Crossref journal-article
Springer Science and Business Media LLC
Nature Reviews Microbiology (297)
Bibliography

Brochier-Armanet, C., Boussau, B., Gribaldo, S., & Forterre, P. (2008). Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nature Reviews Microbiology, 6(3), 245–252.

Authors 4
  1. Céline Brochier-Armanet (first)
  2. Bastien Boussau (additional)
  3. Simonetta Gribaldo (additional)
  4. Patrick Forterre (additional)
References 61 Referenced 963
  1. Pace, N. R. A molecular view of microbial diversity and the biosphere. Science 276, 734–740 (1997). (10.1126/science.276.5313.734) / Science by NR Pace (1997)
  2. Woese, C. R. & Fox, G. E. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl Acad. Sci. USA 74, 5088–5090 (1977). (10.1073/pnas.74.11.5088) / Proc. Natl Acad. Sci. USA by CR Woese (1977)
  3. Fox, G. E. et al. The phylogeny of prokaryotes. Science 209, 457–463 (1980). (10.1126/science.6771870) / Science by GE Fox (1980)
  4. Woese, C. R. Bacterial evolution. Microbiol. Rev. 51, 221–271 (1987). (10.1128/MMBR.51.2.221-271.1987) / Microbiol. Rev. by CR Woese (1987)
  5. Woese, C. R. in Archaea: Evolution, Physiology and Molecular Biology (eds Garrett, R. A. & Klenk, H. P.) 1–15 (Blackwell publishing, Oxford, 2006). An eloquent historical review that reported, for the first time, all the steps that led to the discovery of Archaea. Forms the introduction of an interesting book that covers the various aspects of archaeal physiology and molecular biology and focuses on the similarities between Archaea and Eukaryotes. (10.1002/9780470750865.ch1) / Archaea: Evolution, Physiology and Molecular Biology by CR Woese (2006)
  6. Woese, C. R., Kandler, O. & Wheelis, M. L. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl Acad. Sci. USA 87, 4576–4579 (1990). (10.1073/pnas.87.12.4576) / Proc. Natl Acad. Sci. USA by CR Woese (1990)
  7. Woese, C. R., Gupta, R., Hahn, C. M., Zillig, W. & Tu, J. The phylogenetic relationships of three sulfur dependent archaebacteria. Syst. Appl. Microbiol. 5, 97–105 (1984). (10.1016/S0723-2020(84)80054-5) / Syst. Appl. Microbiol. by CR Woese (1984)
  8. Prangishvilli, D., Zillig, W., Gierl, A., Biesert, L. & Holz, I. DNA-dependent RNA polymerase of thermoacidophilic archaebacteria. Eur. J. Biochem. 122, 471–477 (1982). (10.1111/j.1432-1033.1982.tb06461.x) / Eur. J. Biochem. by D Prangishvilli (1982)
  9. Makarova, K. S. & Koonin, E. V. Comparative genomics of archaea: how much have we learned in six years, and what's next? Genome Biol. 4, 115 (2003). (10.1186/gb-2003-4-8-115) / Genome Biol. by KS Makarova (2003)
  10. Brochier, C., Forterre, P. & Gribaldo, S. An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences. BMC Evol. Biol. 5, 36 (2005). Revealed a conserved core of vertically inherited genes in different cellular systems, which proved that reconstructing the phylogeny of species is a feasible task in Archaea. (10.1186/1471-2148-5-36) / BMC Evol. Biol. by C Brochier (2005)
  11. Gribaldo, S. & Brochier-Armanet, C. The origin and evolution of Archaea: a state of the art. Phil. Trans. R. Soc. Lond. B 361, 1007–1022 (2006). (10.1098/rstb.2006.1841) / Phil. Trans. R. Soc. Lond. B by S Gribaldo (2006)
  12. Daubin, V., Gouy, M. & Perriere, G. A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res. 12, 1080–1090 (2002). (10.1101/gr.187002) / Genome Res. by V Daubin (2002)
  13. Wolf, Y. I., Rogozin, I. B., Grishin, N. V., Tatusov, R. L. & Koonin, E. V. Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol. Biol. 1, 8 (2001). (10.1186/1471-2148-1-8) / BMC Evol. Biol. by YI Wolf (2001)
  14. Forterre, P., Gribaldo, S. & Brochier-Armanet, C. in Archaea: Evolution, Physiology and Molecular Biology (eds Garrett, R. A. & Klenk, H. P.) 17–29 (Blackwell publishing, Oxford, 2006). (10.1002/9780470750865.ch2) / Archaea: Evolution, Physiology and Molecular Biology by P Forterre (2006)
