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Deinococcota

From Wikipedia, the free encyclopedia
(Redirected from Hadobacteria)

Deinococcota
Scientific classification Edit this classification
Domain: Bacteria
Kingdom: Thermotogati
Phylum: Deinococcota
Weisburg et al. 2021[1]
Class: Deinococci
Garrity and Holt 2002[2]
Orders & families
Synonyms
  • Deinococcota
    • "Deinobacteria" Cavalier-Smith 2006
    • "Deinococcobacteria" Margulis & Schwartz 1998
    • "Deinococcaeota" Oren et al. 2015
    • "Deinococcota" Whitman et al. 2018
    • "Deinococcus–Thermus" Weisburg et al. 1989
    • "Hadobacteria" Cavalier-Smith 2006[3]
    • "Xenobacteria"
  • Deinococci
    • "Deinococcia" Oren, Parte & Garrity 2016 ex Cavalier-Smith 2020
    • "Thermi" Rinke et al. 2013
    • "Thermia" Cavalier-Smith 2020

Deinococcota (synonym, "Deinococcus-Thermus") is a phylum of bacteria with a single class, Deinococci (from Ancient Greek δεινός (deinós), meaning "terrible", and κόκκος (kókkos), meaning "berry"[4]), that are highly resistant to environmental hazards, also known as extremophiles.[5]

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.[6][7][8]

Taxonomy

[edit]

The phylum Deinococcota consists of a single class (Deinococci) and two orders:

Deinococcales
Includes two families (Deinococcaceae and Trueperaceae), with three genera, Deinococcus, Deinobacterium and Truepera.[9][10][11] Truepera radiovictrix is the earliest diverging member of the order.[9] Within the order, Deinococcus forms a distinct monophyletic cluster with respect to Deinobacterium and Truepera species.[12]
The genus includes 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 survive extremes of heat and cold.[13]
Thermales
Includes several genera resistant to heat (Marinithermus, Meiothermus, Oceanithermus, Thermus, Vulcanithermus, Rhabdothermus) placed within a single family, Thermaceae.[10][11][14] Phylogenetic analyses demonstrate that within the Thermales, Meiothermus and Thermus species form a monophyletic cluster, with respect to Marinithermus, Oceanithermus, Vulcanithermus and Rhabdothermus that branch as outgroups within the order.[12] This suggests that Meiothermus and Thermus species are more closely related to one another relative to other genera within the order.
Thermus aquaticus was important in the development of the polymerase chain reaction where repeated cycles of heating DNA to near boiling make it advantageous to use a thermo-stable DNA polymerase enzyme, the Taq polymerase.[15]

Though these two groups evolved from a common ancestor, the two mechanisms of resistance appear to be largely independent.[12][16]

Molecular signatures

[edit]

Molecular signatures in the form of conserved signature indels (CSIs) and proteins (CSPs) have been found that are uniquely shared by all members belonging to the Deinococcota phylum.[5][12] These CSIs and CSPs are distinguishing characteristics that delineate the unique phylum from all other bacterial organisms, and their exclusive distribution is parallel with the observed differences in physiology. CSIs and CSPs have also been found that support order and family-level taxonomic rankings within the phylum. Some of the CSIs found to support order level distinctions are thought to play a role in the respective extremophilic characteristics.[12] The CSIs found in DNA-directed RNA polymerase subunit beta and DNA topoisomerase I in Thermales species may be involved in thermophilicity,[17] while those found in Excinuclease ABC, DNA gyrase, and DNA repair protein RadA in Deinococcales species may be associated with radioresistance.[18]

Additionally, some genera within this group, including Deinococcus, Thermus, and Meiothermus, also have molecular signatures that demarcate them as individual genera, inclusive of their respective species, providing a means to distinguish them from the rest of the group and all other bacteria.[12] Two CSPs that were found uniquely for all members belonging to the Deinococcus genus are well characterized and are thought to play a role in their characteristic radioresistant phenotype. These CSPs include the DNA damage repair protein PprA and the single-stranded DNA-binding protein DdrB.[12]

CSIs have also been found specific for Truepera radiovictrix.[12]

Phylogeny

[edit]

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[19] and National Center for Biotechnology Information (NCBI)[20]

16S rRNA based LTP_07_2026[21][22][23] 120 marker proteins based GTDB release 11-RS232[24][25][26]
"Deinococcia"
Thermales
Thermaceae

