Thermococcus

Last updated

Thermococcus
Scientific classification
Domain:
Archaea
Kingdom:
Euryarchaeota
Phylum:
Euryarchaeota
Class:
Thermococci
Order:
Thermococcales
Family:
Thermococcaceae
Genus:
Thermococcus

Zillig 1983
Type species
Thermococcus celer
Zillig 1983
Species

See text

In taxonomy, Thermococcus is a genus of thermophilic Archaea in the family the Thermococcaceae. [1]

Contents

Members of the genus Thermococcus are typically irregularly shaped coccoid species, ranging in size from 0.6 to 2.0 μm in diameter. [2] Some species of Thermococcus are immobile, and some species have motility, using flagella as their main mode of movement.[ citation needed ] These flagella typically exist at a specific pole of the organism.[ citation needed ] This movement has been seen at room or at high temperatures, depending on the specific organism. [3] In some species, these microorganisms can aggregate and form white-gray plaques. [4] Species under Thermococcus typically thrive at temperatures between 60 and 105 °C, [5] either in the presence of black smokers (hydrothermal vents), or freshwater springs. [6] Species in this genus are strictly anaerobes, [7] [8] and are thermophilic, [2] [7] found in a variety depths, such as in hydrothermal vents 2500m below the ocean surface, [9] but also centimeters below the water surface in geothermal springs. [10] These organisms thrive at pH levels of 5.6-7.9. [11] Members of this genus have been found in many hydrothermal vent systems in the world, including from the seas of Japan, [12] to off the coasts of California. [13] Sodium Chloride salt is typically present in these locations at 1%-3% concentration, [8] but is not a required substrate for these organisms, [14] [15] as one study showed Thermococcus members living in fresh hot water systems in New Zealand, [6] but they do require a low concentration of lithium ions for growth. [16] Thermococcus members are described as heterotrophic, chemotrophic, [2] [17] [18] and are organotrophic sulfanogens; using elemental sulfur and carbon sources including amino acids, carbohydrates, and organic acids such as pyruvate. [17] [18] [19]

Phylogeny

16S rRNA based LTP_08_2023 [20] [21] [22] GTDB 08-RS214 by Genome Taxonomy Database. [23] [24] [25]
Thermococcus

T. aggregans

T. aegaeusArab et al. 2000

T. alcaliphilus

T. litoralis Neuner et al. 2001

T. argininiproducensPark et al. 2023

T. sibiricus

species‑group 2

Pyrococcus

Thermococcus s.s.

T. barophilus

T. paralvinellae

T. acidaminovoransDirmeier et al. 2001

T. gorgonarius

T. fumicolansGodfroy et al. 1996

T. pacificus

T. waiotapuensisGonzlez et al. 2001

T. zilligii

T. guaymasensis

T. eurythermalis

T. henrietii

T. nautili

T. stetteri

T. cleftensis

T. siculi

T. indicus

T. celericrescens

T. aciditoleransLi et al. 2021

T. camini

T. profundus

T. piezophilus

T. coalescensKuwabara et al. 2005

T. prieuriiGorlas et al. 2013

T. thioreducens

T. hydrothermalis Godfroy et al. 1997

T. barossii

T. atlanticusCambon-Bonavita et al. 2004

T. celer

Thermococcus

T. sibiricusMiroshnichenko et al. 2001

T. aggregansCanganella et al. 1998

T. alcaliphilus Keller et al. 1997

"T. bergensis" Birkeland et al. 2021

species‑group 2
Thermococcus

T. barophilus Marteinsson et al. 1999

T. paralvinellaeHensley et al. 2014

species‑group 3

Pyrococcus

Thermococcus s.s.

