Branching order of bacterial phyla (Woese, 1987)

For the same tree with newly discovered phyla, see Branching order of bacterial phyla (Rappe and Giovanoni, 2003).
Main article: Bacterial phyla

There are several models of the Branching order of bacterial phyla, one of these was proposed in 1987 paper by Carl Woese.[1]

The branching order proposed by Carl Woese was based on molecular phylogeny, which was considered revolutionary as all preceding models were based on discussions of morphology. (v. Monera).[2] Several models have been proposed since and no consensus is reached at present as to the branching order of the major bacterial lineages.[3]

The gene used was the 16S ribosomal DNA.

Tree

The names have been changed to reflect more current nomenclature used by molecular phylogenists.

Archaea + eukaryote


Bacteria

Thermotogae

Chloroflexi

Deinococcus-Thermus


Proteobacteria

Cyanobacteria

Firmicutes

Actinobacteria


Planctomycetes

Chlamydiae

Spirochaetes

Bacteroidetes

Chlorobi









Note on names

Despite the impact of the paper on bacterial classification, it was not a proposal for change of taxonomy. Consequently many clades were given official names. Only subsequently, this occurred: for example, the "purple bacteria and relatives" were renamed Proteobacteria.[4]

Discussion

Atomic structure of the 30S ribosomal Subunit from Thermus thermophilus of which 16S makes up part of. Proteins are shown in blue and the single RNA strand in orange.[5]

In 1987, Carl Woese, regarded as the forerunner of the molecular phylogeny revolution, divided Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences:[1][6]

The "purple bacteria and relatives" were renamed Proteobacteria.[4]

The low and high CG content gram positive subdivisions were renamed Actinobacteria and Firmicutes divisions, making the number of phyla 12.[7] Until recently, it was believed than only Firmicutes and Actinobacteria were Gram-positive. The candidate phylum TM7 may be Gram positive.[8] Chloroflexi however possess a single bilayer, but stain negative (with some exceptions[9]).[10]

"Green non-sulfur bacteria and relatives" was renamed Chloroflexi.[11]

"Radioresistant micrococci and relatives" are commonly referred to as Deinococcus-Thermus clade,[12] although it has been proposed to call the clade Xenobacteria[13] or Hadobacteria[14] (latter is illegitimate).[15]

Last universal ancestor

The root of the tree, i.e. the node of the last universal ancestor, is placed between the domain Bacteria (or kingdom Eubacteria as it was then known) and the clade formed by the domains Archaea (formerly kingdom Archaebacteria) and Eukaryotes. This is consistent with all subsequent studies, bar the study by Thomas Cavalier-Smith in 2002 and 2004, which was not based on molecular phylogeny.[14]

Eukaryotes are a mosaic of different lineages:

Consequently, in Woese (1987) the group is referred to as urkaryote.

The clade composed of Archaea and the nuclear genome of eukaryotes is called Neomura by T. Cavalier-Smith[14]

See also

References

  1. 1 2 Woese, CR (1987). "Bacterial evolution". Microbiological reviews 51 (2): 221–71. PMC 373105. PMID 2439888.
  2. ↑ Olsen GJ, Woese CR, Overbeek R (1994). "The winds of (evolutionary) change: breathing new life into microbiology". Journal of Bacteriology 176 (1): 1–6. doi:10.2172/205047. PMC 205007. PMID 8282683.
  3. ↑ Pace, N. R. (2009). "Mapping the Tree of Life: Progress and Prospects". Microbiology and Molecular Biology Reviews 73 (4): 565–576. doi:10.1128/MMBR.00033-09. PMC 2786576. PMID 19946133.
  4. 1 2 Stackebrandt; et al. (1988). "Proteobacteria classis nov., a name for the phylogenetic taxon that includes the "purple bacteria and their relatives"". Int. J. Syst. Bacteriol. 38: 321–325. doi:10.1099/00207713-38-3-321.
  5. ↑ Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution (2000). "Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution". Cell 102 (5): 615–23. doi:10.1016/S0092-8674(00)00084-2. PMID 11007480.
  6. ↑ Holland L. (22 May 1990). "Woese,Carl in the forefront of bacterial evolution revolution". scientist 4 (10).
  7. ↑ Stackebrandt, E.; Rainey, F. A.; Ward-Rainey, N. L. (1997). "Proposal for a New Hierarchic Classification System, Actinobacteria classis nov.". International Journal of Systematic Bacteriology 47: 479–491. doi:10.1099/00207713-47-2-479.
  8. ↑ Hugenholtz, P.; Tyson, G. W.; Webb, R. I.; Wagner, A. M.; Blackall, L. L. (2001). "Investigation of Candidate Division TM7, a Recently Recognized Major Lineage of the Domain Bacteria with No Known Pure-Culture Representatives". Applied and Environmental Microbiology 67 (1): 411–9. doi:10.1128/AEM.67.1.411-419.2001. PMC 92593. PMID 11133473.
  9. ↑ Yabe, S.; Aiba, Y.; Sakai, Y.; Hazaka, M.; Yokota, A. (2010). "Thermogemmatispora onikobensis gen. nov., sp. nov. And Thermogemmatispora foliorum sp. nov., isolated from fallen leaves on geothermal soils, and description of Thermogemmatisporaceae fam. Nov. And Thermogemmatisporales ord. Nov. Within the class Ktedonobacteria". International Journal of Systematic and Evolutionary Microbiology 61 (4): 903–910. doi:10.1099/ijs.0.024877-0. PMID 20495028.
  10. ↑ Sutcliffe, I. C. (2011). "Cell envelope architecture in the Chloroflexi: A shifting frontline in a phylogenetic turf war". Environmental Microbiology 13 (2): 279–282. doi:10.1111/j.1462-2920.2010.02339.x. PMID 20860732.
  11. ↑ Boone, David R.; Castenholz, Richard W. (May 18, 2001) [1984(Williams & Wilkins)]. George M. Garrity, ed. The Archaea and the Deeply Branching and Phototrophic Bacteria. Bergey's Manual of Systematic Bacteriology 1 (2nd ed.). New York: Springer. p. 721. ISBN 978-0-387-98771-2. British Library no. GBA561951.
  12. ↑ Euzéby, J. P. (December 8, 2011). "List of Prokaryotic names with Standing in Nomenclature (LPSN)". Bacterio.CICT.fr. Toulouse, France: Centre Interuniversitaire de Calcul de Toulouse, Université Toulouse III - Paul Sabatier. Section: "Classification of Deinococcus-Thermus". Retrieved 2011-12-14.
    First published as: Euzéby, J. P. (1997). "List of Bacterial Names with Standing in Nomenclature: A Folder Available on the Internet". Int J Syst Bacteriol 47 (2): 590–2. doi:10.1099/00207713-47-2-590. ISSN 0020-7713. PMID 9103655.
  13. ↑ Bergey's Manual of Systematic Bacteriology 1st Ed.
  14. 1 2 3 Cavalier-Smith, T (2002). "The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification". International Journal of Systematic and Evolutionary Microbiology 52 (Pt 1): 7–76. doi:10.1099/00207713-52-1-7. PMID 11837318.
  15. ↑ Euzéby. "LPSN". op. cit. Section: "Class Hadobacteria".
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