Deinococcus-Thermus
| Deinococcus-Thermus |
| Scientific classification |
| Domain: |
Bacteria |
| Phylum: |
Deinococcus-Thermus |
| Class: |
Deinococci
Garrity and Holt 2002 |
| Orders & Genera |
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Deinococcales Rainey et al. 1997
Deinococcaceae Brooks and Murray 1981 emend. Rainey et al. 1997
Deinococcus Brooks and Murray 1981 emend. Rainey et al. 1997
Deinobacterium Ekman et al. 2011
Trueperaceae Rainey et al. 2005
Truepera da Costa, Rainey and Albuquerque 2005
Thermales Rainey and Da Costa 2002
Thermaceae Da Costa and Rainey 2002
Thermus Brock and Freeze 1969 emend. Nobre et al. 1996
Meiothermus Nobre et al. 1996 emend. Albuquerque et al. 2009
Marinithermus Sako et al. 2003
Oceanithermus Miroshnichenko et al. 2003 emend. Mori et al. 2004
Vulcanithermus Miroshnichenko et al. 2003
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| Synonyms |
- Hadobacteria Cavalier-Smith 1992 emend. Cavalier-Smith 1998
- Xenobacteria
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The Deinococcus-Thermus are a small group of bacteria composed of cocci 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).
Phylogeny
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [5] and National Center for Biotechnology Information (NCBI)[6] and the phylogeny is based on 16S rRNA-based LTP release 106 by The All-Species Living Tree Project [7]
| Thermaceae |
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Vulcanithermus mediatlanticus Miroshnichenko et al. 2003
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| Oceanithermus |
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O. desulfurans Mori et al. 2004
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O. profundus Miroshnichenko et al. 2003
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Marinithermus hydrothermalis Sako et al. 2003
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| Meiothermus |
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?M. granaticius Albuquerque et al. 2010
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?M. rosaceus ♠ Chen et al. 2002
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M. silvanus (Tenreiro et al. 1995) Nobre et al. 1996
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M. chliarophilus (Tenreiro et al. 1995) Nobre et al. 1996
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M. timidus Pires et al. 2005
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M. rufus Albuquerque et al. 2010
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M. cerbereus Chung et al. 1997
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M. ruber (Loginova et al. 1984) Nobre et al. 1996
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M. cateniformans Zhang et al. 2010
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M. taiwanensis Chen et al. 2002
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| Thermus |
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?T. caldophilus ♠ Taguchi et al. 1983
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?T. eggertssonii ♠ Peters 2008
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?T. filiformis Hudson et al. 1987
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?T. kawarayensis ♠ Kurosawa et al. 2005
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?T. murrieta ♠ Benner et al. 2006
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?T. nonproteolyticus ♠
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?T. rehai ♠ Lin et al. 2002
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?T. yunnanensis ♠ Gong et al. 2005
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T. oshimai Williams et al. 1996
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T. thermophilus (ex Oshima and Imahori 1974) Manaia et al. 1995
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T. aquaticus Brock and Freeze 1969
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T. arciformis Zhang et al. 2010
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T. islandicus Bjornsdottir et al. 2009
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T. brockianus Williams et al. 1995
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T. igniterrae Chung et al. 2000
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T. antranikianii Chung et al. 2000
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T. scotoductus Kristjansson et al. 1994
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| Deinococcales |
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Truepera radiovictrix Albuquerque et al. 2005
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| Deinococcaceae |
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Deinococcus pimensis Rainey and da Costa 2005
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Deinococcus peraridilitoris Rainey et al. 2007
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Deinococcus papagonensis Rainey and da Costa 2005
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Deinococcus yavapaiensis Rainey and da Costa 2005
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Deinobacterium chartae Ekman et al. 2011
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| Deinococcus |
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?D. aquivivus ♠ Kaempferet al. 2008
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?D. depolymerans Asker et al. 2011
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?D. xibeiensis Wang et al. 2010
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D. misasensis Asker et al. 2008
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D. cellulosilyticus Weon et al. 2007
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D. roseus Asker et al. 2008
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D. maricopensis Rainey and da Costa 2005
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D. alpinitundrae Callegan et al. 2008
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D. gobiensis Yuan et al. 2009
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D. radiophilus (ex Lewis 1973) Brooks and Murray 1981
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D. piscis Shashidhar and Bandekar 2009
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D. proteolyticus Brooks and Murray 1981
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D. sonorensis Rainey and da Costa 2005
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D. radiomollis Callegan et al. 2008
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D. altitudinis Callegan et al. 2008
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D. aquiradiocola Asker et al. 2009
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D. claudionis Callegan et al. 2008
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D. indicus Suresh et al. 2004
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D. radiodurans (ex Raj et al. 1960) Brooks and Murray 1981
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D. wulumuqiensis Wang et al. 2010
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D. aquaticus Im et al. 2008
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D. caeni Im et al. 2008
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D. grandis (Oyaizu et al. 1987) Rainey et al. 1997
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D. deserti de Groot et al. 2005
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D. navajonensis Rainey and da Costa 2005
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D. hohokamensis Rainey and da Costa 2005
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D. ficus Lai et al. 2006 emend. Kämpfer 2009
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D. aquatilis Kämpfer et al. 2008
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D. yunweiensis Zhang et al. 2007
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D. xinjiangensis Peng et al. 2009
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D. hopiensis Rainey and da Costa 2005
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D. murrayi Ferreira et al. 1997
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D. geothermalis Ferreira et al. 1997
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D. apachensis Rainey and da Costa 2005
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D. aerius Yang et al. 2009
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D. aetherius Yang et al. 2010
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D. aerophilus Yoo et al. 2010
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D. aerolatus Yoo et al. 2010
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D. radiopugnans Brooks and Murray 1981
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D. marmoris Hirsch et al. 2006
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D. saxicola Hirsch et al. 2006
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D. frigens Hirsch et al. 2006
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Note:
♠ Strains found at the National Center for Biotechnology Information (NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LSPN)
Sequenced genomes
Currently there are 10 sequenced genomes of strains in this phylum.[8]
- 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.[9] Currently, the genome of Thermus aquaticus Y51MC23 is in the final stages of assembly by the DOE Joint Genome Institute [10]
References
- ^ 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.
- ^ http://www.bacterio.cict.fr/classifphyla.html#DeinococcusThermus
- ^ 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.
- ^ 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.
- ^ J.P. Euzéby. "Deinococcus-Thermus". List of Prokaryotic names with Standing in Nomenclature (LPSN) [1]. http://www.bacterio.cict.fr/classifphyla.html#Deinococcus-Thermus. Retrieved 2011-11-17.
- ^ Sayers et al.. "Deinococcus-Thermus". National Center for Biotechnology Information (NCBI) taxonomy database [2]. http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=1297&lvl=6&lin. Retrieved 2011-06-05.
- ^ All-Species Living Tree Project."16S rRNA-based LTP release 106 (full tree)". Silva Comprehensive Ribosomal RNA Database [3]. http://www.arb-silva.de/fileadmin/silva_databases/living_tree/LTP_release_106/LTPs106_SSU_tree.pdf. Retrieved 2011-11-17.
- ^ http://www.ncbi.nlm.nih.gov/genomes/MICROBES/microbial_taxtree.html
- ^ 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
- ^ http://www.ncbi.nlm.nih.gov/genomeprj/55053
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| Types |
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Notable
extremophiles |
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G-/
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G+/
no OM |
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Selenomonadales
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Erysipelotrichiales
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gr+f/gr+a(t)/gr-p(c)/gr-o
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