T. gammatolerans Jolivet et al. 2003

T. guaymasensisCanganella et al. 1998

T. eurythermalisZhao et al. 2015

T. henrietiiAlain et al. 2021

T. nautiliSoler et al. 2007

T. stetteri Miroshnichenko 1990

T. kodakarensis Atomi et al. 2005

T. peptonophilus González et al. 1996

T. profundus Kobayashi and Horikoshi 1995

T. gorgonariusMiroshnichenko et al. 1998

T. zilligiiRonimus et al. 1999

"T. onnurineus" Bae et al. 2006

T. piezophilusDalmasso et al. 2017

T. celer Zillig 1983 (type sp.)

T. barossiiDuffaud et al. 2005

"T. radiotolerans" Jolivet et al. 2004

T. thioreducensPikuta et al. 2007

T. cleftensisHensley et al. 2014

T. pacificusMiroshnichenko et al. 1998

T. siculiGrote et al. 2000

T. indicusLim et al. 2021

T. caminiCourtine et al. 2021

T. celericrescensKuwabara et al. 2007

Unassigned species:

Metabolism

Metabolically, Thermococcus spp. have developed a different form of glycolysis from eukaryotes and prokaryotes. [26] [5] One example of a metabolic pathway for these organisms is the metabolism of peptides, [26] which occurs in three steps: first, hydrolysis of the peptides to amino acids is catalyzed by peptidases, [5] then the conversion of the amino acids to keto acids is catalyzed by aminotransferases, [26] and finally CO2 is released from the oxidative decarboxylation or the keto acids by four different enzymes, [5] which produces coenzyme A derivatives that are used in other important metabolic pathways. [5] Thermococcus species also have the enzyme rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase), [27] which is made from enzymes involved in the metabolism of nucleic acids in Thermococcus kodakarensis, [5] [26] [27] showing how integrated these metabolic systems truly are for these hyperthermophilic microorganisms. [27] Some nutrients are limiting in Thermococcus cell growth. [27] Nutrients that affect cell growth the most in thermococcal species are carbon and nitrogen sources. [27] Since thermococcal species do not metabolically generate all necessary amino acids, some have to be provided by the environment in which these organisms thrive. Some of these needed amino acids are leucine, isoleucine, and valine (the branched-chain amino acids). [27] When Thermococcus species are supplemented with these amino acids, they can metabolize them and produce acetyl-CoA or succinyl-CoA, [27] which are important precursors used in other metabolic pathways essential for cellular growth and respiration. [27] Thermococcus onnurineus lacks the genes for purine nucleotide biosynthesis and thus relies on environmental sources to meet its purine requirements. [28] With today's technology, Thermococcus members are relatively easy to grow in labs, [29] and are therefore considered model organisms for studying the physiological and molecular pathways of extremophiles. [30] [31] Thermococcus kodakarensis is one example of a model Thermococcus species, a microorganism in which has had its entire genome examined and replicated. [31] [32] [33]

Ecology

Thermococcal species can grow between 60 and 102 °C, optimal temperature at 85 °C which gives them a great ecological advantage to be the first organisms to colonize new hydrothermal environments. [5] [34] [35] As hyperthermophiles, there is a need for extreme environmental conditions, including temperature, pH, and salt. These conditions lead to the production of stress proteins and molecular chaperones that protect DNA as well as housekeeping cellular machinery. Thermococcus also thrives under gluconeogenic conditions. Some thermococcal species produce CO2, H2, and H2S as products of metabolism and respiration. [31] The releases of these molecules are then used by other autotrophic species, aiding the diversity of hydrothermal microbial communities. [5] This type of continuous enrichment culture plays a crucial role in the ecology of deep-sea hydrothermal vents, [36] suggesting that thermococci interact with other organisms via metabolite exchange, which supports the growth of autotrophs. [5] Thermococcus species that release H2 with the use of multiple hydrogenases (including CO-dependent hydrogenases) have been regarded as potential biocatalysts for water-gas shift reactions. [37]

Transportation mechanisms

Thermococcus species are naturally competent in taking up DNA and incorporating donor DNA into their genomes via homologous recombination. [38] These species can produce membrane vesicles (MVs), [38] formed by budding from the outermost cellular membranes, [38] [39] which can capture and obtain plasmids from neighboring Archaea species to transfer the DNA into either themselves or surrounding species. [38] These MVs are secreted from the cells in clusters, forming nanospheres or nanotubes, [39] keeping the internal membranes continuous. [38] Competence for DNA transfer and integration of donor DNA into the recipient genome by homologous recombination is common in the archaea and appears to be an adaptation for repairing DNA damage in the recipient cells (see Archaea subsection "Gene transfer and genetic exchange").

