Thermophiles

Aquificales and Thermotogales

Along with Thermotogae, members of Aquificae are thermophilic eubacteria.

Learning Objectives

Differentiate Aquificales from Thermotogae

Key Takeaways

Key Points

  • The phylum Thermotogae is composed of gram-negative staining, anaerobic, mostly thermophilic, and hyperthermophilic bacteria.
  • The Aquificae phylum is a diverse collection of bacteria that live in harsh environmental settings. They have been found in hot springs, sulfur pools, and thermal ocean vents.
  • A 51 amino acid insertion has been identified in SecA preprotein translocase which is shared by various members of the phylum Aquificae as well as 2 Thermotoga species. The presence of the insertion in the Thermotoga species may be due to a horizontal gene transfer.
  • However, a close relationship of the Aquificae to Thermotogae and the deep branching of Aquificae is not supported by phylogenetic studies based upon other gene/ protein sequences and also by conserved signature indels in several highly conserved universal proteins.

Key Terms

  • thermophile: 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.
  • hyperthermophile: An organism that thrives in extremely hot environments— from 60 degrees C (140 degrees F) upwards. An optimal temperature for the existence of hyperthermophiles is above 80°C (176°F). Hyperthermophiles are a subset of extremophiles, micro-organisms within the domain Archaea, although some bacteria are able to tolerate temperatures of around 100°C (212°F), as well.

Along with Thermotogae, members of Aquificae are thermophilic eubacteria (thermophiles).

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Thermophile bacteria isolated from deep-sea vent fluids.: This organism eats sulfur and hydrogen and fixes its own carbon from carbon dioxide. (A,B) scanning electron micrographs, and (C,D) transmission electron micrographs in thin sections.

Aquificales

The Aquificae phylum is a diverse collection of bacteria that live in harsh environmental settings. They have been found in hot springs, sulfur pools, and thermal ocean vents. Members of the genus Aquifex, for example, are productive in water between 85 to 95 °C. They are the dominant members of most terrestrial neutral to alkaline hot springs above 60 degrees Celsius. They are autotrophs, and are the primary carbon fixers in these environments. They are true bacteria (domain bacteria) as opposed to the other inhabitants of extreme environments, the Archaea.

Comparative genomic studies have identified six conserved signature indels (CSIs) that are specific for the species from the phylum Aquificae and provide potential molecular markers for this phylum. Additionally, a 51 amino acid insertion has been identified in SecA preprotein translocase which is shared by various members of the phylum Aquificae as well as two Thermotoga species. The presence of the insertion in the Thermotoga species may be due to a horizontal gene transfer. In the 16S rRNA gene trees, the Aquificae species branch in the proximity of the phylum Thermotogae (another phylum comprising hyperthermophiles) close to the archaeal-bacterial branch point. However, a close relationship of the Aquificae to Thermotogae and the deep branching of Aquificae is not supported by phylogenetic studies based upon other gene/protein sequences and also by conserved signature indels in several highly conserved universal proteins.

Thermotogae

The phylum Thermotogae is composed of gram-negative staining, anaerobic, mostly thermophilic, and hyperthermophilic bacteria. The name of this phylum is derived from the existence of many of these organisms at high temperatures along with the characteristic sheath structure, or “toga,” surrounding the cells of these species. Recently, some Thermotogae existing in mesophilic temperatures have also been identified. Although Thermotogae species exhibit Gram-negative staining, they are bounded by a single unit lipid membrane. Therefore, they are monoderm bacteria. Because of the ability of some Thermotogae species to thrive at high temperatures, they are considered attractive targets for use in industrial processes. The metabolic ability of Thermotogae to utilize different complex-carbohydrates for production of hydrogen gas led to these species being cited as a possible biotechnological source for production of energy alternative to fossil fuels.

