Euryarchaeota

Diverse Cell Forms of Methanogens

There are over 50 described species of methanogens, sharing over 30 signature proteins.

Learning Objectives

Outline the physical characteristics associated with methanogens

Key Takeaways

Key Points

  • Methanogens are usually either coccoid (spherical) or bacilli (rod shaped).
  • Methanogens have a cell wall that is composed of pseudopeptidoglycan, which offers lysozyme resistance.
  • There are many diverse strains of methanogens, including M. smithii (found in the human gut), M. kandleri (discovered on the wall of a black smoker), and M acetivorans (found in oil wells, trash dumps, and deep-sea hydrothermal vents ).

Key Terms

  • polysaccharide: Complex sugars. A polymer made of many saccharide units linked by glycosidic bonds.

Methanogens belong to the domain archaea, which are distinctly different than bacteria. There are over 50 described species of methanogens, sharing over 30 signature proteins. These species do not form a monophyletic group, but are split into three clades. Therefore, the large numbers of proteins uniquely shared by all methanogens may be due to lateral gene transfers.

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Methanopyrus kandleri: M. kandleri, a methanogen, is the only strain in the genus Methanopyrus. Methanopyrus kandleri can survive and reproduce at 122°C.

Methanogens are usually either coccoid (spherical) or bacilli (rod shaped). The cell walls of of Methanogens, like other Archaea, lack peptidoglycan, a polymer found in the cell walls of the bacteria. Instead, some methanogens have a cell wall that is composed of pseudopeptidoglycan. Pseudopeptidoglycan differs in chemical structure from bacterial peptidoglycan, but resembles eubacterial peptidoglycan in morphology, function, and physical structure. These differences makes these archaea resistant to the enzyme, lysozyme, which only breaks down β (1,4) sugar linkages like those found in peptidoglycan. Those that do not contain pseudopeptidoglycan have at least one paracrystalline array (S-layer) made up of proteins that fit together like a jigsaw puzzle.

There are many diverse strains of methanogens. Methanobrevibacter smithii is the dominant archaeon in the human gut. M. smithii is pivotal in the removal of excess hydrogen from the human gut. They are important for the efficient digestion of polysaccharides, allowing for an increase in the transformation of nutrients into calories.

Methanocaldococcus jannaschii thermophilic methanogen isolated from a hot spring at Woods hole. It was the first archaeon to have its complete genome sequenced, identifying many genes and synthesis pathways unique to the archaea.

Methanopyrus is a genus of methanogens, with a single described species, M. kandleri. M. kandleri is a hyperthermophile, discovered on the wall of a black smoker from the Gulf of California at a depth of 2000 m, at temperatures of 84-110 °C.

Methanosarcina acetivorans is a versatile methane producing microbe which is found in such diverse environments as oil wells, trash dumps, deep-sea hydrothermal vents, and oxygen-depleted sediments beneath kelp beds. Only M. acetivorans and microbes in the genus Methanosarcina use all three known metabolic pathways for methanogenesis.

Extremely Halophilic Archaea

Halophiles are extremophiles that thrive in environments with very high concentrations of salt.

Learning Objectives

Describe the methods employed by halophilic Archaea to prevent water loss

Key Takeaways

Key Points

  • Halophiles can be found anywhere with a salt concentration at least five times greater than that of the ocean.
  • Most halophilic organisms cope with the high concentrations of salt by expending energy to exclude salt from their cytoplasm.
  • Halophiles prevent this loss of water by increasing the internal osmolarity of the cell by accumulating osmoprotectants or by the selective uptake of potassium ions.

Key Terms

  • halotolerance: The adaptation of a living organism to conditions of high salinity (dissolved salt).
  • zwitterionic: Pertaining to a neutral molecule containing both positive and negative charge.
  • osmoprotectant: Any osmolyte that helps an organism to survive osmotic stress

Halophiles are extremophiles that thrive in environments with very high concentrations of salt. In fact, the very name “halophile” comes from the Greek word for “salt-loving. ” Although some halophilic bacteria and eukaryotes exist, the largest classification of halophiles is in the Archaea domain.

Halophiles can be found anywhere with a salt concentration at least five times greater than that of the ocean. They are categorized as slight, moderate, or extreme halophiles based on the extent of their halotolerance. Halophiles thrive in places such as the Great Salt Lake, Owens Lake in California, evaporation ponds, and the Dead Sea – places that provide an inhospitable environment to most lifeforms.

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Dead Sea: Salt builds up along the Dead Sea. These extreme conditions provides an inhospitable environment to most life forms.

