Pseudomonadati

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Pseudomonadati
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Domain: Bacteria
Kingdom: Pseudomonadati
(Gibbons & Murray 1978) Oren & Göker 2024
Type genus
Pseudomonas
Migula 1894 (Approved Lists 1980) [1]
Phyla [2]
Synonyms

"Hydrobacteria" Battistuzzi & Hedges, 2009 [3]

Pseudomonadati [4] is a kingdom containing approximately one-third of prokaryote species, mostly gram-negative bacteria and their relatives. [3] It is the closest relative of an even larger kingdom of Bacteria, the Bacillati, which are mostly gram-positive bacteria. [5] [3]

Contents

Names

The synonymous name "Hydrobacteria" (hydro = "water") refers to the moist environment inferred for the common ancestor of those species. In contrast, species of Bacillati possess adaptations for life on land. [5] [3] Since 2024, the only validly published name for this group is kingdom Pseudomonadati (there used to be none, because no levels above phylum could exist in earlier versions of the Prokaryotic Code). [6]

"Gracilicutes," which was described in 1978 by Gibbons and Murray, [7] is sometimes used in place of Pseudomonadati. However, "Gracilicutes" included Cyanobacteria (a member of Bacillati) and was not constructed under the now generally accepted three-domain system. [7] More recently, a redefinition of "Gracilicutes" was proposed [8] but it did not include a molecular phylogeny or statistical analyses. Also, it did not follow the three-domain system, claiming instead that the lineage of eukaryotes + Archaea is nested within Bacteria as a close relative of Actinomycetota, a tree not supported in any molecular phylogeny.

Evolution

Pseudomonadati and Bacillati were inferred to have diverged approximately 3 billion years ago, suggesting that land (continents) had been colonized by prokaryotes at that time. [3]

Phylogeny and taxonomy

They include these superphyla and phyla: Acidobacteriota, Aquificota, Bdellovibrionota, Campylobacterota, Deferribacterota, Dependentiae, Desulfobacterota, Desulfuromonadota, Elusimicrobiota, FCB superphylum, Myxococcota, Nitrospirota, Proteobacteria, PVC superphylum, and Spirochaetota. [9] [10]

Some unrooted molecular phylogenetic analyses [11] [12] have not supported this dichotomy of Bacillati and Pseudomonadati, but the most recent genomic analyses, [9] [10] including those that have focused on rooting the tree, [9] have found these two groups to be monophyletic.

Together, Pseudomonadati and Bacillati form a large clade containing 97% of prokaryotes and 99% of all species of Bacteria known by 2009, and placed by Battistuzzi and Hedges in the proposed taxon Selabacteria, in allusion to their phototrophic abilities (Greek σέλας = light). [13] Currently, the bacterial phyla that are outside of Pseudomonadati + Bacillati, and thus justifying the taxon Selabacteria, are debated and may or may not include Fusobacteria. [9] [10]

The definition of two major divisions within the domain Bacteria, Pseudomonadati, and Bacillati, has come largely from rooted phylogenetic analyses of genomes. [5] [3] [9] [10] Unrooted analyses have not fully supported this division, [12] [11] drawing attention to the importance of rooted trees of life.

The two recent analyses of bacterial phylogeny both supported the division of Pseudomonadati and Bacillati. [9] [10] However, they interpreted the evolution of the cell wall differently, with one concluding that the last common ancestor of Bacteria was a monoderm (gram-positive bacteria [9] ) and the other concluding that it was a diderm (gram-negative bacteria [10] ). The following tree is redrawn from one of those two recent studies, [9] showing the phylogeny of bacterial phyla and superphyla, with the position of Fusobacteria being unresolved and DST being the closest relative of Bacillati:

