Thermoproteota

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Thermoproteota
RT8-4.jpg
Archaea Sulfolobus infected with specific virus STSV-1.
Scientific classification OOjs UI icon edit-ltr.svg
Domain: Archaea
Kingdom: Proteoarchaeota
Superphylum: TACK group
Phylum: Thermoproteota
Garrity & Holt 2021 [1]
Class
Synonyms
  • "Eocyta" Lake et al. 1984
    This also applies to TACK group
  • "Crenarchaeota" Garrity and Holt 2001
  • "Gearchaeota" corrig. Kozubal et al. 2013
  • "Marsarchaeota" Jay et al. 2018
  • "Nezhaarchaeota" Wang et al. 2019
  • "Thermoproteaeota" Oren et al. 2015
  • "Thermoproteota" Whitman et al. 2018
  • "Verstraetearchaeota" Vanwonterghem et al. 2016

The Thermoproteota (also known as Crenarchaea) are prokaryotes that have been classified as a phylum of the Archaea domain. [2] [3] [4] Initially, the Thermoproteota were thought to be sulfur-dependent extremophiles but recent studies have identified characteristic Thermoproteota environmental rRNA indicating the organisms may be the most abundant archaea in the marine environment. [5] Originally, they were separated from the other archaea based on rRNA sequences; other physiological features, such as lack of histones, have supported this division, although some crenarchaea were found to have histones. [6] Until recently all cultured Thermoproteota had been thermophilic or hyperthermophilic organisms, some of which have the ability to grow at up to 113 °C. [7] These organisms stain Gram negative and are morphologically diverse, having rod, cocci, filamentous and oddly-shaped cells. [8]

Contents

Thermoproteota were initially classified as a part of Regnum Eocyta in 1984, [9] but this classification has been discarded. The term "eocyte" now applies to either TACK (formerly Crenarchaeota) or to Thermoproteota.

Sulfolobus

One of the best characterized members of the Crenarchaeota is Sulfolobus solfataricus . This organism was originally isolated from geothermally heated sulfuric springs in Italy, and grows at 80 °C and pH of 2–4. [10] Since its initial characterization by Wolfram Zillig, a pioneer in thermophile and archaean research, similar species in the same genus have been found around the world. Unlike the vast majority of cultured thermophiles, Sulfolobus grows aerobically and chemoorganotrophically (gaining its energy from organic sources such as sugars). These factors allow a much easier growth under laboratory conditions than anaerobic organisms and have led to Sulfolobus becoming a model organism for the study of hyperthermophiles and a large group of diverse viruses that replicate within them.

16S rRNA based LTP_06_2022 [11] [12] [13] 53 marker proteins based GTDB 08-RS214 [14] [15] [16]
"TACK"

Nitrososphaerota

Thermoproteota
Thermoproteia

Thermoproteales

Fervidicoccales

Desulfurococcales 1

Desulfurococcales

Sulfolobales

"TACK"

"Korarchaeia"

"BAT"

"Bathyarchaeia" (MCG)

Nitrososphaeria_A ("Aigarchaeota")

Nitrososphaeria

"Sulfobacteria"
"Methanomethylicia"

"Methanomethylicales"

"Nezhaarchaeales"

("Verstraetearchaeota")
"Thermoproteia"

"Gearchaeales"

"Thermofilales"

Thermoproteales

"Sulfolobia"

"Marsarchaeales"

Sulfolobales

Thermoproteota

Recombinational repair of DNA damage

Irradiation of S. solfataricus cells with ultraviolet light strongly induces formation of type IV pili that can then promote cellular aggregation. [17] Ultraviolet light-induced cellular aggregation was shown by Ajon et al. [18] to mediate high frequency inter-cellular chromosome marker exchange. Cultures that were ultraviolet light-induced had recombination rates exceeding those of uninduced cultures by as much as three orders of magnitude. S. solfataricus cells are only able to aggregate with other members of their own species. [18] Frols et al. [17] [19] and Ajon et al. [18] considered that the ultraviolet light-inducible DNA transfer process, followed by homologous recombinational repair of damaged DNA, is an important mechanism for promoting chromosome integrity.