Thermococcus species produce numerous MVs, transferring DNA, metabolites, and even toxins in some species; [39] moreover, these MVs protect their contents against thermodegradation by transferring these macromolecules in a protected environment. [38] [39] MVs also prevent infections by capturing viral particles. [39] Along with transporting macromolecules, Thermococcus species use MVs to communicate to each other. [38] Furthermore, these MVs are used by a specific species (Thermococcus coalescens) to indicate when aggregation should occur, [38] so these typically single-celled miroorganisms can fuse into one massive single cell. [38]

It has been reported that Thermococcus kodakarensis has four virus-like integrated gene elements containing subtilisin-like serine protease precursors. [40] To date, only two viruses have been isolated from Thermococcus spp., PAVE1 and TPV1. [40] These viruses exist in their hosts in a carrier state. [40]
The process of DNA replication and elongation has been extensively studied in T. kodakarensis. [40] The DNA molecule is a circular structure consisting of about 2 million base pairs in length, and has more than 2,000 sequences that code for proteins. [40]

Future technology

An enzyme from Thermococcus, Tpa-S DNA polymerase, has been found to be more efficient in long and rapid polymerase chain reaction (PCR) than Taq polymerase. [41] Tk-SP, another enzyme from T. kodakarensis, [41] [42] can degrade abnormal prion proteins (PrPSc); [41] prions are misfolded proteins that can cause fatal diseases in all organisms. [41] Tk-SP shows broad substrate specificity, and degraded prions exponentially in the lab setting. [41] This enzyme does not require calcium or any other substrate to fold, so is showing great potential in studies this far. [41] Additional studies have been coordinated on the phosphoserine phosphatase (PSP) enzyme of T. onnurineus, which provided an essential component in the regulation of PSP activity. [42] This information is useful for drug companies, because abnormal PSP activity leads to a major decrease in serine levels of the nervous system, causing neurological diseases and complications. [42]

Thermococcus spp. can increase gold mining efficiency up to 95% due to their specific abilities in bioleaching. [43]

See also

Related Research Articles

<span class="mw-page-title-main">Extremophile</span> Organisms capable of living in extreme environments

An extremophile is an organism that is able to live in extreme environments, i.e., environments with conditions approaching or stretching the limits of what known life can adapt to, such as extreme temperature, pressure, radiation, salinity, or pH level.

<span class="mw-page-title-main">Thermophile</span> Organism that thrives at relatively high temperatures

A thermophile is an organism—a type of extremophile—that thrives at relatively high temperatures, between 41 and 122 °C. Many thermophiles are archaea, though some of them are bacteria and fungi. Thermophilic eubacteria are suggested to have been among the earliest bacteria.

<i>Nanoarchaeum equitans</i> Species of archaeon

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. It has been proposed as the first species in a new phylum, and is the only species within the genus Nanoarchaeum. Strains of this microbe were also found on the Sub-polar Mid Oceanic Ridge, and in the Obsidian Pool in Yellowstone National Park. Since it grows in temperatures approaching boiling, at about 80 °C (176 °F), it is considered to be a thermophile. It grows best in environments with a pH of 6, and a salinity concentration of 2%. Nanoarchaeum appears to be an obligate symbiont on the archaeon Ignicoccus; it must be in contact with the host organism to survive. Nanoarchaeum equitans cannot synthesize lipids but obtains them from its host. Its cells are only 400 nm in diameter, making it the smallest known living organism, and the smallest known archaeon.

A hyperthermophile is an organism that thrives in extremely hot environments—from 60 °C (140 °F) upwards. An optimal temperature for the existence of hyperthermophiles is often above 80 °C (176 °F). Hyperthermophiles are often within the domain Archaea, although some bacteria are also able to tolerate extreme temperatures. Some of these bacteria are able to live at temperatures greater than 100 °C, deep in the ocean where high pressures increase the boiling point of water. Many hyperthermophiles are also able to withstand other environmental extremes, such as high acidity or high radiation levels. Hyperthermophiles are a subset of extremophiles. Their existence may support the possibility of extraterrestrial life, showing that life can thrive in environmental extremes.

<span class="mw-page-title-main">Archaeoglobaceae</span> Family of archaea

Archaeoglobaceae are a family of the Archaeoglobales. All known genera within the Archaeoglobaceae are hyperthermophilic and can be found near undersea hydrothermal vents. Archaeoglobaceae are the only family in the order Archaeoglobales, which is the only order in the class Archaeoglobi.