  15. Bernander, R. Chromosome replication, nucleoid segregation and cell division in Archaea. Trends Microbiol. 8, 278–283 (2000). (10.1016/S0966-842X(00)01760-1) / Trends Microbiol. by R Bernander (2000)
  16. Myllykallio, H. et al. Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon. Science 288, 2212–2215 (2000). (10.1126/science.288.5474.2212) / Science by H Myllykallio (2000)
  17. Makarova, K. S. & Koonin, E. V. Evolutionary and functional genomics of the Archaea. Curr. Opin. Microbiol. 8, 586–594 (2005). (10.1016/j.mib.2005.08.003) / Curr. Opin. Microbiol. by KS Makarova (2005)
  18. Klenk, H. P. in Archaea: Evolution, Physiology and Molecular Biology (eds Garrity, G. M. & Klenk, H. P.) 75–95 (Blackwell publishing, Oxford, 2006). (10.1002/9780470750865.ch7) / Archaea: Evolution, Physiology and Molecular Biology by HP Klenk (2006)
  19. Uemori, T., Sato, Y., Kato, I., Doi, H. & Ishino, Y. A novel DNA polymerase in the hyperthermophilic archaeon, Pyrococcus furiosus: gene cloning, expression, and characterization. Genes Cells 2, 499–512 (1997). (10.1046/j.1365-2443.1997.1380336.x) / Genes Cells by T Uemori (1997)
  20. Margolin, W., Wang, R. & Kumar, M. Isolation of an ftsZ homolog from the archaebacterium Halobacterium salinarium: implications for the evolution of FtsZ and tubulin. J. Bacteriol. 178, 1320–1327 (1996). (10.1128/jb.178.5.1320-1327.1996) / J. Bacteriol. by W Margolin (1996)
  21. Allers, T. & Mevarech, M. Archaeal genetics — the third way. Nature Rev. Genet. 6, 58–73 (2005). (10.1038/nrg1504) / Nature Rev. Genet. by T Allers (2005)
  22. Olsen, G. J., Lane, D. J., Giovannoni, S. J., Pace, N. R. & Stahl, D. A. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40, 337–365 (1986). (10.1146/annurev.mi.40.100186.002005) / Annu. Rev. Microbiol. by GJ Olsen (1986)
  23. DeLong, E. F. Archaea in coastal marine environments. Proc. Natl Acad. Sci. USA 89, 5685–5689 (1992). (10.1073/pnas.89.12.5685) / Proc. Natl Acad. Sci. USA by EF DeLong (1992)
  24. Fuhrman, J. A., McCallum, K. & Davis, A. A. Novel major archaebacterial group from marine plankton. Nature 356, 148–149 (1992). (10.1038/356148a0) / Nature by JA Fuhrman (1992)
  25. Schleper, C., Jurgens, G. & Jonuscheit, M. Genomic studies of uncultivated archaea. Nature Rev. Microbiol. 3, 479–488 (2005). A fascinating review that underlines the diversity of Archaea and the importance of using metagenomic approaches to gain insights into their biology and physiology. (10.1038/nrmicro1159) / Nature Rev. Microbiol. by C Schleper (2005)
  26. Schleper, C. in Archaea: Evolution, Physiology and Molecular Biology (eds Garrett, R. A. & Klenk, H. P.) 39–50 (Blackwell publishing, Oxford, 2006). (10.1002/9780470750865.ch4) / Archaea: Evolution, Physiology and Molecular Biology by C Schleper (2006)
  27. Preston, C. M., Wu, K. Y., Molinski, T. F. & DeLong, E. F. A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov. Proc. Natl Acad. Sci. USA 93, 6241–6246 (1996). (10.1073/pnas.93.13.6241) / Proc. Natl Acad. Sci. USA by CM Preston (1996)
  28. Schleper, C., Swanson, R. V., Mathur, E. J. & DeLong, E. F. Characterization of a DNA polymerase from the uncultivated psychrophilic archaeon Cenarchaeum symbiosum. J. Bacteriol. 179, 7803–7811 (1997). (10.1128/jb.179.24.7803-7811.1997) / J. Bacteriol. by C Schleper (1997)
  29. Garrett, R. A. & Klenk, H. P. (eds) Archaea: Evolution, Physiology and Molecular Biology (Blackwell publishing, Oxford, 2006). (10.1002/9780470750865) / Archaea: Evolution, Physiology and Molecular Biology by RA Garrett (2006)
  30. Barns, S. M., Delwiche, C. F., Palmer, J. D. & Pace, N. R. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc. Natl Acad. Sci. USA 93, 9188–9193 (1996). (10.1073/pnas.93.17.9188) / Proc. Natl Acad. Sci. USA by SM Barns (1996)
