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Alphaproteobacteria

January 31, 2023

Alphaproteobacteria is a class of bacteria in the phylum Pseudomonadota (formerly Proteobacteria).[4] The Magnetococcales and Mariprofundales are considered basal or sister to the Alphaproteobacteria.[5][6] The Alphaproteobacteria are highly diverse and possess few commonalities, but nevertheless share a common ancestor. Like all Proteobacteria, its members are gram-negative and some of its intracellular parasitic members lack peptidoglycan and are consequently gram variable.[4][3]

Alphaproteobacteria
Transmission electron micrograph of Wolbachia within an insect cell.
Credit:Public Library of Science / Scott O'Neill
Scientific classification
Domain: Bacteria
Phylum: Pseudomonadota
Class: Alphaproteobacteria
Garrity et al. 2006
Subclasses[1] and Orders[3]
Synonyms[3]
  • Caulobacteria Cavalier-Smith 2020
  • Anoxyphotobacteria (Gibbons and Murray 1978) Murray 1988
  • Photobacteria Gibbons and Murray 1978 (Approved Lists 1980)
  • Alphabacteria Cavalier-Smith 2002

Characteristics

The Alphaproteobacteria are a diverse taxon and comprises several phototrophic genera, several genera metabolising C1-compounds (e.g., Methylobacterium spp.), symbionts of plants (e.g., Rhizobium spp.), endosymbionts of arthropods (Wolbachia) and intracellular pathogens (e.g. Rickettsia). Moreover, the class is sister to the protomitochondrion, the bacterium that was engulfed by the eukaryotic ancestor and gave rise to the mitochondria, which are organelles in eukaryotic cells (See endosymbiotic theory).[1][7] A species of technological interest is Rhizobium radiobacter (formerly Agrobacterium tumefaciens): scientists often use this species to transfer foreign DNA into plant genomes.[8] Aerobic anoxygenic phototrophic bacteria, such as Pelagibacter ubique, are alphaproteobacteria that are a widely distributed and may constitute over 10% of the open ocean microbial community.

Evolution and genomics

There is some disagreement on the phylogeny of the orders, especially for the location of the Pelagibacterales, but overall there is some consensus. The discord stems from the large difference in gene content (e.g. genome streamlining in Pelagibacter ubique) and the large difference in GC-content between members of several orders.[1] Specifically, Pelagibacterales, Rickettsiales and Holosporales contain species with AT-rich genomes.[jargon] It has been argued[by whom?] that it could be a case of convergent evolution that would result in an artefactual clustering.[9][10][11] However, several studies disagree.[1][12][13][14]

Furthermore, it has been found that the GC-content of ribosomal RNA (the traditional phylogenetic marker for prokaryotes) little reflects the GC-content of the genome. One example of this atypical decorrelation of ribosomal GC-content with phylogeny is that members of the Holosporales have a much higher ribosomal GC-content than members of the Pelagibacterales and Rickettsiales, even though they are more closely related to species with high genomic GC-contents than to members of the latter two orders.[1]

The Class Alphaproteobacteria is divided into three subclasses Magnetococcidae, Rickettsidae and Caulobacteridae.[1] The basal group is Magnetococcidae, which is composed by a large diversity of magnetotactic bacteria, but only one is described, Magnetococcus marinus.[15] The Rickettsidae is composed of the intracellular Rickettsiales and the free-living Pelagibacterales. The Caulobacteridae is composed of the Holosporales, Rhodospirillales, Sphingomonadales, Rhodobacterales, Caulobacterales, Kiloniellales, Kordiimonadales, Parvularculales and Sneathiellales.

Comparative analyses of the sequenced genomes have also led to discovery of many conserved insertion-deletions (indels) in widely distributed proteins and whole proteins (i.e. signature proteins) that are distinctive characteristics of either all Alphaproteobacteria, or their different main orders (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales) and families (viz. Rickettsiaceae, Anaplasmataceae, Rhodospirillaceae, Acetobacteraceae, Bradyrhiozobiaceae, Brucellaceae and Bartonellaceae).

