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Archaea

Taxonomy

The Archaea represent a monophyletic group distinct from both Bacteria and Eukarya. The Archaea fall into two major phyla: Euryarchaea and Crenarchaea. Phenotypically, cultivated crenarchaea and some euryarchaea are sulfur-metabolizing thermophiles (yellow in the tree above), whereas the euryarchaea also include the methanogens (green) and extreme halophiles (red). Both major phyla are also home to a large number of ssu-rRNA sequences apparently from planktonic marine species; the phenotypes of these organisms are not known. Two potential minor phyla are the Nanoarchaea and Korarchaea; the relationships between these minor phyla and either the Euryarchaea of Crenarchaea remain unclear.

General properties of the Archaea

Although they superficially resemble Bacteria, the Archaea are neither Bacteria nor Eukarya. In some respects, Archaea do resemble Bacteria. Most metabolic proteins are similar to those of Bacteria, as are gene and chromosome structure, the processes of replication, transcription, and translation, and the cytoskeleton. In many other respects, however, the Archaea are more similar to Eukarya. Most of the information-processing machinery (replication, transcription, translation) is eukaryal-like. Archaea also have nucleosomes, nucleolar enzymes, and cell-cycle proteins not present (or at least very different) in Bacteria. And in some ways, Archaea are different that either Bacteria or Eukarya, the most obvious being membrane lipids.

Morphology
Phenotypically, the Archaea are a lot like Bacteria. Most are small (0.5-5 microns) rods, cocci, spirilla, and filaments. Archaea most often reproduce by fission, like most Bacteria and most unicellular Eukarya, and reproduction is asexual.

Cell envelop
One of the unique features of Archaea are their membrane lipids, which are quite different than those of either Bacteria or Eukarya. They are ether-linked (not ester-linked) glycerol derivatives of 20 or 40 carbon branched (isoprenyl) lipids. Unsaturations in the lipid chain are generally conjugated (those of Bacteria & eukaryotes are unconjugated). 40-carbon lipids are ether-linked to glycerol at both ends, and if these glycerol moieties are on opposite sides of the membrane form lipid monolayers rather than bilayers. These lipids can be used as chemical signatures for the presence of Archaea in a sample.

Archaea have a cytoplasm membrane only; they do not have an outer membrane.

The Archaea have a wide various cell walls, but none contain peptidoglycan, the signature of bacterial cell walls. Protein or glycoprotein S-layers are common, as are cell walls containing pseudomurien, which is chemically related to peptidoglycan in that it is a fabric of linear disaccharide polymer crosslinked with oligopeptides.

Flagella
Although the flagella of Archaea (those that have them) resemble bacterial flagella superficially, they are fundamentally different structures. Like bacterial flagella, archaeal flagella are composed of a motor embedded in the cell envelop, and a long semi-flexible helical filament that is turned by the motor and drives the cell. The similarity ends there. The archaeal flagellar motor proteins and structure are related to type II secretion systems and type IV pili, whereas bacterial flagella are related to type III secretion systems. The archaeal flagellar motor is driven directly by ATP hydrolysis rather than the flow of protons across the cell membrane - it is a chemical motor rather than an electric motor. Archaeal flagellar filaments are much thinner than are those of bacteria, and are not hollow; protein subunits are added to the base to lengthen the filament, rather than the tip as in Bacteria. Clearly these structures are analogous rather than homologous; they evolved from independent origins, and are a classic example of evolutionary convergence.

Transcription and translation
The transcriptional/translational machinery in Archaea is fundamentally like those of Bacteria and Eukarya, with 70S (bacterial-sized) ribosomes. Genes are arranged in co-transcribed clusters (operons). Ribosomes recognize translational start sites and bind to the mRNAs directly at 'Shine-Dalgarno' (SD) sequences as in Bacteria. Also as in Bacteria, transcription and translation are linked - that is, they occur simultaneously.

However, in many ways transcription and translation in Archaea is like it is in Eukarya. Although each promoter drives the expression of an entire operon, the promoters are very much like eukaryotic RNA polymerase II promoters, and as in eukaryotes, are binding sites for transcription factors rather than the RNA polymerase itself, as in Bacteria. Archaea have a single RNA polymerase (like Bacteria), but this RNA polymerase is essentially a eukaryotic RNA polymerase II, and requires the same general transcription factors for promoter recognition. Translation is initiated with methionine (like Eukarya) rather than formyl-methionine (Bacteria). Translation is inhibited by diphtheria toxin, as are eukaryal ribosomes, but is not inhibited by most bacterial-translation-inhibiting antibiotics. Chimeric archaeal/eukaryal ribosomes are functional; neither bacterial/archaeal nor bacterial/eukaryal are functional.