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Great Salt Lake: Halophiles are adapted to conditions of extreme salt concentration, such as the Great Salt Lake in Utah.

High salinity represents an extreme environment that relatively few organisms have been able to adapt to and occupy. Most halophilic organisms cope with the high concentrations of salt by expending energy to exclude salt from their cytoplasm to avoid protein aggregation, or “salting out. ” “Normal” organisms would desiccate in these conditions, losing water via osmosis out of the cytoplasm. Halophiles prevent this loss of water by increasing the internal osmolarity of the cell. One way halophilic archaea can increase their internal osmolarity is by accumulating organic compounds – called osmoprotectants – in their cytoplasm. These compatible solutes can be accumulated from the environment or synthesized. The most common compatible solutes are neutral or zwitterionic, and include amino acids, sugars, polyols, betaines and ectoines, as well as derivatives of some of these compounds.

A more radical adaptation to preventing water loss employs the selective influx of potassium (K+) ions into the cytoplasm. In archaea, this adaptation is restricted to the the extremely halophilic family Haloarchaea (often known as Halobacteriaceae). To use this method, the entire intracellular machinery – including enzymes, structural proteins, and charged amino acids that allow the retention of water molecules on their surfaces – must be adapted to high salt levels. In the compatible solute adaptation, little or no adjustment is required of intracellular macromolecules – in fact, the compatible solutes often act as general stress protectants as well as osmoprotectants.

The extremely halophilic Haloarchaea require at least a 2 M salt concentration and are usually found in saturated solutions (about 36% w/v salts). These are the primary inhabitants of salt lakes, inland seas, and evaporating ponds of seawater. The red color of deep salterns is due to the carotenoids (organic pigment) in these archaea. These archaea require salt for growth and they will lyse if they are exposed to less salty environment.

The high concentration of NaCl in halophilic environment limits the availability of oxygen for respiration. Halophiles are chemoheterotrophs, using light for energy and methane as a carbon source under aerobic or anaerobic conditions.

Methane-Producing Archaea: Methanogens

Methanogens are an important group of microoraganisms that produce methane as a metabolic byproduct under anaerobic conditions.

Learning Objectives

Discuss the characteristics associated with methane-producing archaea

Key Takeaways

Key Points

  • Methanogens are responsible for the methane in the belches of ruminants and in the flatulence in humans.
  • Methanogens play a vital ecological role in anaerobic environments by removing excess hydrogen and fermentation products produced by other forms of anaerobic respiration.
  • Methanogens play a key role in the remineralization of organic carbon and under the right conditions can form reservoirs of methanogen, a potent greenhouse gas.

Key Terms

  • extremophiles: An extremophile (from Latin extremus, meaning “extreme,” and Greek philiā (φ), meaning “love”) is an organism that thrives in physically or geochemically extreme conditions that are detrimental to most life on earth.

Methanogenic archaea, or methanogens, are an important group of microoraganisms that produce methane as a metabolic byproduct under anaerobic conditions. Methanogens belong to the domain archaea, which is distinct from bacteria. Methanogens are commonly found in the guts of animals, deep layers of marine sediment, hydrothermal vents, and wetlands. They are responsible for the methane in the belches of ruminants, as in, the flatulence in humans, and the marsh gas of wetlands. Methanogens should not be confused with methanotrophs, which consume methane rather than produce it.

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Methane: The flatulence of cows is only a small portion of cows’ methane release. Cows also burp methane due to methanogens in their digestive systems.

Methanogens play a vital ecological role in anaerobic environments by removing excess hydrogen and fermentation products produced by other forms of anaerobic respiration. Because of this, methanogens thrive in environments in which all electron acceptors other than CO2 (such as oxygen, nitrate, trivalent iron, and sulfate) have been depleted.

In the human gut, accumulation of hydrogen reduces the efficiency of microbial processes, reducing energy yield. Methanogens such as M. smithii are pivotal in the removal of this excess hydrogen from the gut and may be useful therapeutic targets for reducing energy harvest in obese humans.

In marine sediments, biomethanation is generally confined to where sulfates are depleted, below the top layers. Methanogens play a key role in the remineralization of organic carbon in continental margin sediments and other aquatic sediments with high rates of sedimentation and organic matter. Under the correct temperatures and pressure, biogenic methane can accumulate in massive deposits, which account for significant fractions of organic carbon and key reservoirs of a potent greenhouse gas.

