Thermoproteota

The Thermoproteota are prokaryotes that have been classified as a phylum of the domain Archaea.[1][2][3] 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.[4] 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.[5] Until 2005 all cultured Thermoproteota had been thermophilic or hyperthermophilic organisms, some of which have the ability to grow at up to 113 °C.[6] These organisms stain Gram negative and are morphologically diverse, having rod, cocci, filamentous and oddly-shaped cells.[7] Recent evidence shows that some members of the Thermoproteota are methanogens.

Thermoproteota were initially classified as a part of regnum Eocyta in 1984,[8] but this classification has been discarded. The term "eocyte" now applies to either TACK (formerly Crenarchaeota) or to Thermoproteota.

## Contents

* 1 Sulfolobus
* 2 Recombinational repair of DNA damage
* 3 Marine species
* 4 Possible connections with eukaryotes
* 5 See also
* 6 References
* 6.1 Scientific journals
* 6.2 Scientific handbooks
* 7 External links

## 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.[9] 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[10][11][12] | 53 marker proteins based GTDB 10-RS226[13][14][15]

|

| "TACK"  |  |  |

Nitrososphaerota

|

|  | Thermoproteota  |  |  |

Thermoproteales

|

|  |  |  |  |

Fervidicoccales

|

Desulfurococcales 1

|  |  |

Desulfurococcales

|

Sulfolobales

Thermoproteia
|  |  |  |  | "Korarchaeota"  |  | "Korarchaeia"  |

"Korarchaeales"

|

|  | Promethearchaeati  |

Promethearchaeota

|

Thermoproteota  |  | "BAT"  |  |  |  | "Bathyarchaeia"  |  |  |

"Bifangarchaeales" [B24]

|

|  |  |  |  |

"Xuanwuarculales" [RBG-16-48-13]

|

|  |  |

"Hecatellales" [B25]

|

"Houtuarculales" [40CM-2-53-6]

|  |  |

"Wuzhiqiibiales" [TCS64]

|

|  |  |

"Zhuquarculales" [EX4484-135]

|

"Bathyarchaeales" [B26-1]

(MCG)
|  | Nitrososphaeria_A  |

"Caldarchaeales"

|

Nitrososphaeria  |  |  |

"Geothermarchaeales"

|

|  |  |

PSMU01

|

|  |  |

Conexivisphaerales

|

Nitrososphaerales

"Sulfobacteria"  |  |  |  | Methanosuratincolia  |  |  |

"Nezhaarchaeales"

|

|  |  |

"Culexarchaeles"

|

Methanosuratincolales

"Thermoproteia"  |  |  |

"Gearchaeales"

|

|  |  |

Thermofilales

|

Thermoproteales

|  | "Sulfolobia"  |  |  |

"Marsarchaeales" (sic)

|

Sulfolobales

## 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.[16] Ultraviolet light-induced cellular aggregation was shown by Ajon et al.[17] 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.[17] Frols et al.[16][18] and Ajon et al.[17] 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.[19][20] 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 .[21] 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 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.[8] 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

* Euryarchaeota
* List of Archaea genera
* Two-domain system
* Asgard (archaea)

