Archaea

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Archaea
Fossil range: Paleoarchean - Recent
Halobacteria sp. strain NRC-1, each cell about 5 μm in length.
Halobacteria sp. strain NRC-1, each cell about 5 μm in length.
Scientific classification
Superdomain: Neomura
Domain: Archaea
Woese, Kandler & Wheelis, 1990
Phyla

Crenarchaeota
Euryarchaeota
Korarchaeota
Nanoarchaeota
ARMAN

The Archaea (pronounced /ɑrˈkiːə/) are a group of prokaryotic, single-celled microorganisms. In this they are similar to bacteria but these two groups evolved differently, and are classified as different domains in the three-domain system. Originally these organisms were named archaebacteria. However, this term has not been favored since the three-domain system became popular.

Although there is still uncertainty in the phylogeny, Archaea, Eukaryota and Bacteria were introduced as the fundamental classifications in what would later become the three-domain system by Carl Woese in 1977. As prokaryotes, archaea are also classified in kingdom Monera in the traditional five-kingdom Linnaean taxonomy. While their prokaryotic cell structure is similar to Bacteria, the genes of Archaea and several of their metabolic pathways are more closely related to those of eukaryotes. One way to account for this is to group archaeans and eukaryotes together in the clade Neomura, which might have arisen from gram-positive bacteria. On the other hand, other studies have suggested that Archaea may instead be the most ancient lineage in the world, with bacteria and eukaryotes diverging from this group.[1]

Archaea were originally described in extreme environments, but have since been found in all habitats and may contribute up to 20% of total biomass.[2] These cells are particularly common in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet.[3] A single individual or species from this domain is called an archaeon (sometimes spelled "archeon"),[4] while the adjectival form is archaeal or archaean. The etymology is Ancient Greek, from ἀρχαία meaning "ancient things".

Contents

Microbiology

Further information: Microbiology

Early in the 20th century, prokaryotes were regarded as a single group of organisms and classified based on their biochemistry, morphology and metabolism. For example, microbiologists tried to classify microorganisms based on the substances they consume, their shapes, and the structures of their cell walls.[5] However, a new approach was proposed in 1965,[6] and microbiologists began to examine the sequences of the genes in these organisms and use this genetic information to work out which prokaryotes are genuinely related to each other: this is known as phylogenetics.

Archaea were first detected in extreme environments, such as volcanic hot springs.
Archaea were first detected in extreme environments, such as volcanic hot springs.

Archaea were identified as a separate group of prokaryotes in 1977 by Carl Woese and George E. Fox due to their separation from other prokaryotes in phylogenetic trees that were based on the sequences of ribosomal RNA (rRNA) genes.[7] These two groups were originally named the Archaebacteria and Eubacteria and treated as kingdoms or subkingdoms, which Woese and Fox termed Urkingdoms. Woese argued that this group of prokaryotes represented a fundamentally different branch of living things. He later renamed the two groups of prokaryotes Archaea and Bacteria to emphasize this, and argued that together with Eukarya they compose three Domains of living organisms.[8] At first, only the methanogens were placed in this new domain, but gradually microbiologists realized that the archaea are a large and diverse group of organisms.

Initially, archaea were thought of as extremophiles that existed only in apparently-inhospitable habitats, such as hot springs and salt lakes, but in the late 20th century it became increasingly clear that archaea are in fact widely distributed in nature and are common inhabitants of much less extreme habitats, such as soils and oceans.[9] This new appreciation of the importance and ubiquity of archaea came mostly from the increasing application of molecular biology techniques that could detect prokaryotes in samples of water or soil from their nucleic acids alone, avoiding the need to find ways to culture the organisms in the laboratory.[10][11]

Origin and early evolution

Further information: Timeline of evolution

The Archaea should not be confused with the geological term Archean eon, also known as the Archeozoic era. This refers to the primordial period of earth history when prokaryotes were the only cellular organisms living on the planet.[12][13] Probable fossils of these ancient cells have been dated to almost 3.5 billion years ago,[14] and the remains of lipids that may be either archaean or eukaryotic have been detected in shales dating from 2.7 billion years ago.[15]

Phylogenetic tree showing the relationship between the archaea and other forms of life. Eukaryotes are colored red, archaea green and bacteria blue.
Phylogenetic tree showing the relationship between the archaea and other forms of life.[16] Eukaryotes are colored red, archaea green and bacteria blue.