Some methanogens, called extremophiles, can thrive in extreme environments such as hot springs, submarine hydrothermal vents, and hot, dry deserts. Methanogens have been found buried under kilometers of ice in Greenland, as well as in the “solid” rock of the Earth’s crust, kilometers below the surface.

Thermoplasmatales, Thermocaccales, and Methanopyrus

There are many classes in the phylum Euryarchaeota, many of which are extremophiles.

Learning Objectives

Recognize the characteristics associated with the Euryarchaeota classes of thermophiles: Thermoplasmatales, Thermococcales and Methanopyri

Key Takeaways

Key Points

  • Thermoplasmatales are an order of the class Thermoplasmata. All are acidophiles, growing optimally at pH below 2.
  • Another anaerobic Euryarchaeota, often hyperthermophiles, are the Thermococcales of the class Thermocococci.
  • Methanopyrus is a genus of methanogen, with a single described species, M. kandleri.

Key Terms

  • acidophiles: an organism that thrives under highly acidic conditions (usually at pH 2.0 or below)
  • hyperthermophile: An organism that lives and thrives in an extremely hot environment like a deep sea smoker vent; often a member of the Archaea.

There are many classes in the phylum Euryarchaeota, many of which are extremophiles, surviving in extreme conditions that are uninhabitable for most other organisms. Thermoplasmatales, Thermococcales, and Methanopyri are all Euryarchaeota Classes of thermophiles.

Thermoplasmatales are an order of the class Thermoplasmata. All are acidophiles, growing optimally at pH below 2. Picrophilus is currently the most acidophilic of all known organisms growing at a minimum pH of 0.06. Many of these organisms do not contain a cell wall, although this is not true in the case of Picrophilus. Most members of the Thermotoplasmata are thermophilic. A thermophile is an extremophile that thrives at relatively high temperatures, between 45 and 122 °C. Many of them are archaea. Thermophilic eubacteria are suggested to have been among the earliest bacteria. Thermophiles contain enzymes that can function at high temperatures, and can even survive at much higher temperatures, whereas other bacteria would be damaged and sometimes killed if exposed to the same temperatures.

Another anaerobic Euryarchaeota, often hyperthermophiles, are the Thermococcales of the class Thermocococci.

Methanopyrus is a genus of methanogen, with a single described species, Methanopyrus kandleri . It is a hyperthermophile, discovered on the wall of a black smoker from the Gulf of California at a depth of 2000 m, at temperatures of 84-110 °C. Strain 116 was discovered in black smoker fluid of the Kairei hydrothermal field; it can survive and reproduce at 122 °C. It lives in a hydrogen-carbon dioxide rich environment, and like other methanogens reduces the latter to methane. It is placed among the Euryarchaeota, in its own class, Methanopyri.

Archaeoglobus

Archaeoglobus is a genus of Euryarchaeota found in high-temperature oil fields.

Learning Objectives

Outline the unique traits associated with Archaeoglobus

Key Takeaways

Key Points

  • Archaeoglobus are sulfate-reducing archaea, coupling the reduction of sulfate to sulfide with the oxidation of many different organic carbon sources, including complex polymers.
  • Archaeoglobus grow at extremely high temperatures and are found in hydrothermal vents, oil deposits, and hot springs.
  • Comparative genomic studies on archaeal genomes provide evidence that members of the genus Archaeoglobus are the closest relatives of methanogenic archaea.

Key Terms

  • lithoautotroph: A microbe that takes energy from reduced compounds of minerals.
  • heterotroph: An organism that requires an external supply of energy in the form of food as it cannot synthesize its own.
  • hyperthermophiles: An organism that thrives in extremely hot environments-from 60 degrees C (140 degrees F) upwards.

Archaeoglobus is a genus of Euryarchaeota found in high-temperature oil fields, where they may contribute to oil field souring. Archaeoglobus are sulfate-reducing archaea, coupling the reduction of sulfate to sulfide with the oxidation of many different organic carbon sources, including complex polymers.

Archaeoglobus grow at extremely high temperatures between 60 and 95 °C, with optimal growth at 83 °C. These hyperthermophiles can be found in hydrothermal vents, oil deposits, and hot springs. They can produce biofilm to form a protective environment when subjected to environmental stresses such as extreme pH or temperature, high concentrations of metal, or the addition of antibiotics, xenobiotics, or oxygen. These archaeons are known to cause the corrosion of iron and steel in oil and gas processing systems by producing iron sulphide. Their bioflims, however, may have industrial or research applications in the detoxification of metal contaminated samples or to gather metals in an economically recoverable form.