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Thermotoga sketch: Outline of a Thermotoga maritima section showing the “toga. “

This phylum presently consists of a single class (Thermotogae), order (Thermotogales), and family (Thermotogaceae). It contains a total of nine genera (viz. Thermotoga, Petrotoga, Thermosipho, Fervidobacterium, Marinitoga, Kosmotoga, Geotoga, Thermopallium, and Thermococcoides), all of which are currently part of the family Thermotogaceae. In the 16S rRNA trees the Thermotogae have been observed to branch with the Aquificae in close proximity to the archaeal-bacterial branch point. The Thermotogae have also been scrutinized for their supposedly profuse lateral gene transfer (LGT) with Archaeal organisms. However, recent studies based on more robust methodologies suggest that incidence of LGT between Thermotogae and other groups including Archaea is not as high as suggested in earlier studies.

Until recently, no biochemical or molecular markers were known that could distinguish the species from the phylum Thermotogae from all other bacteria. However, a recent comparative genomic study has identified large numbers of conserved signature indels (CSIs) in important proteins that are specific for either all Thermotogae species or a number of its sub-groups. The newly discovered molecular markers provide novel means for identification and circumscription of species from the Thermotogae phylum in molecular terms and for future revisions to the taxonomy of this phylum.

Deinococcus and Thermus

The Deinococcus-Thermus are a small group of bacteria composed of cocci highly resistant to environmental hazards.

Learning Objectives

Compare Deinococcus and Thermus bacteria

Key Takeaways

Key Points

  • The Deinococcales include two families with three genera, Deinococcus and Truepera, the former with several species that are resistant to radiation; they are famous for their ability to eat nuclear waste and other toxic materials, survive in the vacuum of space and in extremes of heat and cold.
  • The Thermales include several genera resistant to heat, including Thermus.
  • These bacteria have thick cell walls that give them Gram-positive stains, but they include a second membrane and so are closer in structure to those of Gram-negative bacteria.

Key Terms

  • radioresistance: Any form of resistance that an organism has to protect itself against the harmful effects of ionizing radiation
  • clade: A group of animals or other organisms derived from a common ancestor species.
  • polyextremophile: An organism which can tolerate two or more extreme environmental factors.

The Deinococcus-Thermus are a small group of bacteria composed of cocci that are highly-resistant to environmental hazards. There are two main groups: the Deinococcales include two families, with three genera, Deinococcus and Truepera.

The Thermales include several genera resistant to heat (Marinithermus, Meiothermus, Oceanithermus, Thermus, Vulcanithermus).

Though these two groups evolved from a common ancestor, the two mechanisms of resistance appear to be largely independent.

DEINOCOCCUS

This is the one genus of three of the Deinococcales group from the Deinococcus-Thermus phylum, and is highly-resistant to environmental hazards. It has several species that are resistant to radiation (they have become famous for their ability to eat nuclear waste and other toxic materials), survive in the vacuum of space, and in extremes of heat and cold. There are 47 species of Deinococcus described according to NCBI on 25 August 2011.

These bacteria have thick cell walls that give them Gram-positive stains, but they include a second membrane and so are closer in structure to those of Gram-negative bacteria. Cavalier-Smith calls this clade Hadobacteria (from Hades, the Greek underworld).

They are also characterized by the presence of the carotenoid pigment Deinoxanthin that give them their pink color, and a high resistance to gamma and UV radiation. They are usually isolated according to these two criteria.

D. RADIODURANS

Deinococcus radiodurans is an extremophilic bacterium, one of the most radioresistant organisms known. It can survive cold, dehydration, vacuum, and acid, and is therefore known as a polyextremophile and has been listed as the world’s toughest bacterium in The Guinness Book of World Records.

D. radiodurans is a rather large, spherical bacterium, with a diameter of 1.5 to 3.5 µm. Four cells normally stick together, forming a tetrad. The bacteria are easily cultured and do not appear to cause disease. Colonies are smooth, convex, and pink to red in color. D. radiodurans does not form endospores and is nonmotile. It is an obligate aerobic chemoorganoheterotroph, i.e., it uses oxygen to derive energy from organic compounds in its environment.