Genomes
The genomes of Archaea are generally ca. 2-4Mbp, usually in one main circular DNA molecule, as to most Bacteria. However, as in eukaryotes, Archaea have abundant histone-like proteins and the DNA is packaged in the form of nucleosome-like particles. Hyperthermophilic species contain a reverse gyrase that positively supercoils this genomic DNA, rendering it more resistant to thermal denaturation.

In the same way that transcription and translation processes are generally like those of Bacteria although the machinery that carries these out is essentially like those of Eukarya, so too the genome replication process is similar in Archaea and Bacteria, with one (or a small number of) replication origin and a replication terminus, but this process is carried out by replication machinery that closely resembles the eukaryal replisome. In addition, chromosome replication and segregation/mitosis seem to be distinct processes in the cell cycle of Archaea, as in Eukarya.

Phylum Crenarchaea

Taxonomy

• Phylum Crenarchaeota
  • Class Thermoprotei
    • Order Thermoproteales
      • Family Thermoproteaceae (e.g. Thermoproteus, Pyrobaculum)
      • Family Thermofilaceae (Thermofilum)
    • Order Caldisphaerales
      • Family Caldisphaeraceae (Caldisphaera)
    • Order Desulfurococcales
      • Family Desulforococcaceae (e.g. Desulfurococcus, Aeropyrum)
      • Family Pyrodictiaceae (Pyrodictium, Pyrolobus, Hyperthermus)
    • Order Sulfolobales
      • Family Sulfolobaceae (e.g.Sulfolobus, Acidianus, Desulfurolobus)
        
        
  • Incertae sedis
    • Group I marine Archaea (e.g. Cenarchaeum symbiosum)

About this phylum

Diversity
Cultivated crenarchaea are all relatively closely-related and primitive (at least in terms of their ssu-rRNA branch sequences). Crenarchaeal sequences from environmental surveys are much more diverse, and are often abundant in non-thermophilic environments from which no cultivated crenarchaea are known. A large phylogenetic group of cultivated crenarchaea known as the “marine group I Archaea” was first seen in marine water surveys but since found in many other non-thermophilic environments,

Metabolism
Cultivated crenarchaeal generally oxidize and/or reduce sulfur and sulfur compounds (at least facultatively) by one of three biochemical processes:

1. Sulfur reduction

Sulfur + H2 ---> H2S + protons

These organisms are autotrophic anaerobes that fix carbon from CO2. Hydrogen is the electron donor for electron transport and elemental sulfur (or sulfur compounds such as thiosulfate) is the terminal electron acceptor.

2. Sulfur respiration

Sulfur + organics ---> CO2 + H2S

These organisms are heterotrophic anaerobes. Both carbon and energy are from organic compounds. Organics are the electron donor for electron transport and sulfur (or sulfur compounds) is the terminal electron acceptor. This process is much like aerobic respiration, except that sulfur compounds take the place of O2. In fact, many organisms that grow by sulfur respiration can also grow by aerobic respiration.

3. Sulfur oxidation

Sulfur + O2 ---> H2SO4

These organisms can usually grow heterotrophically, getting fixed carbon from low concentrations of organics in the medium. Most can also be grown autotrophically, fixing carbon from CO2 via the reverse TCA cycle. All are aerobes, of course, since it is the terminal electron acceptor (sulfur is the electron donor) for electron transport.

In most cases reduced sulfur compounds such as thiosulfate or sulfite are also usable in place of elemental sulfur. Cultivated crenarchaea are all thermophilic, and most are extremely thermophilic, with optimal growth temperatures above 80°C. As a group, these are the most thermophilic organisms known. Many are also acidophilic and autotrophic. Because this phenotype is shared by the most primitive and deepest branches of the Euryarchaea, it is probably the primitive phenotype of the Archaea.

At least some of the “marine group I” crenarchaea are anaerobic ammonia oxidizers.

Morphology
Cellular morphology of crenarchaea generally follow the phylogenetic subgroups: most Thermoproteales are rod-shaped or filamentous, most Desulfurococcales are flattened ovoids, an most Sulfolobales are irregular cocci.

Habitat
Cultivated crenarchaea are common in hydrothermal environments, especially acidic hot springs, solfataras, and marine hydrothermal vents. Uncultivated crenarchaea are apparently very common in some non-thermophilic environments, including ocean water, soil, and cave rock surfaces. One uncultivated specie, Cenaerchaeum symbiosum, is a symbiont of a marine sponge, but no other crenarchaeal symbionts or parasites of plants or animals are known.

Example species

Thermoproteus tenax

Thermoproteus tenax, like other Thermoproteales, are strict anaerobes that grow best (at least in cultivation) by sulfur respiration. It is an extreme thermophile, and so anaerobiosis is not surprizing; the solubility of oxygen in water at temperatures above 85°C is extremely low. Although it grows best in culture by sulfur respiration, the more usual growth conditions for these organisms in the wild is probably autotrophic sulfur reduction. So, T. tenax can either respire heterotrophically or reduce sulfur autotrophically for a living, and the switch between growth modes is a distinct developmental process.

