Pseudomonadota
Escherichia coli
Scientific classification Edit this classification
Domain: Bacteria
Phylum: Pseudomonadota
Garrity et al. 2021[1]
Classes
Synonyms
  • "Proteobacteria" Stackebrandt et al. 1988[6]
  • "Proteobacteria" Gray and Herwig 1996[7]
  • "Proteobacteria" Garrity et al. 2005[8]
  • "Proteobacteria" Cavalier-Smith 2002[9]
  • Alphaproteobacteraeota Oren et al. 2015
  • "Alphaproteobacteriota" Whitman et al. 2018
  • "Caulobacterota" corrig. Garrity et al. 2021
  • "Neoprotei" Pelletier 2012
  • Rhodobacteria Cavalier-Smith 2002

Pseudomonadota (synonym Proteobacteria) is a major phylum of Gram-negative bacteria. The renaming of several prokaryote phyla in 2021, including Pseudomonadota, remains controversial among microbiologists, many of whom continue to use the earlier name Proteobacteria, of long standing in the literature.[10] The phylum Proteobacteria includes a wide variety of pathogenic genera, such as Escherichia, Salmonella, Vibrio, Yersinia, Legionella, and many others.[11] Others are free-living (non-parasitic) and include many of the bacteria responsible for nitrogen fixation.

Carl Woese established this grouping in 1987, calling it informally the "purple bacteria and their relatives".[12] Because of the great diversity of forms found in this group, it was later informally named Proteobacteria, after Proteus, a Greek god of the sea capable of assuming many different shapes (not after the Proteobacteria genus Proteus).[6][13] In 2021 the International Committee on Systematics of Prokaryotes designated the synonym Pseudomonadota.[1]

Characteristics

All Pseudomonadota (Proteobacteria) are diverse. They are nominally Gram-negative, although in practice some may actually stain Gram-positive or Gram-variable. Their outer membrane is mainly composed of lipopolysaccharides. Many move about using flagella, but some are nonmotile, or rely on bacterial gliding.

Pseudomonadota have a wide variety of metabolism types. Most are facultatively or obligately anaerobic, chemolithoautotrophic, and heterotrophic, but numerous exceptions occur. A variety of genera, which are not closely related to each other, convert energy from light through conventional photosynthesis or anoxygenic photosynthesis.

Some Alphaproteobacteria can grow at very low levels of nutrients and have unusual morphology such as stalks and buds. Others include agriculturally important bacteria capable of inducing nitrogen fixation in symbiosis with plants. The type order is the Caulobacterales, comprising stalk-forming bacteria such as Caulobacter. The mitochondria of eukaryotes are thought to be descendants of an alphaproteobacterium.[14]

The Betaproteobacteria are highly metabolically diverse and contain chemolithoautotrophs, photoautotrophs, and generalist heterotrophs. The type order is the Burkholderiales, comprising an enormous range of metabolic diversity, including opportunistic pathogens.

The Gammaproteobacteria are the largest class in terms of species with validly published names. The type order is the Pseudomonadales, which include the genera Pseudomonas and the nitrogen-fixing Azotobacter.

The Zetaproteobacteria are iron-oxidizing neutrophilic chemolithoautotrophs, distributed worldwide in estuaries and marine habitats. The type order is the Mariprofundales.

The Hydrogenophilalia are obligate thermophiles and include heterotrophs and autotrophs. The type order is the Hydrogenophilales.

The Acidithiobacillia contain only sulfur, iron, and uranium-oxidising autotrophs. The type order is the Acidithiobacillales, which includes economically important organisms used in the mining industry such as Acidithiobacillus spp.

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)[15] and the National Center for Biotechnology Information (NCBI).[16]

The group is defined primarily in terms of ribosomal RNA (rRNA) sequences. The Pseudomonadota are divided into several classes. These were previously regarded as subclasses of the phylum, but they are now treated as classes. These classes are monophyletic.[17][18][19] The genus Acidithiobacillus, part of the Gammaproteobacteria until it was transferred to class Acidithiobacillia in 2013,[2] was previously regarded as paraphyletic to the Betaproteobacteria according to multigenome alignment studies.[20] In 2017, the Betaproteobacteria was subject to major revisions and the class Hydrogenophilalia was created to contain the order Hydrogenophilales[4]

