Gracilicutes

Gracilicutes
Escherichia coli cells magnified 25,000 times
Scientific classification
Domain:	Bacteria
(unranked):	Gracilicutes Gibbons and Murray 1978 [1]
Superphyla/Phyla
Various definitions, see text

Gracilicutes (Latin: gracilis, slender, and cutis, skin, referring to the cell wall) is a clade in bacterial phylogeny. ^[2]

Traditionally gram staining results were most commonly used as a classification tool, consequently until the advent of molecular phylogeny, the Kingdom Monera (as the domains Bacteria and Archaea were known then) was divided into four phyla, ^{[1] [3]}

• Gracilicutes (gram-negative, it is split in many groups, but some authors still use it in a narrower sense)
• Firmacutes [sic] (gram-positive, subsequently corrected to Firmicutes, ^[4] today it excludes the Actinomycetota)
• Mollicutes (gram variable, later renamed Tenericutes and now Mycoplasmatota, e.g. Mycoplasma )
• Mendosicutes (uneven gram stain, "methanogenic bacteria" now known as methanogens and classed as Archaea)

This classification system was abandoned in favour of the three-domain system based on molecular phylogeny started by C. Woese. ^{[5] [6]}

Using hand-drawn schematics rather than standard molecular phylogenetic analysis, Gracilicutes was revived in 2006 by Cavalier-Smith as an infrakindgom containing the phyla Spirochaetota, Sphingobacteria (FCB), Planctobacteria (PVC), and Proteobacteria. ^[7] It is a gram-negative clade that branched off from other bacteria just before the evolutionary loss of the outer membrane or capsule, and just after the evolution of flagella. ^[7] Most notably, this author assumed an unconventional tree of life placing Chloroflexota near the origin of life and Archaea as a close relative of Actinomycetota. This taxon is not generally accepted and the three-domain system is followed. ^[8]

A taxon called Hydrobacteria was defined in 2009 from a molecular phylogenetic analysis of core genes. It is in contrast to the other major group of eubacteria called Terrabacteria . ^[9] Some researchers have used the name Gracilicutes in place of Hydrobacteria , but this does not agree with the original description of Gracilicutes by Gibbons and Murray, noted above, which included cyanobacteria and did not follow the three-domain system. Also as noted above, the use of Gracilicutes by Cavalier-Smith can be rejected because it was a major alteration of an earlier taxonomic name, was not based on a statistical analysis, and did not follow the three-domain system. The most recent genomic analyses have supported the division of Bacteria into two major superphyla, corresponding to Terrabacteria and Hydrobacteria . ^{[10] [11]}

Relationships

The phylogenetic tree according to the phylogenetic analyzes of Battistuzzi and Hedges (2009) is the following and with a molecular clock calibration. ^[9]

Recent phylogenetic analyzes have found that proteobacteria are a paraphyletic phylum that could encompass several recently discovered candidate phyla and other phyla such as Acidobacteriota, Chrysiogenota, Deferribacterota, and possibly Aquificota. This suggests that Gracilicutes or Hydrobacteria as a clade may comprise several candidates more closely related to Proteobacteria, Spirochaetes, PVC group, and FCB group than to bacteria from the clade Terrabacteria . Some of these phyla were classified as part of the proteobacteria. For example, Cavalier-Smith in his proposal of the 6 kingdoms included Acidobacteriota, Aquificota, Chrysiogenota, and Deferribacterota as part of the proteobacteria. ^[7]

Phylogenetic analyzes have found roughly the following phylogeny between the major and some more closely related phyla. ^{[12] [13] [14] [15]}

Hydrobacteria

Fusobacteriota (sometimes included in Terrabacteria.) Spirochaetota Poribacteria FCB/"Sphingobacteria" PVC/"Planctobacteria" Elusimicrobiota Aerophobetes "Proteobacteria" sensu lato Rokubacteria Acidobacteriota Aminicenantes Dadabacteria Thermodesulfobacteriota Myxococcota Modulibacteria Tectomicrobia Nitrospinota Nitrospirota Chrysiogenota Deferribacterota Dependentiae Campylobacterota Aquificota (sometimes included in Terrabacteria.) Pseudomonadota Alphaproteobacteria Zetaproteobacteria Acidithiobacillia Betaproteobacteria Gammaproteobacteria

According to the phylogenetic analysis of Hug (2016), the relationships could be the following. ^[16]

The following graph shows Cavalier-Smith's version of the tree of life, indicating the status of Gracilicutes. However, this tree is not supported by any molecular analysis so it should not be considered phylogenetic.