T. tenax is a long rod-shaped organism that reproduces by branch formation; the branch bud forms near the end of a cell and grows into a new individual cell. It is a common solfatara inhabitant, with an optimal growth temperature of 85°C. T. tenax is motile, but this is not usually seen microscopically; after all, the room temperature of a microscope slide is 65°C below the optimal growth temperature of the organism!

Pyrodictium occultum

Pyrodictium is a marine organism common in deep sea hydrothermal vents. It is a flat irregular coccus (think of the body of a prickly-pear cactus) with a network of tubular fibriles that connect cells together. The optimal growth temperature is 105°C, and cultures grow well at temperatures up to 115°C, making it one of the most thermophilic species known. They are also one the most primitive organisms known; this is a general rule, that thermophiles, and especially extreme thermophiles, are primitive, at least in terms of their ssu-rRNA sequences. P. occultum can grow either by sulfur respiration or sulfur reduction.

Sulfolobus solfataricus

S. solfataricus is a lobed coccus; the lobes seem to be budding scars from reproduction, and often these buds can be almost like appendages that hold the cell to the sulfur granules they're growing on. S. solfataricus and its relatives are common, even predominant organisms of solfataras and boiling mud pots.

S. solfataricus is an obligate aerobe or microaerophile, capable of autotrophic sulfur oxidation, chemolithoheterotrophy (using sulfur oxidation for energy but requiring organic carbon for growth), or heterotrophy by oxidative respiration. S. solfataricus is an obligate thermoacidophile, requiring a pH of ca. 4.5 and temperature of 87°C for optimal growth. Like most acidophiles, they are sensitive to fatty acid toxicity; fatty acids are protonated and so uncharged at these environmental pH’s, diffuse readily through the cytoplasmic membrane, then ionize at the more moderate cytoplasmic pH. This results in an uncoupling of the proton gradient and acidification of the cytoplasm.

Phylum Euryarchaea

• Phylum Euryarchaeota
  • Class Methanobacteria
    • Order Methanobacteriales
      • Family Methanobacteriaceae (e.g. Methanothermobacter)
      • Family Methanothermaceae (Methanthermus)
  • Class Methanococci
    • Order Methanococcales
      • Family Methanococcaceae (e,g, Methanococcus)
      • Family Methanocaldococcaceae (e.g. Methanocaldococcus)
  • Class Methanomicrobia
    • Order Methanomicrobiales
      • Family Methanomicrobiaceae (e.g. Methanogenium)
      • Family Methanocorpusculaceae (e.g. Methanocorpusculum)
      • Family Methanospirillaceae (Methanospirillum)
    • Order Methanosarcinales
      • Family Methanosarcinaceae (e.g. Methanosarcina, Methanolobus)
      • Family Methanosaetaceae (Methanosaeta, Methanothrix)
      • Family Methanocalculus (Methanocalculus)
  • Class Methanopyri
    • Order Methanopyrales
      • Family Methanopyraceae (Methanopyrus)
  • Class Halobacteria
    • Order Halobacteriales
      • Family Halobacteriaceae (e.g. Halobacterium, Natronobacterium)
  • Class Thermoplasmata
    • Order Thermoplasmatales
      • Family Thermoplasmataceae (Thermoplasma)
      • Family Picrophilaceae (Picrophilus)
      • Family Ferroplasmataceae (Ferroplasma)
  • Class Thermococci
    • Order Thermococcales
      • Family Thermococcaceae (e.g. Thermococcus, Pyrococcus)
  • Class Archaeoglobi
  • Order Archaeoglobales
    • Family Archaeoglobaceae (e.g. Archaeoglobus, Geoglobus)
      

About this phylum

Diversity
The euryarchaea are more diverse both phylogenetically (as measured by ssu-rRNA sequence) and phenotypically than are the crenarchaea. The primitive phenotype of the euryarchaea seems to have been sulfur-metabolizing thermophily, and because this is also the general phenotype of the crenarchaea, this is the most likely phenotype of the ancestral archaeon. However, methanogenesis arose early in the evolution of the euryarchaea, and is the predominant phenotype of this phylum (at least among cultivated species). Two groups with methanogenic ancestry have reverted to sulfur-metabolizing thermophily (defined broadly); the Thermoplasmata, relatives of the Methanomicrobia and Halobacteria, and the Archaeoglobi, perhaps related to the Methanococci, although their placement in the tree is not entirely clear. The extreme halophiles are a third group with methanogenic ancestry and are, like the Thermoplasmata, specifically related to the Methanomicrobia.

The placement of Methanopyrus as a very primitive branch at the base of the euryarchaea in ssu-rRNA-based trees seems to be a long-branch attraction artifact; most trees based on non-rRNA sequences indicate that Methanopyrus is a relative of the Methanobacteria.

