Crenarchaeota



Habitats and Energy Metabolism of Crenarchaeota

Crenarchaeota exist in a wide range of habitats and exhibit a great variety of chemical reactions in their metabolism.

Learning Objectives

Outline the various types of energy metabolism used by Crenarchaeota

Key Takeaways

Key Points

  • The first-discovered archaeans were extremophiles.
  • Extremophile archaea are members of four main physiological groups: halophiles, thermophiles, alkaliphiles, and acidophiles.
  • Some archaea obtain energy from inorganic compounds such as sulfur or ammonia (they are lithotrophs).
  • Other groups of archaea use sunlight as a source of energy (phototrophs) or CO2 in the atmosphere as a source of carbon (autotrophs).

Key Terms

  • extremophile: An organism that lives under extreme conditions of temperature, salinity, and so on. They are commercially important as a source of enzymes that operate under similar conditions.
  • phototroph: An organism that carries out photon capture to acquire energy. They use the energy from light to carry out various cellular metabolic processes.
  • autotroph: Any organism that can synthesize its food from inorganic substances, using heat or light as a source of energy.

The Crenarchaeota are Archaea that have been classified as either a phylum of the Archaea kingdom, or in a kingdom of its own. Archaea exist in a broad range of habitats, and as a major part of global ecosystems, they may contribute up to 20% of earth’s biomass.

The first-discovered archaeans were extremophiles. Indeed, some archaea survive high temperatures, often above 100 °C (212 °F), as found in geysers, black smokers, and oil wells. Other common habitats include very cold habitats and highly saline, acidic, or alkaline water. However, archaea also include mesophiles that grow in mild conditions, in marshland, sewage, the oceans, and soils.

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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

Extremophile archaea are members of four main physiological groups. These are the:

  • halophiles
  • thermophiles
  • alkaliphiles
  • acidophiles

These groups are not comprehensive or phylum-specific, nor are they mutually exclusive, since some archaea belong to several groups. Nonetheless, they are a useful starting point for classification Halophiles live in extremely saline environments such as salt lakes. Thermophiles grow best at temperatures above 45 °C (113 °F), in places such as hot springs; hyperthermophilic archaea grow optimally at temperatures greater than 80 °C (176 °F). Other archaea exist in very acidic or alkaline conditions.

Recently, several studies have shown that archae exist not only in mesophilic and thermophilic environments but are also present, sometimes in high numbers, at low temperatures as well, as found in cold oceanic environments.

Chemical reactions and energy sources

Archaea exhibit a great variety of chemical reactions in their metabolism and use many sources of energy. These reactions are classified into nutritional groups, depending on energy and carbon sources.

Some archaea obtain energy from inorganic compounds such as sulfur or ammonia (they are lithotrophs). These include nitrifiers, methanogens and anaerobic methane oxidisers. In these reactions one compound passes electrons to another (in a redox reaction), releasing energy to fuel the cell’s activities. One compound acts as an electron donor and one as an electron acceptor. The energy released generates adenosine triphosphate ( ATP ) through chemiosmosis, in the same basic process that happens in the mitochondrion of eukaryotic cells.

Other groups of archaea use sunlight as a source of energy (phototrophs). However, oxygen–generating photosynthesis does not occur in any of these organisms. Many basic metabolic pathways are shared between all forms of life; for example, archaea use a modified form of glycolysis (the Entner–Doudoroff pathway) and either a complete or partial citric acid cycle. These similarities to other organisms probably reflect both early origins in the history of life and their high level of efficiency.

Some Euryarchaeota are methanogens living in anaerobic environments such as swamps. This form of metabolism evolved early, and it is even possible that the first free-living organism was a methanogen. A common reaction involves the use of carbon dioxide as an electron acceptor to oxidize hydrogen. Methanogenesis involves a range of coenzymes that are unique to these archaea, such as coenzyme M and methanofuran. These reactions are common in gut-dwelling archaea. Acetic acid is also broken down into methane and carbon dioxide directly, by acetotrophic archaea. These acetotrophs are archaea in the order Methanosarcinales, and are a major part of the communities of microorganisms that produce biogas.

Other archaea use CO2 in the atmosphere as a source of carbon, in a process called carbon fixation (they are autotrophs). This process involves either a highly modified form of the Calvin cycle or a recently discovered metabolic pathway called the 3-hydroxypropionate/4-hydroxybutyrate cycle. The Crenarchaeota also use the reverse Krebs cycle while the Euryarchaeota also use the reductive acetyl-CoA pathway. Carbon–fixation is powered by inorganic energy sources. No known archaea carry out photosynthesis.

Archaeal energy sources are extremely diverse, and range from the oxidation of ammonia by the Nitrosopumilales to the oxidation of hydrogen sulfide or elemental sulfur by species of Sulfolobus, using either oxygen or metal ions as electron acceptors.

