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Pseudomonadati

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Pseudomonadati
Escherichia coli cells magnified 25,000 times
Scientific classification Edit this classification
Domain: Bacteria
Kingdom: Pseudomonadati
(Gibbons & Murray 1978) Oren & Göker 2024
Phyla[1]
Synonyms
  • "Hydrobacteria" Battistuzzi & Hedges, 2009[2]

Pseudomonadati[3] is a kingdom containing approximately one-third of prokaryote species, mostly gram-negative bacteria and their relatives.[2] It is the closest relative of an even larger kingdom of Bacteria, the Bacillati, which are mostly gram-positive bacteria.[4][2]

Names

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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.[4][2] 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).[5]

"Gracilicutes," which was described in 1978 by Gibbons and Murray,[6] 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.[6] More recently, a redefinition of "Gracilicutes" was proposed[7] 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

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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.[2]

Phylogeny and taxonomy

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They include these superphyla and phyla: Acidobacteriota, Aquificota, Bdellovibrionota, Campylobacterota, Deferribacterota, Dependentiae, Desulfobacterota, Desulfuromonadota, Elusimicrobiota, FCB superphylum, Myxococcota, Nitrospirota, Proteobacteria, PVC superphylum, and Spirochaetota.[8][9]

Some unrooted molecular phylogenetic analyses[10][11] have not supported this dichotomy of Bacillati and Pseudomonadati, but the most recent genomic analyses,[8][9] including those that have focused on rooting the tree,[8] 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 (selas = light).[12] 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.[8][9]

The definition of two major divisions within the domain Bacteria, Pseudomonadati, and Bacillati, has come largely from rooted phylogenetic analyses of genomes.[4][2][8][9] Unrooted analyses have not fully supported this division,[11][10] drawing attention to the importance of rooted trees of life.

  • A timetree redrawn showing the division of Hydrobacteria and Terrabacteria.
    A timetree redrawn from Battistuzzi and Hedges (2009) shows the division of Pseudomonadati (syn. "Hydrobacteria") and Bacillati (syn. "Terrabacteria").[4][2]

The two recent analyses of bacterial phylogeny both supported the division of Pseudomonadati and Bacillati.[8][9] 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[8]) and the other concluding that it was a diderm (gram-negative bacteria[9]). The following tree is redrawn from one of those two recent studies,[8] showing the phylogeny of bacterial phyla and superphyla, with the position of Fusobacteria being unresolved and DST being the closest relative of Bacillati:

  • A phylogeny of bacterial phyla and superphyla according to Coleman et al. (2021). Pseudomonadati was referred to as "Gracilicutes" in that study.
    A phylogeny of bacterial phyla and superphyla according to Coleman et al. (2021).[8] Pseudomonadati was referred to as "Gracilicutes" in that study.

References

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  1. ^ 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
  2. ^ a b c d e f g 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.
  3. ^ "Kingdom: Pseudomonadati". lpsn.dsmz.de. Retrieved 2025-04-02.
  4. ^ a b c d 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.
  5. ^ 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.
  6. ^ a b 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.
  7. ^ 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.
  8. ^ a b c d e f g h i 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.
  9. ^ a b c d e f 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.
  10. ^ a b 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.
  11. ^ a b 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.
  12. ^ 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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