Methanogens

Other than the fact that they all make a living the same general way (by methanogenesis), methanogens are a diverse phenotypic and ecological group.The methanogens fall into three main groups: Methanococci, Methanobacteria, and Methanomicrobia. They are chemolithotrophic, generating energy by the production of methane, and often autotrophic. All are extreme anaerobes, much more sensitive to oxygen or oxidizing environments than are most other anaerobes, and so cultivation requires specialized equipment and techniques. Many methanogens are thermophilic, but this is not a general property of these organisms; mesophily is also common.

Metabolism

Methanogens obtain energy by the reduction of one- or two-carbon compounds to methane. C1 compounds (formate, CO2, CO) are reduced using hydrogen as the electron donor and covalently attached to methanofuran in the form of a formyl group. This formyl is transfered to tetrahydromethanopterin (H4MPT) and sequentially reduced through methenyl and methylene to methyl, with is transfered to coenzyme M, and finally reduced to free methane. The source of reducing power in these steps is hydrogen; the F420 hydrogenase transfers the electrons from hydrogen to cofactor F420, which supplies the electrons for C1-H4MPT reduction. In the final step of methanogenesis, electrons from H2 are transfered to F430 rather than F420 by a specific F430 hydrogenase. The protons released from hydrogen are released externally from the membrane-hydrogenase, and protons required (in addition to electrons) during the C1 reduction are taken from the cytoplasm; the result is a proton gradient which can be used to generate ATP via a traditional ATPase.

Some methanogens, the methanomicrobia, can make methane from acetate and/or methanol rather than CO2, CO or formate; in these cases, only the ultimate or penultimate steps of methanogenesis are used. In the case of methanogenesis from acetate, the methyl group of acetate is transfered directly to H4MPT - the carboxy group is released as CO2, which in some methanogens can be fed into the methanogenesis pathway as well. In the case of methanogenesis using methanol, the methyl group of methanol is transfered to a corrinoid protein and then to the final methyl carrier, coenzyme M, before release of methane. Other methyl-containing substrates for methanogenesis (e.g. methylamines) can be utilized by some methanogens by transfer of their methyl groups to the corrinoid protein.

Most methanogens are autotrophs, and use the methanogenic pathway for carbon fixation as well as energy production. Methyl-H4MPT is carboxylated and transfered to coenzyme A to produce acetyl-CoA; this is the reverse of the reaction otherwise used by acetoclastic (acetate utilizing) methanogens to make methane from acetate. Acetyl-CoA can then be fed into catabolism via the “intermediate” reaction or TCA cycle.

Morphology
Members of the Methanococci and Methanobacteria are, as might be expected, cocci and rod-shaped, respectively. The Methanomicrobia are more diverse in morphology; usually the genus name is a good indication of their general morphology.

Habitat
The enzymes in the methanogenic pathway are extremely oxygen sensitive, and so all methanogens are extreme anaerobes. However, they are common organisms, found in all types of anaerobic environments, and are certainly the most prevalent cultivable Archaea in the “moderate” world. For example:

• Sediments and soils - swamp gas is methane which, because of its low ignition temperature and threshold concentration, is readily ignited and glows very faintly as 'will-o-the-wisps' visible at night in swamps. Methanogens are also crucial components of the microbial populations of the 'rhizosphere', the plant root environment.
• Animal GI tracts - especially wood-eating insects and ruminants, but most other animals as well. African termite mounds are scrupulously aerated by the insects, not just for oxygenation, but to keep methane concentrations below ignitable levels. Cows may produce enough methane to be a significant source of this potent greenhouse gas.
• Wastewater and landfills - The wastewater process converts organics in the wastewater into methane and CO2. Landfills must be carefully vented; houses near older unvented landfills have exploded because of the buildup of methane that seeped through the ground into their basements. Alternatively, methane can be collected from wastewater or landfill facilities and used for energy production.
• Oil deposits - natural gas is methane, and at least some natural gas is produced not geochemically but by methanogens living in the subterranean oil deposits.

Methanogens form a variety of symbioses with plants, animals and protists, but despite these close associations there are no known pathogenic methanogens. None of the other Archaea are pathogens either, but considering the conditions under which most of them grow, this is perhaps not surprizing. Methanogens also form close syntrophic associations with heterotrophic Bacteria that generate hydrogen (i.e. use protons as the terminal electron acceptor). Hydrogen-generating heterotrophism is only energetically-favorable where the ambient concentration of hydrogen is kept extremely low. Methanogens associate with these organisms, utilizing the hydrogen they generate for methanogenesis, and keep the hydrogen concentration low enough for the heterotrophs to make a living. Neither of these organisms could persist in the environment alone, but together they are successful.