Phototrophic archaea use light to produce chemical energy in the form of ATP. In the Halobacteria, light-activated ion pumps like bacteriorhodopsin and halorhodopsin generate ion gradients by pumping ions out of the cell across the plasma membrane. The energy stored in these electrochemical gradients is then converted into ATP by ATP synthase (photophosphorylation).

Some marine Crenarchaeota are capable of nitrification, suggesting these organisms may affect the oceanic nitrogen cycle, although these oceanic Crenarchaeota may also use other sources of energy. Vast numbers of archaea are also found in the sediments that cover the sea floor, with these organisms making up the majority of living cells at depths over 1 meter below the ocean bottom.

Hyperthermophiles from Terrestrial Volcanic Habitats

A hyperthermophile thrives at relatively high temperatures and can be found in geothermally heated regions of the Earth.

Learning Objectives

Summarize the traits that define Hyperthermophiles

Key Takeaways

Key Points

  • Unlike other types of bacteria, thermophiles can survive at much hotter temperatures, whereas other bacteria would be damaged or killed if exposed to the same temperatures.
  • Thermophiles contain enzymes that can function at high temperatures.
  • Hyperthermophiles are particularly extreme thermophiles for which the optimal temperatures are above 80°C, and their membranes and proteins are unusually stable at these extremely high temperatures.

Key Terms

  • lithotroph: An organism that obtains its energy from inorganic compounds (such as ammonia) via electron transfer.
  • thermophile: An organism that lives and thrives at relatively high temperatures; a form of extremophile; many are members of the Archaea.

A thermophile is an organism —a type of extremophile—that thrives at relatively high temperatures, between 45 and 122 °C (113 and 252 °F). Many thermophiles are archaea. Thermophilic eubacteria are suggested to have been among the earliest bacteria. Thermophiles are found in various geothermally heated regions of the Earth, such as the hot springs found in Yellowstone National Park.

Unlike other types of bacteria, thermophiles can survive at much hotter temperatures, whereas other bacteria would be damaged or killed if exposed to the same temperatures. As a prerequisite for their survival, thermophiles contain enzymes that can function at high temperatures. Some of these enzymes are used in molecular biology (for example, heat-stable DNA polymerases for PCR), and in washing agents. Thermophiles are classified into obligate and facultative thermophiles; obligate thermophiles (also called extreme thermophiles) require such high temperatures for growth, whereas facultative thermophiles (also called moderate thermophiles) can thrive at high temperatures, but also at lower temperatures (below 50°C).

Hyperthermophiles are particularly extreme thermophiles for which the optimal temperatures are above 80°C. Thermophiles, meaning “heat-loving,” are organisms with an optimum growth temperature of 50°C or more, a maximum of up to 70°C or more, and a minimum of about 40°C, but these are only approximate. Some extreme thermophiles (hyperthermophiles) require a very high temperature (80°C to 105°C) for growth. Their membranes and proteins are unusually stable at these extremely high temperatures. Thus, many important biotechnological processes use thermophilic enzymes because of their ability to withstand intense heat.

Many of the hyperthermophiles Archea require elemental sulfur for growth. Some are anaerobes that use the sulfur instead of oxygen as an electron acceptor during cellular respiration. Some are lithotrophs that oxidize sulfur to sulfuric acid as an energy source, thus requiring the microorganism to be adapted to very low pH (i.e., it is an acidophile as well as thermophile). These organisms are inhabitants of hot, sulfur-rich environments usually associated with volcanism, such as hot springs, geysers, and fumaroles. In these places, especially in Yellowstone National Park, zonation of microorganisms according to their temperature optima occurs. Often, these organisms are colored due to the presence of photosynthetic pigments.

Hyperthermophiles from Submarine Volcanic Habitats

Hyperthermophiles live in dark regions of the oceans and use chemosynthesis to produce biomass from single carbon molecules.

Learning Objectives

Describe the metabolic processes used by hyperthermophiles found in submarine volcanic habitats

Key Takeaways

Key Points

  • Chemosynthesis is the biological conversion of one or more carbon molecules and nutrients into organic matter using the oxidation of inorganic molecules (e.g. hydrogen gas, hydrogen sulfide ) or methane as a source of energy.
  • The energy for chemosynthesis can be derived from hydrogen, hydrogen sulfide or ammonia.
  • Many chemosynthetic microorganisms are consumed by other organisms in the ocean, and symbiotic associations between chemosynthesizers and respiring heterotrophs are quite common.

Key Terms

  • hydrothermal vent: a hot spring, on the floor of the ocean, mostly along the central axes of the mid-ocean ridges, where heated fluids emerge from fissures in the Earth’s crust
  • symbiotic: Of a relationship with mutual benefit between two individuals or organisms.
  • chemosynthesis: The production of carbohydrates and other compounds from simple compounds such as carbon dioxide, using the oxidation of chemical nutrients as a source of energy rather than sunlight; it is limited to certain bacteria and fungi.