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.[17] 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.[18] One possibility is that the last common ancestor of the bacteria and archaea may have been a non-methanogenic thermophile, which raises the possibility that lower temperatures are extreme environments in archaeal terms, and organisms that can survive in cooler environments appeared later in the evolution of these organisms.[19]

The relationship between archaea and eukaryotes remains an important problem. Aside from the similarities noted above, many genetic trees group the two together, with some analyses even suggesting that eukaryotes have a closer relationship to the archaeal phylum Euryarchaeota than the relationship between the Euryarchaeota and the phylum Crenarchaeota: although the shared similarities in the cell structure of the archaea might suggest otherwise. However, the discovery of archaean-like genes in certain bacteria, such as Thermotoga maritima, makes these relationships difficult to determine, as horizontal gene transfer has occurred.[20]

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.[21] However, a recent large scale phylogenetic analysis of the structure of proteins encoded in almost 200 completely sequenced genomes showed that the origin of Archaea is much more ancient and that the archaeal lineage may represent the most ancient that exists on earth.[1] In fact, the study shows that the ancestor of all life had a proteome with a rather complex collection of protein structures, many of which are widely spread in modern metabolism. Single gene sequencing for systematics has led to whole genome sequencing; by March, 2008, 49 archaeal genomes have been completed with 34 in progress.[22]

In 1998, Woese described a novel hypothesis that posits that during early life on earth, horizontal gene transfer within a common "colony" dominated the evolutionary process, eventually giving rise to the division into the three domains, where vertical gene transfer became dominant.[23] According to Woese, this combination of horizontal and vertical gene transfer could explain the differing pictures of the evolutionary history of Archaea, Bacteria and Eukaryotes that are given by analyses that examine different genes; since although the set of genes within the genomes of a species will be inherited as a group in modern organisms, these genes might not have been inherited together in the past. Instead genomes could have been assembled by the free exchange of genes between the members of an ancestral community of ancient organisms.

Classification

Phylogenetic tree showing extensive horizontal gene transfer between domains and an ancestral colony as the root of the tree.
Phylogenetic tree showing extensive horizontal gene transfer between domains and an ancestral colony as the root of the tree.
Further information: Biological classification and Systematics

The classification of archaea, and of prokaryotes in general, is a rapidly-moving and contentious field. These classification systems aim to organize archaea into groups of organisms that share structural features and common ancestors.[24] This follows the classification of other organisms, with a popular definition of a species in animals being a set of actually or potentially interbreeding populations that are reproductively isolated from other such groups.[25] However, efforts to classify prokaryotes such as archaea into species are complicated by the fact that they are asexual and show high levels of horizontal gene transfer between lineages. The area is controversial, with for example, some arguing that in groups such as the genus Ferroplasma, related archaea form population clusters that can be seen as species.[26] On the other hand, studies in Halorubrum found significant genetic exchange between such population clusters.[27] Such results have led to the argument that prokaryotic species are points within an interconnected net of gene transfer events, rather than parts of a standard phylogenetic tree.[28]

The current state of knowledge on archaean diversity is fragmentary.[29] Estimates of the total number of phylum-level lineages in the archaea range from 18 to 23, of which only 8 phyla have representatives that have been grown in culture and studied directly. Many of these hypothetical groups are known from only a single rRNA sequence, indicating that the vast majority of the diversity among these organisms remains completely unknown.[30] This problem of how to study and classify an uncultured microbial majority is common across all prokaryotes.[31]

Most of the well-studied species of archaea are members of two main phyla, the Euryarchaeota and Crenarchaeota. Other groups have been tentatively created, such as the peculiar species Nanoarchaeum equitans that was discovered in 2003 has been given its own phylum, the Nanoarchaeota;[32] and the phylum Korarchaeota that contains a small group of thermophilic species, which are most closely related to the Crenarchaeota.[33] Other recently-detected species of archaea cannot be easily classified within any of these groups, such as the Archael Richmond Mine Acidophilic Nanoorganisms (ARMAN) that were discovered in 2006.[34]

Morphology and physiology

The sizes of prokaryotic cells relative to other cells and biomolecules.
The sizes of prokaryotic cells relative to other cells and biomolecules.

Size and shape

Individual archaeans range from 0.1 micrometres (μm) to over 15 μm in diameter, and occur in various shapes, commonly as spheres, rods, spirals or plates.[35] Other morphologies in the Crenarchaeota include irregularly-shaped lobed cells in Sulfolobus, thin needle-like filaments that are less than half a micometre in diameter in Thermofilum, and almost perfectly rectangular rods in Thermoproteus and Pyrobaculum.[36] Recently, even a species of flat, square archaea called Haloquadra walsbyi that lives in hypersaline pools has been discovered.[37] These unusual shapes are probably maintained both by their cell walls and a prokaryotic cytoskeleton, but in contrast to the bacteria, these cellular structures are poorly understood in archaea.[38] However, proteins related to the cytoskeleton components of other organisms have been identified in the archaea,[39] and filaments have been observed within these cells.[40]

Some species of archaea form aggregates or filaments of cells up to 200 μm in length,[35] and these organisms can be prominent members of the communities of microbes that make up biofilms.[41] A particularly elaborate form of multicellular colonies are produced by archaea in the genus Pyrodictium. Here, the cells produce arrays of long, thin hollow tubes called cannulae, that stick out from the cells' surfaces and connect them together into a dense bush-like colony.[42] The function of these cannulae is not known, but they may allow the cells to communicate or exchange nutrients with their neighbors.[43]

Comparison of archaeal, bacterial and eukaryotic cells

Archaea are similar to other prokaryotes in many aspects of their cell structure and metabolism, but other characteristics set the Archaea apart.

