Archaea

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, "old ones"; also called Archaebacteria , (AmE [ɑɹkɪbækˈtɪɹɪə], BrE [ɑːkɪbækˈtɪəɹɪə]), adjective: archaeal, is a major division of living organisms. Although there is still uncertainty in the exact phylogenic origins of the groups, Archaea, Eukaryota and Bacteria are the fundamental classifications in what is called the three-domain system and constitute three clearly defined patterns of life forms. The patterns are most clearly exhibited by the ribosomes and other components of the protein synthesis system (translation machinery) and these clearcut distinctions have been dubbed canonical patterns.

Like bacteria, Archaea are single-celled organisms lacking nuclei and are therefore prokaryotes, classified as Monera in the alternative five-kingdom taxonomy. They were originally described in extreme environments, but have since been found in all types of habitats.

A single organism from this domain is called an archaeon.

History

Archaea were identified in 1977 by Carl Woese and George Fox as being a separate branch based on their separation from other prokaryotes on 16S rRNA phylogenetic trees. 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.

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).

A phylogenetic tree of life based on differences in rRNA, showing the separation of bacteria, archaea, and eukaryotes.

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 phosphate in membrane phospho-lipids is the mirror image of that found in bacteria and eukaryotes. Distinctly different enzymes are needed to form these membrane components. Thus in Archaea the membrane fats contain sn-glycerol-1-phosphate (G1P), compared to sn-glycerol-3-phosphate (G3P) of bacteria.

• 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. Even in this case, 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.

Habitats

Many archaeans are extremophiles. Some live at very high temperatures, often above 100°C, as found in geysers and black smokers. 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. Archaea are usually harmless to other organisms and none are known to cause disease.

Archaea are usually placed into three groups based on preferred habitat. These are the halophiles, methanogens, and thermophiles. Halophiles 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. 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 (Könneke et al, 2006) has shown, however, that one group of marine crenarchaeota are capable of nitrification, a trait previously unknown among the archaea.

Form

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.[1]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.

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.

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. 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.

Single gene sequencing for systematics has led to whole genome sequencing; by Sept 16, 2006, 28 archaeal genomes have been completed with 25 partially completed [2].

Famous 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

References

Further reading

• Howland, John L. (2000). The Surprising Archaea: Discovering Another Domain of Life. Oxford: Oxford University Press. ISBN 0-19-511183-4. 
• Giovannoni, S.J. and Stingl, U. (2005). "Molecular diversity and ecology of microbial plankton". Nature 437: 343-348.

• Könneke, M., Bernhard, A.E., de la Torre, J.R., Walker, C.B., Waterbury, J.B. and Stahl, D.A. (2005). "Isolation of an autotrophic ammonia-oxidizing marine archaeon". Nature 437: 543-546.

• Lake, J.A. (1988). "Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences". Nature 331: 184–186.

• Woese, Carl R.; Fox, George E. (1977). "Phylogenetic Structure of the Prokaryotic Domain: The Primary Kingdoms". Proceedings of the National Academy of Sciences of the United States of America 74 (11): 5088–5090.

• 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.

Further reading

• Archaea
• ArchaeaWeb - by UNSW - Information about Archaea
• Introduction to the Archaea, ecology, systematics and morphology
• Archaea at The Encyclopedia of Astrobiology, Astronomy, & Spaceflight
• Extremophiles Bioprospecting for antimicrobials, Dr Sarah Maloney Citat: "...Ground breaking research on extremophiles continues to this day, with the recently-discovered 22nd genetically-encoded amino acid – pyrrolysine – from the archaeon, Methanosarcina barkeri, (Hao et al., 2002; Srinivasan et al., 2002)...."
• BBC News July 21, 1999: Toughest bug reveals genetic secrets Citat: "...It [Pyrococcus abyssi] likes conditions that the vast majority of other organisms would find impossible to live in. It thrives best at temperatures of about 103 degrees [Celsius] and under pressures of about 200 atmospheres...."
• Pyrococcus abyssi Home page at Genoscope
• Browse any completed archaeal genome at UCSC