In biochemistry, chemosynthesis is the biological conversion of one or more carbon molecules (usually carbon dioxide or methane) and nutrients into organic matter using the oxidation of inorganic molecules (e.g. hydrogen gas, hydrogen sulfide) or methane as a source of energy. Chemoautotrophs, organisms that obtain carbon through chemosynthesis, are phylogenetically diverse. Groups that include conspicuous or biogeochemically-important taxa include the sulfur-oxidizing gamma and epsilon proteobacteria, the Aquificaeles, the methanogenic archaea and the neutrophilic iron-oxidizing bacteria.

A thermophile is an organism that thrives at relatively high temperatures, between 45 and 122 °C (113 and 252 °F). Thermophiles are found in various geothermally heated regions of the Earth, such as deep sea hydrothermal vents. As a prerequisite for their survival, thermophiles contain enzymes that can function at high temperatures. Some of these enzymes are used in molecular biology (for example, heat-stable DNA polymerases for PCR), and in washing agents.

Thermophiles are classified into obligate and facultative thermophiles: Obligate thermophiles (also called extreme thermophiles) require such high temperatures for growth, whereas facultative thermophiles (also called moderate thermophiles) can thrive at high temperatures, but also at lower temperatures (below 50°C). For example, Venenivibrio stagnispumantis gains energy by oxidizing hydrogen gas.

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Venenivibrio: Scanning Electron Microscopy image of Venenivibrio stagnispumantis, a species which gains energy by oxidizing hydrogen gas.

Many microorganisms in dark regions of the oceans also use chemosynthesis to produce biomass from single carbon molecules. Two categories can be distinguished. In the rare sites at which hydrogen molecules (H2) are available, the energy available from the reaction between CO2 and H2 (leading to production of methane, CH4) can be large enough to drive the production of biomass. Alternatively, in most oceanic environments, energy for chemosynthesis derives from reactions in which substances such as hydrogen sulfide or ammonia are oxidized to produce formaldehyde (which will be used to make carbohydrates) and solid globules of sulfur. This may occur with or without the presence of oxygen. In bacteria that can do this, such as purple sulfur bacteria, yellow globules of sulfur are present and visible in the cytoplasm.

Many chemosynthetic microorganisms are consumed by other organisms in the ocean, and symbiotic associations between chemosynthesizers and respiring heterotrophs are quite common. Large populations of animals can be supported by chemosynthetic secondary production at hydrothermal vents, methane clathrates, cold seeps, whale falls, and isolated cave water. Indeed, it has been hypothesized that chemosynthesis may support life below the surface of Mars, Jupiter’s moon Europa, and other planets. Giant tube worms use bacteria in their trophosome to react hydrogen sulfide with oxygen as a source of energy.

Nonthermophilic Crenarchaeota

Nonthermophilic Crenarchaeota can be extreme halophiles living in highly salty environments.

Learning Objectives

Discuss the characteristics of nonthermophilic crenarchaeota, specifically Halococcus, that allow it to survive in extreme environments

Key Takeaways

Key Points

  • Halococcus is a genus of extreme halophilic archaea.
  • Halophiles are found mainly in inland bodies of water with high salinity, where their pigments (from a protein called rhodopsinprotein) tint the sediment bright colors.
  • Halococcus and similar halophilic organisms have been utilized economically in the food industry and even in skin-care production.
  • Halococcus is able to survive in its high-saline habitat by preventing the dehydration of its cytoplasm using a solute which is either found in their cell structure or is drawn from the external environment.

Key Terms

  • halophile: An organism that lives and thrives in an environment of high salinity, often requiring such an environment; a form of extremophile.

Crenarchaeota can be extreme halophiles, and include organisms living in highly salty environments (for example, halococcus).

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Archaea: Cluster of halobacterium (archaea)

Halococcus is a genus of extremely halophilic archaea, meaning that they require high salt levels, sometimes as high as 32% NaCl, for optimal growth. Halophiles are found mainly in inland bodies of water with high salinity, where their pigments (from a protein called rhodopsinprotein) tint the sediment bright colors. Rhodopsin protein and other proteins serve to protect Halococcus from the extreme salinities of the environment. Some Halococcus may be located in highly salted soil or foods. Because they can function under such high-salt conditions, Halococcus and similar halophilic organisms have been utilized economically in the food industry and even in skin-care production. Halococcus’ genome has not been sequenced yet, although studies of its 16s rDNA have demonstrated its placement on the phylogenetic tree. Due to the organisms’ potential longevity, Halococcus may be a good candidate for exploring taxonomic similarities to life found in outer space.