These molecular signatures provide novel means for the circumscription of these taxonomic groups and for identification/assignment of new species into these groups.[16] Phylogenetic analyses and conserved indels in large numbers of other proteins provide evidence that Alphaproteobacteria have branched off later than most other phyla and Classes of Bacteria except Betaproteobacteria and Gammaproteobacteria.[17][18]

The phylogeny of Alphaproteobacteria has constantly been revisited and updated.[19][20] There are some debates for the inclusion of Magnetococcidae in Alphaproteobacteria. For example, an independent proteobacterial class (Etaproteobacteria) for Magnetococcidae has been proposed.[21][22] A recent phylogenomic study suggests the placement of the protomitochondrial clade between Magnetococcidae and all other alphaproteobacterial taxa,[5] which suggests an early divergence of the protomitochondrial lineage from the rest of alphaproteobacteria, except for Magnetococcidae. This phylogeny also suggests that the protomitochondrial lineage does not necessarily have a close relationship to Rickettsidae.

Incertae Sedis

The following taxa have been assigned to the Alphaproteobacteria, but have not been assigned to one or more intervening taxonomic ranks:[23]

  • Orders not assigned to a subclass
  • Genera not assigned to a family
    • "Candidatus Anoxipelagibacter" Ruiz-Perez et al. 2021
    • "Bilophococcus" Moench 1988
    • "Charonomicrobium" Csotonyi et al. 2011
    • "Candidatus Endolissoclinum" Kwan et al. 2012
    • "Candidatus Endowatersipora" Anderson and Haygood 2007
    • "Candidatus Halyseomicrobium" Levantesi et al. 2004
    • "Candidatus Halyseosphaera" Kragelund et al. 2006
    • "Candidatus Hodgkinia" McCutcheon et al. 2009
    • "Candidatus Lariskella" Matsuura et al. 2012
    • "Marinosulfonomonas" Holmes et al. 1997
    • "Candidatus Mesopelagibacter" Ruiz-Perez et al. 2021
    • "Methylosulfonomonas" Holmes et al. 1997
    • "Candidatus Monilibacter" Kragelund et al. 2006
    • "Nanobacterium" Ciftcioglu et al. 1997
    • "Oleomonas" Kanamori et al. 2002
    • "Candidatus Paraholospora" Eschbach et al. 2009
    • "Candidatus Phycosocius" Tanabe et al. 2015
    • "Candidatus Puniceispirillum" Oh et al. 2010
    • "Tetracoccus" Blackall et al. 1997
    • "Tuberoidobacter" Nikitin 1983[24][25][26]
  • Species not assigned to a genus

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN).[3] The phylogeny is based on whole-genome analysis.[6][a] Subclass names are based on Ferla et al. (2013).[1]

Natural genetic transformation

Although only a few studies have been reported on natural genetic transformation in the Alphaproteobacteria, this process has been described in Agrobacterium tumefaciens,[28] Methylobacterium organophilum,[29] and Bradyrhizobium japonicum.[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 by homologous recombination.

Notes

  1. ^ Holosporales and Minwuiales are omitted from this phylogenetic tree.