## References

1. ↑ See the NCBI webpage on Crenarchaeota
2. ↑ C.Michael Hogan. 2010. Archaea. eds. E.Monosson & C.Cleveland, Encyclopedia of Earth. National Council for Science and the Environment, Washington DC.
3. ↑ Data extracted from the "NCBI taxonomy resources". National Center for Biotechnology Information. https://ftp.ncbi.nih.gov/pub/taxonomy/.
4. ↑ Brock Biology of Microorganisms (11th ed.). Prentice Hall. 2005. ISBN 978-0-13-144329-7.
5. ↑ "Histones in Crenarchaea". Journal of Bacteriology 187 (15): 5482–5485. Aug 2005. doi:10.1128/JB.187.15.5482-5485.2005. PMID 16030242.
6. ↑ "Pyrolobus fumarii, gen. and sp. nov., represents a novel group of archaea, extending the upper temperature limit for life to 113 °C". Extremophiles: Life Under Extreme Conditions 1 (1): 14–21. Feb 1997. doi:10.1007/s007920050010. PMID 9680332.
7. ↑ Bergey's Manual of Systematic Bacteriology Volume 1: The Archaea and the Deeply Branching and Phototrophic Bacteria (2nd ed.). Springer. 2001. ISBN 978-0-387-98771-2. https://archive.org/details/bergeysmanualofs00boon.
8. ↑ 8.0 8.1 "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. June 1984. doi:10.1073/pnas.81.12.3786. PMID 6587394. Bibcode: 1984PNAS...81.3786L.
9. ↑ "The Sulfolobus-"Caldariellard" group: Taxonomy on the basis of the structure of DNA-dependent RNA polymerases". Arch. Microbiol. 125 (3): 259–269. 1980. doi:10.1007/BF00446886. Bibcode: 1980ArMic.125..259Z.
10. ↑ "The LTP". https://imedea.uib-csic.es/mmg/ltp/#LTP.
11. ↑ "LTP_all tree in newick format". https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_all_06_2022.ntree.
12. ↑ "LTP_06_2022 Release Notes". https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_06_2022_release_notes.pdf.
13. ↑ "GTDB release 10-RS226". https://gtdb.ecogenomic.org/about#4|.
14. ↑ "ar53_r226.sp_label". https://data.gtdb.ecogenomic.org/releases/release226/226.0/auxillary_files/ar53_r226.sp_labels.tree.
15. ↑ "Taxon History". https://gtdb.ecogenomic.org/taxon_history/.
16. ↑ 16.0 16.1 "UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation". Molecular Microbiology 70 (4): 938–952. November 2008. doi:10.1111/j.1365-2958.2008.06459.x. PMID 18990182.
17. ↑ 17.0 17.1 17.2 "UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili". Molecular Microbiology 82 (4): 807–817. November 2011. doi:10.1111/j.1365-2958.2011.07861.x. PMID 21999488.
18. ↑ "Reactions to UV damage in the model archaeon Sulfolobus solfataricus". Biochemical Society Transactions 37 (Pt 1): 36–41. February 2009. doi:10.1042/BST0370036. PMID 19143598.
19. ↑ "Novel major archaebacterial group from marine plankton". Nature 356 (6365): 148–149. Mar 1992. doi:10.1038/356148a0. PMID 1545865. Bibcode: 1992Natur.356..148F.
20. ↑ "Archaea in coastal marine environments". Proceedings of the National Academy of Sciences of the United States of America 89 (12): 5685–5689. Jun 1992. doi:10.1073/pnas.89.12.5685. PMID 1608980. Bibcode: 1992PNAS...89.5685D.
21. ↑ "Thermoproteota Garrity & Holt, 2021" (in en). https://www.gbif.org/species/144094900.
22. ↑ "Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences". Proceedings of the National Academy of Sciences of the United States of America 93 (17): 9188–9193. Aug 1996. doi:10.1073/pnas.93.17.9188. PMID 8799176. Bibcode: 1996PNAS...93.9188B.
23. ↑ "Isolation of an autotrophic ammonia-oxidizing marine archaeon". Nature 437 (7058): 543–546. Sep 2005. doi:10.1038/nature03911. PMID 16177789. Bibcode: 2005Natur.437..543K.
24. ↑ "The deep archaeal roots of eukaryotes". Molecular Biology and Evolution 25 (8): 1619–1630. 2008. doi:10.1093/molbev/msn108. PMID 18463089.