It is often found in habitats rich in organic materials, such as soil, feces, meat, or sewage, but has also been isolated from dried foods, room dust, medical instruments and textiles. It is extremely resistant to ionizing radiation, ultraviolet light, desiccation, and oxidizing and electrophilic agents.

Its genome consists of two circular chromosomes, one 2.65 million base pairs long and the other 412 thousand base pairs long, as well as a megaplasmid of 177 thousand base pairs and a plasmid of 46 thousand base pairs. It has about 3,195 genes. In its stationary phase, each bacterial cell contains four copies of this genome; when rapidly multiplying, this increases to eight to 10 copies.

D. radiodurans is capable of withstanding an acute dose of five thousand Gy (five hundred thousand rad) of ionizing radiation with almost no loss of viability, and an acute dose of 15 thousand Gy with 37% viability. A dose of five thousand Gy is estimated to introduce several hundred double-strand breaks (DSBs) into the organism’s DNA (~0.005 DSB/Gy/Mbp (haploid genome)). For comparison, a chest X-ray or Apollo mission involves about one mGy, five Gy can kill a human, two to eight hundred Gy will kill E. coli, and over four thousand Gy will kill the radiation-resistant tardigrade.

Several bacteria of comparable radioresistance are now known, including some species of the genus Chroococcidiopsis (phylum cyanobacteria ) and some species of Rubrobacter (phylum actinobacteria); among the archaea, the species Thermococcus gammatolerans shows comparable radioresistance.

D. radiodurans also has a unique ability to repair damaged DNA. It isolates the damaged segments in a controlled area and repairs it. This bacteria can also repair many small fragments from an entire chromosome.

THERMUS

A genus of thermophilic bacteria that can tolerate high temperatures, it is one of several bacteria belonging to the Deinococcus-Thermus group and includes the following three species: T. aquaticus, T. antranikianii, and T. igniterrae.

Thermus aquaticus is the source of the heat-resistant enzyme Taq DNA polymerase, one of the most important enzymes in molecular biology because of its use in the polymerase chain reaction (PCR) DNA-amplification technique.

It thrives at 70°C (160°F), but can survive at temperatures of 50°C to 80°C (120°F to 175°F). This bacterium is a chemotroph — it performs chemosynthesis to obtain food. However, since its range of temperature overlaps somewhat with that of the photosynthetic cyanobacteria that share its ideal environment, it is sometimes found living jointly with its neighbors, obtaining energy for growth from their photosynthesis.

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Thermus aquaticus: Electron microscopy of thermus aquaticus.

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A tetrad of D. radiodurans: Transmission electron microgragh (TEM) of D. radiodurans.

Chloroflexus and Relatives

Chloroflexus are Gram-negative filamentous anoxygenic phototrophic organisms that utilize type II photosynthetic reaction centers.

Learning Objectives

Show the unique features of chloroflexus

Key Takeaways

Key Points

  • These anoxygenic phototrophs do not produce oxygen as a byproduct of photosynthesis, in contrast to oxygenic phototrophs like cyanobacteria. While oxygenic phototrophs use water as an electron donor for phototrophy, Chloroflexus uses reduced sulfur compounds such as thiosulfate or elemental sulfur.
  • The complete electron transport chain for Chloroflexus spp. is not yet known. Particularly, Chloroflexus aurantiacus has not been demonstrated to have a cytochrome bc1 complex, and may use different proteins to reduce cytochrome c.
  • The Chloroflexi are a phylum of bacteria containing isolates with a diversity of phenotypes including aerobic thermophiles, which use oxygen and grow well in high temperatures, anoxygenic phototrophs, which use light for photosynthesis, and anaerobic halorespirers, which uses halogenated organics.
  • Recent phylogenetic analysis of the Chloroflexi has found very weak support for the grouping together of the different classes currently part of the phylum.

Key Terms

  • trichome: Certain (usually filamentous) algae have the terminal cell produced into an elongate “hair-like” structure called a trichome. The same term is applied to such structures in some cyanobacteria.