<i>Pyrococcus furiosus</i> Species of archaeon

Pyrococcus furiosus is a heterotrophic, strictly anaerobic, extremophilic, model species of archaea. It is classified as a hyperthermophile because it thrives best under extremely high temperatures, and is notable for having an optimum growth temperature of 100 °C. P. furiosus belongs to the Pyrococcus genus, most commonly found in extreme environmental conditions of hydrothermal vents. It is one of the few prokaryotic organisms that has enzymes containing tungsten, an element rarely found in biological molecules.

Caldococcus is a genus of Archaea in the order Desulfurococcales.

Thermococcus litoralis is a species of Archaea that is found around deep-sea hydrothermal vents as well as shallow submarine thermal springs and oil wells. It is an anaerobic organotroph hyperthermophile that is between 0.5–3.0 μm (20–118 μin) in diameter. Like the other species in the order thermococcales, T. litoralis is an irregular hyperthermophile coccus that grows between 55–100 °C (131–212 °F). Unlike many other thermococci, T. litoralis is non-motile. Its cell wall consists only of a single S-layer that does not form hexagonal lattices. Additionally, while many thermococcales obligately use sulfur as an electron acceptor in metabolism, T. litoralis only needs sulfur to help stimulate growth, and can live without it. T. litoralis has recently been popularized by the scientific community for its ability to produce an alternative DNA polymerase to the commonly used Taq polymerase. The T. litoralis polymerase, dubbed the vent polymerase, has been shown to have a lower error rate than Taq but due to its proofreading 3’–5’ exonuclease abilities, but higher than Pfu polymerase.

<span class="mw-page-title-main">Archaea</span> Domain of single-celled organisms

Archaea is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotic. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this term has fallen out of use.

Thermococcus celer is a Gram-negative, spherical-shaped archaeon of the genus Thermococcus. The discovery of T. celer played an important role in rerooting the tree of life when T. celer was found to be more closely related to methanogenic Archaea than to other phenotypically similar thermophilic species. T. celer was the first archaeon discovered to house a circularized genome. Several type strains of T. celer have been identified: Vu13, ATCC 35543, and DSM 2476.

<i>Thermococcus gammatolerans</i> Species of archaeon

Thermococcus gammatolerans is an archaea extremophile and the most radiation-resistant organism known to exist.

Methanocaldococcus jannaschii is a thermophilic methanogenic archaean in the class Methanococci. It was the first archaeon, and third organism, to have its complete genome sequenced. The sequencing identified many genes unique to the archaea. Many of the synthesis pathways for methanogenic cofactors were worked out biochemically in this organism, as were several other archaeal-specific metabolic pathways.

Thermococcus kodakarensis is a species of thermophilic archaea. The type strain T. kodakarensis KOD1 is one of the best-studied members of the genus.

Thermoplasma volcanium is a moderate thermoacidophilic archaea isolated from acidic hydrothermal vents and solfatara fields. It contains no cell wall and is motile. It is a facultative anaerobic chemoorganoheterotroph. No previous phylogenetic classifications have been made for this organism. Thermoplasma volcanium reproduces asexually via binary fission and is nonpathogenic.

Thermococcus profundus is a hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent. It is coccoid-shaped with 1–2 μm in diameter, designated as strain DT5432.

Thermococcus chitonophagus is a chitin-degrading, hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent. It is anaerobic, round to slightly irregular coccus-shaped, 1.2–2.5 μm in diameter, and motile by means of a tuft of flagella.

Thermococcus barophilus is a piezophilic and hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent. It is anaerobic and sulfur-metabolising, with type strain MPT.

Thermococcus peptonophilus is a fast-growing hyperthermophilic archaeon. It is coccus-shaped, obligately anaerobic and about 0.7–2 μm in diameter. It is a strict anaerobe and grows exclusively on complex substrates, such as peptone, casein, tryptone, and yeast extract. It cannot use carbon dioxide as a source of carbon. Although it can grow somewhat in the absence of elemental sulfur, it prefers sulfur.

Saccharolobus solfataricus is a species of thermophilic archaeon. It was transferred from the genus Sulfolobus to the new genus Saccharolobus with the description of Saccharolobus caldissimus in 2018.

References

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