References

  1. ^ a b c d e f g h i j Ferla MP, Thrash JC, Giovannoni SJ, Patrick WM (2013). "New rRNA gene-based phylogenies of the Alphaproteobacteria provide perspective on major groups, mitochondrial ancestry and phylogenetic instability". PLOS ONE. 8 (12): e83383. Bibcode:2013PLoSO...883383F. doi:10.1371/journal.pone.0083383. PMC 3859672. PMID 24349502.
  2. ^ Grote J, Thrash JC, Huggett MJ, Landry ZC, Carini P, Giovannoni SJ, Rappé MS (2012). "Streamlining and core genome conservation among highly divergent members of the SAR11 clade". mBio. 3 (5): e00252-12. doi:10.1128/mBio.00252-12. PMC 3448164. PMID 22991429.
  3. ^ a b c d Euzéby JP, Parte AC. "Alphaproteobacteria". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved May 31, 2021.
  4. ^ a b Brenner DJ, Krieg NR, Staley T (July 26, 2005) [1984(Williams & Wilkins)]. Garrity GM (ed.). The Proteobacteria. Bergey's Manual of Systematic Bacteriology. Vol. 2C (2nd ed.). New York: Springer. p. 1388. ISBN 978-0-387-24145-6. British Library no. GBA561951.
  5. ^ a b Martijn J, Vosseberg J, Guy L, Offre P, Ettema TJ (May 2018). "Deep mitochondrial origin outside the sampled alphaproteobacteria". Nature. 557 (7703): 101–105. Bibcode:2018Natur.557..101M. doi:10.1038/s41586-018-0059-5. PMID 29695865. S2CID 13740626.
  6. ^ a b Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, et al. (7 April 2020). "Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of 'Alphaproteobacteria'". Frontiers in Microbiology. 11: 468. doi:10.3389/fmicb.2020.00468. PMC 7179689. PMID 32373076.
  7. ^ Martijn, Joran; Vosseberg, Julian; Guy, Lionel; Offre, Pierre; Ettema, Thijs J. G. (2018-05-01). "Deep mitochondrial origin outside the sampled alphaproteobacteria". Nature. 557 (7703): 101–105. Bibcode:2018Natur.557..101M. doi:10.1038/s41586-018-0059-5. ISSN 1476-4687. PMID 29695865. S2CID 13740626.
  8. ^ Chilton MD, Drummond MH, Merio DJ, Sciaky D, Montoya AL, Gordon MP, Nester EW (June 1977). "Stable incorporation of plasmid DNA into higher plant cells: the molecular basis of crown gall tumorigenesis". Cell. 11 (2): 263–71. doi:10.1016/0092-8674(77)90043-5. PMID 890735. S2CID 7533482.
  9. ^ Rodríguez-Ezpeleta N, Embley TM (2012). "The SAR11 group of alpha-proteobacteria is not related to the origin of mitochondria". PLOS ONE. 7 (1): e30520. Bibcode:2012PLoSO...730520R. doi:10.1371/journal.pone.0030520. PMC 3264578. PMID 22291975.  
  10. ^ Viklund J, Ettema TJ, Andersson SG (February 2012). "Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade". Molecular Biology and Evolution. 29 (2): 599–615. doi:10.1093/molbev/msr203. PMID 21900598.
  11. ^ Viklund J, Martijn J, Ettema TJ, Andersson SG (2013). "Comparative and phylogenomic evidence that the alphaproteobacterium HIMB59 is not a member of the oceanic SAR11 clade". PLOS ONE. 8 (11): e78858. Bibcode:2013PLoSO...878858V. doi:10.1371/journal.pone.0078858. PMC 3815206. PMID 24223857.  
  12. ^ Georgiades K, Madoui MA, Le P, Robert C, Raoult D (2011). "Phylogenomic analysis of Odyssella thessalonicensis fortifies the common origin of Rickettsiales, Pelagibacter ubique and Reclimonas americana mitochondrion". PLOS ONE. 6 (9): e24857. Bibcode:2011PLoSO...624857G. doi:10.1371/journal.pone.0024857. PMC 3177885. PMID 21957463.  
  13. ^ Thrash JC, Boyd A, Huggett MJ, Grote J, Carini P, Yoder RJ, et al. (2011). "Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade". Scientific Reports. 1: 13. Bibcode:2011NatSR...1E..13T. doi:10.1038/srep00013. PMC 3216501. PMID 22355532.
  14. ^ Williams KP, Sobral BW, Dickerman AW (July 2007). "A robust species tree for the alphaproteobacteria". Journal of Bacteriology. 189 (13): 4578–86. doi:10.1128/JB.00269-07. PMC 1913456. PMID 17483224.