Like bacteria and eukaryotes, archaea possess glycerol-based phospholipids called ether lipids.[44] However, three features of archaeal lipids are highly unusual:[45]

Membrane structures. Top: archaeal membrane, 1-isoprene sidechain, 2-ether linkage, 3-L-glycerol, 4-phosphate moieties. Middle: bacterial and eukaryan membrane: 5-fatty acid, 6-ester linkage, 7-D-glycerol, 8-phosphate moieties. Bottom: 9-lipid bilayer of bacteria and eukarya, 10-lipid monolayer of some archaea.
Membrane structures. Top: archaeal membrane, 1-isoprene sidechain, 2-ether linkage, 3-L-glycerol, 4-phosphate moieties. Middle: bacterial and eukaryan membrane: 5-fatty acid, 6-ester linkage, 7-D-glycerol, 8-phosphate moieties. Bottom: 9-lipid bilayer of bacteria and eukarya, 10-lipid monolayer of some archaea.
  • The archaeal lipids are unique because the stereochemistry of the glycerol is the reverse of that found in bacterial and eukaryotic lipids - the glycerol components of these lipids are mirror images of each other. In archaea, acyl chains are attached to the sn-2 and sn-3 positions of the glycerol, while bacterial and eucaryal lipids have acyl chains at the sn-1 and sn-2 positions. 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. 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 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.

Cell wall and flagella

Further information: Cell wall

Although not unique, archaeal cell walls are also unusual. For instance, in most archaea they are formed by surface-layer proteins or an S-layer.[46] S-layers are also found in some 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).[47]

Archaeans also have flagella that are notably different in composition and development from the superficially similar flagella of bacteria.[48] The bacterial flagellum is a modified type III secretion system, while archeal flagella appear to be homologous to the bacterial type IV pili.[49]

Metabolism

Further information: Microbial metabolism

Archaea exhibit a variety of different types of metabolism; there are nitrifiers, methanogens and anaerobic methane oxidisers.[4] Methanogens live in anaerobic environments and produce methane. Of note are the halobacteria, which use light to produce energy. Although no archaea fix carbon through photosynthesis, in some archaea light-activated ion pumps like bacteriorhodopsin and halorhodopsin generate ion gradients, which are converted into adenosine triphosphate (ATP).[35]

Reproduction

Further information: Asexual reproduction

Archaea reproduce asexually by binary or multiple fission, fragmentation, or budding; meiosis does not occur, so if a species of archaea exists in more than one form, these will all have the same number of chromosomes (they have the same karyotype).[35] Cell division is controlled in the archaea as part of a complex cell cycle where the cell's chromosome is replicated, the two daughter chromosomes are separated, and the cell then divides.[50] The details of the archaeal cell cycle have only been investigated in the genus Sulfolobus, but here it has characters that are similar to both bacterial and eukaryotic systems: with the chromosomes being replicated from multiple starting-points (origins of replication) using DNA polymerases that are similar to the equivalent eukaryotic enzymes.[51] However, the proteins that direct cell division, such as the 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, appear to be closer to their bacterial equivalents.[50]

Spores, such as the endospores made by some bacteria, are not formed in any of the known archaea,[52] although some species of haloarchaea can undergo phenotypic switching and grow as several different types of cell, including thick-walled structures that are resistant to osmotic shock and allow them to survive in water at low concentrations of salt.[53] These are not reproductive structures, but may instead help these species disperse to new habitats.

Genetics

Further information: Plasmid, Genome

Archaea are similar to bacteria in that they usually have a single circular chromosome.[54] These range in size from 5,751,492 base pairs in Methanosarcina acetivorans,[55] the largest archaean genome sequenced to date, to the tiny 490,885 base-pair genome of Nanoarchaeum equitans, which is the smallest microbial genome known and may contain only 537 protein-encoding genes.[56] Plasmids are also found in archaea, and can spread between cells by physical contact, in a process that may be similar to bacterial conjugation.[57][58] Archaeal plasmids are increasingly important as genetic tools and allow the performance of genetic studies in archaea.[59]

Sulfolobus infected with the DNA virus STSV1. Bar is 1 micrometre.
Sulfolobus infected with the DNA virus STSV1.[60] Bar is 1 micrometre.