Halococcus is able to survive in its high-saline habitat by preventing the dehydration of its cytoplasm. To do this they use a solute, which is either found in their cell structure or is drawn from the external environment. Special chlorine pumps allow the organisms to retain chloride to maintain osmotic balance with the salinity of their habitat. The cells are cocci, 0.6-1.5 micrometres long, with sulfated polysaccharide walls. The cells are organtrophic, using amino acids, organic acids, or carbohydrates for energy. In some cases they are also able to photosynthesize.

Psychrophilic Crenarchaeota

Psychrophiles crenarchaeotes are extremophilic organisms that are capable of growth and reproduction in cold temperatures.

Learning Objectives

Discuss the specific characteristics associated with psychrophilic crenarchaeotes

Key Takeaways

Key Points

  • Psychrophiles are characterized by lipid cell membranes chemically resistant to the stiffening caused by extreme cold, and often create protein ‘antifreezes’ to keep their internal space liquid and protect their DNA even in temperatures below water’s freezing point.
  • Crenarchaea are thought to be very abundant and one of the main contributors to the fixation of carbon.
  • Crenarchaeote are abundant in the ocean and some species have a 200 times greater affinity for ammonia than ammonia oxidizing bacteria, leading researchers to challenge the previous belief that ammonia oxidizing bacteria are primarily responsible for nitrification in the ocean.

Key Terms

  • crenarchaeota: Archae that have been recently identified to be present in marine environments where they responsible for nitrification.
  • psychrophile: An organism that can live and thrive at temperatures much lower than normal; a form of extremophile.

Psychrophiles or cryophiles (adj. cryophilic) are extremophilic organisms that are capable of growth and reproduction in cold temperatures, ranging from −15°C to +10°C. Temperatures as low as −15°C are found in pockets of very salty water (brine) surrounded by sea ice. They can be contrasted with thermophiles, which thrive at unusually hot temperatures. The environments they inhabit are ubiquitous on Earth, as a large fraction of our planetary surface experiences temperatures lower than 15°C. They are present in alpine and arctic soils, high-latitude and deep ocean waters, polar ice, glaciers, and snowfields. Most psychrophiles are bacteria or archaea, and psychrophily is present in widely diverse microbial lineages within those broad groups. Psychrophiles are characterized by lipid cell membranes chemically resistant to the stiffening caused by extreme cold, and often create protein ‘antifreezes’ to keep their internal space liquid and protect their DNA even in temperatures below water’s freezing point.

The Crenarchaeota (Greek for “spring old quality”) (also known as Crenarchaea or eocytes) are Archaea that have been classified as either a phylum of the Archaea kingdom or a kingdom of its own. Initially, the Crenarchaeota were thought to be sulfur-dependent extremophiles but recent studies have identified characteristic Crenarchaeota environmental rRNA indicating the organism may be the most abundant archaea in the marine environment. Originally, they were separated from the other archaea based on rRNA sequences. However, other physiological features, such as lack of histones have supported this division, although some crenarchaea were found to have histones. Until recently all cultured Crenarchaea had been thermophilic or hyperthermophilic organisms, some of which have the ability to grow at up to 113 °C. These organisms stain Gram negative and are morphologically diverse having rod, cocci, filamentous and oddly shaped cells. Beginning in 1992, data were published that reported sequences of genes belonging to the Crenarchaea in marine environments making these bacteria psychrophiles or cryophiles. Since then, analysis of the abundant lipids from the membranes of Crenarchaea taken from the open ocean have been used to determine the concentration of these “low temperature Crenarchaea.” Based on these measurements of their signature lipids, Crenarchaea are thought to be very abundant and one of the main contributors to the fixation of carbon. DNA sequences from Crenarchaea have also been found in soil and freshwater environments, suggesting that this phylum is ubiquitous to most environments.

Nitrification, as stated above, is formally a two-step process; in the first step ammonia is oxidized to nitrite, and in the second step nitrite is oxidized to nitrate. Different microbes are responsible for each step in the marine environment. Several groups of ammonia oxidizing bacteria (AOB) are known in the marine environment, including Nitrosomonas, Nitrospira, and Nitrosococcus. All contain the functional gene ammonia monooxygenase (AMO) which, as its name implies, is responsible for the oxidation of ammonia. More recent metagenomic studies have revealed that some Crenarchaeote Archaea possess AMO. Crenarchaeote are abundant in the ocean and some species have a 200 times greater affinity for ammonia than AOB, leading researchers to challenge the previous belief that AOB are primarily responsible for nitrification in the ocean.

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Nitrogen Cycling: Nitrification is the biological oxidation of ammonia with oxygen into nitrite followed by the oxidation of these nitrites into nitrates. Degradation of ammonia to nitrite is usually the rate limiting step of nitrification. Nitrification is an important step in the nitrogen cycle in soil.