Deinococcus-Thermus


Deinococcus-Thermus
Deinococcus-Thermus
Scientific classification
Domain: Bacteria
Phylum: Deinococcus-Thermus
Class: Deinococci
L. Margulis & K.V. Schwartz, 1998
Orders & Genera

Deinococcales
  Deinococcaceae
    Deinococcus
    Deinobacterium
  Trueperaceae
    Truepera
Thermales
  Thermaceae
    Thermus
    Meiothermus
    Marinithermus
    Oceanithermus
    Vulcanithermus

Synonyms
  • Hadobacteria Cavalier-Smith 1992 emend. Cavalier-Smith 1998
  • Xenobacteria

The Deinococcus-Thermus are a small group of bacteria composed of cocci[citation needed] highly resistant to environmental hazards.[1]

There are two main groups.

  • The Deinococcales include two families, with three genera, Deinococcus and Truepera, the former with 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.
  • The Thermales include several genera resistant to heat (Marinithermus, Meiothermus, Oceanithermus, Thermus, Vulcanithermus).[2] 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.

Though these two groups evolved from a common ancestor, the two mechanisms of resistance appear to be largely independent.[3]

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[4] (from Hades, the Greek underworld).

Taxonomy[5][6]

Class Deinococci

  • Order Thermales
    • Family Thermaceae
      • Genus Marinithermus Sako et al. 2003
        • Marinithermus hydrothermalis Sako et al. 2003
      • Genus Meiothermus Nobre et al. 1996 emend. Albuquerque et al. 2009
        • M. cateniformans Zhang et al. 2010
        • M. cerbereus Chung et al. 1997
        • M. chliarophilus (Tenreiro et al. 1995) Nobre et al. 1996
        • M. granaticius Albuquerque et al. 2010
        • M. rosaceus Chen et al. 2002
        • M. ruber (Loginova et al. 1984) Nobre et al. 1996
        • M. rufus Albuquerque et al. 2010
        • M. silvanus (Tenreiro et al. 1995) Nobre et al. 1996
        • M. taiwanensis Chen et al. 2002
        • M. timidus Pires et al. 2005
      • Genus Oceanithermus Miroshnichenko et al. 2003 emend. Mori et al. 2004
        • O. desulfurans Mori et al. 2004
        • O. profundus Miroshnichenko et al. 2003
      • Genus Thermus Brock and Freeze 1969 emend. Nobre et al. 1996
        • T. antranikianii Chung et al. 2000
        • T. aquaticus Brock and Freeze 1969
        • T. arciformis Zhang et al. 2010
        • T. brockianus Williams et al. 1995
        • T. caldophilusTaguchi et al. 1983
        • T. eggertssoniiPeters 2008
        • T. filiformis Hudson et al. 1987
        • T. igniterrae Chung et al. 2000
        • T. islandicus Bjornsdottir et al. 2009
        • T. kawarayensisKurosawa et al. 2005
        • T. murrietaBenner et al. 2006
        • T. nonproteolyticus
        • T. oshimai Williams et al. 1996
        • T. rehai
        • T. scotoductus Kristjansson et al. 1994
        • T. thermophilus (ex Oshima and Imahori 1974) Manaia et al. 1995
        • T. yunnanensisGong et al. 2005
      • Genus Vulcanithermus Miroshnichenko et al. 2003
        • Vulcanithermus mediatlanticus Miroshnichenko et al. 2003
  • Order Deinococcales (Radio-resistant micrococci)
    • Family Trueperaceae
      • Genus Truepera Albuquerque, da Costa and Rainey 2005
        • Truepera radiovictrix Albuquerque, da Costa and Rainey 2005
    • Family Deinococcaceae
      • Genus DeinobacteriumEkman et al. 2010
        • Deinobacterium chartaeEkman et al. 2010
      • Genus Deinococcus Brooks and Murray 1981 emend. Rainey et al. 1997
        • D. aerius Yang et al. 2009
        • D. aerolatus Yoo et al. 2010
        • D. aerophilus Yoo et al. 2010
        • D. aetherius Yang et al. 2009
        • D. alpinitundrae Callegan et al. 2008
        • D. altitudinis Callegan et al. 2008
        • D. apachensis Rainey and da Costa 2005
        • D. aquaticus Im et al. 2008
        • D. aquatilis Kämpfer et al. 2008
        • D. aquiradiocola Asker et al. 2009
        • D. aquivivusKaempferet al. 2008
        • D. caeni Im et al. 2008
        • D. cellulosilyticus Weon et al. 2007
        • D. claudionis Callegan et al. 2008
        • D. deserti de Groot et al. 2005
        • D. ficus Lai et al. 2006 emend. Kämpfer 2009
        • D. frigens Hirsch et al. 2006
        • D. geothermalis Ferreira et al. 1997
        • D. gobiensis Yuan et al. 2009
        • D. grandis (Oyaizu et al. 1987) Rainey et al. 1997
        • D. hohokamensis Rainey and da Costa 2005
        • D. hopiensis Rainey and da Costa 2005
        • D. indicus Suresh et al. 2004
        • D. maricopensis Rainey and da Costa 2005
        • D. marmoris Hirsch et al. 2006
        • D. misasensis Asker et al. 2008
        • D. murrayi Ferreira et al. 1997
        • D. navajonensis Rainey and da Costa 2005
        • D. papagonensis Rainey and da Costa 2005
        • D. peraridilitoris Rainey et al. 2007
        • D. pimensis Rainey and da Costa 2005
        • D. piscis Shashidhar and Bandekar 2009
        • D. proteolyticus Brooks and Murray 1981
        • D. radiodurans (ex Raj et al. 1960) Brooks and Murray 1981
        • D. radiomollis Callegan et al. 2008
        • D. radiophilus (ex Lewis 1973) Brooks and Murray 1981
        • D. radiopugnans Brooks and Murray 1981
        • D. roseus Asker et al. 2008
        • D. saxicola Hirsch et al. 2006
        • D. sonorensis Rainey and da Costa 2005
        • D. wulumuqiensis Wang et al. 2010
        • D. xibeiensis Wang et al. 2010
        • D. xinjiangensis Peng et al. 2009
        • D. yavapaiensis Rainey and da Costa 2005
        • D. yunweiensis Zhang et al. 2007