As with the bacteriophages that infect bacteria, viruses exist that replicate within archaea: these are double-stranded DNA viruses that appear to be unrelated to any other form of virus and can have a variety of unusual shapes, with some resembling bottles, hooked rods, or teardrops.[61] These viruses have been studied in most detail in the thermophilic archaea, particularly the orders Sulfolobales and Thermoproteale.[62] Defenses against these viruses may involve RNA interference from repetitive DNA sequences within archaean genomes that are related to the genes of the viruses.[63][64]

Archaea are genetically distinct from other organisms, with up to 15% of the proteins encoded by any one archaeal genome being unique to the Archaea, although most of these unique genes have no known function.[65] Of the remainder of the genes that are unique to archaea and do have an identified function, most are involved in methanogenesis. The genes that are shared between archaea, bacteria and eukaryotes form a common core of cell function, relating mostly to transcription, translation, and nucleotide metabolism.[66] Other characteristic features of archaean genomes are the organization of genes of related function, such as enzymes catalysing steps in the same metabolic pathway, into novel operons, and large differences in tRNA genes and their aminoacyl tRNA synthetases.[66]

Transcription and translation in archaea are more similar to that in eukaryotes than in bacteria, with both the RNA polymerase II and the ribosomes of archaea sharing both subunits and sequence similarity with their equivalents in eukaryotes.[54] The function and interactions of the archaeal RNA polymerase in transcription also seems to be related to that of eukaryotes, with similar assemblies of proteins (the general transcription factors) directing the binding of the RNA polymerase to a gene's promoter. However, many other archaean transcription factors are similar to those seen in bacteria.[67]

Habitats and interactions with other organisms

Multiple archaeans are extremophiles, and some would say this is their ecological niche.[4] They can survive high temperatures, often above 100 °C, as found in geysers, black smokers, and oil wells. Some are found in very cold habitats and others in highly saline, acidic, or alkaline water. Mesophiles favor milder conditions in marshland, sewage 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 archaeal pathogens are known,[68][69] although a relationship has been proposed between the presence of some methanogens and human periodontal disease.[70]

Image of plankton in the oceans; archaea form a major part of oceanic life.
Image of plankton in the oceans; archaea form a major part of oceanic life.

Archaea are commonly placed into three physiological groups. These are the halophiles, thermophiles and acidophiles. These groups are not necessarily comprehensive or monophyletic, nor even mutually exclusive. Nonetheless, they are a useful starting point for ecological studies. Halophiles, including the genus Halobacterium, live in extremely saline environments and start outnumbering their bacterial counterparts at salinities greater than 20-25%.[4] These can be found in sediments or in the intestines of animals.[71] Thermophiles live in places that have high temperatures, such as hot springs. Where optimal growth occurs at greater than 80 °C, the archaeon is a hyperthermophyle, and the highest recorded temperature survived was 121 °C. Although thermophilic bacteria predominate at some high temperatures, archaea generally have the edge when acidity exceeds pH 5. True acidophiles withstand pH 0 and below.[4]

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. 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.[72] 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.[73]

Significance in technology and industry

Further information: Biotechnology

Extremophile archaea, particularly organisms that are resistant to heat, or extremes of acidity and alkalinity, are a source of enzymes that can function under these harsh conditions.[74][75] These enzymes have a wide range of uses. For example, thermostable DNA polymerases, such as the Pfu DNA polymerase from Pyrococcus furiosus, have revolutionized molecular biology by allowing the polymerase chain reaction to be used as a simple and rapid technique for cloning DNA. In industry, amylases, galactosidases and pullulanases in other species of Pyrococcus that function at over 100 °C allow food processing at high temperatures, such as the production of low lactose milk and whey.[76] Enzymes from these thermophilic archaea also tend to be very stable in organic solvents, so can be used in a broad range of environmentally-friendly processes in green chemistry that synthesize organic compounds.[75]

In contrast to the range of applications of archaean enzymes, the use of the organisms themselves in biotechnology are more restricted. However, methanogenic archaea are a vital part of sewage treatment, since they are part of the community of microorganisms that carry out anaerobic digestion and produce biogas.[77] Acidophillic archaea also show promise in the extraction of metals such as gold, cobalt and copper from ores in mineral processing.[78]

A new class of potentially useful antibiotics are derived from the Archaea group of organisms. Eight of these archaeocins have been characterized, but hundreds more are believed to exist, especially within the haloarchaea. The discovery of new archaeocins hinges on recovery and cultivation of archaeal organisms from the environment. [79]

See also

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