Methanococci

The methanococci are typically found in marine and freshwater sediments. Some species are thermophiles, but many mesophilic species have been isolated as well. They are motile via tufted flagella, but they are so sensitive to oxygen that motility can only be observed if samples are taken and observed microscopically in a strictly anaerobic environment. Their cell walls are made up of an extracellular protein S-layer. The Methanococci can only grow on H2 + CO2 or formate for energy, although some can use organics to avoid the need for carbon fixation. Some are complete prototrophs; can make everything they need from inorganic compounds. They can fix their own carbon from CO2, synthesize all their vitamins, fix their own nitrogen from N2, fix sulfur from H2S, &c. These organisms are more sensitive to oxygen than any other cultivated species, and are also very sensitive to UV light, because they lack the enzymes required for repair of UV-damaged DNA (photolyase).

Example : Methanocaldococcus jannaschii

Methanocaldococcus (previously Methanococcus) jannaschii is a motile coccus with a single 'tuft' of many flagella. It is an obligate autotroph (using the Calvin cycle for carbon fixation), reducing only CO2 or CO with H2 to produce methane. M. jannaschii is an extreme thermophile, growing optimally at 80°C; it was isolated from a deep sea hydrothermal vent environment. The sequence of the genome of M. jannaschii was the first archaeal genome sequence available. It consists of 3 circular chromosomes: one large (ca. 2Mbp) chromosome containing all of the identifiable genes, and 2 small (138Kbp and 38Kbp) chromosomes that could also be considered single-copy plasmids.

Methanobacteria

The methanobacteria are nonmotile rod-shaped or filamentous organisms with pseudomurein cell walls. They can only use H2 + CO2 (sometimes CO and/or formate) to make energy, and fix carbon using the Acetyl-CoA pathway (see Chapter 9). They are mostly thermophiles, and are more easily isolated that other methanogens because they are more resistant to exposure to oxygen. Mesophilic or moderately thermophilic species are common colon and rumen inhabitants in animals.

Example : Methanothermobacter thermoautotrophicus

Methanothermobacter thermoautotrophicus (previous Methanbacterium thermoautotrophicum strain ΔH) was isolated from municipal wastewater sludge, and is one of the best-studied of methanogens. Cells are rod-shaped, ca. 0.5μm x 3-7μm, that form chains or filaments. M. thermoautotrophicus is moderately thermophilic, growing optimally at 65°C, and requires no growth factors

Methanomicrobia

Members of the methanomicrobia are usually nonmotile, and come in various shapes - rods, cocci, spirals, pleomorphs. Most can use only H2 + CO2 or formate for energy, but some are capable of methanogenesis using acetate, methanol, or methylamines. Although they are generally autotrophic, many species can't fix their own carbon - they require acetate for growth. In these instances, they don't make methane from acetate, but use it only as a carbon source. Unlike the methanococci and methanobacteria, this group is mostly mesophilic. These organisms are specifically related to both Thermoplasma and the extreme halophiles.

Example : Methanosarcina barkeri

A particularly important genus in this group is Methanosarcina, exemplified by M. barkeri. These organisms are unique in that they can make methane from hydrogen and CO2 or CO, like other methangens, or from acetate, methylamines, or methanol alone. M. barkeri is common in soils, sediment, swamp, and wastewater treatment sludge. In fact, M. barkeri is the organism responsible for the success of wastewater treatment. In this process, organic material is concentrated and converted to biomass during aerobic digestion, then converted to acetate (and some CO2) by Bacteria during anaerobic digestion. M. barkeri converts this acetate to CO2 + methane, which bubbles away. Because it gets so little energy from this abbreviated form of methanogenesis, it turns vast quantities of acetate over into methane, generating only a little biomass in the process. This is, after all, the point of wastewater treatment - to convert as much of the organic carbon into gas as possible.

Extreme Halophiles

The extremely halophilic Archaea are mesophilic organisms that require at least 2M NaCl or equivalent ionic strength for growth - most grow in saturated or near-saturated brines. They are the primary inhabitant of saturated salt lakes. Red pigments make it obvious when large numbers of these organisms are present - blooms often occurs after a rain carries organic material into a salt lake, and the Red Sea gets its name from such blooms. So does the well-known “Red Herring”, from foul-smelling but hound-diverting salted fish being spoiled by Halobacterium.

Other halophilic organisms (e.g. some fungi, brine shrimp) have essentially normal cytoplasmic salt concentrations, expend energy to continuously pump salt out of the cell and water into the cell, and contain organic osmolytes such as glycerol or sugars. Halophilic Archaea generally grow at even higher salt concentrations, but don't fight back at all - the internal salt concentrations are as high or higher than they are outside! However, Na+ and Cl- are not particularly biologically-friendly, and so the extremely halophilic Archaea replace K+ for Na+ (by active transport) and organic acids (e.g. glutamate) for Cl- in the cytoplasm.

