Branching order of bacterial phyla (Cavalier-Smith, 2002)

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There are several models of the Branching order of bacterial phyla, one of these was proposed in 2002 and 2004 by Thomas Cavalier-Smith. [1] [2] In this frame of work, the branching order of the major lineage of bacteria are determined based on some morphological characters, such as cell wall structure, and not based on the molecular evidence (molecular phylogeny).

Whereas modern molecular studies point towards the root of the tree of life being between a monophyletic Bacteria and Archaea+Eukarya (Neomura), in the Cavalier-Smith theory, the last common ancestor (cenansestor) was a Gram-negative diderm bacterium with peptidoglycan, while Archaea and Eukaryotes stem from Actinobacteria. [1] [2]

LUA

Chlorobacteria (accepted name = Chloroflexi)

Hadobacteria (= Deinococcus-Thermus group)

Glycobacteria

Cyanobacteria

Gracilicutes

Spirochaetae

Sphingobacteria

Fibrobacteres

Chlorobi

Bacteroidetes

Planctobacteria

Planctomycetes

Chlamydiae

Lentisphaerae

Verrucomicrobia

Proteobacteria
Geobacteria

Deferribacteres

Acidobacteria

Thiobacteria

Deltaproteobacteria

Epsilonproteobacteria

Rhodobacteria

Alphaproteobacteria

Chromatibacteria

Betaproteobacteria

Gammaproteobacteria

Unibacteria
Eurybacteria

Thermotogae

Fusobacteria

Negativicutes

Endobacteria (=Firmicutes, Mollicutes)

Actinobacteria

Neomura

Archaea

Eukarya

See also

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In biology, kingdom is the second highest taxonomic rank, just below domain. Kingdoms are divided into smaller groups called phyla. Traditionally, some textbooks from the United States and Canada used a system of six kingdoms while textbooks in Great Britain, India, Greece, Brazil and other countries use five kingdoms only. Some recent classifications based on modern cladistics have explicitly abandoned the term kingdom, noting that the traditional kingdoms are not monophyletic, meaning that they do not consist of all the descendants of a common ancestor.

Euryarchaeota Phylum of archaea

Euryarchaeota is a phylum of archaea. It is one of two phyla of archaea, the other being crenarchaeota. Euryarchaeota are highly diverse and include methanogens, which produce methane and are often found in intestines, halobacteria, which survive extreme concentrations of salt, and some extremely thermophilic aerobes and anaerobes, which generally live at temperatures between 41 and 122 °C. They are separated from the other archaeans based mainly on rRNA sequences and their unique DNA polymerase.

The Aquificae phylum is a diverse collection of bacteria that live in harsh environmental settings. The name 'Aquificae' was given to this phylum based on an early genus identified within this group, Aquifex, which is able to produce water by oxidizing hydrogen. They have been found in springs, pools, and oceans. They are autotrophs, and are the primary carbon fixers in their environments. These bacteria are Gram-negative, non-spore-forming rods. They are true bacteria as opposed to the other inhabitants of extreme environments, the Archaea.

<i>Deinococcus</i>–<i>Thermus</i> Phylum of Gram-negative bacteria

Deinococcus–Thermus is a phylum of bacteria that are highly resistant to environmental hazards, also known as extremophiles. 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.

Two-empire system

The two-empire system was the top-level biological classification system in general use before the establishment of the three-domain system. It classified cellular life into Prokaryota and Eukaryota as either "empires" or "superkingdoms". When the three-domain system was introduced, some biologists preferred the two-superkingdom system, claiming that the three-domain system overemphasized the division between Archaea and Bacteria. However, given the current state of knowledge and the rapid progress in biological scientific advancement, especially due to genetic analyses, that view has all but vanished.

Neomura

Neomura is a possible clade composed of the two domains of life of Archaea and Eukaryota. The group was named by Thomas Cavalier-Smith in 2002. Its name means "new walls", reflecting his hypothesis that it evolved from Bacteria, and one of the major changes was the replacement of peptidoglycan cell walls with other glycoproteins. As of August 2017, the neomuran hypothesis is not accepted by most workers; molecular phylogenies suggest that eukaryotes are most closely related to one group of archaeans and evolved from them, rather than forming a clade with all archaeans.

Gracilicutes

Gracilicutes is a clade in bacterial phylogeny.

Planctobacteria Superphylum of bacteria

The PVC group is a superphylum of bacteria named after its three important members, Planctomycetes, Verrucomicrobia, and Chlamydiae. Cavalier-Smith postulated that the PVC bacteria probably lost or reduced their peptidoglycan cell wall twice. It has been hypothesised that a member of the PVC clade might have been the host cell in the endosymbiotic event that gave rise to the first proto-eukaryotic cell.

Methanomicrobia Class of archaea

In the taxonomy of microorganisms, the Methanomicrobia are a class of the Euryarchaeota.

Archaea Domain of single-celled organisms

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

There are several models of the Branching order of bacterial phyla, one of these was proposed in 2006 by Ciccarelli et al. for their iTOL project.

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There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved indels, however, they are in agreement with several groupings of classes and phyla. One feature of the cladogram obtained with this method is the clustering of cell wall morphology from monoderms to transitional diderms to traditional diderms.

Conserved signature inserts and deletions (CSIs) in protein sequences provide an important category of molecular markers for understanding phylogenetic relationships. CSIs, brought about by rare genetic changes, provide useful phylogenetic markers that are generally of defined size and they are flanked on both sides by conserved regions to ensure their reliability. While indels can be arbitrary inserts or deletions, CSIs are defined as only those protein indels that are present within conserved regions of the protein.

The Scotokaryotes (Cavalier-Smith) is a proposed basal Neokaryote clade as sister of the Diaphoretickes. Basal Scotokaryote groupings are the Metamonads, the Malawimonas and the Podiata. In this phylogeny the Discoba are sometimes seen as paraphyletic and basal Eukaryotes.

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References

  1. 1 2 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.
  2. 1 2 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. Archived from the original on 18 December 2019. Retrieved 21 November 2011.