  31. Hershberger, K. L., Barns, S. M., Reysenbach, A. L., Dawson, S. C. & Pace, N. R. Wide diversity of Crenarchaeota. Nature 384, 420 (1996). (10.1038/384420a0) / Nature by KL Hershberger (1996)
  32. Lopez-Garcia, P., Brochier, C., Moreira, D. & Rodriguez-Valera, F. Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers. Environ. Microbiol. 6, 19–34 (2004). (10.1046/j.1462-2920.2003.00533.x) / Environ. Microbiol. by P Lopez-Garcia (2004)
  33. Robertson, C. E., Harris, J. K., Spear, J. R. & Pace, N. R. Phylogenetic diversity and ecology of environmental Archaea. Curr. Opin. Microbiol. 8, 638–642 (2005). A recent, exhaustive archaeal phylogeny that was based on an analysis of SSU rRNA sequences. Despite the use of a large number of sequences, this marker was unable to resolve the deepest nodes of the archaeal phylogeny. (10.1016/j.mib.2005.10.003) / Curr. Opin. Microbiol. by CE Robertson (2005)
  34. Cubonova, L., Sandman, K., Hallam, S. J., Delong, E. F. & Reeve, J. N. Histones in Crenarchaea. J. Bacteriol. 187, 5482–5485 (2005). (10.1128/JB.187.15.5482-5485.2005) / J. Bacteriol. by L Cubonova (2005)
  35. Ochsenreiter, T., Selezi, D., Quaiser, A., Bonch-Osmolovskaya, L. & Schleper, C. Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR. Environ. Microbiol. 5, 787–797 (2003). (10.1046/j.1462-2920.2003.00476.x) / Environ. Microbiol. by T Ochsenreiter (2003)
  36. Wuchter, C. et al. Archaeal nitrification in the ocean. Proc. Natl Acad. Sci. USA 103, 12317–12322 (2006). (10.1073/pnas.0600756103) / Proc. Natl Acad. Sci. USA by C Wuchter (2006)
  37. Leininger, S. et al. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442, 806–809 (2006). (10.1038/nature04983) / Nature by S Leininger (2006)
  38. Konneke, M. et al. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437, 543–546 (2005). The first report of the isolation of a member of the Thaumarchaeota, and the first demonstration of the ability of an isolated archaeon to oxidize ammonium. (10.1038/nature03911) / Nature by M Konneke (2005)
  39. Nunoura, T. et al. Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragments. Environ. Microbiol. 7, 1967–1984 (2005). (10.1111/j.1462-2920.2005.00881.x) / Environ. Microbiol. by T Nunoura (2005)
  40. Woese, C. R., Achenbach, L., Rouviere, P. & Mandelco, L. Archaeal phylogeny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts. Syst. Appl. Microbiol. 14, 364–371 (1991). (10.1016/S0723-2020(11)80311-5) / Syst. Appl. Microbiol. by CR Woese (1991)
  41. Boussau, B. & Gouy, M. Efficient likelihood computations with nonreversible models of evolution. Syst. Biol. 55, 756–768 (2006). (10.1080/10635150600975218) / Syst. Biol. by B Boussau (2006)
  42. Hallam, S. J. et al. Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc. Natl Acad. Sci. USA 103, 18296–18301 (2006). (10.1073/pnas.0608549103) / Proc. Natl Acad. Sci. USA by SJ Hallam (2006)
  43. Matte-Tailliez, O., Brochier, C., Forterre, P. & Philippe, H. Archaeal phylogeny based on ribosomal proteins. Mol. Biol. Evol. 19, 631–639 (2002). (10.1093/oxfordjournals.molbev.a004122) / Mol. Biol. Evol. by O Matte-Tailliez (2002)
  44. Waters, E. et al. The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc. Natl Acad. Sci. USA 100, 12984–12988 (2003). (10.1073/pnas.1735403100) / Proc. Natl Acad. Sci. USA by E Waters (2003)
  45. Slesarev, A. I. et al. The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc. Natl Acad. Sci. USA 99, 4644–4649 (2002). (10.1073/pnas.032671499) / Proc. Natl Acad. Sci. USA by AI Slesarev (2002)
  46. Gribaldo, S. & Philippe, H. Ancient phylogenetic relationships. Theor. Popul. Biol. 61, 391–408 (2002). (10.1006/tpbi.2002.1593) / Theor. Popul. Biol. by S Gribaldo (2002)
  47. Huber, H. et al. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417, 63–67 (2002). (10.1038/417063a) / Nature by H Huber (2002)