  15. ^ Bazylinski DA, Williams TJ, Lefèvre CT, Berg RJ, Zhang CL, Bowser SS, Dean AJ, Beveridge TJ (2012). "Magnetococcus marinus gen. nov., sp. nov., a marine, magnetotactic bacterium that represents a novel lineage (Magnetococcaceae fam. nov.; Magnetococcales ord. nov.) at the base of the Alphaproteobacteria ". Int J Syst Evol Microbiol. 63 (Pt 3): 801–808. doi:10.1099/ijs.0.038927-0. PMID 22581902.
  16. ^ Gupta RS (2005). "Protein signatures distinctive of alpha proteobacteria and its subgroups and a model for alpha-proteobacterial evolution". Critical Reviews in Microbiology. 31 (2): 101–35. doi:10.1080/10408410590922393. PMID 15986834. S2CID 30170035.
  17. ^ Gupta RS (October 2000). "The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes". FEMS Microbiology Reviews. 24 (4): 367–402. doi:10.1111/j.1574-6976.2000.tb00547.x. PMID 10978543.
  18. ^ Gupta RS, Sneath PH (January 2007). "Application of the character compatibility approach to generalized molecular sequence data: branching order of the proteobacterial subdivisions". Journal of Molecular Evolution. 64 (1): 90–100. Bibcode:2007JMolE..64...90G. doi:10.1007/s00239-006-0082-2. PMID 17160641. S2CID 32775450.
  19. ^ Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, et al. (2020-04-07). "Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of 'Alphaproteobacteria'". Frontiers in Microbiology. 11: 468. doi:10.3389/fmicb.2020.00468. PMC 7179689. PMID 32373076.
  20. ^ Muñoz-Gómez SA, Hess S, Burger G, Lang BF, Susko E, Slamovits CH, Roger AJ (February 2019). Rokas A, Wittkopp PJ, Irisarri I (eds.). "An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins". eLife. 8: e42535. doi:10.7554/eLife.42535. PMC 6447387. PMID 30789345.
  21. ^ Ji B, Zhang SD, Zhang WJ, Rouy Z, Alberto F, Santini CL, et al. (March 2017). "The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of Proteobacteria". Environmental Microbiology. 19 (3): 1103–1119. doi:10.1111/1462-2920.13637. PMID 27902881. S2CID 32324511.
  22. ^ Lin W, Zhang W, Zhao X, Roberts AP, Paterson GA, Bazylinski DA, Pan Y (June 2018). "Genomic expansion of magnetotactic bacteria reveals an early common origin of magnetotaxis with lineage-specific evolution". The ISME Journal. 12 (6): 1508–1519. doi:10.1038/s41396-018-0098-9. PMC 5955933. PMID 29581530.
  23. ^ Euzéby JP, Parte AC. "Alphaproteobacteria, not assigned to a family". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved June 7, 2021.
  24. ^ Rose AH, Tempest DW, Morris JG (1983). Advances in Microbial Physiology. Vol. 24. Academic Press. p. 111. ISBN 0-12-027724-7.
  25. ^ Tuberoidobacter, on: IniProt Taxonomy
  26. ^ Tuberoidobacter, on: NCBI Taxonomy Browser
  27. ^ Roger AJ, Muñoz-Gómez SA, Kamikawa R (November 2017). "The Origin and Diversification of Mitochondria". Current Biology. 27 (21): R1177–R1192. doi:10.1016/j.cub.2017.09.015. PMID 29112874.
  28. ^ Demanèche S, Kay E, Gourbière F, Simonet P (June 2001). "Natural transformation of Pseudomonas fluorescens and Agrobacterium tumefaciens in soil". Applied and Environmental Microbiology. 67 (6): 2617–21. Bibcode:2001ApEnM..67.2617D. doi:10.1128/AEM.67.6.2617-2621.2001. PMC 92915. PMID 11375171.
  29. ^ O'Connor M, Wopat A, Hanson RS (January 1977). "Genetic transformation in Methylobacterium organophilum". Journal of General Microbiology. 98 (1): 265–72. doi:10.1099/00221287-98-1-265. PMID 401866.
  30. ^ Raina JL, Modi VV (August 1972). "Deoxyribonucleate binding and transformation in Rhizobium jpaonicum". Journal of Bacteriology. 111 (2): 356–60. doi:10.1128/jb.111.2.356-360.1972. PMC 251290. PMID 4538250.

