Editing Pseudomonadota

{{short description|Phylum of Gram-negative bacteria}}
{{use dmy dates|cs1-dates=ly|date=April 2024}}
{{cs1 config|name-list-style=vanc|display-authors=6}}
{{Automatic taxobox
| image =  E. coli Bacteria (7316101966).jpg
| image_caption = ''[[Escherichia coli]]''
| taxon = Pseudomonadota
| authority = Garrity et al. 2021<ref name="Phynally">{{cite journal | vauthors = Oren A, Garrity GM | title = Valid publication of the names of forty-two phyla of prokaryotes | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 71 | issue = 10 | pages = 5056 | date = October 2021 | pmid = 34694987 | doi = 10.1099/ijsem.0.005056 | s2cid = 239887308 | doi-access = free}}</ref><ref name=LPSN/>
| subdivision_ranks = Classes
| subdivision_ref = <ref name=NCBI/>
| subdivision =
* [[Acidithiobacillia]]<ref name=WilliamsKelly />
* [[Alphaproteobacteria]]<ref name=GarrityBellLilburn>{{cite book | vauthors = Garrity GM, Bell JA, Lilburn T | chapter = Class&nbsp;I. ''Alphaproteobacteria'' class. nov. | veditors = Brenner DJ, Krieg NR, Staley JT, Garrity GM | title = Bergey's Manual of Systematic Bacteriology | volume = ((2 (Proteobacteria), Part C (The Alpha-, Beta-, Delta- and Epsilonproteobacteria) )) | edition=2nd | publisher = Springer | year = 2005 | page=1 | doi=10.1002/9781118960608.cbm00041 | isbn = 978-1-118-96060-8}}</ref>
* "Anaeropigmentatia"
* [[Betaproteobacteria]]<ref name=Bodenetal2017>{{cite journal | vauthors = Boden R, Hutt LP, Rae AW | title = 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 | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 67 | issue = 5 | pages = 1191–1205 | date = May 2017 | pmid = 28581923 | doi = 10.1099/ijsem.0.001927 | hdl-access = free | doi-access = free | hdl = 10026.1/8740}}</ref>
* [[Gammaproteobacteria]]<ref name=WilliamsKelly>{{cite journal | vauthors = Williams KP, Kelly DP | title = Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 63 | issue = Pt 8 | pages = 2901–2906 | date = August 2013 | pmid = 23334881 | doi = 10.1099/ijs.0.049270-0 | s2cid = 39777860}}</ref>
<!-- Deltaproteobacteria was reclassified as Myxococcota. -->
<!-- Epsilonproteobacteria was reclassified as Campylobacterota. -->
* [[Hydrogenophilalia]]<ref name=Bodenetal2017 />
<!-- Oligoflexia was reclassified as Bdellovibrionota. -->
* [[Magnetococcia]]
* [[Zetaproteobacteria]]<ref name="Emerson2007">{{cite journal | vauthors = Emerson D, Rentz JA, Lilburn TG, Davis RE, Aldrich H, Chan C, Moyer CL | title = A novel lineage of proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities | journal = PLOS ONE | volume = 2 | issue = 7 | pages = e667 | date = August 2007 | pmid = 17668050 | pmc = 1930151 | doi = 10.1371/journal.pone.0000667 | bibcode = 2007PLoSO...2..667E | doi-access = free}}</ref>
| synonyms =
* "Proteobacteria" <small>Stackebrandt et al. 1988</small><ref name=stack>{{cite journal | vauthors = Stackebrandt E, Murray RG, Trüper HG |year=1988 |title=Proteobacteria classis nov., a name for the phylogenetic taxon that includes the "purple bacteria and their relatives" |journal=International Journal of Systematic Bacteriology |volume=38 |issue=3 |pages=321–325 |doi=10.1099/00207713-38-3-321 |doi-access=free}}</ref>
* "Proteobacteria" <small>Gray and Herwig 1996</small><ref name = "Gray_1996">{{cite journal | vauthors = Gray JP, Herwig RP | title = Phylogenetic analysis of the bacterial communities in marine sediments | journal = Applied and Environmental Microbiology | volume = 62 | issue = 11 | pages = 4049–4059 | date = November 1996 | pmid = 8899989 | pmc = 168226 | doi = 10.1128/aem.62.11.4049-4059.1996 | bibcode = 1996ApEnM..62.4049G}}</ref>
* "Proteobacteria" <small>Garrity et al. 2005</small><ref>{{cite book | vauthors = Garrity GM, Bell JA, Lilburn T |year=2005 |section=Phylum&nbsp;XIV. Proteobacteria phyl. nov. |title=Bergey's Manual of Systematic Bacteriology | volume = ((2 (Proteobacteria), Part B (Gammaproteobacteria) )) |edition=2nd |page=1 | veditors = Brenner DJ, Krieg NR, Staley JT, Garrity GM |place=New York, NY |publisher=Springer}}</ref>
* "Proteobacteria" <small>[[Cavalier-Smith]] 2002</small><ref>{{cite journal | vauthors = Cavalier-Smith T | title = The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 52 | issue = Pt 1 | pages = 7–76 | date = January 2002 | pmid = 11837318 | doi = 10.1099/00207713-52-1-7 | doi-access = free}}</ref>
* "Alphaproteobacteraeota" <small>Oren et al. 2015</small>
* "Alphaproteobacteriota" <small>Whitman et al. 2018</small>
* "Caulobacterota" <small>corrig. Garrity et al. 2021</small>
* "Neoprotei" <small>Pelletier 2012</small>
* Rhodobacteria <small>Cavalier-Smith 2002</small>
}}