This DNA transfer process can be regarded as a primitive form of sexual interaction.

Marine species

Beginning in 1992, data were published that reported sequences of genes belonging to the Thermoproteota in marine environments. [20] , [21] Since then, analysis of the abundant lipids from the membranes of Thermoproteota taken from the open ocean have been used to determine the concentration of these “low temperature Crenarchaea” (See TEX-86). Based on these measurements of their signature lipids, Thermoproteota are thought to be very abundant and one of the main contributors to the fixation of carbon .[ citation needed ] DNA sequences from Thermoproteota have also been found in soil and freshwater environments, suggesting that this phylum is ubiquitous to most environments. [22]

In 2005, evidence of the first cultured “low temperature Crenarchaea” was published. Named Nitrosopumilus maritimus , it is an ammonia-oxidizing organism isolated from a marine aquarium tank and grown at 28 °C. [23]

Possible connections with eukaryotes

The research about two-domain system of classification has paved the possibilities of connections between crenarchaea and eukaryotes. [24]

DNA analysis from 2008 (and later, 2017) has shown that eukaryotes possible evolved from thermoproteota-like organisms. Other candidates for the ancestor of eukaryotes include closely related asgards. This could suggest that eukaryotic organisms possibly evolved from prokaryotes.

These results are similar to the eocyte hypothesis of 1984, proposed by James A. Lake. [9] The classification according to Lake, states that both crenarchaea and asgards belong to Kingdom Eocyta. Though this has been discarded by scientists, the main concept remains. The term "Eocyta" now either refers to the TACK group or to Phylum Thermoproteota itself.

However, the topic is highly debated and research is still going on.

See also

Related Research Articles

<span class="mw-page-title-main">Nanoarchaeota</span> Phylum of archaea

Nanoarchaeota is a proposed phylum in the domain Archaea that currently has only one representative, Nanoarchaeum equitans, which was discovered in a submarine hydrothermal vent and first described in 2002.

<span class="mw-page-title-main">Korarchaeota</span> Proposed phylum within the Archaea

The Korarchaeota is a proposed phylum within the Archaea. The name is derived from the Greek noun koros or kore, meaning young man or young woman, and the Greek adjective archaios which means ancient. They are also known as Xenarchaeota. The name is equivalent to Candidatus Korarchaeota, and they go by the name Xenarchaeota or Xenarchaea as well.

The Thermoprotei is a class of the Thermoproteota.

Mollicutes is a class of bacteria distinguished by the absence of a cell wall. The word "Mollicutes" is derived from the Latin mollis, and cutis. Individuals are very small, typically only 0.2–0.3 μm in size and have a very small genome size. They vary in form, although most have sterols that make the cell membrane somewhat more rigid. Many are able to move about through gliding, but members of the genus Spiroplasma are helical and move by twisting. The best-known genus in the Mollicutes is Mycoplasma. Colonies show the typical "fried-egg" appearance.

<i>Sulfolobus</i> Genus of archaea

Sulfolobus is a genus of microorganism in the family Sulfolobaceae. It belongs to the archaea domain.

Methanococcus is a genus of coccoid methanogens of the family Methanococcaceae. They are all mesophiles, except the thermophilic M. thermolithotrophicus and the hyperthermophilic M. jannaschii. The latter was discovered at the base of a “white smoker” chimney at 21°N on the East Pacific Rise and it was the first archaeal genome to be completely sequenced, revealing many novel and eukaryote-like elements.

In taxonomy, the Methanococcales are an order of the Methanococci.

In the taxonomy of microorganisms, the Methanomicrobiales are an order of the Methanomicrobia. Methanomicrobiales are strictly carbon dioxide reducing methanogens, using hydrogen or formate as the reducing agent. As seen from the phylogenetic tree based on 'The All-Species Living Tree' Project the family Methanomicrobiaceae is highly polyphyletic within the Methanomicrobiales.

