Gracilicutes Explained

Gracilicutes (Latin: gracilis, slender, and cutis, skin, referring to the cell wall) is a clade in bacterial phylogeny.[1]

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,[2]

This classification system was abandoned in favour of the three-domain system based on molecular phylogeny started by C. Woese.[4] [5]

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.[6] 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.[6] 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.[7]

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.[8] 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.[9] [10]

Relationships

The phylogenetic tree according to the phylogenetic analyzes of Battistuzzi and Hedges (2009) is the following and with a molecular clock calibration.[8]

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.

Phylogenetic analyzes have found roughly the following phylogeny between the major and some more closely related phyla.[11] [12] [13] [14]

According to the phylogenetic analysis of Hug (2016), the relationships could be the following.[15]

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.

Notes and References

  1. Boussau B, Guéguen L, Gouy M . Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria . BMC Evolutionary Biology . 8 . 272 . October 2008 . 18834516 . 2584045 . 10.1186/1471-2148-8-272 . Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of Aquificales in the phylogeny of Bacteria . free .
  2. Book: Krieg NR, Holt JC . 1984 . Bergey's Manual of Systematic Bacteriology . 1st . 1 . Williams and Wilkins . Baltimore .
  3. Book: Murray RG . The higher taxa, or, a place for everything...? . Krieg NR, Holt JC . 1984 . Bergey's Manual of Systematic Bacteriology . 1st . 1 . Williams and Wilkins . Baltimore . 31–34 .
  4. Woese CR . Bacterial evolution . Microbiological Reviews . 51 . 2 . 221–271 . June 1987 . 2439888 . 373105 . 10.1128/MMBR.51.2.221-271.1987 .
  5. Book: Bergey's Manual of Systematic Bacteriology. 2A. Introductory Essays. Garrity GM . Brenner DJ, Krieg NA, Staley JT . Springer. New York . 2nd. 978-0-387-24143-2 . 304 . July 26, 2005. 1984(Williams & Wilkins). British Library no. GBA561951.
  6. Cavalier-Smith T . Rooting the tree of life by transition analyses . Biology Direct . 1 . 19 . July 2006 . 16834776 . 1586193 . 10.1186/1745-6150-1-19 . free .
  7. Book: Krieg NR, Ludwig W, Whitman WB, Hedlund BP, Paster BJ, Staley JT, Ward N, Brown D, Parte A . 6 . The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes . Bergey's Manual of Systematic Bacteriology. 4. Garrity GM . Springer . New York . 2nd. 978-0-387-95042-6 . 908 . November 24, 2010. 1984(Williams & Wilkins). British Library no. GBA561951.
  8. Battistuzzi FU, Hedges SB . A major clade of prokaryotes with ancient adaptations to life on land . Molecular Biology and Evolution . 26 . 2 . 335–343 . February 2009 . 18988685 . 10.1093/molbev/msn247 . free .
  9. Coleman GA, Davín AA, Mahendrarajah TA, Szánthó LL, Spang A, Hugenholtz P, Szöllősi GJ, Williams TA . 6 . A rooted phylogeny resolves early bacterial evolution . Science . 372 . 6542 . eabe0511 . May 2021 . 33958449 . 10.1126/science.abe0511 . 233872903 . 1983/51e9e402-36b7-47a6-91de-32b8cf7320d2 . free .
  10. Léonard RR, Sauvage E, Lupo V, Perrin A, Sirjacobs D, Charlier P, Kerff F, Baurain D . 6 . Was the Last Bacterial Common Ancestor a Monoderm after All? . Genes . 13 . 2 . 376 . February 2022 . 35205421 . 8871954 . 10.3390/genes13020376 . free .
  11. Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, Thomas BC, Singh A, Wilkins MJ, Karaoz U, Brodie EL, Williams KH, Hubbard SS, Banfield JF . 6 . Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system . Nature Communications . 7 . 13219 . October 2016 . 27774985 . 5079060 . 10.1038/ncomms13219 . 2016NatCo...713219A .
  12. Coleman GA, Davín AA, Mahendrarajah TA, Szánthó LL, Spang A, Hugenholtz P, Szöllősi GJ, Williams TA . A rooted phylogeny resolves early bacterial evolution . Science . New York, N.Y. . 372 . 6542 . May 2021 . 33958449 . 10.1126/science.abe0511 . 233872903 . 1983/51e9e402-36b7-47a6-91de-32b8cf7320d2 . free .
  13. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T . 6 . Insights into the phylogeny and coding potential of microbial dark matter . Nature . 499 . 7459 . 431–437 . July 2013 . 23851394 . 10.1038/nature12352 . 2013Natur.499..431R . 4394530 . free . 10453/27467 . free .
  14. Zhu Q, Mai U, Pfeiffer W, Janssen S, Asnicar F, Sanders JG, Belda-Ferre P, Al-Ghalith GA, Kopylova E, McDonald D, Kosciolek T, Yin JB, Huang S, Salam N, Jiao JY, Wu Z, Xu ZZ, Cantrell K, Yang Y, Sayyari E, Rabiee M, Morton JT, Podell S, Knights D, Li WJ, Huttenhower C, Segata N, Smarr L, Mirarab S, Knight R . 6 . Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea . Nature Communications . 10 . 1 . 5477 . December 2019 . 31792218 . 6889312 . 10.1038/s41467-019-13443-4 . 2019NatCo..10.5477Z .
  15. Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfield CN, Hernsdorf AW, Amano Y, Ise K, Suzuki Y, Dudek N, Relman DA, Finstad KM, Amundson R, Thomas BC, Banfield JF . 6 . A new view of the tree of life . Nature Microbiology . 1 . 5. 16048 . April 2016 . 27572647 . 10.1038/nmicrobiol.2016.48 . 3833474 . free .

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