External links

  • Alphaproteobacteria at the US National Library of Medicine Medical Subject Headings (MeSH)
  • Bacterial (Prokaryotic) Phylogeny Webpage: Alpha Proteobacteria.

January 31, 2023
alphaproteobacteria, class, bacteria, phylum, pseudomonadota, formerly, proteobacteria, magnetococcales, mariprofundales, considered, basal, sister, highly, diverse, possess, commonalities, nevertheless, share, common, ancestor, like, proteobacteria, members, . Alphaproteobacteria is a class of bacteria in the phylum Pseudomonadota formerly Proteobacteria 4 The Magnetococcales and Mariprofundales are considered basal or sister to the Alphaproteobacteria 5 6 The Alphaproteobacteria are highly diverse and possess few commonalities but nevertheless share a common ancestor Like all Proteobacteria its members are gram negative and some of its intracellular parasitic members lack peptidoglycan and are consequently gram variable 4 3 AlphaproteobacteriaTransmission electron micrograph of Wolbachia within an insect cell Credit Public Library of Science Scott O NeillScientific classificationDomain BacteriaPhylum PseudomonadotaClass AlphaproteobacteriaGarrity et al 2006Subclasses 1 and Orders 3 Rickettsidae Ferla et al 2013 1 Rickettsiales Gieszczykiewicz 1939 Approved Lists 1980 Pelagibacterales Grote et al 2012 2 Caulobacteridae Ferla et al 2013 1 Caulobacterales Henrici and Johnson 1935 Approved Lists 1980 Emcibacterales Iino et al 2016 Holosporales Szokoli et al 2020 Hyphomicrobiales Douglas 1957 Approved Lists 1980 Iodidimonadales Iino et al 2016 Kordiimonadales Kwon et al 2005 Micropepsales Harbison et al 2017 Parvularculales Garrity et al 2003 Rhodobacterales Garrity et al 2006 Rhodospirillales Pfennig and Truper 1971 Approved Lists 1980 Rhodothalassiales Venkata Ramana et al 2014 Sneathiellales Kurahashi et al 2008 Sphingomonadales Yabuuchi and Kosako 2006 Taxa incertae sedis see text Synonyms 3 Caulobacteria Cavalier Smith 2020 Anoxyphotobacteria Gibbons and Murray 1978 Murray 1988 Photobacteria Gibbons and Murray 1978 Approved Lists 1980 Alphabacteria Cavalier Smith 2002 Contents 1 Characteristics 2 Evolution and genomics 3 Incertae Sedis 4 Phylogeny 5 Natural genetic transformation 6 Notes 7 References 8 External linksCharacteristics EditThe Alphaproteobacteria are a diverse taxon and comprises several phototrophic genera several genera metabolising C1 compounds e g Methylobacterium spp symbionts of plants e g Rhizobium spp endosymbionts of arthropods Wolbachia and intracellular pathogens e g Rickettsia Moreover the class is sister to the protomitochondrion the bacterium that was engulfed by the eukaryotic ancestor and gave rise to the mitochondria which are organelles in eukaryotic cells See endosymbiotic theory 1 7 A species of technological interest is Rhizobium radiobacter formerly Agrobacterium tumefaciens scientists often use this species to transfer foreign DNA into plant genomes 8 Aerobic anoxygenic phototrophic bacteria such as Pelagibacter ubique are alphaproteobacteria that are a widely distributed and may constitute over 10 of the open ocean microbial community Evolution and genomics EditThere is some disagreement on the phylogeny of the orders especially for the location of the Pelagibacterales but overall there is some consensus The discord stems from the large difference in gene content e g genome streamlining in Pelagibacter ubique and the large difference in GC content between members of several orders 1 Specifically Pelagibacterales Rickettsiales and Holosporales contain species with AT rich genomes jargon It has been argued by whom that it could be a case of convergent evolution that would result in an artefactual clustering 9 10 11 However several studies disagree 1 12 13 14 Furthermore it has been found that the GC content of ribosomal RNA the traditional phylogenetic marker for prokaryotes little reflects the GC content of the genome One example of this atypical decorrelation of ribosomal GC content with phylogeny is that members of the Holosporales have a much higher ribosomal GC content than members of the Pelagibacterales and Rickettsiales even though they are more closely related to species with high genomic GC contents than to members of the latter two orders 1 The Class Alphaproteobacteria is divided into three subclasses Magnetococcidae Rickettsidae and Caulobacteridae 1 The basal group is