'''Pseudomonadota''' (synonym "'''Proteobacteria"''') is a major [[phylum]] of [[Gram-negative bacteria]].<ref name="Rizzatti_2017">{{cite journal | vauthors = Rizzatti G, Lopetuso LR, Gibiino G, Binda C, Gasbarrini A | title = Proteobacteria: A Common Factor in Human Diseases | journal = BioMed Research International | volume = 2017 | pages = 9351507 | date = 2017 | pmid = 29230419 | pmc = 5688358 | doi = 10.1155/2017/9351507 | doi-access = free}}</ref> Currently, they are considered the predominant phylum within the realm of bacteria.<ref name="Kersters_2006" /> They are naturally found as [[pathogen]]ic and free-living (non-[[Parasitism|parasitic]]) genera.<ref name="Kersters_2006" /> The phylum comprises six classes ''[[Acidithiobacillia]], [[Alphaproteobacteria]], [[Betaproteobacteria]], [[Gammaproteobacteria]], [[Hydrogenophilaceae|Hydrogenophilia]]'', and ''[[Zetaproteobacteria]].''<ref name = "Kersters_2006">{{cite book | vauthors = Kersters K, De Vos P, Gillis M, Swings J, Vandamme P, Stackebrandt E | chapter = Introduction to the Proteobacteria |date=2006 |title = The Prokaryotes | volume = ((5: Proteobacteria: Alpha and Beta Subclasses)) |pages=3–37 | veditors = Dworkin M, Falkow S, Rosenberg E, Schleifer KH  |url=https://doi.org/10.1007/0-387-30745-1_1 |access-date=2024-04-12 |place=New York, NY |publisher=Springer |language=en |doi=10.1007/0-387-30745-1_1 |isbn=978-0-387-30745-9}}</ref> The Pseudomonadota are widely diverse, with differences in [[Morphology (biology)|morphology]], [[Metabolism|metabolic]] processes, relevance to humans, and [[Ecology|ecological]] influence.<ref name="Kersters_2006" />

== Classification ==
American microbiologist [[Carl Woese]] established this grouping in 1987, calling it informally the "purple bacteria and their relatives".<ref name="woese87">{{cite journal | vauthors = Woese CR | title = Bacterial evolution | journal = Microbiological Reviews | volume = 51 | issue = 2 | pages = 221–271 | date = June 1987 | pmid = 2439888 | pmc = 373105 | doi = 10.1128/MMBR.51.2.221-271.1987}}</ref> The group was later formally named the 'Proteobacteria' after the Greek god Proteus, who was known to assume many forms.<ref>{{cite journal | vauthors = Moon CD, Young W, Maclean PH, Cookson AL, Bermingham EN | title = Metagenomic insights into the roles of Proteobacteria in the gastrointestinal microbiomes of healthy dogs and cats | journal = MicrobiologyOpen | volume = 7 | issue = 5 | pages = e00677 | date = October 2018 | pmid = 29911322 | pmc = 6182564 | doi = 10.1002/mbo3.677}}</ref> In 2021 the [[International Committee on Systematics of Prokaryotes]] designated the synonym Pseudomonadota, and renamed many other prokaryotic phyla as well.<ref name="Phynally" /> This 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.<ref>{{cite web | vauthors = Robitzski D | date = 4 January 2022 | work = The Scientist | url=https://www.the-scientist.com/news-opinion/newly-renamed-prokaryote-phyla-cause-uproar-69578 | title=Newly Renamed Prokaryote Phyla Cause Uproar}}</ref> The phylum Pseudomonadota encompasses classes ''Acidithiobacillia, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Hydrogenophilia'', and ''Zetaproteobacteria.''<ref name = "Kersters_2006" /> The phylum includes a wide variety of [[pathogen]]ic genera, such as ''[[Escherichia]]'', ''[[Salmonella]]'', ''[[Vibrio]]'', ''[[Yersinia]]'', ''[[Legionella]]'', and many others.<ref name="Slonczewski">{{cite book | vauthors = Slonczewski JL, Foster JW, Foster E | title = Microbiology: An Evolving Science | edition = 5th | publisher = WW Norton & Company | date = 2020}}</ref> Others are free-living (non-[[Parasitism|parasitic]]) and include many of the [[bacteria]] responsible for [[nitrogen fixation]].<ref>{{Cite journal |last1=Sah |first1=Stuti |last2=Krishnani |first2=Shweena |last3=Singh |first3=Rajni |date=December 2021 |title=Pseudomonas mediated nutritional and growth promotional activities for sustainable food security |journal=Current Research in Microbial Sciences |language=en |volume=2 |pages=100084 |doi=10.1016/j.crmicr.2021.100084 |pmc=8645841 |pmid=34917993}}</ref>

Previously, the Pseudomonadota phylum included two additional classes, namely ''Deltaproteobacteria'' and ''[[Oligoflexia]]''. However, further investigation into the phylogeny of these taxa through genomic marker analysis demonstrated their separation from the Pseudomonadota phylum.<ref name="Waite_2020">{{cite journal | vauthors = Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P, Wagner M, Loy A, Naganuma T, Nakai R, Whitman WB, Hahn MW, Kuever J, Hugenholtz P | title = Proposal to reclassify the proteobacterial classes ''Deltaproteobacteria'' and ''Oligoflexia'', and the phylum ''Thermodesulfobacteria'' into four phyla reflecting major functional capabilities | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 70 | issue = 11 | pages = 5972–6016 | date = November 2020 | pmid = 33151140 | doi = 10.1099/ijsem.0.004213 | doi-access = free}}</ref> ''Deltaproteobacteria'' has been identified as a diverse [[Taxonomy|taxonomic]] unit, leading to a proposal for its reclassification into distinct phyla: ''[[Desulfobacterota]]'' (encompassing ''[[Thermodesulfobacteriota|Thermodesulfobacteria]]''), ''[[Myxococcota]]'', and ''[[Bdellovibrionota]]'' (comprising ''Oligoflexia'').<ref name="Waite_2020" />