  48. Brochier, C., Gribaldo, S., Zivanovic, Y., Confalonieri, F. & Forterre, P. Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? Genome Biol. 6, R42 (2005). (10.1186/gb-2005-6-5-r42) / Genome Biol. by C Brochier (2005)
  49. Burggraf, S., Stetter, K. O., Rouviere, P. & Woese, C. R. Methanopyrus kandleri: an archaeal methanogen unrelated to all other known methanogens. Syst. Appl. Microbiol. 14, 346–351 (1991). (10.1016/S0723-2020(11)80308-5) / Syst. Appl. Microbiol. by S Burggraf (1991)
  50. Brochier, C., Forterre, P. & Gribaldo, S. Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox. Genome Biol. 5, R17 (2004). (10.1186/gb-2004-5-3-r17) / Genome Biol. by C Brochier (2004)
  51. Bapteste, E., Brochier, C. & Boucher, Y. Higher-level classification of the Archaea: evolution of methanogenesis and methanogens. Archaea 1, 353–363 (2005). (10.1155/2005/859728) / Archaea by E Bapteste (2005)
  52. Felsenstein, J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27, 401–410 (1978). (10.2307/2412923) / Syst. Zool. by J Felsenstein (1978)
  53. Tatusov, R. L. et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29, 22–28 (2001). (10.1093/nar/29.1.22) / Nucleic Acids Res. by RL Tatusov (2001)
  54. Forterre, P., Gribaldo, S., Gadelle, D. & Serre, M. C. Origin and evolution of DNA topoisomerases. Biochimie 89, 427–446 (2007). (10.1016/j.biochi.2006.12.009) / Biochimie by P Forterre (2007)
  55. Makarova, K. S., Wolf, Y. I., Sorokin, A. V. & Koonin, E. V. Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. Biol. Direct 2, 33 (2007). A dedicated COG database for Archaea that highlights the important differences between Thaumarchaeota and hyperthermophilic crenarchaeota. (10.1186/1745-6150-2-33) / Biol. Direct by KS Makarova (2007)
  56. Nicol, G. W. & Schleper, C. Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle? Trends Microbiol. 14, 207–212 (2006). Together with reference 37, this review revealed the unsuspected role of archaea in the global nitrogen cycle, which was previously assumed to be carried out by bacteria. (10.1016/j.tim.2006.03.004) / Trends Microbiol. by GW Nicol (2006)
  57. Forterre, P., Brochier, C. & Philippe, H. Evolution of the Archaea. Theor. Popul. Biol. 6, 409–422 (2002). (10.1006/tpbi.2002.1592) / Theor. Popul. Biol. by P Forterre (2002)
  58. Edgar, R. C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 113 (2004). (10.1186/1471-2105-5-113) / BMC Bioinformatics by RC Edgar (2004)
  59. Philippe, H. MUST, a computer package of Management Utilities for Sequences and Trees. Nucleic Acids Res. 21, 5264–5272 (1993). (10.1093/nar/21.22.5264) / Nucleic Acids Res. by H Philippe (1993)
  60. Altschul, S. F. & Koonin, E. V. Iterated profile searches with PSI-BLAST — a tool for discovery in protein databases. Trends Biochem. Sci. 23, 444–447 (1998). (10.1016/S0968-0004(98)01298-5) / Trends Biochem. Sci. by SF Altschul (1998)
  61. Guindon, S. & Gascuel, O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696–704 (2003). (10.1080/10635150390235520) / Syst. Biol. by S Guindon (2003)
Dates
Type When
Created 17 years, 6 months ago (Feb. 15, 2008, 12:25 a.m.)
Deposited 2 years, 3 months ago (May 19, 2023, 12:24 a.m.)
Indexed 36 minutes ago (Sept. 3, 2025, 6:25 a.m.)
Issued 17 years, 6 months ago (March 1, 2008)
Published 17 years, 6 months ago (March 1, 2008)
Published Print 17 years, 6 months ago (March 1, 2008)
Funders 0

None

@article{Brochier_Armanet_2008, title={Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota}, volume={6}, ISSN={1740-1534}, url={http://dx.doi.org/10.1038/nrmicro1852}, DOI={10.1038/nrmicro1852}, number={3}, journal={Nature Reviews Microbiology}, publisher={Springer Science and Business Media LLC}, author={Brochier-Armanet, Céline and Boussau, Bastien and Gribaldo, Simonetta and Forterre, Patrick}, year={2008}, month=mar, pages={245–252} }