Biology:Pseudomonadota

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Short description: Phylum of Gram-negative bacteria

Pseudomonadota
EscherichiaColi NIAID.jpg
Escherichia coli
Scientific classification e
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

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.[citation needed]

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.[citation needed]

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.[citation needed]

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

The Hydrogenophilalia are obligate thermophiles and include heterotrophs and autotrophs. The type order is the Hydrogenophilales.[citation needed]

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.[citation needed]

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. ↑ 1.0 1.1 "Valid publication of the names of forty-two phyla of prokaryotes". Int J Syst Evol Microbiol 71 (10): 5056. 2021. doi:10.1099/ijsem.0.005056. PMID 34694987. 
  2. ↑ 2.0 2.1 2.2 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. 
  3. ↑ Garrity, G.M.; Bell, J.A.; Lilburn, T. (2005). "Class I. Alphaproteobacteria class. nov.". Bergey's Manual of Systematic Bacteriology. 2: The Proteobacteria, Part C (The Alpha-, Beta-, Delta- and Epsilonproteobacteria (2nd ed.). Springer. p. 1. doi:10.1002/9781118960608.cbm00041. ISBN 9781118960608. 
  4. ↑ 4.0 4.1 4.2 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. 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. doi:10.1371/journal.pone.0000667. PMID 17668050. Bibcode: 2007PLoSO...2..667E. 
  6. ↑ 6.0 6.1 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. ↑ "Phylogenetic analysis of the bacterial communities in marine sediments". Appl Environ Microbiol 62 (11): 4049–4059. 1996. doi:10.1128/aem.62.11.4049-4059.1996. PMID 8899989. Bibcode: 1996ApEnM..62.4049G. 
  8. ↑ Garrity, G.M.; Bell, J.A.; Lilburn, T. (2005). Bergey's Manual of Systematic Bacteriology. 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". https://www.the-scientist.com/news-opinion/newly-renamed-prokaryote-phyla-cause-uproar-69578. 
  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. PMID 2439888. 
  13. ↑ "Proteobacteria". http://stri.discoverlife.org/mp/20m?tree=Proteobacteria&res=800. 
  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. ↑ "Pseudomonadota". List of Prokaryotic names with Standing in Nomenclature (LPSN). https://lpsn.dsmz.de/phylum/pseudomonadota. 
  16. ↑ Sayers. "Proteobacteria". National Center for Biotechnology Information (NCBI) taxonomy database. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=1224&lvl=3&lin=f&keep=1&srchmode=1&unlock. 
  17. ↑ Krieg, Noel R.; Brenner, Don J.; Staley, James T. (2005). 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. doi:10.1126/science.1123061. PMID 16513982. Bibcode: 2006Sci...311.1283C. 
  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. PMID 20207755. 
  21. ↑ "Interactive Tree of Life" (in en). European Molecular Biology Laboratory. http://itol.embl.de/. 
  22. ↑ "The LTP". https://imedea.uib-csic.es/mmg/ltp/#LTP. 
  23. ↑ "LTP_all tree in newick format". https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/Tree_LTP_all_12_2021.ntree. 
  24. ↑ "LTP_12_2021 Release Notes". https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_12_2021_release_notes.pdf. 
  25. ↑ "GTDB release 08-RS214". https://gtdb.ecogenomic.org/about#4%7C. 
  26. ↑ "bac120_r214.sp_label". https://data.gtdb.ecogenomic.org/releases/release214/214.0/auxillary_files/bac120_r214.sp_labels.tree. 
  27. ↑ "Taxon History". https://gtdb.ecogenomic.org/taxon_history/. 
  28. ↑ "Bacterial transformation: Distribution, shared mechanisms and divergent control". Nat. Rev. Microbiol. 12 (3): 181–196. 2014. doi:10.1038/nrmicro3199. PMID 24509783. 
  29. ↑ "Natural genetic transformation: Prevalence, mechanisms and function". Res. Microbiol. 158 (10): 767–778. 2007. doi:10.1016/j.resmic.2007.09.004. PMID 17997281. 
  30. ↑ 30.0 30.1 "Adaptive value of sex in microbial pathogens". Infect. Genet. Evol. 8 (3): 267–285. 2008. doi:10.1016/j.meegid.2008.01.002. PMID 18295550. 

External links

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