References

  1. ↑ Pseudomonadati in LPSN; Parte, Aidan C.; Sardà Carbasse, Joaquim; Meier-Kolthoff, Jan P.; Reimer, Lorenz C.; Göker, Markus (1 November 2020). "List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ". International Journal of Systematic and Evolutionary Microbiology. 70 (11): 5607–5612. doi: 10.1099/ijsem.0.004332 .
  2. ↑ Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. (2020). List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; DOI: 10.1099/ijsem.0.004332
  3. 1 2 3 4 5 6 7 Battistuzzi, F. U.; Hedges, S. B. (1 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.
  4. ↑ "Kingdom: Pseudomonadati". lpsn.dsmz.de. Retrieved 2025-04-02.
  5. 1 2 3 4 Battistuzzi, Fabia U; Feijao, Andreia; Hedges, S Blair (2004). "A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land". BMC Evolutionary Biology. 4 (1): 44. doi: 10.1186/1471-2148-4-44 . PMC   533871 . PMID   15535883.
  6. ↑ Göker, Markus; Oren, Aharon (22 January 2024). "Valid publication of names of two domains and seven kingdoms of prokaryotes". International Journal of Systematic and Evolutionary Microbiology. 74 (1). doi: 10.1099/ijsem.0.006242 .
  7. 1 2 Gibbons, N. E.; Murray, R. G. E. (1 January 1978). "Proposals Concerning the Higher Taxa of Bacteria". International Journal of Systematic Bacteriology. 28 (1): 1–6. doi: 10.1099/00207713-28-1-1 .
  8. ↑ Cavalier-Smith, Thomas (2006). "Rooting the tree of life by transition analyses". Biology Direct. 1 (1): 19. doi: 10.1186/1745-6150-1-19 . PMC   1586193 . PMID   16834776.
  9. 1 2 3 4 5 6 7 8 9 Coleman, Gareth A.; Davín, Adrián A.; Mahendrarajah, Tara A.; Szánthó, Lénárd L.; Spang, Anja; Hugenholtz, Philip; Szöllősi, Gergely J.; Williams, Tom A. (7 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.
  10. 1 2 3 4 5 6 Léonard, Raphaël R.; Sauvage, Eric; Lupo, Valérian; Perrin, Amandine; Sirjacobs, Damien; Charlier, Paulette; Kerff, Frédéric; Baurain, Denis (18 February 2022). "Was the Last Bacterial Common Ancestor a Monoderm after All?". Genes. 13 (2): 376. doi: 10.3390/genes13020376 . PMC   8871954 . PMID   35205421.
  11. 1 2 Hug, Laura A.; Baker, Brett J.; Anantharaman, Karthik; Brown, Christopher T.; Probst, Alexander J.; Castelle, Cindy J.; Butterfield, Cristina N.; Hernsdorf, Alex W.; Amano, Yuki; Ise, Kotaro; Suzuki, Yohey; Dudek, Natasha; Relman, David A.; Finstad, Kari M.; Amundson, Ronald; Thomas, Brian C.; Banfield, Jillian F. (May 2016). "A new view of the tree of life". Nature Microbiology. 1 (5): 16048. doi: 10.1038/nmicrobiol.2016.48 . PMID   27572647. S2CID   3833474.
  12. 1 2 Zhu, Qiyun; Mai, Uyen; Pfeiffer, Wayne; Janssen, Stefan; Asnicar, Francesco; Sanders, Jon G.; Belda-Ferre, Pedro; Al-Ghalith, Gabriel A.; Kopylova, Evguenia; McDonald, Daniel; Kosciolek, Tomasz; Yin, John B.; Huang, Shi; Salam, Nimaichand; Jiao, Jian-Yu; Wu, Zijun; Xu, Zhenjiang Z.; Cantrell, Kalen; Yang, Yimeng; Sayyari, Erfan; Rabiee, Maryam; Morton, James T.; Podell, Sheila; Knights, Dan; Li, Wen-Jun; Huttenhower, Curtis; Segata, Nicola; Smarr, Larry; Mirarab, Siavash; Knight, Rob (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.
  13. ↑ Battistuzzi, FU; Hedges, SB (2009). "Eubacteria". In Hedges, SB; Kumar, S (eds.). The Timetree of Life. New York: Oxford University Press. pp. 106–115.
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