Biology:Deinococcota

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Short description: Phylum of Gram-negative bacteria

Deinococcota
Deinococcus radiodurans.jpg
Scientific classification e
Domain: Bacteria
Subkingdom: Negibacteria
Phylum: Deinococcota
Weisburg et al. 2021[2]
Class: Deinococci
Garrity and Holt 2002[1]
Orders & families
Synonyms
  • "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"

Deinococcota (synonym, Deinococcus-Thermus) is a phylum of bacteria with a single class, Deinococci, that are highly resistant to environmental hazards, also known as extremophiles.[4] 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.[5][6][7]

Taxonomy

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

  • The Deinococcales include two families (Deinococcaceae and Trueperaceae), with three genera, Deinococcus, Deinobacterium and Truepera.[8][9][10] Truepera radiovictrix is the earliest diverging member of the order.[8] Within the order, Deinococcus forms a distinct monophyletic cluster with respect to Deinobacterium and Truepera species.[11] 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.[12]
  • The Thermales include several genera resistant to heat (Marinithermus, Meiothermus, Oceanithermus, Thermus, Vulcanithermus, Rhabdothermus) placed within a single family, Thermaceae.[9][10][13] 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.[11] 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.[14]

Though these two groups evolved from a common ancestor, the two mechanisms of resistance appear to be largely independent.[11][15]

Molecular signatures

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.[4][11] 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.[11] The CSIs found in DNA-directed RNA polymerase subunit beta and DNA topoisomerase I in Thermales species may be involved in thermophilicity,[16] while those found in Excinuclease ABC, DNA gyrase, and DNA repair protein RadA in Deinococcales species may be associated with radioresistance.[17] 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.[11] These CSPs include the DNA damage repair protein PprA the single-stranded DNA-binding protein DdrB.

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

Phylogeny

16S rRNA based LTP_08_2023[18][19][20] 120 marker proteins based GTDB 08-RS214[21][22][23]
"Deinococcia"
 
Thermales
Thermaceae
 
 

Allomeiothermus

 
 
 

Calidithermus

 
 

Meiothermus

 
 
 
 
 
 

Rhabdothermus

 
 

Vulcanithermus

 
 
 
 

Oceanithermus

 
 
 

Marinithermus

 
 

Thermus

 
 
 
 
 
 
 
 
Trueperales
Trueperaceae

Truepera

 
 
Deinococcales
Deinococcaceae
 

Deinobacterium

 
 

Deinococcus

 
 
 
 
 
"Deinococcia"
Deinococcales
 
"Marinithermaceae"
 

Marinithermus

 
 

Oceanithermus

 
 
Thermaceae
 
 

Allomeiothermus

 
 
 

Calidithermus

 
 

Meiothermus

 
 
 
 

Thermus

 
 
 
 
Trueperaceae

Truepera

 
Deinococcaceae
 
 

Deinobacterium

 
 

Deinococcus species-group 2

 
 
 

Deinococcus

 
 
 
 
 

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[24] and National Center for Biotechnology Information (NCBI)[25]

  • Phylum Deinococcota Oren and Garrity 2021
    • Class Deinococci Garrity & Holt 2002 ["Deinococcia" Oren, Parte & Garrity 2016 ex Cavalier-Smith 2020; "Thermi" Rinke et al. 2013; "Thermia" Cavalier-Smith 2020]
      • Order Deinococcales Rainey et al. 1997 [Trueperales García-López et al. 2020]
        • Family Deinococcaceae Brooks and Murray 1981 emend. Rainey et al. 1997
        • Family Trueperaceae Rainey et al. 2005
          • Genus Truepera da Costa, Rainey and Albuquerque 2005
      • Order Thermales Rainey and Da Costa 2002
        • Family Thermaceae Da Costa and Rainey 2002
          • Genus Allomeiothermus Jiao et al. 2023
          • Genus Calidithermus Raposo et al. 2019
          • Genus Marinithermus Sako et al. 2003
          • Genus Meiothermus Nobre et al. 1996 emend. Albuquerque et al. 2009
          • Genus Oceanithermus Miroshnichenko et al. 2003 emend. Mori et al. 2004
          • Genus Rhabdothermus Steinsbu et al. 2011
          • Genus Thermus Brock and Freeze 1969 emend. Nobre et al. 1996
          • Genus Vulcanithermus Miroshnichenko et al. 2003

Sequenced genomes

Currently there are 10 sequenced genomes of strains in this phylum.[26]

  • 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.[27]