### Scientific journals

* "The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification". International Journal of Systematic and Evolutionary Microbiology 52 (Pt 1): 7–76. Jan 2002. doi:10.1099/00207713-52-1-7. PMID 11837318.
* "Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology". International Journal of Systematic and Evolutionary Microbiology 52 (Pt 3): 1043–1047. May 2002. doi:10.1099/00207713-52-3-1043. PMID 12054223.
* "Genomic approaches to typing, taxonomy and evolution of bacterial isolates". International Journal of Systematic and Evolutionary Microbiology 51 (Pt 1): 3–16. Jan 2001. doi:10.1099/00207713-51-1-3. PMID 11211268.
* "A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data". International Journal of Systematic and Evolutionary Microbiology 51 (Pt 2): 385–391. Mar 2001. doi:10.1099/00207713-51-2-385. PMID 11321083.
* "Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes". International Journal of Systematic and Evolutionary Microbiology 51 (Pt 2): 667–678. Mar 2001. doi:10.1099/00207713-51-2-667. PMID 11321113.
* "Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy". International Journal of Systematic and Evolutionary Microbiology 51 (Pt 3): 945–953. May 2001. doi:10.1099/00207713-51-3-945. PMID 11411719.
* "Is characterization of a single isolate sufficient for valid publication of a new genus or species? Proposal to modify recommendation 30b of the Bacteriological Code (1990 Revision)". International Journal of Systematic and Evolutionary Microbiology 51 (Pt 6): 2221–2225. Nov 2001. doi:10.1099/00207713-51-6-2221. PMID 11760965.
* "DNA-DNA hybridization determined in micro-wells using covalent attachment of DNA". International Journal of Systematic and Evolutionary Microbiology 50 (3): 1095–1102. May 2000. doi:10.1099/00207713-50-3-1095. PMID 10843050.
* "A rapid method for determining the G+C content of bacterial chromosomes by monitoring fluorescence intensity during DNA denaturation in a capillary tube". International Journal of Systematic and Evolutionary Microbiology 50 (4): 1463–1469. Jul 2000. doi:10.1099/00207713-50-4-1463. PMID 10939651.
* "Suggestions for avoiding on-going confusion from the Bacteriological Code". International Journal of Systematic and Evolutionary Microbiology 50 (4): 1687–1689. Jul 2000. doi:10.1099/00207713-50-4-1687. PMID 10939677.
* "Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis". International Journal of Systematic and Evolutionary Microbiology 50 (4): 1655–1663. Jul 2000. doi:10.1099/00207713-50-4-1655. PMID 10939673.
* "Proposal to change the Rule governing the designation of type strains deposited under culture collection numbers allocated for patent purposes". International Journal of Systematic Bacteriology 49 (3): 1317–1319. Jul 1999. doi:10.1099/00207713-49-3-1317. PMID 10490293.
* "Proposal to change Rule 18a, Rule 18f and Rule 30 to limit the retroactive consequences of changes accepted by the ICSB". International Journal of Systematic Bacteriology 49 (3): 1321–1322. Jul 1999. doi:10.1099/00207713-49-3-1321. PMID 10425797.
* "Misunderstanding the Bacteriological Code". International Journal of Systematic Bacteriology 49 (3): 1313–1316. Jul 1999. doi:10.1099/00207713-49-3-1313. PMID 10425796.
* "Proposals to update and make changes to the Bacteriological Code". International Journal of Systematic Bacteriology 49 (3): 1309–1312. Jul 1999. doi:10.1099/00207713-49-3-1309. PMID 10425795.
* "Reclassification of the crenarchael orders and families in accordance with 16S rRNA sequence data". International Journal of Systematic Bacteriology 47 (3): 657–660. Jul 1997. doi:10.1099/00207713-47-3-657. PMID 9226896.
* "Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data". International Journal of Systematic Bacteriology 47 (4): 1145–1156. Oct 1997. doi:10.1099/00207713-47-4-1145. PMID 9336922.
* "List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet". International Journal of Systematic Bacteriology 47 (2): 590–592. Apr 1997. doi:10.1099/00207713-47-2-590. PMID 9103655.
* "Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa". International Journal of Systematic Bacteriology 45 (3): 595–599. Jul 1995. doi:10.1099/00207713-45-3-595. PMID 8590690.
* "Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes". International Journal of Systematic Bacteriology 44 (1): 174–176. Jan 1994. doi:10.1099/00207713-44-1-174. PMID 8123559.
* "A definition of the domains Archaea, Bacteria and Eucarya in terms of small subunit ribosomal RNA characteristics". Systematic and Applied Microbiology 14 (4): 305–310. 1991. doi:10.1016/s0723-2020(11)80303-6. PMID 11540071. Bibcode: 1991SyApM..14..305W.
* "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya". Proceedings of the National Academy of Sciences of the United States of America 87 (12): 4576–4579. Jun 1990. doi:10.1073/pnas.87.12.4576. PMID 2112744. Bibcode: 1990PNAS...87.4576W.
* "The ribosomal gene spacer region in archaebacteria". Systematic and Applied Microbiology 10 (3): 211–214. 1988. doi:10.1016/s0723-2020(88)80002-x. PMID 11542149. Bibcode: 1988SyApM..10..211A.
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### Scientific handbooks

* "Phylum AI. Crenarchaeota phy. nov.". Bergey's Manual of Systematic Bacteriology Volume 1: The Archaea and the deeply branching and phototrophic Bacteria (2nd ed.). New York: Springer Verlag. 2001. pp. 169. ISBN 978-0-387-98771-2. https://archive.org/details/bergeysmanualofs00boon.

## External links

* "Crenarchaeota". University of Wisconsin. http://www.bact.wisc.edu/Microtextbook/index.php?name=Sections&req=viewarticle&artid=97&page=1.
* "Comparative analysis of crenarchaeal genomes". United States Department of Energy. http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=TaxonList&page=lineageMicrobes&phylum=Crenarchaeota.