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Microbial Mats Around the Grand Prismatic Spring: Thermophiles produce some of the bright colors of Grand Prismatic Spring, Yellowstone National Park

Archaeoglobus are lithotrophs, and can be either autotrophic or heterotrophic.The archaeoglobus strain A. lithotrophicus are lithoautotrophs, and derive their energy from hydrogen, sulfate and carbon dioxide. The strain A. profundus are also lithotrophic, but as they require acetate and CO2 for biosynthesis, and are therefore heterotrophs. Archaeoglobus species utilize their environment by acting as scavengers with many potential carbon sources. They can obtain carbon from fatty acids, the degradation of amino acids, aldehydes, organic acids, and possibly carbon monoxide (CO) as well.

Comparative genomic studies on archaeal genomes provide evidence that members of the genus Archaeoglobus are the closest relatives of methanogenic archaea. This is supported by the presence of 10 conserved signature proteins that are uniquely found in all methanogens and Archaeoglobus. Additionally, 18 proteins which are uniquely found in members of Thermococci, Archaeoglobus and methanogens have been identified, suggesting that these three groups of Archaea may have shared a common relative exclusive of other Archaea. However, the possibility that the shared presence of these signature proteins in these archaeal lineages is due to lateral gene transfer cannot be excluded.

The complete genome sequence from Archaeoglobus fulgidus reveals the presence of a complete set of genes for methanogenesis. The function of these genes in A. fulgidus remains unknown, and the lack of the enzyme methyl-CoM reductase does not allow for methanogenesis to occur by a mechanism similar to that found in other methanogens.

The A. fulgidus genome is a circular chromosome of 2,178,000 base pairs, roughly half the size of E. coli. A quarter of the genome encodes preserved proteins whose functions are not yet determined, but are expressed in other archaeons such as Methanococcus jannaschii. Another quarter encodes proteins unique to the archaeal domain. One observation about the genome is that there are many gene duplications and the duplicated proteins are not identical. This suggests metabolic differentiation specifically with respect to the decomposing and recycling carbon pathways through scavenged fatty acids. The duplicated genes also gives the genome a larger genome size than its fellow archaeon M. jannaschii.

Nanoarchaeum and Aciduliprofundum

Nanoarchaeum equitans is a species of marine Archaea discovered in a hydrothermal vent off the coast of Iceland.

Learning Objectives

Discuss the unique characteristics associated with Nanoarchaeum

Key Takeaways

Key Points

  • Nanoarchaeum grows best in environments with a pH of six and a salinity concentration of 2%.
  • Nanoarchaeum cannot synthesize lipids but obtains them from its host, Ignicoccus.
  • The genome and proteome composition of N. equitans are marked with the signatures of dual adaptation – one to high temperature and the other to obligatory parasitism.

Key Terms

  • nanobes: A tiny filamental structure that may or not be a living organism, and if living, would be the smallest form of life, 1/10 the size of the smallest known bacteria.

Nanoarchaeum equitans is a species of marine Archaea that was discovered in 2002 in a hydrothermal vent off the coast of Iceland on the Kolbeinsey Ridge by Karl Stetter. Strains of this microbe were also found on the Sub-polar Mid Oceanic Ridge and in the Obsidian Pool in Yellowstone National Park. It is a thermophile that grows in temperatures approaching boiling (80 degrees Celsius). Nanoarchaeum grows best in environments with a pH of six, and a salinity concentration of 2%. Nanoarchaeum cannot synthesize lipids but obtains them from its host, Ignicoccus. Nanoarchaeum appears to be an obligatory symbiont of this archaeon Ignicoccus, and must be in contact with it to survive.

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Nanoarchaeum equitans: Image of Nanoarchaeum equitans (and its host Ignicoccus).

Nanoarchaeum cells are only 400 nm in diameter, making it the next smallest known living organism to nanobacteria and nanobes, whose status as living organisms is controversial. Its genome is only 490,885 nucleotides long; the smallest non-viral genome ever sequenced next to that of Candidatus Carsonella ruddii. N. equitans genome consists of a single circular chromosome, and lacks almost all genes required for synthesis of amino acids, nucleotides, cofactors, and lipids, but encodes everything needed for repair and replication. 95% of its DNA encodes for proteins for stable RNA molecules. Nanoarchaeum has small appendages that come out of its circular structure. The cell surface is covered by a thin, lattice-shaped S-layer, which provides structure and protection for the entire cell. Genetically, Nanoarchaeum is peculiar in that its 16S RNA sequence is undetectable by the most common methods.

