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Pseudomonadati

From Wikipedia, the free encyclopedia
(Redirected from Negibacteria)

Pseudomonadati
Escherichia coli cells magnified 25,000 times
Scientific classification Edit this classification
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[5]
  • "Hydrobacterida" Luketa 2012

Pseudomonadati[6] is a prokaryotic kingdom containing approximately one-third of prokaryote species, mostly gram-negative bacteria and their relatives. The grouping was originally proposed under the name "Hydrobacteria".[5]

Hydrobacteria is the closest relative of an even larger kingdom of Bacteria, the Bacillati ("Terrabacteria"), which are mostly gram-positive bacteria.[7][5] 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.[5]

Names

[edit]

The synonymous name "Hydrobacteria" (hydro = "water") refers to the moist environment inferred for the common ancestor of those species. In contrast, species of Bacillati ("Terrabacteria") possess adaptations for life on land.[7][5] 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).[8]

"Gracilicutes," which was described in 1978 by Gibbons and Murray,[9] 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.[9] More recently, a redefinition of "Gracilicutes" was proposed[10] 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.

Phylogeny and taxonomy

[edit]

They include these superphyla and phyla: Acidobacteriota, Aquificota, Bdellovibrionota, Campylobacterota, Deferribacterota, Dependentiae, Desulfobacterota, Desulfuromonadota, Elusimicrobiota, FCB superphylum, Myxococcota, Nitrospirota, Proteobacteria, PVC superphylum, and Spirochaetota.[11][12]

Some unrooted molecular phylogenetic analyses[13][14] have not supported this dichotomy of Bacillati and Pseudomonadati, but the most recent genomic analyses,[11][12] including those that have focused on rooting the tree,[11] 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).[15] 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.[11][12]

The definition of two major divisions within the domain Bacteria, Pseudomonadati, and Bacillati, has come largely from rooted phylogenetic analyses of genomes.[7][5][11][12] Unrooted analyses have not fully supported this division,[14][13] 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.[11][12] 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[11]) and the other concluding that it was a diderm (gram-negative bacteria[12]). The following tree is redrawn from one of those two recent studies,[11] showing the phylogeny of bacterial phyla and superphyla, with the position of Fusobacteria being unresolved and DST being the closest relative of Bacillati:

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[16] and National Center for Biotechnology Information (NCBI).[17]

16S rRNA based LTP_07_2026[18][19][20] 120 marker proteins based GTDB 11-RS232[21][22][23]

Minisyncoccota
Pseudomonadati

"Muiribacteriota" [incl. "Riflebacteria", "Wallbacteria"]

"Poribacteriota"

"Oederibacteriota" [incl. "Firestoneibacteriota"; "Goldiibacteriota"; "Muellerivitota"]

"Planctochlora"
"FCB group"
⊞
⊟

"Hinthialibacterota" (OLB16)

"Tangaroaeota" (RBG-13-66-14; Coatesbacteria)

"Edwardsiibacteriota"

Caldifarciminota [incl. "Hydrothermota"; "Caldipriscota"; "Stahliibacteriota" ]

"Fermentibacterota" [incl. "Aegiribacterota"]

"Cloacimonadota"

"Eiseniibacteriota"

"Joyebacterota" [incl. "Effluvivivacota"]

"Krumholzibacteriota" [incl. "Delphinibacteriota"]

Gemmatimonadota [incl. "Glassiibacteriota"]

"Latescibacterota" [incl. "Handelsmaniibacteriota"]

"Blakebacterota"

"Zixiibacteriota"

"Delongiibacteriota" (UBA4055)

Fibrobacterota [incl. "Raymondiibacteriota"]

"Electryoneota" (AABM5-125-24)

Fidelibacterota [incl. "Marinisomatota"]

"Zhuqueibacterota" [incl. "Cosmopoliota"]

Calditrichota

Bacteroidota [incl. Chlorobiota; Balneolota; Ignavibacteriota; "Kapaibacteriota"; "Kryptoniota"; Rhodothermota]

"Proteobacteria"
⊞
⊟

Acidobacteriota [incl. "Aminicenantota"; "Fischeribacteriota"]

"Aquificida"

"Acidulodesulfobacteriota" (sic) (SZUA-79)

Nitrospirota [incl. "Leptospirillaeota" (sic)]

Thermodesulfobacteriota [incl. Desulfobacterota; "Desulfuromonadota"; "Binatota"; "Deferrisomatota"; "Deferrimicrobiota"; "Desulfovibrionota"; "Tharpellota"]

Unassigned phyla:

See also

[edit]

References

[edit]
  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. ↑ "Phylum Caldifarciminota". LPSN - List of Prokaryotic names with Standing in Nomenclature. Retrieved 13 July 2026.
  4. ↑ Mori, Koji; Hidaka, Kohei; Tamazawa, Satoshi; Hosoyama, Akira; Tamaki, Hideyuki; Kakegawa, Takeshi; Hanada, Satoshi (3 July 2026). "Caldifarcimen microaerophilum gen. nov., sp. nov., a facultatively anaerobic, thermophilic bacterium of a novel bacterial phylum, Caldifarciminota phyl. nov., formerly called candidate phylum WOR-3, description of Caldifarciminaceae fam. nov., Caldifarciminales ord. nov. and Caldifarciminia classis nov". International Journal of Systematic and Evolutionary Microbiology. 76 (7). doi:10.1099/ijsem.0.007229. PMID 42397696.
  5. 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.
  6. ↑ "Kingdom: Pseudomonadati". lpsn.dsmz.de. Retrieved 2025-04-02.
  7. 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.
  8. ↑ 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.
  9. 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.
  10. ↑ 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. ↑ Battistuzzi, FU; Hedges, SB (2009). "Eubacteria". In Hedges, SB; Kumar, S (eds.). The Timetree of Life. New York: Oxford University Press. pp. 106–115.
  16. ↑ Pseudomonadati in LPSN; Freese, H. M.; Meier-Kolthoff, J. P.; Sardà Carbasse, J.; Afolayan, A. O.; Göker, M. (2026). "TYGS and LPSN in 2025: a Global Core Biodata Resource for genome-based classification and nomenclature of prokaryotes within DSMZ Digital Diversity". Nucleic Acids Research. 54 (D1): D884–D891. doi:10.1093/nar/gkaf1110.
  17. ↑ Schoch CL; et al. "Pseudomonadati". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2025-06-05.
  18. ↑ "The LTPlus". The All-Species Living Tree Project. Retrieved 1 August 2026.
  19. ↑ "LTP_all tree in newick format". The All-Species Living Tree Project. Retrieved 1 August 2026.
  20. ↑ Rossello-Mora, Ramon; Viver, Tomeu; Palmer-Rodríguez, Pere; Westram, Ralf; Bustos-Caparros, Esteban; Gago, Joan Francisco; Gonzalez-Mendez, Jaime; Llabrés, Mercè; Ludwig, Wolfgang; Amann, Rudolf (22 April 2026). "A pipeline for improved 16S rRNA gene-based phylogeny and diversity analyses of Bacteria and Archaea". Nature Portfolio. doi:10.21203/rs.3.rs-9370187/v1.
  21. ↑ "GTDB release 11-RS232". Genome Taxonomy Database. Retrieved 1 May 2026.
  22. ↑ "bac120_r232.sp_label". Genome Taxonomy Database. Retrieved 1 May 2026.
  23. ↑ "Taxon History". Genome Taxonomy Database. Retrieved 1 May 2026.
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