Allomeiothermus Jiao et al. 2023

Calidithermus Raposo et al. 2019

Meiothermus Nobre et al. 1996

Oceanithermus Miroshnichenko et al. 2003

Marinithermus Sako et al. 2003

Rhabdothermus Steinsbu et al. 2011

Vulcanithermus Miroshnichenko et al. 2003

Thermus Brock & Freeze 1969

Trueperales
Trueperaceae

Truepera Albuquerque, da Costa & Rainey 2005

Deinococcales
Deinococcaceae

Deinococcus peraridilitoris

Deinobacterium Ekman et al. 2011

Deinococcus~

Deinococcus Brooks & Murray 1981

Sequenced genomes

[edit]

By 2009 there were 10 sequenced genomes of strains in this phylum.[27]

  • Deinococcus radiodurans R1
  • Thermus thermophilus HB27
  • Thermus thermophilus HB8
  • Deinococcus geothermalis DSM 11300
  • Deinococcus deserti VCD115
  • Meiothermus ruber DSM 1279
  • Meiothermus silvanus DSM 9946
  • Truepera radiovictrix DSM 17093
  • Oceanithermus profundus DSM 14977

The two Meiothermus species were sequenced under the auspices of the Genomic Encyclopedia of Bacteria and Archaea project (GEBA), which aims at sequencing organisms based on phylogenetic novelty and not on pathogenicity or notoriety.[28]

As of August 2026, the number of sequenced genomes is 1,341, of which 138 are labelled "reference genome" by NCBI and 921 are metagenome-assembled genomes.[29]

See also

[edit]