<span class="mw-page-title-main">Sulfolobales</span> Order of archaea

Sulfolobales is an order of archaeans in the class Thermoprotei.

<span class="mw-page-title-main">Thermococcales</span> Order of archaea

In taxonomy, the Thermococcales are an order of microbes within the Thermococci. The species within the Thermococcales are used in laboratories as model organisms. All these species are strict anaerobes and can ferment sugars as sources of carbon, but they also need elemental sulfur.

In taxonomy, the Methanocorpusculaceae are a family of microbes within the order Methanomicrobiales. It contains exactly one genus, Methanocorpusculum. The species within Methanocorpusculum were first isolated from anaerobic digesters and anaerobic wastewater treatment plants. In the wild, they prefer freshwater environments. Unlike many other methanogenic archaea, they do not require high temperatures or extreme salt concentrations to live and grow.

Methanomicrobiaceae are a family of archaea in the order the Methanomicrobiales.

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

In taxonomy, the Methanosarcinaceae are a family of the Methanosarcinales.

Methanospirillaceae are a family of microbes within Methanomicrobiales.

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

In taxonomy, the Thermococcaceae are a family of the Thermococcales. Almost all species within the three genera of Thermococcaceae were isolated from hydrothermal vents in the ocean. All are strictly anaerobes.

Pseudomonas avellanae is a Gram-negative plant pathogenic bacterium. It is the causal agent of bacterial canker of hazelnut. Based on 16S rRNA analysis, P. avellanae has been placed in the P. syringae group. This species was once included as a pathovar of Pseudomonas syringae, but following DNA-DNA hybridization, it was instated as a separate species. Following ribotypical analysis Pseudomonas syringae pv. theae was incorporated into this species.

In taxonomy, Methanimicrococcus is a genus of the Methanosarcinaceae. The members of this genus have been found in pharmaceutical wastewater, and they can contribute to the degradation of organic contaminants.

Methanocalculus is a genus of the Methanomicrobiales, and is known to include methanogens.

In the taxonomy of microorganisms, Candidatus Methanoregula is a genus of the Methanomicrobiales. It was is isolated from an acidic peat bog. It produces methane at the lowest pH of any known organism.

