almost none have been isolated in [[pure culture]].<ref>{{cite journal | author = Giovannoni SJ, Stingl U. | title = Molecular diversity and ecology of microbial plankton | journal = Nature | volume = 427 | issue = 7057 | pages = 343-8 | year = 2005 | pmid =  16163344 }}</ref> Currently we have almost no information regarding the physiology of these organisms meaning that their effects on global biogeochemical cycles remain unknown. One recent study has shown, however, that one group of marine [[crenarchaeota]] are capable of [[nitrification]], a trait previously unknown among the archaea.<ref>{{cite journal | author = Konneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA. | title = Isolation of an autotrophic ammonia-oxidizing marine archaeon | journal = Nature | volume = 437 | issue = 7057 | pages = 543-6 | year = 2005 | pmid =  16177789 }}</ref>
+==Form==
 [[Image:Relative scale.png|thumb|300px|left|The sizes of prokaryotes relative to other organisms and biomolecules.]]
-Individual archaeans range from 0.1 μm to over 15 μm in diameter, and some form aggregates or filaments up to 200 μm in length.  They occur in various shapes, such as spherical, rod-shape, spiral, lobed, or rectangular.  Recently, a species of flat, square archaean that lives in hypersaline pools has been discovered.<ref>{{cite journal | author = Burns DG, Camakaris HM, Janssen PH, Dyall-Smith ML. | title = Cultivation of Walsby's square haloarchaeon. | journal = FEMS Microbiol Lett. | | volume = 238| issue = 2 | pages = 469-73 | year = 2004 | id = PMID 15358434 | url = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15358434&query_hl=36&itool=pubmed_docsum}}</ref> They also exhibit a variety of different types of metabolism.  Of note, the [[halobacteria]] can use light to produce [[adenosine triphosphate|ATP]], although no Archaea conduct [[photosynthesis]] with an [[electron transport chain]], as occurs in other groups.  Rather light-activated ion pumps like [[bacteriorhodopsin]] and [[halorhodopsin]] play a role in generating ion gradients, whose energy then leads to production of ATP.
+Individual archaeans range from 0.1 μm to over 15 μm in diameter, and some form aggregates or filaments up to 200 μm in length.  They occur in various shapes, such as spherical, rod-shape, spiral, lobed, or rectangular. Archaea have no murein in their cell walls. Recently, a species of flat, square archaean that lives in hypersaline pools has been discovered.<ref>{{cite journal | author = Burns DG, Camakaris HM, Janssen PH, Dyall-Smith ML. | title = Cultivation of Walsby's square haloarchaeon. | journal = FEMS Microbiol Lett. | | volume = 238| issue = 2 | pages = 469-73 | year = 2004 | pmid =  15358434 | url = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15358434&query_hl=36&itool=pubmed_docsum}}</ref> They also exhibit a variety of different types of metabolism.  Of note, the [[halobacteria]] can use light to produce [[adenosine triphosphate|ATP]], although no Archaea conduct [[photosynthesis]] with an [[electron transport chain]], as occurs in other groups.  Rather light-activated ion pumps like [[bacteriorhodopsin]] and [[halorhodopsin]] play a role in generating ion gradients, whose energy then leads to production of ATP. Archaea can reproduce using binary and multiple fission, fragmentation, and budding.
 ==Evolution and classification==
-Archaea are divided into two main groups based on rRNA trees, the [[Euryarchaeota]] and [[Crenarchaeota]].  Two other groups have been tentatively created for certain environmental samples and the peculiar species ''[[Nanoarchaeum|Nanoarchaeum equitans]]'', discovered in 2002 by [[Karl Stetter]], but their affinities are uncertain.<ref>{{cite journal | author = Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO. | title = A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. | journal = Nature  | volume = 417 | issue = 6884 | pages = 27–8 | year = 2002| id = PMID 11986665}}</ref>
+Archaea are divided into two main groups based on rRNA trees, the [[Euryarchaeota]] and [[Crenarchaeota]].  Two other groups have been tentatively created for certain environmental samples and the peculiar species ''[[Nanoarchaeum|Nanoarchaeum equitans]]'', discovered in 2002 by [[Karl Stetter]], but their affinities are uncertain.<ref>{{cite journal | author = Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO. | title = A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. | journal = Nature  | volume = 417 | issue = 6884 | pages = 27–8 | year = 2002| pmid =  11986665}}</ref>