Pseudomonadota classes with validly published names include some prominent genera:[21] e.g.:

according to ARB living tree, iTOL, Bergey's and others. 16S rRNA based LTP_12_2021[22][23][24] 120 single copy marker proteins based GTDB 08-RS214[25][26][27]

Alphaproteobacteria

Zetaproteobacteria

Gammaproteobacteria

Betaproteobacteria

Hydrogenophilalia

Alphaproteobacteria

"Mariprofundia" (Zetaproteobacteria)

"Chromatibacteria"

"Thiohalorhabdales"

Methylothermaceae 2

Algiphilaceae

Methylothermaceae

Acidithiobacillia

Gammaproteobacteria (nested Betaproteobacteria & Hydrogenophilalia)

"Caulobacteria" (Alphaproteobacteria)

"Mariprofundia" (Zetaproteobacteria)

"Magnetococcia"

"Pseudomonadia"

clade 1

"Foliamicales"

clade 3

Immundisolibacterales

clade 5

"Acidithiobacillidae" (Acidithiobacillia)

"Neisseriidae" (Betaproteobacteria & nested Hydrogenophilalia)

"Pseudomonadidae" (Gammaproteobacteria)

Transformation

Transformation, a process in which genetic material passes from one bacterium to another,[28] has been reported in at least 30 species of Pseudomonadota distributed in the classes alpha, beta, and gamma.[29] The best-studied Pseudomonadota with respect to natural genetic transformation are the medically important human pathogens Neisseria gonorrhoeae (class beta), and Haemophilus influenzae (class gamma).[30] Natural genetic transformation is a sexual process involving DNA transfer from one bacterial cell to another through the intervening medium and the integration of the donor sequence into the recipient genome. In pathogenic Pseudomonadota, transformation appears to serve as a DNA repair process that protects the pathogen's DNA from attack by their host's phagocytic defenses that employ oxidative free radicals.[30]

