Branching order of bacterial phyla (Woese, 1987)

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

	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

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, listed below.^[1]^[6] Many new phyla have been proposed since then.

Purple Bacteria and their relatives (later renamed Proteobacteria^[7])
- alpha subdivision (purple non-sulfur bacteria, rhizobacteria, Agrobacterium, Rickettsiae, Nitrobacter)
- beta subdivision (Rhodocyclus, (some) Thiobacillus, Alcaligenes, Spirillum, Nitrosovibrio)
- gamma subdivision (enterics, fluorescent pseudomonads, purple sulfur bacteria, Legionella, (some) Beggiatoa)
- delta subdivision (Sulfur and sulfate reducers (Desulfovibrio), Myxobacteria, Bdellovibrio)
Gram-positive Eubacteria^{[Note 1]}
- High-G+C species (later renamed Actinobacteria^[11]) (Actinomyces, Streptomyces, Arthrobacter, Micrococcus, Bifidobacterium)
- Low-G+C species (later renamed Firmicutes^[11]) (Clostridium, Peptococcus, Bacillus, Mycoplasma)
- Photosynthetic species (Heliobacteria)
- Species with Gram-negative walls (Megasphaera, Sporomusa)
Cyanobacteria and chloroplasts (Aphanocapsa, Oscillatoria, Nostoc, Synechococcus, Gloeobacter, Prochloron)
Spirochetes and relatives
- Spirochetes (Spirochaeta, Treponema, Borrelia)
- Leptospiras (Leptospira, Leptonema)
Green sulfur bacteria (Chlorobium, Chloroherpeton)
Bacteroides, Flavobacteria and relatives (later renamed Bacteroidetes
- Bacteroides (Bacteroides, Fusobacterium)
- Flavobacterium group (Flavobacterium, Cytophaga, Saprospira, Flexibacter)
Planctomyces and relatives (later renamed Planctomycetes)
- Planctomyces group (Planctomyces, Pasteuria [sic]^{[Note 2]})
- Thermophiles (Isocystis pallida)
Chlamydiae (Chlamydia psittaci, Chlamydia trachomatis)
Radioresistant micrococci and relatives (now commonly referred to as Deinococcus–Thermus^[12] or Thermi)^{[Note 3]}
- Deinococcus group (Deinococcus radiodurans)
- Thermophiles (Thermus aquaticus)
Green non-sulfur bacteria and relatives (later renamed Chloroflexi^[16])
- Chloroflexus group (Chloroflexus, Herpetosiphon)
- Thermomicrobium group (Thermomicrobium roseum)
Thermotogae (Thermotoga maritima)

Last universal common ancestor

The root of the tree, i.e. the node of the last universal common 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.^[17]

Eukaryotes are a mosaic of different lineages:

The genome in the nucleus descends from the first organelle-less eukaryote, the "urkaryote" a sister species to the ancestral archeon
The mitochondria are organelles that descended from the proto-mitochondrion, a species of Rickettsiales (Alphaproteobacteria) (v. Reclinomonas and retortamonads).
The chloroplasts are organelles of cyanobacterial origin.

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^[17]

Footnotes

^ Until recently, it was believed than only Firmicutes and Actinobacteria were Gram-positive. However, the candidate phylum TM7 may also be Gram positive.^[8] Chloroflexi however possess a single bilayer, but stain negative (with some exceptions^[9]).^[10]
^ Pasteuria is now assigned to phylum Bacilli, not to phylum Planctomycetes.
^ It has been proposed to call the clade Xenobacteria^[13] or Hadobacteria^[14] (the latter is considered an illegitimate name^[15]).

References

^ ^a ^b Woese, CR (1987). "Bacterial evolution". Microbiological Reviews. 51 (2): 221–71. doi:10.1128/MMBR.51.2.221-271.1987. PMC 373105. PMID 2439888.
^ 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.
^ 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.
^ 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 (3): 321–325. doi:10.1099/00207713-38-3-321.
^ Schluenzen F; et al. (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.
^ Holland L (22 May 1990). "Carl Woese in forefront of bacterial evolution revolution". The Scientist. 3 (10).
^ 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 (3): 321–325. doi:10.1099/00207713-38-3-321.
^ 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.
^ 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.
^ 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.
^ ^a ^b 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 (2): 479–491. doi:10.1099/00207713-47-2-479.
^ J.P. Euzéby. "List of Prokaryotic names with Standing in Nomenclature: classification of Deinococcus–Thermus". Archived from the original on 27 January 2013. Retrieved 30 December 2010.
^ Bergey's Manual of Systematic Bacteriology 1st Ed.
^ 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.
^ "List of Prokaryotic names with Standing in Nomenclature—Class Hadobacteria". LPSN. Archived from the original on 19 April 2012. Retrieved 30 December 2010. 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.
^ Boone DR; Castenholz RW (18 May 2001) [1984 (Williams & Wilkins)]. Garrity GM (ed.). The Archaea and the Deeply Branching and Phototrophic Bacteria. Bergey's Manual of Systematic Bacteriology. Vol. 1 (2nd ed.). New York: Springer. pp. 721. ISBN 978-0-387-98771-2. British Library no. GBA561951.
^ ^a ^b 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.

[GramPos-11] Until recently, it was believed than only Firmicutes and Actinobacteria were Gram-positive. However, the candidate phylum TM7 may also be Gram positive.^[8] Chloroflexi however possess a single bilayer, but stain negative (with some exceptions^[9]).^[10]

[Pasteuria-13] Pasteuria is now assigned to phylum Bacilli, not to phylum Planctomycetes.

[Thermi-18] It has been proposed to call the clade Xenobacteria^[13] or Hadobacteria^[14] (the latter is considered an illegitimate name^[15]).

[woese87-1] Woese, CR (1987). "Bacterial evolution". Microbiological Reviews. 51 (2): 221–71. doi:10.1128/MMBR.51.2.221-271.1987. 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.

[pace09-3] 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.

[Stackebrandt_et_al._1988_321–325-4] 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 (3): 321–325. doi:10.1099/00207713-38-3-321.

[Schluenzen-5] Schluenzen F; et al. (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). "Carl Woese in forefront of bacterial evolution revolution". The Scientist. 3 (10).

[7] 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 (3): 321–325. doi:10.1099/00207713-38-3-321.

[fish-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.

[Stackebrandt-12] 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 (2): 479–491. doi:10.1099/00207713-47-2-479.

[14] J.P. Euzéby. "List of Prokaryotic names with Standing in Nomenclature: classification of Deinococcus–Thermus". Archived from the original on 27 January 2013. Retrieved 30 December 2010.

[15] Bergey's Manual of Systematic Bacteriology 1st Ed.

[Neomura-16] 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.

[17] "List of Prokaryotic names with Standing in Nomenclature—Class Hadobacteria". LPSN. Archived from the original on 19 April 2012. Retrieved 30 December 2010. 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.

[I-19] Boone DR; Castenholz RW (18 May 2001) [1984 (Williams & Wilkins)]. Garrity GM (ed.). The Archaea and the Deeply Branching and Phototrophic Bacteria. Bergey's Manual of Systematic Bacteriology. Vol. 1 (2nd ed.). New York: Springer. pp. 721. ISBN 978-0-387-98771-2. British Library no. GBA561951.

[CS02-20] 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.

[1]

[2]

[3]

[4]

[5]

[6]

[7]

[Note 1]

[11]

[Note 2]

[12]

[Note 3]

[16]

[17]

[8]

[9]

[10]

[13]

[14]

[15]