The class ''[[Epsilonproteobacteria]]'' was additionally identified within the Pseudomonadota phylum. This class is characterized by its significance as [[chemolithotrophic]] primary producers and its metabolic prowess in deep-sea [[hydrothermal vent]] ecosystems.<ref name="Waite_2017">{{cite journal | vauthors = Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, Sievert SM, Simon J, Campbell BJ, Hanson TE, Woyke T, Klotz MG, Hugenholtz P | title = Comparative Genomic Analysis of the Class ''Epsilonproteobacteria'' and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.) | journal = Frontiers in Microbiology | volume = 8 | pages = 682 | date = 2017 | pmid = 28484436 | pmc = 5401914 | doi = 10.3389/fmicb.2017.00682 | doi-access = free}}</ref> Noteworthy pathogenic genera within this class include ''[[Campylobacter]], [[Helicobacter]], and [[Arcobacter]]''. Analysis of phylogenetic tree topology and genetic markers revealed the direct divergence of ''Epsilonproteobacteria'' from the Pseudomonadota phylum.<ref name="Waite_2017" /> Limited [[Outgroup (cladistics)|outgroup]] data and low bootstrap values support these discoveries. Despite further investigations, consensus has not been reached regarding the [[Monophyly|monophyletic]] nature of ''Epsilonproteobacteria'' within Proteobacteria, prompting researchers to propose its taxonomic separation from the phylum. The proposed reclassification of the name ''Epsilonproteobacteria'' is ''Epsilonbacteraeota'',<ref name="Waite_2017" /> later revised to ''[[Campylobacterota]]'' in 2018.<ref>{{cite journal | vauthors = Oren A, Garrity GM | title = Valid publication of the names of forty-two phyla of prokaryotes | journal = Int J Syst Evol Microbiol | year = 2021 | volume = 71 | issue = 10 | pages = 5056 | doi = 10.1099/ijsem.0.005056 | pmid = 34694987 | s2cid = 239887308 | doi-access = free }}</ref>

==Taxonomy==
The currently accepted taxonomy is based on the [[List of Prokaryotic names with Standing in Nomenclature]] (LPSN)<ref name=LPSN>{{cite web |author=A.C. Parte |url=https://lpsn.dsmz.de/phylum/pseudomonadota |title=Pseudomonadota |access-date=2025-02-28 |publisher=[[List of Prokaryotic names with Standing in Nomenclature]] (LPSN) |display-authors=et al.}}</ref> and [[National Center for Biotechnology Information]] (NCBI).<ref name=NCBI>{{cite web |author=C.L. Schoch |url=https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=1224&lvl=3&lin=f&keep=1&srchmode=1&unlock |title=Pseudomonadota |access-date=2025-02-28 |publisher=[[National Center for Biotechnology Information]] (NCBI) taxonomy database |display-authors=et al.}}</ref>

The group Pseudomonadota is defined based on [[ribosomal RNA]] (rRNA) sequencing, and are divided into several subclasses. These subclasses were regarded as such for many years, but are now treated as various classes of the phylum. These classes are [[monophyly|monophyletic]].<ref>{{cite book | vauthors = Krieg NR, Brenner DJ, Staley JT |title=Bergey's Manual of Systematic Bacteriology  |publisher=Springer |year=2005 |isbn=978-0-387-95040-2 |volume= ((2: The Proteobacteria))}}</ref><ref>{{cite journal | vauthors = Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P | title = Toward automatic reconstruction of a highly resolved tree of life | journal = Science | volume = 311 | issue = 5765 | pages = 1283–1287 | date = March 2006 | pmid = 16513982 | doi = 10.1126/science.1123061 | bibcode = 2006Sci...311.1283C | s2cid = 1615592 | citeseerx = 10.1.1.381.9514}}</ref><ref>{{cite journal | vauthors = Yarza P, Ludwig W, Euzéby J, Amann R, Schleifer KH, Glöckner FO, Rosselló-Móra R | title = Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses | journal = Systematic and Applied Microbiology | volume = 33 | issue = 6 | pages = 291–299 | date = October 2010 | pmid = 20817437 | doi = 10.1016/j.syapm.2010.08.001| bibcode = 2010SyApM..33..291Y }}</ref> The genus ''[[Acidithiobacillus]]'', part of the Gammaproteobacteria until it was transferred to class Acidithiobacillia in 2013,<ref name="WilliamsKelly" /> was previously regarded as [[paraphyly|paraphyletic]] to the ''Betaproteobacteria'' according to [[Phylogenomics|multigenome alignment studies]].<ref name=":3">{{cite journal | vauthors = Williams KP, Gillespie JJ, Sobral BW, Nordberg EK, Snyder EE, Shallom JM, Dickerman AW | title = Phylogeny of gammaproteobacteria | journal = Journal of Bacteriology | volume = 192 | issue = 9 | pages = 2305–2314 | date = May 2010 | pmid = 20207755 | pmc = 2863478 | doi = 10.1128/JB.01480-09}}</ref> In 2017, the [[Betaproteobacteria]] was subject to major revisions and the class [[Hydrogenophilalia]] was created to contain the order [[Hydrogenophilales]]<ref name="Bodenetal2017" />