Metabolism
Halophilic Archaea are generally facultative phototrophs. Under aerobic conditions, they are traditional heterotrophs, using organic material from the environment for both carbon and energy. Energy production is respiratory, using oxygen as the terminal electron acceptor. Under anaerobic conditions, they grow photochemotrophically, using light for energy, but require organic material for carbon.

Halophilic Archaea do not contain the usual photosystems, nor do they use their electron transport chain for gathering energy from light, as do other phototrophs. Phototrophy is driven by a single protein, bacteriorhodopsin, that is a light-driven proton pump. This proton pump generates a proton gradient used to make ATP via ATPase, just like in other organisms. It is not as efficient as the bacterial photosystems, but light is rarely limiting for growth in the desert salt lakes where they predominate.

Some halophiles grow at high pH (up to pH10-10.5) i.e. Natronobacterium in soda lakes. This is a problem for them (or at least for us, trying to understand how they get away with it). At high pH values, protons pumped to the outside by either electron transport or bacteriorhodopsin will react with hydroxide in the environment very quickly. At any higher pH, protons are too low a concentration outside the cell to drive ATPase. Although the electrical potential is would still be there, it can't be harvested by an ATPase unless it can get protons from the outside; and in any case the cell needs the protons back to maintain the internal pH of the cytoplasm. This problem probably limits the maximum pH for life.

Morphology
Most halophilic Archaea are rod-shaped (often irregular) or coccoid. However, there is little net osmotic pressure on the cell wall (high salt both inside and out), and some species take advantage of this by adopting high surface-area flattened shapes (disks, squares, or triangles) that are not possible for organisms with 'normal' cell turgor. Gas vacuoles are common, nd many are motile

Habitat
Extremely halophilic Archaea are common in hypersaline seas and lakes, salt evaporation pools, salted meats, salt marshes, and subterranean salt deposit. They can also be found in unexpected low water-content environments such as soil and sludges.

Example : Halobacterium salinarium

H. salinarium (this species also includes what was classically known as H. halobium) is a very common extreme halophile, originally isolated from salted cod. The bacteriorhodopsin of this organism, which accumulates to such high concentrations in the cell membrane that it forms a semicrystalline array and is known as “purple membrane”, is the model system for the study of these proteins for use a biosensors. H. salinarium is motile via a single polar flagellum, and in stationary phase produces gas vacuoles. It is non-fermentative; anaerobic or microaerophilic growth is strictly phototrophic. Requires a minimum of 3M NaCl for growth, and cultures will lyse immediately if exposed to less than 1.5-2M salt. Cells are rod-shaped, but are often irregular in cultivation or in stationary phase. Most strains of this species contain one large and two small chromosomes, but the smaller “plasmids” are sometimes integrated or rearranged relative to the main chromosome. The genome is extraordinarily rich in transposons and insertion elements, resulting (at least in domesticated strains) in a great deal of genetic instability.

Sulfur-metabolizing thermophiles

Sulfur-metabolizing Euryarchaea can be separated into two classes: the Thermococci, a primitive deep branch in the tree that probably retain this phenotype from the ancestral state shared with the Crenarchaea, and the Archaeoglobi and Thermoplasmata, that seem to have reverted to sulfur metabolism from a methanogenic ancestry. All are thermophilic, and all sulfur metabolizers (a very general phenotype, to be sure), but are otherwise not much alike and represent independent branches on the euryarchaeal phylogenetic tree.

Example : Pyrococcus furiosus

Pyrococcus and its close relative Thermococcus are perhaps the most primitive organisms known, i.e. it is closer to the root of the universal tree than are any other known organisms. Pyrococcus furiosus (loosely translated from the latin, this means “Great Balls of Fire”) is a neutral pH heterotroph, and is extremely thermophilic, growing optimally at 100°C; as such, it is only of only a few of known organisms that grow at or about the boiling point of water at atmospheric pressure (cultures are kept under more than atmospheric pressure). P. furiosus is a heterotroph, growing by anaerobic sulfur respiration using a wide range of peptides, sugars and polysaccharides. This specie is apparently common in deep-sea hydrothermal vent areas and marine hydrothermal sediments. Cells or all members of this group are motile cocci, with a distinct tuft of flagella.

Example : Archaeoglobus fulgidus

A. fulgidus is an inhabitant of deep-sea hydrothermal vents and heated marine sediments. It is a thermophilic (ca. 85°C) coccus; some species are motile with tufted flagella (much like Thermococcus, see above) and others are nonmotile. Archaeglobus can grow autotrophically by sulfate reduction, using H2 as the electron donor. Carbon fixation is apparently by the reductive (or “reverse”) TCA cycle, despite the fact that the genome contains two very different RuBPCase genes (the key enzyme in the Calvin cycle). Alternatively, it can grow heterotrophically from lactate or acetate, plucking the methyl group from these and in essence using the methanogenic pathway in reverse to generate H2 and CO2.