As a genus, Chloroflexus spp. are Gram-negative filamentous anoxygenic phototrophic (FAP) organisms that utilize type II photosynthetic reaction centers containing bacteriochlorophyll a similar to the purple bacteria, and light-harvesting chlorosomes containing bacteriochlorophyll c similar to green sulfur bacteria of the Chlorobi. As the name implies, these anoxygenic phototrophs do not produce oxygen as a byproduct of photosynthesis, in contrast to oxygenic phototrophs such as cyanobacteria, algae, and higher plants. While oxygenic phototrophs use water as an electron donor for phototrophy, Chloroflexus uses reduced sulfur compounds such as hydrogen sulfide, thiosulfate, or elemental sulfur. This belies their antiquated name green non-sulfur bacteria. However, Chloroflexus spp. can also utilize hydrogen (H2) as a source of electrons.

Chloroflexus aurantiacus is thought to grow photoheterotrophically in nature, but it has the capability of fixing inorganic carbon through photoautotrophic growth. Instead of using the Calvin-Benson-Bassham Cycle typical of plants, Chloroflexus aurantiacus has been demonstrated to use a novel autotrophic pathway known as the 3-Hydroxypropionate pathway.The complete electron transport chain for Chloroflexus spp. is not yet known. Particularly, Chloroflexus aurantiacus has not been demonstrated to have a cytochrome bc1 complex. It may use different proteins to reduce cytochrome c.

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3-Hydroxypropionate Pathway: A schematic representation of the 3-Hydroxypropionate CO2 assimilatory pathway observed in Chloroflexus bacteria.

Chloroflexus aurantiacus is a photosynthetic bacterium isolated from hot springs, belonging to the green non-sulfur bacteria. This organism is thermophilic and can grow at temperatures from 35 °C to 70 °C. Chloroflexus aurantiacus can survive in the dark if oxygen is available. When grown in the dark, Chloroflexus aurantiacus has a dark orange color. When grown in sunlight it is dark green. The individual bacteria tend to form filamentous colonies enclosed in sheaths, which are known as trichomes. One of the main reasons for interest in Chloroflexus aurantiacus is in the study of the evolution of photosynthesis.

How did photosynthesis arise in bacteria? The answer to this question is complicated by the fact that there are several types of light-harvesting energy capture systems. Chloroflexus aurantiacus has been of interest in the search for origins of the so-called type II photosynthetic reaction center. One idea is that bacteria with respiratory electron transport evolved photosynthesis by coupling a light-harvesting energy capture system to the pre-existing respiratory electron transport chain. Therefore, rare organisms like Chloroflexus aurantiacus that can survive using either respiration or photosynthesis are of interest in on-going attempts to trace the evolution of photosynthesis.

The Chloroflexi or Chlorobacteria are a phylum of bacteria containing isolates with a diversity of phenotypes including members that are aerobic thermophiles, which use oxygen and grow well in high temperatures, anoxygenic phototrophs, which use light for photosynthesis, and anaerobic halorespirers, which use halogenated organics (such as the toxic chlorinated ethenes and polychlorinated biphenyls) as energy sources. Whereas most bacteria, in terms of diversity, are diderms and stain Gram negative with the exception of the Firmicutes (low CG Gram positives), Actinobacteria (high CG gram positives), and the Deinococcus-Thermus group (Gram positive, but diderms with thick peptidoglycan), the members of the phylum Chloroflexi are monoderms and stain mostly Gram negative.

In 1987, Carl Woese, regarded as the forerunner of the molecular phylogeny revolution, divided Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences and grouped the genera Chloroflexus, Herpetosiphon, and Thermomicrobium into the “Green non-sulfur bacteria and relatives,” which was temporarily renamed as “Chloroflexi” in Volume One of Bergey’s Manual of Systematic Bacteriology.