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

  1. ↑ Oren A, Garrity GM (2021). "Valid publication of the names of forty-two phyla of prokaryotes". Int J Syst Evol Microbiol. 71 (10): 5056. doi: 10.1099/ijsem.0.005056 . PMID   34694987. S2CID   239887308.
  2. ↑ See the NCBI webpage on Crenarchaeota
  3. ↑ C.Michael Hogan. 2010. Archaea. eds. E.Monosson & C.Cleveland, Encyclopedia of Earth. National Council for Science and the Environment, Washington DC.
  4. ↑ Data extracted from the "NCBI taxonomy resources". National Center for Biotechnology Information . Retrieved 2007-03-19.
  5. ↑ Madigan M; Martinko J, eds. (2005). Brock Biology of Microorganisms (11th ed.). Prentice Hall. ISBN   978-0-13-144329-7.
  6. ↑ Cubonova L, Sandman K, Hallam SJ, Delong EF, Reeve JN (2005). "Histones in Crenarchaea". Journal of Bacteriology. 187 (15): 5482–5485. doi:10.1128/JB.187.15.5482-5485.2005. PMC   1196040 . PMID   16030242.
  7. ↑ Blochl E, Rachel R, Burggraf S, Hafenbradl D, Jannasch HW, Stetter KO (1997). "Pyrolobus fumarii, gen. and sp. nov., represents a novel group of archaea, extending the upper temperature limit for life to 113 °C". Extremophiles. 1 (1): 14–21. doi:10.1007/s007920050010. PMID   9680332. S2CID   29789667.
  8. ↑ Garrity GM, Boone DR, eds. (2001). Bergey's Manual of Systematic Bacteriology Volume 1: The Archaea and the Deeply Branching and Phototrophic Bacteria (2nd ed.). Springer. ISBN   978-0-387-98771-2.
  9. 1 2 Lake JA, Henderson E, Oakes M, Clark MW (June 1984). "Eocytes: a new ribosome structure indicates a kingdom with a close relationship to eukaryotes". Proceedings of the National Academy of Sciences of the United States of America. 81 (12): 3786–3790. Bibcode:1984PNAS...81.3786L. doi: 10.1073/pnas.81.12.3786 . PMC   345305 . PMID   6587394.
  10. ↑ Zillig W, Stetter KO, Wunderl S, Schulz W, Priess H, Scholz I (1980). "The Sulfolobus-"Caldariellard" group: Taxonomy on the basis of the structure of DNA-dependent RNA polymerases". Arch. Microbiol. 125 (3): 259–269. doi:10.1007/BF00446886. S2CID   5805400.
  11. ↑ "The LTP" . Retrieved 10 May 2023.
  12. ↑ "LTP_all tree in newick format" . Retrieved 10 May 2023.
  13. ↑ "LTP_06_2022 Release Notes" (PDF). Retrieved 10 May 2023.
  14. ↑ "GTDB release 08-RS214". Genome Taxonomy Database . Retrieved 10 May 2023.
  15. ↑ "ar53_r214.sp_label". Genome Taxonomy Database . Retrieved 10 May 2023.
  16. ↑ "Taxon History". Genome Taxonomy Database . Retrieved 10 May 2023.
  17. 1 2 Fröls S, Ajon M, Wagner M, Teichmann D, Zolghadr B, Folea M, Boekema EJ, Driessen AJ, Schleper C, Albers SV. UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation. Mol Microbiol. 2008 Nov;70(4):938-52. doi: 10.1111/j.1365-2958.2008.06459.x. PMID 18990182
  18. 1 2 3 Ajon M, Fröls S, van Wolferen M, Stoecker K, Teichmann D, Driessen AJ, Grogan DW, Albers SV, Schleper C. UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili. Mol Microbiol. 2011 Nov;82(4):807-17. doi: 10.1111/j.1365-2958.2011.07861.x. Epub 2011 Oct 18. PMID 21999488
  19. ↑ Fröls S, White MF, Schleper C. Reactions to UV damage in the model archaeon Sulfolobus solfataricus. Biochem Soc Trans. 2009 Feb;37(Pt 1):36-41. doi: 10.1042/BST0370036. PMID 19143598
  20. ↑ Fuhrman JA, McCallum K, Davis AA (1992). "Novel major archaebacterial group from marine plankton". Nature. 356 (6365): 148–9. Bibcode:1992Natur.356..148F. doi:10.1038/356148a0. PMID   1545865. S2CID   4342208.
  21. ↑ DeLong EF (1992). "Archaea in coastal marine environments". Proc Natl Acad Sci USA. 89 (12): 5685–9. Bibcode:1992PNAS...89.5685D. doi: 10.1073/pnas.89.12.5685 . PMC   49357 . PMID   1608980.
  22. ↑ Barns SM, Delwiche CF, Palmer JD, Pace NR (1996). "Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences". Proc Natl Acad Sci USA. 93 (17): 9188–93. Bibcode:1996PNAS...93.9188B. doi: 10.1073/pnas.93.17.9188 . PMC   38617 . PMID   8799176.
  23. ↑ Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA (2005). "Isolation of an autotrophic ammonia-oxidizing marine archaeon". Nature. 437 (7058): 543–6. Bibcode:2005Natur.437..543K. doi:10.1038/nature03911. PMID   16177789. S2CID   4340386.
  24. ↑ Yutin, Natalya; Makarova, Kira S.; Mekhedov, Sergey L.; Wolf, Yuri I.; Koonin, Eugene V. (2008). "The deep archaeal roots of eukaryotes". Molecular Biology and Evolution. 25 (8): 1619–1630. doi:10.1093/molbev/msn108. PMC   2464739 . PMID   18463089.

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