Pseudomonadota classes with validly published names include some prominent genera:<ref>{{cite web |title=Interactive Tree of Life |url=http://itol.embl.de/ |url-status=live |archive-url=https://web.archive.org/web/20220223203638/http://itol.embl.de/ |archive-date=23 February 2022 |access-date=23 February 2022 |publisher=[[European Molecular Biology Laboratory]] |place=Heidelberg, DE |language=en}}</ref> e.g.:
* [[Acidithiobacillia]]: ''[[Acidithiobacillus thiooxidans|Acidithiobacillus]]'', ''[[Thermithiobacillus tepidarius|Thermithiobacillus]]''
* [[Alphaproteobacteria]]: ''[[Brucella]], [[Rhizobium]], [[Agrobacterium]], [[Caulobacter]], [[Rickettsia]], [[Wolbachia]]'', etc.
* [[Betaproteobacteria]]: ''[[Bordetella]], [[Ralstonia]], [[Neisseria]], [[Nitrosomonas]]'', etc.
* [[Gammaproteobacteria]]: ''[[Escherichia]], [[Shigella]], [[Salmonella]], [[Yersinia]], [[Buchnera (bacterium)|Buchnera]], [[Haemophilus]], [[Vibrio]], [[Pseudomonas]]'', [[Pasteurella]]'',  etc.''
* [[Zetaproteobacteria]]: ''[[Mariprofundus ferrooxydans|Mariprofundus]]''

{| class="wikitable"
|-
! colspan="1" | according to iTOL, Bergey's <br/>and others.
! colspan=1 | 16S rRNA based [[The All-Species Living Tree Project|LTP]]_10_2024<ref>{{cite web |title=The LTP |url=https://imedea.uib-csic.es/mmg/ltp/#LTP| access-date=10 December 2024}}</ref><ref>{{cite web |title=LTP_all tree in newick format |url=https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_all_10_2024.ntree |access-date=10 December 2024}}</ref><ref>{{cite web |title=LTP_10_2024 Release Notes |url=https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_10_2024_release_notes.pdf |access-date=10 December 2024}}</ref>
! colspan=1 | 120 marker proteins based [[Genome Taxonomy Database|GTDB]] 09-RS220<ref name="about">{{cite web |title=GTDB release 09-RS220 |url=https://gtdb.ecogenomic.org/about#4%7C |website=[[Genome Taxonomy Database]] |access-date=10 May 2024}}</ref><ref name="tree">{{cite web |title=bac120_r220.sp_labels |url=https://data.gtdb.ecogenomic.org/releases/release220/220.0/auxillary_files/bac120_r220.sp_labels.tree |website=[[Genome Taxonomy Database]] |access-date=10 May 2024}}</ref><ref name="taxon_history">{{cite web |title=Taxon History |url=https://gtdb.ecogenomic.org/taxon_history/ |website=[[Genome Taxonomy Database]] |access-date=10 May 2024}}</ref>
|-
| style="vertical-align:top" |
{{Clade | style=font-size:90%;line-height:80%
|1={{clade
  |1=[[Alphaproteobacteria]]
  |2={{clade
    |1=[[Zetaproteobacteria]]
    |2={{clade
      |1=[[Gammaproteobacteria]]
      |2=[[Betaproteobacteria]]
      |3=[[Hydrogenophilalia]]        
       }}
     }}
   }}
}}
|
{{Clade | style=font-size:90%;line-height:80%
|1={{clade
  |1={{clade
    |1=other
    |2={{clade
      |1=other
      |2={{clade
      |label1="Caulobacterota"
      |sublabel1=("Alphaproteobacteriota")
      |1="[[Caulobacteria]]" ([[Alphaproteobacteria]])
         }}
       }}
     }}
  |2={{clade
    |1=other
    |2={{clade
    |label1="Chromatibacteria"
    |1={{clade
      |1={{clade
        |1={{clade
          |1=[[Thiohalorhabdales]]
          |2={{clade
            |1=[[Magnetococcales|Magnetococcia]]
            |2="[[Mariprofundales|Mariprofundia]]" ([[Zetaproteobacteria]])
             }}
           }}
        |2={{clade
          |1=[[Methylohalomonadales]]
          |2={{clade
            |1=[[Thiohalomonadales]]
            |2={{clade
              |1=[[Thiomicrospirales]]
              |2={{clade
                |1=[[Hydrogenophilalia]]
                |2=[[Betaproteobacteria]]
                 }}
               }}
             }}
           }}
         }}
      |2="Pseudomonadia" ([[Gammaproteobacteria]]<br/> and nested [[Acidithiobacillia]])
       }}
       }}
     }}  
   }}
}}
|
{{Clade | style=font-size:90%;line-height:80%
|1={{clade
  |1={{clade
  |label1="[[Caulobacteria]]"
  |sublabel1=([[Alphaproteobacteria]])
  |1={{clade
    |1=Clade 1
    |2={{clade
      |1="Rickettsiidae"
      |2="Caulobacteridae"
       }}
     }}
     }}
  |2={{clade
    |1="[[Mariprofundales|Mariprofundia]]" ([[Zetaproteobacteria]])
    |2={{clade
      |1=[[Magnetococcales|Magnetococcia]]
      |2={{clade
      |label1="[[Pseudomonadia]]"
      |1={{clade
        |1="Neisseriidae" ([[Betaproteobacteria]]<br/> & nested [[Hydrogenophilalia]])
        |2="Pseudomonadidae" ([[Gammaproteobacteria]]<br/> & nested [[Acidithiobacillia]])
         }}
         }}
       }}
     }}
   }}
}}
|}