Recent phylogenetic analysis of the Chloroflexi has found very weak support for the grouping together of the different classes currently part of the phylum. The six classes that make up the phylum did not consistently form a well-supported monophyletic clade in phylogenetic trees based on concatenated sequences for large datasets of proteins. No conserved signature indels were identified that were uniquely shared by the entire phylum. However, the classes “Chloroflexi” and Thermomicrobia were found to group together consistently by both phylogenetic means and the identification of shared conserved signature indels in the 50S ribosomal protein L19 and the enzyme UDP-glucose 4-epimerase. It has been suggested that the phylum Chloroflexi “sensu stricto” should comprise only the classes Chloroflexi and Thermomicrobia, and the other four classes (“Dehalococcoidetes,” Anaerolineae, Caldilineae, and Ktedonobacteria) may represent one or more independent phyla branching in the neighborhood of the Chloroflexi.

Nitrospirae and Deferribacter

Nitrospirae is a phylum of bacteria; some nitrospirae species perform important functions in the nitrogen cycle.

Learning Objectives

Describe nitrospirae

Key Takeaways

Key Points

  • Nitrospirae is a phylum of bacteria. It contains only one class, (Nitrospira), which itself contains one order (Nitrospirales), and one family (Nitrospiraceae). It includes multiple genera, such as Nitrospira, the largest. The first member of this phylum, Nitrospira marina, was discovered in 1985.
  • Nitrospira is a genus of bacteria in the phylum Nitrospirae. The second member of this genus was discovered in 1995 from a corroded iron pipe in a Moscow heating system.
  • In the nitrogen cycle, nitrites are converted to nitrates by Nitrobacter or Nitrospira.
  • Deferribacter is a genus in the phylum Deferribacteres (Bacteria).The genus contains 4 species.

Key Terms

  • nitrogen cycle: The natural circulation of nitrogen, in which atmospheric nitrogen is converted to nitrogen oxides by lightning and deposited in the soil by rain where it is assimilated by plants and either eaten by animals (and returned as feces) or decomposed back to elemental nitrogen by bacteria.

Nitrospirae is a phylum of bacteria containing only one class: Nitrospira, which itself contains one order: Nitrospirales, and one family: Nitrospiraceae.

However, it includes multiple genera, the largest of which is Nitrospira. The first member of this phylum, Nitrospira marina, was discovered in 1986 by Watson et al., isolated from the Gulf of Maine. The second member of this phylum, Thermodesulfovibrio yellowstonii, was discovered in 1994. The third, Nitrospira moscoviensis, was discovered in 1995 from a corroded iron pipe in a Moscow heating system. It is a Gram-negative nitrite-oxidizing organism with a helical to vibroid morphology 0.9-2.2 x 0.2-0.4 micrometers in size.

Some nitrospirae species perform important functions in the Nitrogen Cycle:

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Nitrogen cycle in aquarium: Legend: (1) Addition of food and nutrients, (2) Production of urea and ammonia by fish, (3) Ammonia is converted to nitrites by beneficial nitrosomonas bacteria, (4) Nitrites are converted to nitrates by beneficial nitrospira bacteria. Less toxic nitrates are removed by plants and periodic water changes. (5) Evaporation. (6) Light. (7) Soil. (8) O2 produced by plants. (9) CO2 produced by fish.

The Nitrogen Cycle describes the changes in nitrogenous compounds in the environment. Because many of them are toxic, it is important to know something about this cycle. Luckily, these compounds are converted to less and less toxic forms through this Nitrogen Cycle.

To simplify, if you start with your organisms, they release a compound, ammonia, as a waste product or a product of decomposition. Ammonia is both quite toxic and dangerous. By a process known as nitrification , bacteria convert these waste products to less toxic forms. These bacteria live in aerobic conditions and benefit from the presence of oxygen.

First the ammonia is converted to nitrites by Nitrosomonas; this compound is still toxic. Next, nitrites are converted to nitrates by Nitrobacter or Nitrospira. Nitrates are much less toxic compared to ammonia and nitrite. In an environment with a healthy colony of these nitrifying bacteria, ammonia and nitrites levels will reach zero.