References

[edit]
  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. ↑ Garrity GM, Holt JG (2001). "The Road Map to the Manual". In Boone DR, Castenholz RW, Garrity GM (eds.). Bergey's Manual of Systematic Bacteriology. Vol. 1 (The Archaea and the deeply branching and phototrophic Bacteria) (2nd ed.). New York, NY: Springer–Verlag. pp. 119–166.
  3. ↑ Cavalier-Smith T (2006). "Rooting the tree of life by transition analyses". Biol. Direct. 1: 19. doi:10.1186/1745-6150-1-19. PMC 1586193. PMID 16834776.
  4. ↑ Deinococcus in LPSN; Parte, Aidan C.; Sardà Carbasse, Joaquim; Meier-Kolthoff, Jan P.; Reimer, Lorenz C.; Göker, Markus (1 November 2020). "List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ". International Journal of Systematic and Evolutionary Microbiology. 70 (11): 5607–5612. doi:10.1099/ijsem.0.004332.
  5. 1 2 Griffiths E, Gupta RS (September 2007). "Identification of signature proteins that are distinctive of the Deinococcus–Thermus phylum" (PDF). Int. Microbiol. 10 (3): 201–8. PMID 18076002. Archived from the original (PDF) on 2011-06-14.
  6. ↑ Gupta RS (2011). "Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes". Antonie van Leeuwenhoek. 100 (2): 171–182. doi:10.1007/s10482-011-9616-8. PMC 3133647. PMID 21717204.
  7. ↑ Campbell C, Sutcliffe IC, Gupta RS (2014). "Comparative proteome analysis of Acidaminococcus intestini supports a relationship between outer membrane biogenesis in Negativicutes and Proteobacteria" (PDF). Arch Microbiol. 196 (4): 307–310. Bibcode:2014ArMic.196..307C. doi:10.1007/s00203-014-0964-4. PMID 24535491. S2CID 10721294. Archived from the original (PDF) on 2019-12-22. Retrieved 2019-07-10.
  8. ↑ Sutcliffe IC (2010). "A phylum level perspective on bacterial cell envelope architecture". Trends Microbiol. 18 (10): 464–470. doi:10.1016/j.tim.2010.06.005. PMID 20637628.
  9. 1 2 Albuquerque L, Simões C, Nobre MF, et al. (2005). "Truepera radiovictrix gen. nov., sp. nov., a new radiation resistant species and the proposal of Trueperaceae fam. nov". FEMS Microbiol Lett. 247 (2): 161–169. doi:10.1016/j.femsle.2005.05.002. PMID 15927420.
  10. 1 2 Garrity GM, Holt JG. (2001) Phylum BIV. "Deinococcus–Thermus". In: Bergey’s manual of systematic bacteriology, pp. 395-420. Eds D. R. Boone, R. W. Castenholz. Springer-: New York.
  11. 1 2 Garrity GM, Bell JA, Lilburn TG. (2005) Phylum BIV. The revised road map to the Manual. In: Bergey’s manual of systematic bacteriology, pp. 159-220. Eds Brenner DJ, Krieg NR, Staley JT, Garrity GM. Springer-: New York.
  12. 1 2 3 4 5 6 7 8 Ho J, Adeolu M, Khadka B, Gupta RS (2016). "Identification of distinctive molecular traits that are characteristic of the phylum "Deinococcus–Thermus" and distinguish its main constituent groups". Syst Appl Microbiol. 39 (7): 453–463. doi:10.1016/j.syapm.2016.07.003. PMID 27506333.
  13. ↑ Battista JR, Earl AM, Park MJ (1999). "Why is Deinococcus radiodurans so resistant to ionizing radiation?". Trends Microbiol. 7 (9): 362–5. doi:10.1016/S0966-842X(99)01566-8. PMID 10470044.
  14. ↑ "Classification of bacteria". www.bacterio.cict.fr. Archived from the original on 2013-01-27.
  15. ↑ Nelson RM, Long GL (1989). "A general method of site-specific mutagenesis using a modification of the Thermus aquaticus". Anal Biochem. 180 (1): 147–151. doi:10.1016/0003-2697(89)90103-6. PMID 2530914.
  16. ↑ Omelchenko MV, Wolf YI, Gaidamakova EK, et al. (2005). "Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: Divergent routes of adaptation to thermophily and radiation resistance". BMC Evol. Biol. 5 (1): 57. Bibcode:2005BMCEE...5...57O. doi:10.1186/1471-2148-5-57. PMC 1274311. PMID 16242020.
  17. ↑ Zhang G, Campbell EA, Minakhin L, Richter C, Severinov K, Darst SA (1999). "Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution". Cell. 98 (6): 811–824. doi:10.1016/S0092-8674(00)81515-9. PMID 10499798. S2CID 15695915.
  18. ↑ Tanaka M, Earl AM, Howell HA, Park MJ, Eisen JA, Peterson SN, Battista JR (2004). "Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance". Genetics. 168 (1): 21–23. doi:10.1534/genetics.104.029249. PMC 1448114. PMID 15454524.
  19. ↑ Deinococcota in LPSN; Freese, H. M.; Meier-Kolthoff, J. P.; Sardà Carbasse, J.; Afolayan, A. O.; Göker, M. (2026). "TYGS and LPSN in 2025: a Global Core Biodata Resource for genome-based classification and nomenclature of prokaryotes within DSMZ Digital Diversity". Nucleic Acids Research. 54 (D1): D884–D891. doi:10.1093/nar/gkaf1110.
  20. ↑ C.L. Schoch. "Deinococcota". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2026-08-01.
  21. ↑ "The LTPlus". The All-Species Living Tree Project. Retrieved 1 August 2026.
  22. ↑ "LTP_all tree in newick format". The All-Species Living Tree Project. Retrieved 1 August 2026.
  23. ↑ Rossello-Mora, Ramon; Viver, Tomeu; Palmer-Rodríguez, Pere; Westram, Ralf; Bustos-Caparros, Esteban; Gago, Joan Francisco; Gonzalez-Mendez, Jaime; Llabrés, Mercè; Ludwig, Wolfgang; Amann, Rudolf (22 April 2026). "A pipeline for improved 16S rRNA gene-based phylogeny and diversity analyses of Bacteria and Archaea". Nature Portfolio. doi:10.21203/rs.3.rs-9370187/v1.
  24. ↑ "GTDB release 11-RS232". Genome Taxonomy Database. Retrieved 1 May 2026.
  25. ↑ "bac120_r232.sp_label". Genome Taxonomy Database. Retrieved 1 May 2026.
  26. ↑ "Taxon History". Genome Taxonomy Database. Retrieved 1 May 2026.
  27. ↑ "Microbial Genomes".
  28. ↑ Wu, D.; Hugenholtz, P.; Mavromatis, K.; Pukall, R. D.; Dalin, E.; Ivanova, N. N.; Kunin, V.; Goodwin, L.; Wu, M.; Tindall, B. J.; Hooper, S. D.; Pati, A.; Lykidis, A.; Spring, S.; Anderson, I. J.; d'Haeseleer, P.; Zemla, A.; Singer, M.; Lapidus, A.; Nolan, M.; Copeland, A.; Han, C.; Chen, F.; Cheng, J. F.; Lucas, S.; Kerfeld, C.; Lang, E.; Gronow, S.; Chain, P.; Bruce, D. (2009). "A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea". Nature. 462 (7276): 1056–1060. Bibcode:2009Natur.462.1056W. doi:10.1038/nature08656. PMC 3073058. PMID 20033048.
  29. ↑ "Genome (taxon 1297)". NCBI.
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