==Characteristics==
Pseudomonadota are a diverse group. Though some species may stain Gram-positive or Gram-variable in the laboratory, they are nominally [[Gram-negative]]. Their unique [[Bacterial outer membrane|outer membrane]] is mainly composed of [[lipopolysaccharide]]s, which helps differentiate them from the Gram-positive species.<ref>{{Cite journal |last1=Silhavy |first1=Thomas J. |last2=Kahne |first2=Daniel |last3=Walker |first3=Suzanne |date=2010-05-01 |title=The Bacterial Cell Envelope |url=http://cshperspectives.cshlp.org/content/2/5/a000414 |journal=Cold Spring Harbor Perspectives in Biology |language=en |volume=2 |issue=5 |pages=a000414 |doi=10.1101/cshperspect.a000414 |issn=1943-0264 |pmc=2857177 |pmid=20452953}}</ref> Most Pseudomonadota are motile and move using flagella. Many move about using [[Flagellum|flagella]], but some are nonmotile, or rely on [[bacterial gliding]].<ref name=":4">{{Cite web |title=Pseudomonadota Garrity et al., 2021 |url=https://www.gbif.org/species/113662549 |access-date=2024-04-18 |website=www.gbif.org |language=en}}</ref>

Pseudomonadota have a wide variety of [[metabolism]] types. Most are facultative or obligate [[Anaerobic organism|anaerobes]], [[Chemolithoautotrophic|chemolithoautotrophs]], and [[Heterotrophic|heterotrophs]], though numerous exceptions exist. A variety of distantly related genera within the Pseudomonadota obtain their energy from light through conventional [[photosynthesis]] or [[anoxygenic photosynthesis]].<ref name=":4" />

The [[Acidithiobacillia]] contain only sulfur, iron, and uranium-oxidizing [[autotroph]]s. The type order is the [[Acidithiobacillales|Acidithiobacillaceae]], which includes five different ''Acidithiobacillus'' species used in the mining industry. In particular, these microbes assist with the process of [[bioleaching]], which involves microbes assisting in metal extraction from mining waste that typically extraction methods cannot remove.<ref name=":6">{{Citation |last1=Kelly |first1=Donovan P. |title=The Family Acidithiobacillaceae |date=2014 |work=The Prokaryotes: Gammaproteobacteria |pages=15–25 |editor-last=Rosenberg |editor-first=Eugene |url=https://doi.org/10.1007/978-3-642-38922-1_250 |access-date=2024-04-18 |place=Berlin, Heidelberg |publisher=Springer |language=en |doi=10.1007/978-3-642-38922-1_250 |isbn=978-3-642-38922-1 |last2=Wood |first2=Ann P. |editor2-last=DeLong |editor2-first=Edward F. |editor3-last=Lory |editor3-first=Stephen |editor4-last=Stackebrandt |editor4-first=Erko}}</ref>

Some [[Alphaproteobacteria]] can grow at very low levels of nutrients and have unusual morphology within their life cycles. Some form stalks to help with colonization, and form buds during cell division. 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]]''.<ref name=":5">{{Citation |last1=Bandopadhyay |first1=Sreejata |title=Soil bacteria and archaea |date=2024 |work=Soil Microbiology, Ecology and Biochemistry |pages=41–74 |url=https://doi.org/10.1016/b978-0-12-822941-5.00003-x |access-date=2024-04-18 |publisher=Elsevier |doi=10.1016/b978-0-12-822941-5.00003-x |isbn=978-0-12-822941-5 |last2=Shade |first2=Ashley}}</ref> The [[mitochondria]] of eukaryotes are thought to be descendants of an alphaproteobacterium.<ref>{{Cite journal |last1=Roger |first1=Andrew J. |last2=Muñoz-Gómez |first2=Sergio A. |last3=Kamikawa |first3=Ryoma |date=November 2017 |title=The Origin and Diversification of Mitochondria |journal=Current Biology |volume=27 |issue=21 |pages=R1177–R1192 |doi=10.1016/j.cub.2017.09.015 |pmid=29112874 |bibcode=2017CBio...27R1177R |issn=0960-9822|doi-access=free}}</ref>

The [[Betaproteobacteria]] are highly metabolically diverse and contain [[chemolithoautotroph]]s, [[photoautotroph]]s, and generalist [[heterotroph]]s. The type order is the [[Burkholderiales]], comprising an enormous range of metabolic diversity, including [[opportunistic pathogen]]s. These pathogens are primary for both humans and animals, such as the horse pathogen ''Burkholderia mallei'', and ''Burkholderia cepacia'' which causes respiratory tract infections in people with cystic fibrosis.<ref>{{Citation |last=Coenye |first=Tom |title=The Family Burkholderiaceae |date=2014 |work=The Prokaryotes: Alphaproteobacteria and Betaproteobacteria |pages=759–776 |editor-last=Rosenberg |editor-first=Eugene |url=https://doi.org/10.1007/978-3-642-30197-1_239 |access-date=2024-04-18 |place=Berlin, Heidelberg |publisher=Springer |language=en |doi=10.1007/978-3-642-30197-1_239 |isbn=978-3-642-30197-1 |editor2-last=DeLong |editor2-first=Edward F. |editor3-last=Lory |editor3-first=Stephen |editor4-last=Stackebrandt |editor4-first=Erko}}</ref>

The [[Gammaproteobacteria]] are one of the largest classes in terms of genera, containing approximately 250 validly published names.<ref name=":3" /> The type order is the [[Pseudomonadales]], which include the genera ''[[Pseudomonas]]'' and the nitrogen-fixing ''[[Azotobacter]]'', along with many others. Besides being a well-known pathogenic genus, ''Pseudomonas'' is also capable of biodegradation of certain materials, like cellulose.<ref name=":5" />