Deferribacter is a genus in the phylum Deferribacteres (Bacteria).The genus contains 4 species:

  • D. abyssi
  • D. autotrophicus
  • D. desulfuricans
  • D. thermophilus

Aquifex, Thermocrinis, and Related Bacteria

The Aquificae phylum is a diverse collection of bacteria found in harsh environments: hot springs, sulfur pools, and thermal ocean vents.

Learning Objectives

Outline the similarities of Aquifex, Thermocrinis and related bacteria

Key Takeaways

Key Points

  • Along with Thermotogae, members of Aquificae are thermophilic eubacteria. The Aquificaceae family in the phylum Aquificae contains five genera, including Aquifex and Thermocrinis.
  • Aquifex is a genus of bacteria, one of the few in the phylum Aquificae. The two species generally classified in Aquifex are A. pyrophilus and A. aeolicus. Both are highly thermophilic, growing best in water temperature of 85 °C to 95 °C.
  • The genome of A. aeolicus has been successfully mapped. Comparison of its genome to other organisms showed that around 16% of its genes originated from the Archaea domain. Members of this genus are thought to be some of the earliest members of the eubacteria domain.

Key Terms

  • indel: Either an insertion or deletion mutation in the genetic code.
  • gene silencing: Any technique or mechanism in which the expression of a gene is prevented.

The Aquificae phylum is a diverse collection of bacteria that live in harsh environmental settings. They have been found in hot springs, sulfur pools, and thermal ocean vents.

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Aquificae habitat: White flocculent mats in and around the extremely gassy, high-temperature (>100°C, 212°F) white smokers at Champagne Vent.

Members of the genus Aquifex, for example, are productive in water between 85 to 95 °C. They are the dominant members of most terrestrial neutral-to-alkaline hot springs above 60 °C. They are autotrophs, and the primary carbon fixers in these environments. They are true bacteria (domain bacteria).

Comparative genomic studies have identified six conserved signature indels (CSIs) that are specific for the species from the phylum Aquificae and provide potential molecular markers for it. Along with Thermotogae, members of Aquificae are thermophilic eubacteria.

A 51 amino acid insertion has been identified in SecA preprotein translocase which is shared by various members of the phylum Aquificae as well as two Thermotogae species. The presence of the insertion in the Thermotogae species may be due to a horizontal gene transfer. In the 16S rRNA gene trees, the Aquificae species branch in the proximity of the phylum Thermotogae (another phylum comprising hyperthermophilic organisms) close to the archaeal-bacterial branch point. However, a close relationship of the Aquificae to Thermotogae, and the deep branching of Aquificae, is not supported by phylogenetic studies based upon other gene/ protein sequences and also by conserved signature indels in several highly-conserved universal proteins.

The Aquificaceae family in the phylum Aquificae contains contains five genera, including Aquifex and Thermocrinis.

Aquifex is a genus of bacteria, one of the few in the phylum Aquificae. The two species generally classified in Aquifex are A. pyrophilus and A. aeolicus. Both are highly thermophilic, growing best in water temperature of 85 °C to 95 °C. Both known species are rod-shaped bacteria with a length of two to six µm and a diameter of around 0.5 µm. They are non-sporeforming, Gram-negative autotrophs. Aquifex means “water-maker” in Latin, and refers to the fact that its method of respiration creates water. They tend to form cell aggregates composed of up to one hundred individual cells. A. pyrophilus can even grow anaerobically by reducing nitrogen instead of oxygen. Like other thermophilic bacteria, Aquifex has important uses in industrial processes.

The genome of A. aeolicus has been successfully mapped. This was made easier by the fact that the length of the genome is only about a third of that for E. coli. Comparison of the A. aeolicus genome to other organisms showed that around 16% of its genes originated from the Archaea domain. Members of this genus are thought to be some of the earliest members of the eubacteria domain.

A. aeolicus was discovered north of Sicily, while A. pyrophilus was first found just north of Iceland. A. aeolicus is also known as one of the few bacterial species capable of doing gene silencing.