 Woese argued that the bacteria, archaea, and eukaryotes each represent a primary line of descent that diverged early on from an ancestral ''[[progenote]]'' with poorly-developed genetic machinery.  This hypothesis is reflected in the name Archaea, from the Greek ''archae'' or ancient.  Later he treated these groups formally as [[three-domain system|domain]]s, each comprising several kingdoms.  This division has become very popular, although the idea of the progenote itself is not generally supported.  Some biologists, however, have argued that the archaebacteria and eukaryotes arose from specialized eubacteria.
-The relationship between Archaea and Eukarya remains an important problem.  Aside from the similarities noted above, many genetic trees group the two together.  Some place eukaryotes closer to Eurarchaeota than Crenarchaeota are, although the membrane chemistry suggests otherwise.  However, the discovery of archaean-like genes in certain [[bacterium|bacteria]], such as ''Thermotoga'', makes their relationship difficult to determine, as [[horizontal gene transfer]] may have occurred<ref>{{cite journal | author = Nelson KE. et al. | title = Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima | journal = Nature | volume = 399 | issue = 6734 | pages = 323-9 | year = 1999 | id = PMID 10360571}}</ref>.  Some have suggested that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and cytoplasm, which accounts for various genetic similarities but runs into difficulties explaining cell structure.<ref>{{cite journal | author = Lake JA. | title = Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences | journal = Nature | volume = 331 | issue = 6152 | pages = 184-6 | year = 1988 | id = PMID 3340165}}</ref>
+The relationship between Archaea and Eukarya remains an important problem.  Aside from the similarities noted above, many genetic trees group the two together.  Some place eukaryotes closer to Eurarchaeota than Crenarchaeota are, although the membrane chemistry suggests otherwise.  However, the discovery of archaean-like genes in certain [[bacterium|bacteria]], such as ''Thermotoga'', makes their relationship difficult to determine, as [[horizontal gene transfer]] may have occurred<ref>{{cite journal | author = Nelson KE. et al. | title = Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima | journal = Nature | volume = 399 | issue = 6734 | pages = 323-9 | year = 1999 | pmid =  10360571}}</ref>.  Some have suggested that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and cytoplasm, which accounts for various genetic similarities but runs into difficulties explaining cell structure.<ref>{{cite journal | author = Lake JA. | title = Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences | journal = Nature | volume = 331 | issue = 6152 | pages = 184-6 | year = 1988 | pmid =  3340165}}</ref>
 Single gene [[sequencing]] for [[systematics]] has led to whole [[genome sequencing]]; by January, 2007, 31 archaeal genomes have been completed with 29 partially completed <ref>http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi</ref>.
@@ Line 81: / Line 83: @@
 {{wiktionary}}
 {{wikispecies}}
-* {{cite book | author=Howland, John L. | title=The Surprising Archaea: Discovering Another Domain of Life | location=Oxford | publisher=Oxford University Press | year=2000 | id=ISBN 0-19-511183-4}}
+* {{cite book | author=Howland, John L. | title=The Surprising Archaea: Discovering Another Domain of Life | location=Oxford | publisher=Oxford University Press | year=2000 | isbn= 0-19-511183-4}}
 * [http://www.microbe.org/microbes/archaea.asp Archaea]
 * [http://www.archaea.unsw.edu.au/ ArchaeaWeb - by UNSW - Information about Archaea]
@@ Line 91: / Line 93: @@
 * [http://archaea.ucsc.edu/ Browse any completed archaeal genome at UCSC]
 * [http://opm.phar.umich.edu/localization.php?localization=Archaebacterial%20membrane 3D structures of proteins from archaebacterial membranes]
 {{Extremophile}}
 [[Category:Life sciences]]
-{{credit|103481574}}
+{{credit|111285897}}

Difference between revisions of "Archaea" - New World Encyclopedia

Revision as of 03:01, 28 February 2007

Contents

History

Archaea, Bacteria and Eukaryotes

Habitats

Form

Evolution and classification

Biologists who have studied Archaea

See also

References
ISBN links support NWE through referral fees

Further reading and external links

Credits

Difference between revisions of "Archaea" - New World Encyclopedia

Revision as of 03:01, 28 February 2007

History

Archaea, Bacteria and Eukaryotes

Habitats

Form

Evolution and classification

Biologists who have studied Archaea

See also

ReferencesISBN links support NWE through referral fees

Further reading and external links

Credits

References
ISBN links support NWE through referral fees