The [[Hydrogenophilalia]] are thermophilic chemoheterotrophs and autotrophs.<ref>{{Cite journal |last1=Wakai |first1=Satoshi |last2=Masanari |first2=Misa |last3=Ikeda |first3=Takumi |last4=Yamaguchi |first4=Naho |last5=Ueshima |first5=Saori |last6=Watanabe |first6=Kaori |last7=Nishihara |first7=Hirofumi |last8=Sambongi |first8=Yoshihiro |date=April 2013 |title=Oxidative phosphorylation in a thermophilic, facultative chemoautotroph, H ydrogenophilus thermoluteolus, living prevalently in geothermal niches |url=https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1758-2229.12005 |journal=Environmental Microbiology Reports |language=en |volume=5 |issue=2 |pages=235–242 |doi=10.1111/1758-2229.12005 |pmid=23584967 |bibcode=2013EnvMR...5..235W |issn=1758-2229}}</ref> The bacteria typically use hydrogen gas as an electron donor, but can also use reduced sulfuric compounds. Because of this ability, scientists have begun to use certain species of Hydrogenophilalia to remove sulfides that contaminate industrial wastewater systems. The type order is the [[Hydrogenophilales|Hydrogenophilaceae]] which contains the genera ''Thiobacillus, Petrobacter, Sulfuricella,'' ''Hydrogenophilus'' and ''Tepidiphilus''. Currently, no members of this class have been identified as pathogenic.<ref>{{Citation |last1=Orlygsson |first1=Johann |title=The Family Hydrogenophilaceae |date=2014 |work=The Prokaryotes: Alphaproteobacteria and Betaproteobacteria |pages=859–868 |editor-last=Rosenberg |editor-first=Eugene |url=https://doi.org/10.1007/978-3-642-30197-1_244 |access-date=2024-04-18 |place=Berlin, Heidelberg |publisher=Springer |language=en |doi=10.1007/978-3-642-30197-1_244 |isbn=978-3-642-30197-1 |last2=Kristjansson |first2=Jakob K. |editor2-last=DeLong |editor2-first=Edward F. |editor3-last=Lory |editor3-first=Stephen |editor4-last=Stackebrandt |editor4-first=Erko}}</ref>

The [[Zetaproteobacteria]] are the [[Microbial metabolism#Ferrous iron (Fe2+) oxidation|iron-oxidizing]] [[Neutrophile|neutrophilic]] [[Chemolithotrophic|chemolithoautotrophs]], distributed worldwide in estuaries and marine habitats.<ref name=":4" /> This group is so successful in its environment due to their microaerophilic nature. Because they require less oxygen than what is present in the atmosphere, they are able to compete with the abiotic iron(II) oxidation that is already occurring in the environment.<ref>{{Cite journal |url=https://academic.oup.com/femsec/article/95/4/fiz015/5304609 |access-date=2024-04-18 |journal=FEMS Microbiology Ecology |doi=10.1093/femsec/fiz015 |pmc=6443915 |pmid=30715272 |title=The Fe(II)-oxidizing ''Zetaproteobacteria'': Historical, ecological and genomic perspectives |date=2019 |volume=95 |issue=4 | vauthors = McAllister SM, Moore RM, Gartman A, Luther GW, Emerson D, Chan CS}}</ref> The only confirmed type order for this class is the [[Mariprofundales|Mariprofundaceae]], which does not contain any known pathogenic species.<ref>{{Citation |last1=Moreira |first1=Ana Paula B. |title=The Family Mariprofundaceae |date=2014 |work=The Prokaryotes: Deltaproteobacteria and Epsilonproteobacteria |pages=403–413 |editor-last=Rosenberg |editor-first=Eugene |url=https://doi.org/10.1007/978-3-642-39044-9_378 |access-date=2024-04-18 |place=Berlin, Heidelberg |publisher=Springer |language=en |doi=10.1007/978-3-642-39044-9_378 |isbn=978-3-642-39044-9 |last2=Meirelles |first2=Pedro M. |last3=Thompson |first3=Fabiano |editor2-last=DeLong |editor2-first=Edward F. |editor3-last=Lory |editor3-first=Stephen |editor4-last=Stackebrandt |editor4-first=Erko}}</ref>

==Transformation==

[[Transformation (genetics)|Transformation]], a process in which genetic material passes from one bacterium to another,<ref name="Johnston">{{cite journal | vauthors = Johnston C, Martin B, Fichant G, Polard P, Claverys JP | title = Bacterial transformation: distribution, shared mechanisms and divergent control | journal = Nature Reviews. Microbiology | volume = 12 | issue = 3 | pages = 181–196 | date = March 2014 | pmid = 24509783 | doi = 10.1038/nrmicro3199 | s2cid = 23559881}}</ref> has been reported in at least 30 species of Pseudomonadota distributed in the classes alpha, beta, and gamma.<ref name="pmid17997281">{{cite journal | vauthors = Johnsborg O, Eldholm V, Håvarstein LS | title = Natural genetic transformation: prevalence, mechanisms and function | journal = Research in Microbiology | volume = 158 | issue = 10 | pages = 767–778 | date = December 2007 | pmid = 17997281 | doi = 10.1016/j.resmic.2007.09.004 | doi-access = free}}</ref>  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).<ref name="Michod">{{cite journal | vauthors = Michod RE, Bernstein H, Nedelcu AM | title = Adaptive value of sex in microbial pathogens | journal = Infection, Genetics and Evolution | volume = 8 | issue = 3 | pages = 267–285 | date = May 2008 | pmid = 18295550 | doi = 10.1016/j.meegid.2008.01.002| bibcode = 2008InfGE...8..267M }}</ref> 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 [[Reactive oxygen species|oxidative free radicals]].<ref name="Michod" />

==Habitat==
Due to the distinctive nature of each of the six classes of Pseudomonadota, this phylum occupies a multitude of habitats. These include:

* Human oral cavity<ref name="Leão_2023">{{cite journal | vauthors = Leão I, de Carvalho TB, Henriques V, Ferreira C, Sampaio-Maia B, Manaia CM | title = Pseudomonadota in the oral cavity: a glimpse into the environment-human nexus | journal = Applied Microbiology and Biotechnology | volume = 107 | issue = 2–3 | pages = 517–534 | date = February 2023 | pmid = 36567346 | pmc = 9842593 | doi = 10.1007/s00253-022-12333-y}}</ref>
* Microbial mats in the deep sea<ref>{{cite journal | vauthors = Williams KP, Kelly DP | title = Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 63 | issue = Pt 8 | pages = 2901–2906 | date = August 2013 | pmid = 23334881 | doi = 10.1099/ijs.0.049270-0}}</ref>
* Marine sediments<ref name = "Gray_1996" />
* Thermal sulfur springs<ref name="Boden_2017">{{cite journal | vauthors = Boden R, Hutt LP, Rae AW | title = 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 | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 67 | issue = 5 | pages = 1191–1205 | date = May 2017 | pmid = 28581923 | doi = 10.1099/ijsem.0.001927 | hdl-access = free | hdl = 10026.1/8740}}</ref>
* Agricultural soil<ref name="Boden_2017" />
* Hydrothermal vents<ref>{{cite journal | vauthors = Emerson D, Rentz JA, Lilburn TG, Davis RE, Aldrich H, Chan C, Moyer CL | title = A novel lineage of proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities | journal = PLOS ONE | volume = 2 | issue = 7 | pages = e667 | date = August 2007 | pmid = 17668050 | pmc = 1930151 | doi = 10.1371/journal.pone.0000667 | doi-access = free | bibcode = 2007PLoSO...2..667E}}</ref>
* Stem nodules of legumes<ref name = "Kersters_2006" />
* Within aphids as endosymbionts<ref name="Kersters_2006" />
* Gastrointestinal tract of warm-blooded species<ref name="Kersters_2006" />
* Brackish, estuary waters<ref name="Kersters_2006" />
* Microbiomes of shrimp and mollusks<ref name="Kersters_2006" />
* Human vaginal tract<ref name="Rizzatti_2017" />
* Potato rhizosphere microbiome<ref name=":0"/>

== Significance ==

=== Human health ===
Studies have suggested Pseudomonadota as a relevant signature of disease in the human [[Gastrointestinal tract|gastrointestinal]] (GI) tract, by operating as a marker for microbiota instability.<ref name="Rizzatti_2017" /> The human gut [[microbiome]] consists mainly of four phyla: [[Firmicutes]], [[Bacteroidetes]], [[Actinobacteria]], and Pseudomonadota.<ref name="Rizzatti_2017" /> Microorganism gut colonization is dynamic from birth to death, with stabilization at the first few years of life, to higher diversity in adults, to reduced diversity in the elderly.<ref name="Rizzatti_2017" /> The gut microbiome conducts processes like nutrient synthesis, chemical [[metabolism]], and the formation of the gut barrier.<ref name="Rizzatti_2017" /> Additionally, the gut microbiome facilitates host interactions with its surrounding environment through regulation of nutrient absorption and bacterial intake. In 16s rRNA and [[Metagenomics|metagenome]] sequencing studies, Proteobacteria have been identified as bacteria that prompts [[endotoxemia]] (an inflammatory gut response) and metabolic disorders in human GI tracts.<ref name="Rizzatti_2017" /> Another study by Michail et al. showed a correlation of microbial composition in children with and without [[nonalcoholic fatty liver disease]] (NAFLD), wherein patients with NAFLD have a higher abundance of [[Gammaproteobacteria]] than patients without the disease.<ref>{{cite journal | vauthors = Michail S, Lin M, Frey MR, Fanter R, Paliy O, Hilbush B, Reo NV | title = Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease | journal = FEMS Microbiology Ecology | volume = 91 | issue = 2 | pages = 1–9 | date = February 2015 | pmid = 25764541 | pmc = 4358749 | doi = 10.1093/femsec/fiu002 | doi-access = free}}</ref>

Classes Betaproteobacteria and Gammaproteobacteria are prevalent within the human oral cavity, and are markers for good oral health.<ref name="Leão_2023" /> The oral microbiome consists of 11 habitats, including the tongue dorsum, [[hard palate]], tonsils, throat, saliva, and more.<ref name="Jia_2018">{{cite journal | vauthors = Jia G, Zhi A, Lai PF, Wang G, Xia Y, Xiong Z, Zhang H, Che N, Ai L | title = The oral microbiota - a mechanistic role for systemic diseases | journal = British Dental Journal | volume = 224 | issue = 6 | pages = 447–455 | date = March 2018 | pmid = 29569607 | doi = 10.1038/sj.bdj.2018.217 | doi-access = free}}</ref> Changes in the oral microbiome are due to [[Endogeny (biology)|endogenous]] and [[Exogeny|exogenous]] factors like host lifestyle, [[genotype]], environment, immune system, and [[Socioeconomic status|socioeconomic]] status.<ref name="Jia_2018" /> Considering diet as a factor, high [[saturated fatty acid]] (SAF) content, achieved through poor diet, has been correlated to increased abundance of Betaproteobacteria in the oral cavity.<ref name="Jia_2018" />

