Phylum Euryarchaea

OLD Audio recording

Video recording (.mov format, 1.8Gbytes)
Video recording (480p .mp4 format, 0.2Gbytes)
Video recording (1080p .mp4 format, 1.5Gbytes

 

tree

  • 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

methanogenesis

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
Methanocaldococcus jannaschii
: B. Boonyaratanakornkit & D.S. Clark, University of California Berkeley.

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
Methanothermobacter thermoautotrophicus : The prokaryotes, pp732

Methanothermobacter thermoautotrophicus (previous Methanobacterium 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

Methanosarcina
Methanosarcina barkeri : Dr. Jan Keltjens, http://www.microbiology.science.ru.nl/galleries/

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 halophilic Archaea.

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, and 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

saltern
This is a salina in Namibia, red with the growth of halophiles : Alice Lee

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

black smoker
A deep-sea black smoker, habitat for Pyrococcus furiosus : Geosciences Department, University of Bremen
http://www.geo.uni-bremen.de/Ozeankruste/smoker.jpg

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

Archaeoglobus
Archaeoglobus fulgidus : from Karl Stetter - The Prokaryotes pp709

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

Thermoplasma
Thermoplasma acidophilum : William Hixon, Cell research (2003); 13(4):219-227

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.