The sequencing of the Nanoarchaeum genome has revealed a wealth of information about the organism’s biology. The genes for several vital metabolic pathways appear to be missing. Nanoarchaeum cannot synthesize most nucleotides, amino acids, lipids, and cofactors. The cell most likely obtains these biomolecules from Ignicoccus. However, unlike many parasitic microbes, Nanoarchaeum has many DNA repair enzymes, as well as everything necessary to carry out DNA replication, transcription, and translation. This may explain why the genome lacks the large stretches of non-coding DNA characteristic of other parasites. The organism’s ability to produce its own ATP is also in question. Nanoarchaeum lacks the ability to metabolize hydrogen and sulfur for energy, as many thermophiles do. It does have five subunits of an ATP synthase as well as pathways for oxidative deamination. Whether it obtains energy from biological molecules imported from Ignicoccus, or whether it receives ATP directly is currently unknown. The genome and proteome composition of N. equitans are marked with the signatures of dual adaptation – one to high temperature and the other to obligatory parasitism (or symbiosis).

Aciduliprofundum is another genus of the Euryarchaeota, though relatively less is known about it.

Hyperthermophilic Archaea, H2, and Microbial Evolution

A hyperthermophile is an organism that thrives in extremely hot environments, from 60 degrees C (140 degrees F) and up.

Learning Objectives

Discuss the characteristics associated with hyperthermophiles

Key Takeaways

Key Points

  • Many hyperthermophiles are also able to withstand other environmental extremes like high acidity or radiation levels.
  • The current record growth temperature is 122°C for Methanopyrus kandleri.
  • Although no hyperthermophile has yet been discovered living at temperatures above 122°C, their existence is very possible.
  • It is thought unlikely that microbes could survive at temperatures above 150°C, as the cohesion of DNA and other vital molecules begins to break down at this point.
  • The protein molecules in hyperthermophiles exhibit hyperthermostability and can maintain structural stability (and therefore function) to adapt to high temperatures.

Key Terms

  • hyperthermophile: An organism that lives and thrives in an extremely hot environment like a deep sea smoker vent; often a member of the Archaea.

A hyperthermophile is an organism that thrives in extremely hot environments, from 60 degrees C (140 degrees F) and up. Hyperthermophiles are a subset of extremophiles within the domain Archaea. An optimal temperature for the existence of hyperthermophiles is above 80°C (176°F). Some bacteria are even able to tolerate temperatures of around 100°C (212°F). Many hyperthermophiles are also able to withstand other environmental extremes like high acidity or radiation levels.

Hyperthermophiles were first discovered by Thomas D. Brock in hot springs in Yellowstone National Park, Wyoming. Since then, more than 70 species have been discovered. The most hardy hyperthermophiles yet discovered live on the superheated walls of deep-sea hydrothermal vents, requiring temperatures of at least 90°C for survival.

One extraordinary heat-tolerant hyperthermophile is the recently discovered Strain 121, an archaeon living at 121°C in the Pacific Ocean. Strain 121 has been able to double its population during 24 hours in an autoclave at 121°C (hence its name). Strain 121 survived being heated to 130°C for two hours, but was unable to reproduce until it was transferred to fresh growth medium at the relatively cooler temperature of 103°C. The current record growth temperature is 122°C for Methanopyrus kandleri ,an archaeon found in a Central Indian Ridge. Other hyperthermophile archaea include Pyrolobus fumarii, which lives at 113°C in Atlantic hydrothermal vents, and Pyrococcus furiosus, first discovered in Italy near a volcanic vent.

Although no hyperthermophile has yet been discovered living at temperatures above 122°C, their existence is very possible. However, it is thought unlikely that microbes could survive at temperatures above 150°C, as the cohesion of DNA and other vital molecules begins to break down at this point.

There are a number of proposed high temperature adaptions of hyperthermophiles. Early research into hyperthermophiles speculated that their genome could be characterized by high guanine-cytosine content; however, recent studies show that there is no obvious correlation between the GC content of the genome and the optimal environmental growth temperature of the organism. The protein molecules in the hyperthermophiles exhibit hyperthermostability – that is, they can maintain structural stability (and therefore function) at high temperatures. Such proteins are homologous to their functional analogues in organisms which thrive at lower temperatures, but have evolved to exhibit optimal function at much greater temperatures. Most of the low-temperature homologues of the hyperthermostable proteins would be denatured above 60°C. Such hyperthermostable proteins are often commercially important, as chemical reactions proceed faster at high temperatures. The cell membrane of hyperthermophiles contains high levels of saturated fatty acids, which are usually arranged in a C40 monolayer to retain its shape at high temperatures.