=== Economic value ===
Pseudomonadota bacteria have a [[Symbiosis|symbiotic]] or [[Mutualism (biology)|mutualistic]] association with plant roots, an example being in the [[rhizome]]s of potato plants.<ref name=":0">{{Cite journal |last1=García-Serquén |first1=Aura L. |last2=Chumbe-Nolasco |first2=Lenin D. |last3=Navarrete |first3=Acacio Aparecido |last4=Girón-Aguilar |first4=R. Carolina |last5=Gutiérrez-Reynoso |first5=Dina L. |date=2024-02-17 |title=Traditional potato tillage systems in the Peruvian Andes impact bacterial diversity, evenness, community composition, and functions in soil microbiomes |journal=Scientific Reports |language=en |volume=14 |issue=1 |page=3963 |doi=10.1038/s41598-024-54652-2 |issn=2045-2322 |pmc=10874408 |pmid=38368478|bibcode=2024NatSR..14.3963G}}</ref> Because of this symbiotic relationship, farmers have the ability to increase their crop yields.<ref name=":0" /> Healthier root systems can lead to better nutrient uptake, improved water retention, increased resistance to diseases and pests, and ultimately higher crop yields per acre.<ref>{{Cite journal |last1=Hartman |first1=Kyle |last2=Schmid |first2=Marc W. |last3=Bodenhausen |first3=Natacha |last4=Bender |first4=S. Franz |last5=Valzano-Held |first5=Alain Y. |last6=Schlaeppi |first6=Klaus |last7=van der Heijden |first7=Marcel G.A. |date=2023-07-31 |title=A symbiotic footprint in the plant root microbiome |journal=Environmental Microbiome |language=en |volume=18 |issue=1 |page=65 |doi=10.1186/s40793-023-00521-w |doi-access=free |issn=2524-6372 |pmc=10391997 |pmid=37525294|bibcode=2023EMicb..18...65H}}</ref> Increased agricultural output can spark economic growth, contribute to food security, and lead to job creation in rural areas.<ref>{{Cite journal |last1=Mozumdar |first1=Lavlu |date=2012 |title=Agricultural productivity and food security in the developing world |url=https://ageconsearch.umn.edu/record/196764 |journal=Bangladesh Journal of Agricultural Economics |language=en |volume=35 |doi=10.22004/AG.ECON.196764}}</ref>

As briefly mentioned in previous sections, members of ''Pseudomonadota'' have vast metabolic abilities that allow them to utilize and produce a variety of compounds. [[Bioleaching]], done by various ''Thiobacillus'' species, are a primary example of this.<ref>{{cite journal |last1=Bosecker |first1=Klaus |title=Bioleaching: metal solubilization by microorganisms |journal=FEMS Microbiology Reviews |date=July 1997 |volume=20 |issue=3–4 |pages=591–604 |doi=10.1111/j.1574-6976.1997.tb00340.x}}</ref> Any iron and sulfur oxidizing species has the potential to uncover metals and low-grade ores that conventional mining techniques were unable to extract. At present, they are most often used for recovering copper and uranium, but researchers are looking to expand this field in the future. The downside of this method is that the bacteria produce acidic byproducts that end up in [[acid mine drainage]]. Bioleaching has significant economic promise if it can be controlled and not cause any further harm to the environment.<ref name=":6" />

=== Ecological impact ===
Pseudomonadota are microbes commonly found within soil systems.<ref name=":0" /> Microbes play a crucial role in the surrounding ecosystem by performing functions such as [[Nutrient cycle|nutrient cycling]], carbon dioxide fixation, [[decomposition]], and nitrogen fixation.<ref name=":1">{{Citation |last1=Gupta |first1=Ankit |title=Microbes and Environment |date=2017 |journal=Principles and Applications of Environmental Biotechnology for a Sustainable Future |pages=43–84 |editor-last=Singh |editor-first=Ram Lakhan |place=Singapore |publisher=Springer Singapore |language=en |doi=10.1007/978-981-10-1866-4_3 |isbn=978-981-10-1865-7 |pmc=7189961 |last2=Gupta |first2=Rasna |last3=Singh |first3=Ram Lakhan}}</ref> Pseudomonadota can be described as [[phototroph]]s, [[heterotroph]]s, and [[lithotroph]]s. As heterotrophs (examples ''[[Pseudomonas]]'' and ''[[Xanthomonas]]'') these bacteria are effective in breaking down organic matter, contributing to nutrient cycling.<ref name=":1" /> Additionally, photolithotrophs within the phylum are able to perform photosynthesis using sulfide or elemental sulfur as [[electron donor]]s, which enables them to participate in carbon fixation and oxygen production even in [[Anaerobic respiration|anaerobic]] conditions.<ref name=":1" /> These Pseudomonadota bacteria are also considered [[copiotroph]]ic organisms, meaning they can be found in environments with high nutrient availability.<ref name=":1" /> These environments have ample sources of carbon and other nutrients, environments like fertile soils, compost, and sewage. These copiotrophic bacteria are able to enhance soil health by performing nutrient cycling and waste decomposition.<ref name=":1" />

Because this phylum are able to form a symbiotic relationship with plant roots, incorporating Pseudomonadota into agricultural practices aligns with principles of [[Sustainable agriculture|sustainable farming]].<ref name=":2">{{Cite journal |last1=Mapelli |first1=Francesca |last2=Mengoni |first2=Alessio |last3=Riva |first3=Valentina |last4=Borin |first4=Sara |date=January 2023 |title=Bacterial culturing is crucial to boost sustainable agriculture |url=https://linkinghub.elsevier.com/retrieve/pii/S0966842X22002888 |journal=Trends in Microbiology |language=en |volume=31 |issue=1 |pages=1–4 |doi=10.1016/j.tim.2022.10.005|hdl=2434/945499 |hdl-access=free}}</ref><ref name=":0" /> These bacteria contribute to soil health and fertility, promote natural pest management, and enhance the resilience of crops to environmental stressors.<ref name=":2" />

== See also ==
* [[List of bacteria genera]]
* [[List of bacterial orders]]

<!-- ==Notes==
{{Notelist}} -->

== References ==
{{reflist|30em}}

== External links ==
{{Wikispecies}}
* [http://www.palaeos.org/Proteobacteria Pseudomonadota information] from [[Palaeos]]. {{Webarchive|url=https://web.archive.org/web/20100523075109/http://www.palaeos.org/Proteobacteria |date=2010-05-23}}

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[[Category:Pseudomonadota| ]]
[[Category:Gram-negative bacteria]]
[[Category:Bacteria phyla]]