See also

References

  1. 1 2 Oren A, Garrity GM (2021). "Valid publication of the names of forty-two phyla of prokaryotes". Int J Syst Evol Microbiol. 71 (10): 5056. doi:10.1099/ijsem.0.005056. PMID 34694987. S2CID 239887308.
  2. 1 2 3 Williams, K.P.; Kelly, D.P. (2013). "Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria". International Journal of Systematic and Evolutionary Microbiology. 63 (8): 2901–2906. doi:10.1099/ijs.0.049270-0. PMID 23334881. S2CID 39777860.
  3. ↑ Garrity, G.M.; Bell, J.A.; Lilburn, T. (2005). "Class I. Alphaproteobacteria class. nov.". In Brenner, D.J.; Krieg, N.R.; Staley, J.T.; Garrity, G.M. (eds.). Bergey's Manual of Systematic Bacteriology. Vol. 2: The Proteobacteria, Part C (The Alpha-, Beta-, Delta- and Epsilonproteobacteria (2nd ed.). Springer. p. 1. doi:10.1002/9781118960608.cbm00041. ISBN 9781118960608.
  4. 1 2 3 Boden, R.; Hutt, L.P.; Rae, A.W. (2017). "Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov., transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the "Proteobacteria", and four new families within the orders Nitrosomonadales and Rhodocyclales". International Journal of Systematic and Evolutionary Microbiology. 67 (5): 1191–1205. doi:10.1099/ijsem.0.001927. hdl:10026.1/8740. PMID 28581923.
  5. ↑ Emerson, D.; Rentz, J.A.; Lilburn, T.G.; Davis, R.E.; Aldrich, H.; Chan, C.; Moyer, C.L. (2007). "A novel lineage of proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities". PLOS ONE. 2 (8): e667. Bibcode:2007PLoSO...2..667E. doi:10.1371/journal.pone.0000667. PMC 1930151. PMID 17668050.
  6. 1 2 Stackebrandt, E.; Murray, R.G.E.; Truper, H.G. (1988). "Proteobacteria classis nov., a name for the phylogenetic taxon that includes the "purple bacteria and their relatives"". International Journal of Systematic Bacteriology. 38 (3): 321–325. doi:10.1099/00207713-38-3-321.
  7. ↑ Gray JP, Herwig RP. (1996). "Phylogenetic analysis of the bacterial communities in marine sediments". Appl Environ Microbiol. 62 (11): 4049–4059. Bibcode:1996ApEnM..62.4049G. doi:10.1128/aem.62.11.4049-4059.1996. PMC 168226. PMID 8899989.
  8. ↑ Garrity, G.M.; Bell, J.A.; Lilburn, T. (2005). "Phylum XIV. Proteobacteria phyl. nov.". In Brenner, D.J.; Krieg, N.R.; Staley, J.T.; Garrity, G.M. (eds.). Bergey's Manual of Systematic Bacteriology. Vol. 2 (Proteobacteria), part B (Gammaproteobacteria) (2nd ed.). New York, NY: Springer. p. 1.
  9. ↑ Cavalier-Smith T. (2002). "The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification". Int J Syst Evol Microbiol. 52 (1): 7–76. doi:10.1099/00207713-52-1-7. PMID 11837318.
  10. ↑ "Newly Renamed Prokaryote Phyla Cause Uproar".
  11. ↑ Slonczewski JL, Foster JW, Foster E. Microbiology: An Evolving Science 5th Ed. WW Norton & Company; 2020.
  12. ↑ Woese, C.R. (1987). "Bacterial evolution". Microbiological Reviews. 51 (2): 221–271. doi:10.1128/MMBR.51.2.221-271.1987. PMC 373105. PMID 2439888.
  13. ↑ "Proteobacteria". Discover Life. Tree of Life. Retrieved 2007-02-09.
  14. ↑ Roger, A.J.; Muñoz-Gómez, S.A.; Kamikawa, R. (2017). "The origin and diversification of mitochondria". Current Biology. 27 (21): R1177–R1192. doi:10.1016/j.cub.2017.09.015. PMID 29112874.
  15. ↑ Euzéby JP. "Pseudomonadota". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2016-03-20.
  16. ↑ Sayers. "Proteobacteria". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20.
  17. ↑ Krieg, Noel R.; Brenner, Don J.; Staley, James T. (2005). "The Proteobacteria". Bergey's Manual of Systematic Bacteriology. Springer. ISBN 978-0-387-95040-2.
  18. ↑ Ciccarelli, F.D.; Doerks, T.; von Mering, C.; Creevey, C.J.; Snel, B.; Bork, P. (2006). "Toward automatic reconstruction of a highly resolved tree of life". Science. 311 (5765): 1283–1287. Bibcode:2006Sci...311.1283C. CiteSeerX 10.1.1.381.9514. doi:10.1126/science.1123061. PMID 16513982. S2CID 1615592.
  19. ↑ Yarza, P.; Ludwig, W.; Euzéby, J.; Amann, R.; Schleifer, K.H.; Glöckner, F.O.; Rosselló-Móra, R. (2010). "Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses". Systematic and Applied Microbiology. 33 (6): 291–299. doi:10.1016/j.syapm.2010.08.001. PMID 20817437.
  20. ↑ Williams, K.P.; Gillespie, J.J.; Sobral, B.W.S.; Nordberg, E.K.; Snyder, E. E.; Shallom, J.M.; Dickerman, A.W. (2010). "Phylogeny of Gammaproteobacteria". Journal of Bacteriology. 192 (9): 2305–2314. doi:10.1128/JB.01480-09. PMC 2863478. PMID 20207755.
  21. ↑ "Interactive Tree of Life". Heidelberg, DE: European Molecular Biology Laboratory. Archived from the original on 23 February 2022. Retrieved 23 February 2022.
  22. ↑ "The LTP". Retrieved 23 February 2021.
  23. ↑ "LTP_all tree in newick format". Retrieved 23 February 2021.
  24. ↑ "LTP_12_2021 Release Notes" (PDF). Retrieved 23 February 2021.
  25. ↑ "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
  26. ↑ "bac120_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
  27. ↑ "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.
  28. ↑ Johnston C, Martin B, Fichant G, Polard P, Claverys JP (2014). "Bacterial transformation: Distribution, shared mechanisms and divergent control". Nat. Rev. Microbiol. 12 (3): 181–196. doi:10.1038/nrmicro3199. PMID 24509783. S2CID 23559881.
  29. ↑ Johnsborg O, Eldholm V, Håvarstein LS (2007). "Natural genetic transformation: Prevalence, mechanisms and function". Res. Microbiol. 158 (10): 767–778. doi:10.1016/j.resmic.2007.09.004. PMID 17997281.
  30. 1 2 Michod RE, Bernstein H, Nedelcu AM (2008). "Adaptive value of sex in microbial pathogens". Infect. Genet. Evol. 8 (3): 267–285. doi:10.1016/j.meegid.2008.01.002. PMID 18295550.
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