Example : Thermoplasma acidophilum

T, acidophilum is a facultatively anaerobic thermoacidophilic heterotroph, using either O2 (aerobically, of course) or sulfur (anaerobically) as the terminal electron acceptors for respiration. T. acidophilum, as the name suggests, is also acidophilic, most isolates growing best at a pH of about 2, but some isolated grow at pH’s somewhat below 1. This specie is also moderately thermophilic, preferring about 60°C. It is irregular in shape with cytoplasm extensions similar to the pseudopods of amoeboid eukaryotes, but is motile via monotrichous flagella. It lack a traditional cell wall, crosslinking of the carbohydrate chains of membrane glycoproteins provide what cell rigidity and osmotic tolerance they require. Like Archaeoglobus, they reveal their methanogenic ancestry by containing F420 (a major methanogenic hydrogenase cofactor) & other components of the methanogenic pathway, but it is not known what use they make of these. Thermoplasma has been isolated almost exclusively from smouldering coal refuse piles, and it is presumed that subterranean coal deposits are their natural habitat.

Phylum Korarchaea

The Korarchaea are known almost exclusively from ssu-rRNA sequences from a variety of hydrothermal environments. They are probably best-known from the site of their original discovery: Obsidian Pool, in Yellowstone National Park. This anaerobic pool varies from 65°C to boiling (94°C at this altitude), pH 6.5, and is a slurry of silica, pyrite, and elemental sulfur. The exact placement of the korarchaeal branch relative to other Archaea remains uncertain; it may originate before the split separating Euryarchaea and Crenarchaea, or may be specifically affiliated with the Crenarchaea. Resolving this issue will probably require additional genome sequences. No members of this group have been grown in pure culture.

Example species : Korarchaeum cryptofilum

K. cryptophilum is a very thin filamentous (0.17μm x 5-100μm) thermophilic heterotrophic korarchaeote. It has not been grown in pure culture, but has been maintained in an 85°C anaerobic community culture originating from a sample from Obsidian Pool. The genome sequence of its single 1.59Mbp circular chromosome has been determined from cells physically isolated from this culture on the basis of their unusually high resistance to the detergent SDS; this resistance is presumably due to its very dense and orderly S-layer. The composition of its genome suggests that K. cryptophilum is a peptidolytic heterotroph, but unlike other peptidolytic hyperthermophilic Archaea (e.g. Pyrococcus), it seems to use only protons as the terminal electron acceptor, (generating H2), lacking the ability to use either oxygen or sulfur (or anything else) as terminal electron acceptors. The genes required for the biosynthesis of a number of cofactors/vitamins are absent; this may explain the inability of K. cryptophilum to grow in pure culture.

Phylum Nanoarchaeum

This phylum, which may be a deep sister-group to the euryarchaea, is known only from a single cultivated specie and a small number of environmental ssu-rRNA sequences from thermal and hypersaline environments. Because commonly-used primers are not able to amplify ssu-rRNA sequences from this group, they may have been missed in surveys of other environments. Therefore, the phylogenetic and phenotypic diversity of this group remains largely unknown.

Nanoarchaeum equitans

N. equitans is an obligate parasite of the crenarchaeote Ignicoccus. The cells are very small cocci, only about 400nm in diameter, that grow attached to the outside of the host cells (which are also cocci). They cannot be cultivated in the absence of the host, but have been isolated as a pure co-culture from a single Ignicoccus cell harboring a single N. equitans parasite. N. equitans is the only hyperthermophilic symbiont known, and the only archaeal parasite or pathogen. It is also one of the smallest cellular organisms known. The N. equitans genome consists of a single circular molecule of slightly less than 0.5Mbp, and lacks almost all biosynthetic genes. Even the ATPase is a minimal version; it may be used in reverse to generate a proton gradient (at the expense of ATP) for use by active transport pumps. In is probably an energy parasite. Most of the genes that remain are those of information processing; replication, transcription, translation, signal transduction, and the cell cycle.

An interesting aspect of the N. equitans genome is how disorganized it is. In most Bacteria and Archaea, genes are organized in operons, with structurally or functionally related proteins generally encoded together. Not so it N. equitans; not even the ribosomal proteins are grouped together in operons (this is otherwise very highly conserved), nor are the ribosomal RNAs (which are almost always encoded together in the order 16S-23S-5S in Bacteria and Archaea, and the homologous 18S-5.8S-28S rRNA genes in Eukarya). Even the functional domains of some enzymes are encoded separately, and some of the tRNAs are encoded in two pieces that are joined by splicing in trans.

Archaea as ...