* v
* t
* e

Prokaryotes: Archaea classification

Domain
Archaea
Bacteria
Eukaryota
(Supergroup
Plant
Hacrobia
Heterokont
Alveolata
Rhizaria
Excavata
Amoebozoa
Opisthokonta

Animal
Fungi)

Euryarchaeota|

| Euryarchaeota|

| Archaeoglobi|

* Archaeoglobales

|

Halobacteria|

* Halobacteriales

Methanobacteria|

* Methanobacteriales

Methanococci|

* Methanococcales

Methanomicrobia|

* Methanocellales
* Methanomicrobiales
* Methanosarcinales

Methanopyri|

* Methanopyrales

Thermococci|

* "Methanofastidiosales"
* Thermococcales

Thermoplasmata|

* Methanomassiliicoccales
* Thermoplasmatales

"Altiarchaeia"|

* "Altiarchaeales"
* "Itiarchaeales"

"Thalassoarchaeia"|

* "Ca. Thalassoarchaeum"

"Methanonatronarchaeia"|

"Methanonatronarchaeales"

"Theionarchaeia"

DPANN|

| Diapherotrites|

* "Huberarchaea"
* "Iainarchaeia"
* "Micrarchaeia"

|

Parvarchaeota|

* "Ca. Parvarchaeum"

Aenigmarchaeota|

* "Ca. Aenigmarchaeum"

Nanohaloarchaea|

* "Ca. Nanosalina"
* "Ca. Nanosalinarum"
* "Ca. Haloredivivus"

Nanoarchaeota|

* "Nanoarchaeaceae"
* "Nanopusillaceae"

Woesearchaeota|

* "Woesearchaeia"

Proteoarchaeota|

| TACK|

| Crenarchaeota|

| "Methanomethylia"|

* "Methanomethyliales"

|

Thermoprotei|

* Acidilobales
* Desulfurococcales
* Fervidicoccales
* Sulfolobales
* Thermoproteales

Thaumarchaeota|

| Nitrososphaeria|

* "Nitrosocaldales"
* Cenarchaeales
* "Nitrosopumilales"
* Nitrososphaerales

|

Korarchaeota|

* "Korarchaeia"

Aigarchaeota|

* "Caldiarchaeaceae"
* "Geothermarchaeaceae"

Geoarchaeota|

"Geoarchaeia"

Bathyarchaeota|

"Bathyarchaeia"

Asgard|

* Lokiarchaeota
* Odinarchaeota
* Thorarchaeota
* Heimdallarchaeota

* v
* t
* e

Extant life phyla/divisions by domain

| Bacteria|

* Acidobacteria
* Actinobacteria
* Aquificae
* Bacteroidetes
* Chlamydiae
* Chlorobi
* Chloroflexi
* Chrysiogenetes
* Cyanobacteria
* Deferribacteres
* Deinococcus–Thermus
* Dictyoglomi
* Fibrobacteres
* Firmicutes
* Fusobacteria
* Gemmatimonadetes
* Nitrospirae
* Planctomycetes
* Proteobacteria
* Spirochaetes
* Thermodesulfobacteria
* Thermomicrobia
* Thermotogae
* Verrucomicrobia

|

| Archaea|

* Crenarchaeota
* Euryarchaeota
* Korarchaeota
* Nanoarchaeota
* Archaeal Richmond Mine acidophilic nanoorganisms

|

Eukaryote|

| Protista|

* Heterokontophyta
* Haptophyta
* Cryptophyta
* Ciliophora
* Apicomplexa
* Dinoflagellata
* Euglenozoa
* Percolozoa
* Metamonada
* Radiolaria
* Foraminifera
* Cercozoa
* Rhodophyta
* Glaucophyta
* Amoebozoa

|

Fungi|

* Chytridiomycota
* Blastocladiomycota
* Neocallimastigomycota
* Glomeromycota
* Zygomycota
* Ascomycota
* Basidiomycota

Plant|

* Chlorophyta
* Charophyta
* Marchantiophyta
* Anthocerotophyta
* Moss
* Lycopodiophyta
* Pteridophyta
* Cycadophyta
* Ginkgophyta
* Pinophyta
* Gnetophyta
* Flowering plant

Animal|

* Sponge
* Ctenophora
* Placozoa
* Cnidaria
* Xenacoelomorpha
* Chordata
* Hemichordata
* Echinodermata
* Chaetognatha
* Kinorhyncha
* Loricifera
* Priapulida
* Nematoda
* Nematomorpha
* Onychophora
* Tardigrada
* Arthropoda
* Flatworm
* Gastrotricha
* Orthonectida
* Dicyemida
* Rotifera
* Acanthocephala
* Gnathostomulida
* Micrognathozoa
* Cycliophora
* Nemertea
* Phoronida
* Bryozoa
* Entoprocta
* Brachiopoda
* Mollusca
* Annelida

Incertae sedis|

Parakaryon

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