Magnetococcidae which is composed by a large diversity of magnetotactic bacteria but only one is described Magnetococcus marinus 15 The Rickettsidae is composed of the intracellular Rickettsiales and the free living Pelagibacterales The Caulobacteridae is composed of the Holosporales Rhodospirillales Sphingomonadales Rhodobacterales Caulobacterales Kiloniellales Kordiimonadales Parvularculales and Sneathiellales Comparative analyses of the sequenced genomes have also led to discovery of many conserved insertion deletions indels in widely distributed proteins and whole proteins i e signature proteins that are distinctive characteristics of either all Alphaproteobacteria or their different main orders viz Rhizobiales Rhodobacterales Rhodospirillales Rickettsiales Sphingomonadales and Caulobacterales and families viz Rickettsiaceae Anaplasmataceae Rhodospirillaceae Acetobacteraceae Bradyrhiozobiaceae Brucellaceae and Bartonellaceae These molecular signatures provide novel means for the circumscription of these taxonomic groups and for identification assignment of new species into these groups 16 Phylogenetic analyses and conserved indels in large numbers of other proteins provide evidence that Alphaproteobacteria have branched off later than most other phyla and Classes of Bacteria except Betaproteobacteria and Gammaproteobacteria 17 18 The phylogeny of Alphaproteobacteria has constantly been revisited and updated 19 20 There are some debates for the inclusion of Magnetococcidae in Alphaproteobacteria For example an independent proteobacterial class Etaproteobacteria for Magnetococcidae has been proposed 21 22 A recent phylogenomic study suggests the placement of the protomitochondrial clade between Magnetococcidae and all other alphaproteobacterial taxa 5 which suggests an early divergence of the protomitochondrial lineage from the rest of alphaproteobacteria except for Magnetococcidae This phylogeny also suggests that the protomitochondrial lineage does not necessarily have a close relationship to Rickettsidae Incertae Sedis EditThe following taxa have been assigned to the Alphaproteobacteria but have not been assigned to one or more intervening taxonomic ranks 23 Orders not assigned to a subclass Minwuiales Sun et al 2018 Genera not assigned to a family Candidatus Anoxipelagibacter Ruiz Perez et al 2021 Bilophococcus Moench 1988 Charonomicrobium Csotonyi et al 2011 Candidatus Endolissoclinum Kwan et al 2012 Candidatus Endowatersipora Anderson and Haygood 2007 Candidatus Halyseomicrobium Levantesi et al 2004 Candidatus Halyseosphaera Kragelund et al 2006 Candidatus Hodgkinia McCutcheon et al 2009 Candidatus Lariskella Matsuura et al 2012 Marinosulfonomonas Holmes et al 1997 Candidatus Mesopelagibacter Ruiz Perez et al 2021 Methylosulfonomonas Holmes et al 1997 Candidatus Monilibacter Kragelund et al 2006 Nanobacterium Ciftcioglu et al 1997 Oleomonas Kanamori et al 2002 Candidatus Paraholospora Eschbach et al 2009 Candidatus Phycosocius Tanabe et al 2015 Candidatus Puniceispirillum Oh et al 2010 Tetracoccus Blackall et al 1997 Tuberoidobacter Nikitin 1983 24 25 26 Species not assigned to a genus Vibrio adaptatus Muir et al 1990 Vibrio cyclosites Muir et al 1990Phylogeny EditThe currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature LPSN 3 The phylogeny is based on whole genome analysis 6 a Subclass names are based on Ferla et al 2013 1 Bacteria Alphaproteobacteria Magnetococcales Mariprofundales Rickettsidae Rickettsiales including mitochondria 1 27 Pelagibacterales Caulobacteridae Sphingomonadales Rhodospirillales Rhodothalassiales Iodidimonadales Kordiimonadales Emcibacterales Sneathiellales Hyphomicrobiales Rhodobacterales Micropepsales Parvularculales Caulobacterales outgroup SpirochaetotaNatural genetic transformation EditAlthough only a few studies have been reported on natural genetic transformation in the Alphaproteobacteria this process has been described in Agrobacterium tumefaciens 28 Methylobacterium organophilum 29 and Bradyrhizobium japonicum 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 by homologous recombination Notes Edit Holosporales and Minwuiales are omitted from this phylogenetic tree References Edit a b c d e f g h i j Ferla MP Thrash JC Giovannoni SJ Patrick WM 2013 New rRNA gene based phylogenies of the Alphaproteobacteria provide perspective on major groups mitochondrial ancestry