Note:
♠ Strain found at the National Center for Biotechnology Information (NCBI) but has no standing with the Bacteriological Code (1990 and subsequent Revision) as detailed by List of Prokaryotic names with Standing in Nomenclature (LPSN) as a result of the following reasons:
• No pure culture isolated or available for Prokayotes.
• Not validly published because the effective publication only documents deposit of the type strain in a single recognized culture collection.
• Not approved and published by the International Journal of Systematic Bacteriology or the International Journal of Systematic and Evolutionary Microbiology (IJSB/IJSEM).

Sequenced genomes

Currently there are 10 sequenced genomes of strains in this phylum.[7]

  • 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 sp. 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 pathologenicity or notoriety.[8] Currently, the genome of Thermus aquaticus Y51MC23 is in the final stages of assembly by the DOE Joint Genome Institute [9]

References

  1. ^ Griffiths E, Gupta RS (September 2007). "Identification of signature proteins that are distinctive of the Deinococcus-Thermus phylum". Int. Microbiol. 10 (3): 201–8. PMID 18076002. http://www.im.microbios.org/1003/1003201.pdf. 
  2. ^ http://www.bacterio.cict.fr/classifphyla.html#DeinococcusThermus
  3. ^ 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: 57. doi:10.1186/1471-2148-5-57. PMC 1274311. PMID 16242020. http://www.biomedcentral.com/1471-2148/5/57. 
  4. ^ 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. http://www.biology-direct.com/content/1//19. 
  5. ^ J.P. Euzéby. "Deinoccoci". List of Prokaryotic names with Standing in Nomenclature. http://www.bacterio.cict.fr/classifphyla.html#Deinococcus-Thermus. Retrieved 2011-06-05. 
  6. ^ See the NCBI webpage on Deinococci Data extracted from the "NCBI Taxonomy Browser". National Center for Biotechnology Information. http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi. Retrieved 2011-06-05. 
  7. ^ http://www.ncbi.nlm.nih.gov/genomes/MICROBES/microbial_taxtree.html
  8. ^ Wu, D.; Hugenholtz, P.; Mavromatis, K.; Pukall, R. �D.; Dalin, E.; Ivanova, N. N.; Kunin, V.; Goodwin, L. et al. (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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3073058.  edit
  9. ^ http://www.ncbi.nlm.nih.gov/genomeprj/55053

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