See also

References

  1. ↑ "The Road Map to the Manual". Bergey's Manual of Systematic Bacteriology. 1 (The Archaea and the deeply branching and phototrophic Bacteria) (2nd ed.). New York, NY: Springer–Verlag. 2001. pp. 119–166. 
  2. ↑ "Valid publication of the names of forty-two phyla of prokaryotes". Int J Syst Evol Microbiol 71 (10): 5056. 2021. doi:10.1099/ijsem.0.005056. PMID 34694987. 
  3. ↑ Cavalier-Smith T (2006). "Rooting the tree of life by transition analyses". Biol. Direct 1: 19. doi:10.1186/1745-6150-1-19. PMID 16834776. 
  4. ↑ 4.0 4.1 "Identification of signature proteins that are distinctive of the Deinococcus–Thermus phylum". Int. Microbiol. 10 (3): 201–8. September 2007. PMID 18076002. http://www.im.microbios.org/1003/1003201.pdf. 
  5. ↑ "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. 2011. doi:10.1007/s10482-011-9616-8. PMID 21717204. 
  6. ↑ "Comparative proteome analysis of Acidaminococcus intestini supports a relationship between outer membrane biogenesis in Negativicutes and Proteobacteria". Arch Microbiol 196 (4): 307–310. 2014. doi:10.1007/s00203-014-0964-4. PMID 24535491. http://nrl.northumbria.ac.uk/16439/1/AOMI-D-14-00009.pdf. 
  7. ↑ "A phylum level perspective on bacterial cell envelope architecture". Trends Microbiol 18 (10): 464–470. 2010. doi:10.1016/j.tim.2010.06.005. PMID 20637628. 
  8. ↑ 8.0 8.1 "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. 2005. doi:10.1016/j.femsle.2005.05.002. PMID 15927420. 
  9. ↑ 9.0 9.1 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.
  10. ↑ 10.0 10.1 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.
  11. ↑ 11.0 11.1 11.2 11.3 11.4 11.5 11.6 "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. 2016. doi:10.1016/j.syapm.2016.07.003. PMID 27506333. 
  12. ↑ "Why is Deinococcus radiodurans so resistant to ionizing radiation?". Trends Microbiol 7 (9): 362–5. 1999. doi:10.1016/S0966-842X(99)01566-8. PMID 10470044. 
  13. ↑ "Classification of bacteria". http://www.bacterio.cict.fr/classifphyla.html#DeinococcusThermus. 
  14. ↑ "A general method of site-specific mutagenesis using a modification of the Thermus aquaticus". Anal Biochem 180 (1): 147–151. 1989. doi:10.1016/0003-2697(89)90103-6. PMID 2530914. 
  15. ↑ "Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: Divergent routes of adaptation to thermophily and radiation resistance". BMC Evol. Biol. 5: 57. 2005. doi:10.1186/1471-2148-5-57. PMID 16242020. 
  16. ↑ "Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution". Cell 98 (6): 811–824. 1999. doi:10.1016/S0092-8674(00)81515-9. PMID 10499798. 
  17. ↑ "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. 2004. doi:10.1534/genetics.104.029249. PMID 15454524. PMC 1448114. http://www.genetics.org/content/168/1/21.long. 
  18. ↑ "The LTP". https://imedea.uib-csic.es/mmg/ltp/#LTP. 
  19. ↑ "LTP_all tree in newick format". https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_all_08_2023.ntree. 
  20. ↑ "LTP_08_2023 Release Notes". https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_08_2023_release_notes.pdf. 
  21. ↑ "GTDB release 08-RS214". https://gtdb.ecogenomic.org/about#4%7C. 
  22. ↑ "bac120_r214.sp_label". https://data.gtdb.ecogenomic.org/releases/release214/214.0/auxillary_files/bac120_r214.sp_labels.tree. 
  23. ↑ "Taxon History". https://gtdb.ecogenomic.org/taxon_history/. 
  24. ↑ J.P. Euzéby. "Deinococcota". List of Prokaryotic names with Standing in Nomenclature (LPSN). https://lpsn.dsmz.de/phylum/deinococcota. 
  25. ↑ Sayers. "Deinococcus-Thermus". National Center for Biotechnology Information (NCBI) taxonomy database. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=1297&lvl=6&lin=f&keep=1&srchmode=1&unlock. 
  26. ↑ "Microbial Genomes". https://www.ncbi.nlm.nih.gov/genomes/MICROBES/microbial_taxtree.html. 
  27. ↑ 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. doi:10.1038/nature08656. PMID 20033048. Bibcode: 2009Natur.462.1056W. 

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