and phylogenetic instability PLOS ONE 8 12 e83383 Bibcode 2013PLoSO 883383F doi 10 1371 journal pone 0083383 PMC 3859672 PMID 24349502 Grote J Thrash JC Huggett MJ Landry ZC Carini P Giovannoni SJ Rappe MS 2012 Streamlining and core genome conservation among highly divergent members of the SAR11 clade mBio 3 5 e00252 12 doi 10 1128 mBio 00252 12 PMC 3448164 PMID 22991429 a b c d Euzeby JP Parte AC Alphaproteobacteria List of Prokaryotic names with Standing in Nomenclature LPSN Retrieved May 31 2021 a b Brenner DJ Krieg NR Staley T July 26 2005 1984 Williams amp Wilkins Garrity GM ed The Proteobacteria Bergey s Manual of Systematic Bacteriology Vol 2C 2nd ed New York Springer p 1388 ISBN 978 0 387 24145 6 British Library no GBA561951 a b Martijn J Vosseberg J Guy L Offre P Ettema TJ May 2018 Deep mitochondrial origin outside the sampled alphaproteobacteria Nature 557 7703 101 105 Bibcode 2018Natur 557 101M doi 10 1038 s41586 018 0059 5 PMID 29695865 S2CID 13740626 a b Hordt A Lopez MG Meier Kolthoff JP Schleuning M Weinhold LM Tindall BJ et al 7 April 2020 Analysis of 1 000 Type Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria Frontiers in Microbiology 11 468 doi 10 3389 fmicb 2020 00468 PMC 7179689 PMID 32373076 Martijn Joran Vosseberg Julian Guy Lionel Offre Pierre Ettema Thijs J G 2018 05 01 Deep mitochondrial origin outside the sampled alphaproteobacteria Nature 557 7703 101 105 Bibcode 2018Natur 557 101M doi 10 1038 s41586 018 0059 5 ISSN 1476 4687 PMID 29695865 S2CID 13740626 Chilton MD Drummond MH Merio DJ Sciaky D Montoya AL Gordon MP Nester EW June 1977 Stable incorporation of plasmid DNA into higher plant cells the molecular basis of crown gall tumorigenesis Cell 11 2 263 71 doi 10 1016 0092 8674 77 90043 5 PMID 890735 S2CID 7533482 Rodriguez Ezpeleta N Embley TM 2012 The SAR11 group of alpha proteobacteria is not related to the origin of mitochondria PLOS ONE 7 1 e30520 Bibcode 2012PLoSO 730520R doi 10 1371 journal pone 0030520 PMC 3264578 PMID 22291975 Viklund J Ettema TJ Andersson SG February 2012 Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade Molecular Biology and Evolution 29 2 599 615 doi 10 1093 molbev msr203 PMID 21900598 Viklund J Martijn J Ettema TJ Andersson SG 2013 Comparative and phylogenomic evidence that the alphaproteobacterium HIMB59 is not a member of the oceanic SAR11 clade PLOS ONE 8 11 e78858 Bibcode 2013PLoSO 878858V doi 10 1371 journal pone 0078858 PMC 3815206 PMID 24223857 Georgiades K Madoui MA Le P Robert C Raoult D 2011 Phylogenomic analysis of Odyssella thessalonicensis fortifies the common origin of Rickettsiales Pelagibacter ubique and Reclimonas americana mitochondrion PLOS ONE 6 9 e24857 Bibcode 2011PLoSO 624857G doi 10 1371 journal pone 0024857 PMC 3177885 PMID 21957463 Thrash JC Boyd A Huggett MJ Grote J Carini P Yoder RJ et al 2011 Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade Scientific Reports 1 13 Bibcode 2011NatSR 1E 13T doi 10 1038 srep00013 PMC 3216501 PMID 22355532 Williams KP Sobral BW Dickerman AW July 2007 A robust species tree for the alphaproteobacteria Journal of Bacteriology 189 13 4578 86 doi 10 1128 JB 00269 07 PMC 1913456 PMID 17483224 Bazylinski DA Williams TJ Lefevre CT Berg RJ Zhang CL Bowser SS Dean AJ Beveridge TJ 2012 Magnetococcus marinusgen nov sp nov a marine magnetotactic bacterium that represents a novel lineage Magnetococcaceaefam nov Magnetococcalesord nov at the base of theAlphaproteobacteria Int J Syst Evol Microbiol 63 Pt 3 801 808 doi 10 1099 ijs 0 038927 0 PMID 22581902 Gupta RS 2005 Protein signatures distinctive of alpha proteobacteria and its subgroups and a model for alpha proteobacterial evolution Critical Reviews in Microbiology 31 2 101 35 doi 10 1080 10408410590922393 PMID 15986834 S2CID 30170035 Gupta RS October 2000 The phylogeny of proteobacteria relationships to other eubacterial phyla and eukaryotes FEMS Microbiology Reviews 24 4 367 402 doi 10 1111 j 1574 6976 2000 tb00547 x PMID 10978543 Gupta RS Sneath PH January 2007 Application of the character compatibility approach to generalized molecular sequence data branching order of the proteobacterial subdivisions Journal of Molecular Evolution 64 1 90 100 Bibcode 2007JMolE 64 90G doi 10 1007 s00239 006 0082 2 PMID 17160641 S2CID 32775450 Hordt A Lopez MG Meier Kolthoff JP Schleuning M Weinhold LM 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