Cavalier-Smith's Tree of Life, 2006 ^{[cstol 1]}

[A]	Chlorobacteria  [B]  Hadobacteria  [C]   [D]  Cyanobacteria  [E]   [F] Gracilicutes Spirochaetae Sphingobacteria (FCB) Planctobacteria (PVC) Proteobacteria s.l.  [G]  Eurybacteria  [H] [I]  Endobacteria (Bacillota)  [J]  Actinobacteria  [K]  Neomura     [L]  Archaea  [M]  Eukarya

Legend:
[A] Gram-negative with a peptidoglycan cell wall like Chlorosome.
[B] Oxygenic Photosynthesis, Omp85 and four new catalases.
[C] Glycobacterial revolution: outer membrane with insertion of lipopolysaccharides, hopanoids, diaminopimelic acid, ToIC and TonB.
[D] Phycobilin chromophores.
[E] Flagella.
[F] Four sections: an amino acid in HSP60 and FtsZ and a domain in RNA polymerases β and σ.
[G] Endospores.
[H] Gram-positive Bacteria: hypertrophy of the wall peptidoglycan, sortase enzyme and a loss of the outer membrane.
[I] Glycerol 1-P dehydrogenase.
[J] Proteasome and phosphatidylinositol.
[K] Neomura revolution: Replacement of peptidoglycan by glycoproteins and lipoproteins.
[L] Reverse DNA gyrase and ether lipid isoprenoids.
[M] Phagocytosis.

1. Cavalier-Smith T (2006). "Cell evolution and Earth history: stasis and revolution". Philos Trans R Soc Lond B Biol Sci. 361 (1470): 969–1006. doi:10.1098/rstb.2006.1842. PMC   1578732 . PMID   16754610.

References

1. Gibbons NE, Murray RG (January 1978). "Proposals concerning the higher taxa of bacteria". International Journal of Systematic and Evolutionary Microbiology. 28 (1): 1–6. doi: 10.1099/00207713-28-1-1 .
2. Boussau B, Guéguen L, Gouy M (October 2008). "Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria". BMC Evolutionary Biology. 8: 272. doi: 10.1186/1471-2148-8-272 . PMC   2584045 . PMID   18834516. Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of Aquificales in the phylogeny of Bacteria
3. Krieg NR, Holt JC, eds. (1984). Bergey's Manual of Systematic Bacteriology. Vol. 1 (1st ed.). Baltimore: Williams and Wilkins.
4. Murray RG (1984). "The higher taxa, or, a place for everything...?". In Krieg NR, Holt JC (eds.). Bergey's Manual of Systematic Bacteriology. Vol. 1 (1st ed.). Baltimore: Williams and Wilkins. pp. 31–34.
5. Woese CR (June 1987). "Bacterial evolution". Microbiological Reviews. 51 (2): 221–271. doi:10.1128/MMBR.51.2.221-271.1987. PMC   373105 . PMID   2439888.
6. Brenner DJ, Krieg NA, Staley JT (July 26, 2005) [1984(Williams & Wilkins)]. "Introductory Essays". In Garrity GM (ed.). Bergey's Manual of Systematic Bacteriology. Vol. 2A (2nd ed.). New York: Springer. p. 304. ISBN   978-0-387-24143-2. British Library no. GBA561951.
7. Cavalier-Smith T (July 2006). "Rooting the tree of life by transition analyses". Biology Direct. 1: 19. doi: 10.1186/1745-6150-1-19 . PMC   1586193 . PMID   16834776.
8. Krieg NR, Ludwig W, Whitman WB, Hedlund BP, Paster BJ, Staley JT, et al. (November 24, 2010) [1984(Williams & Wilkins)]. "The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes". In Garrity GM (ed.). Bergey's Manual of Systematic Bacteriology. Vol. 4 (2nd ed.). New York: Springer. p. 908. ISBN   978-0-387-95042-6. British Library no. GBA561951.
9. Battistuzzi FU, Hedges SB (February 2009). "A major clade of prokaryotes with ancient adaptations to life on land". Molecular Biology and Evolution. 26 (2): 335–343. doi: 10.1093/molbev/msn247 . PMID   18988685.
10. Coleman GA, Davín AA, Mahendrarajah TA, Szánthó LL, Spang A, Hugenholtz P, et al. (May 2021). "A rooted phylogeny resolves early bacterial evolution". Science. 372 (6542): eabe0511. doi:10.1126/science.abe0511. hdl: 1983/51e9e402-36b7-47a6-91de-32b8cf7320d2 . PMID   33958449. S2CID   233872903.
11. Léonard RR, Sauvage E, Lupo V, Perrin A, Sirjacobs D, Charlier P, et al. (February 2022). "Was the Last Bacterial Common Ancestor a Monoderm after All?". Genes. 13 (2): 376. doi: 10.3390/genes13020376 . PMC   8871954 . PMID   35205421.
12. Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, et al. (October 2016). "Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system". Nature Communications. 7: 13219. Bibcode:2016NatCo...713219A. doi:10.1038/ncomms13219. PMC   5079060 . PMID   27774985.
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15. Zhu Q, Mai U, Pfeiffer W, Janssen S, Asnicar F, Sanders JG, et al. (December 2019). "Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea". Nature Communications. 10 (1): 5477. Bibcode:2019NatCo..10.5477Z. doi:10.1038/s41467-019-13443-4. PMC   6889312 . PMID   31792218.
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