… the “missing link” between Bacteria and Eukarya
Despite the fact that all of life on Earth is alike in most ways, Bacteria and Eukarya do differ in significant ways. Traditionally, it is assumed that where Bacteria and Eukarya differ, the bacterial version is primitive, because Bacteria are generally simpler than are Eukarya. But simple and primitive are not synonymous, and so this is a bad assumption. What is need is a tie-breaker, an intermediate third distinct phylogenetic group, and the more primitive the better. Such intermediate groups are often called “missing links”; this term is a left-over of the pre-Darwinian “chain of being” view discussed earlier. If a trait is common to two of the three phylogenetic groups, then presumably it was also present in the common ancestor of those two groups. Because the last common ancestor is apparently on the branch between the Bacteria and Archaea/Eukarya, any trait common to Bacteria and either Archaea or Eukarya probably existed in the last common ancestor.

… a deep branch of Eukarya
In order to understand eukaryotic complexity, it would be useful to have a group of primitive organisms that diverged from the rest of the Eukarya early in their evolution. Properties shared by such organisms and more complex Eukarya, but not by Bacteria, would presumably represent the unique traits of the deep ancestor of Eukarya. If these organisms were also relatively simple, they could tell you a lot about the core functionalities of eukaryal cells, unobscured by all the bells and whistles that were added later in their evolutionary history. Where might you look for such an organism? As you can see from the rooted tree above, these organisms are already known - they are the Archaea. For this reason, the Archaea are often studied for their eukaryal-like processes that are simpler and easier to understand than the homologous counterparts in plants, animals or fungi. Examples include RNA polymerase (Archaea have a single RNA polymerase homologous to eukaryal RNA polymerase II), small nucleolar ribonucleoproteins (snoRNPs, involved in RNA modifications), and DNA packaging (Archaea have relatively simple nucleosomes). In addition, archaeal complexes are often easier systems to study using standard biophysical processes such as X-ray diffraction, because of the extreme stability of thermophilic or halophilic complexes.

... reflections of early life on Earth
The Archaea are, as a group, more primitive than are either the Bacteria or Eukaryotes. Primitive Archaea (e.g. Thermococcus, Pyrococcus) are similar to primitive Bacteria (e.g. Aquifex) in being thermophilic sulfur/hydrogen metabolizers, and so this is probably the general phenotype of the last common ancestor, and perhaps primitive life in general. Although modern Archaea are not the ancestors of other modern organisms, they probably do resemble in many ways these ancestral life forms. In may be that they haven't changed much because of their thermophilic environment - evolutionary drift in genes is much more constrained in thermophiles than in mesophiles, because their macromolecules are less tolerant of minor perturbations that are allowed in molecules than function at lower temperatures. For example, most single changes in an RNA-encoding gene will create a mismatch in the secondary structure of the RNA - no big deal for a mesophile, that can tolerate the defect with minimal decrease in fitness until a compensatory change occurs. But the mismatch is a big problem for a thermophile because of the thermal destabilization it causes, making it much less likely that a compensatory change will occur before the decrease in fitness leads to extinction.

Questions for thought

• The observations that most of the deepest branches of the "Big Tree" are thermophiles, and primitive organisms (also judged by evolutionary distance estimated in ssu-rRNA-based trees) are thermophiles, have lead to the conclusion that organisms have a thermophilic ancestry. Why do you think thermophilic organisms seem to have slower rates of evolution than mesophiles?
  
  
• Conceptually, at least, RNA secondary structures are likely to slow their evolutionary rate as the growth temperature of the organism increases. Are the other components of the cell also likely to slow evolutionary rates to a similar extent? How would you expect the relative rate of RNA vs protein evolutionary rate to change at high temperatures? What impact does this have on how we interpret "primitive thermophily" in rRNA-based evolutionary trees?
  
  
• If Archaea are specifically related to eukaryotes to the exclusion of Bacteria, why don't we consider Archaea to be eukaryotes (even if primitive ones)?
  
  
• Acidophiles will always have a proton gradient, since the outside is much lower in pH than the cytoplasm. Why, then, can't they make ATP for free? Why do they still have to run electron transport, pumping protons out?
  
  
• Given that some species can grow at very low pH, e.g. pH 0, what impact do you think this has on the kinds of oxidation/reduction reactions they can derived energy from. Remember that the reaction has to drive the electron transport chain to pump protons out against a very steep proton gradient. How might the organism minimize this resistance to outward proton pumping?
  
  
• Methanogens and Archaeoglobus use the same enzymatic pathway, in opposite directions, to generate energy. Methanogens make methane and fixed carbon from H2 and CO2, whereas Archaeoglobus makes CO2 and H2 from organic carbon. How can these enzymes generate energy forwards and backwards? Isn't this like perpetual motion?
  
  
• How do you suppose organisms like Halobacterium were studied for so long without it being realized that it really wasn't a lot like it's supposed relatives, Pseudomonas?

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