Alphaproteobacteria

The Alphaproteobacteria are a diverse taxon and comprise 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).{{Cite journal |last1=Martijn |first1=Joran |last2=Vosseberg |first2=Julian |last3=Guy |first3=Lionel |last4=Offre |first4=Pierre |last5=Ettema |first5=Thijs J. G. |date=2018-05-01 |title=Deep mitochondrial origin outside the sampled alphaproteobacteria |journal=Nature |language=en |volume=557 |issue=7703 |pages=101–105 |doi=10.1038/s41586-018-0059-5 |pmid=29695865 |bibcode=2018Natur.557..101M |s2cid=13740626 |issn=1476-4687|doi-access=free }} A species of technological interest is Rhizobium radiobacter (formerly Agrobacterium tumefaciens): scientists often use this species to transfer foreign DNA into plant genomes.{{cite journal | vauthors = Chilton MD, Drummond MH, Merio DJ, Sciaky D, Montoya AL, Gordon MP, Nester EW | title = Stable incorporation of plasmid DNA into higher plant cells: the molecular basis of crown gall tumorigenesis | journal = Cell | volume = 11 | issue = 2 | pages = 263–271 | date = June 1977 | pmid = 890735 | doi = 10.1016/0092-8674(77)90043-5 | s2cid = 7533482 }} 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.

Several points of disagreement muddy the recovery of the phylogenetic relationships among the Alphaproteobacteria clades from the genomic data. One such point centers on the placement of the Pelagibacterales stemming from the large differences in gene content (e.g. genome streamlining in Pelagibacter ubique) and GC-content between members of several orders. Specifically, certain species within Pelagibacterales, Rickettsiales, and Holosporales possess AT-rich genomes, containing higher-assayed concentrations of adenine-thymine (AT) pairs than guanine-cytosine (GC) base pairs. While it could be a case of convergent evolution resulting in an artefactual clustering,{{cite journal | vauthors = Rodríguez-Ezpeleta N, Embley TM | title = The SAR11 group of alpha-proteobacteria is not related to the origin of mitochondria | journal = PLOS ONE | volume = 7 | issue = 1 | pages = e30520 | year = 2012 | pmid = 22291975 | pmc = 3264578 | doi = 10.1371/journal.pone.0030520 | doi-access = free | bibcode = 2012PLoSO...730520R }} {{open access}}{{cite journal | vauthors = Viklund J, Ettema TJ, Andersson SG|author3-link=Siv G. E. Andersson | title = Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade | journal = Molecular Biology and Evolution | volume = 29 | issue = 2 | pages = 599–615 | date = February 2012 | pmid = 21900598 | doi = 10.1093/molbev/msr203 | doi-access = }}{{cite journal | vauthors = Viklund J, Martijn J, Ettema TJ, Andersson SG | title = Comparative and phylogenomic evidence that the alphaproteobacterium HIMB59 is not a member of the oceanic SAR11 clade | journal = PLOS ONE | volume = 8 | issue = 11 | pages = e78858 | year = 2013 | pmid = 24223857 | pmc = 3815206 | doi = 10.1371/journal.pone.0078858 | doi-access = free | bibcode = 2013PLoSO...878858V }} {{open access}} several studies disagree{{cite journal | vauthors = Georgiades K, Madoui MA, Le P, Robert C, Raoult D | title = Phylogenomic analysis of Odyssella thessalonicensis fortifies the common origin of Rickettsiales, Pelagibacter ubique and Reclimonas americana mitochondrion | journal = PLOS ONE | volume = 6 | issue = 9 | pages = e24857 | year = 2011 | pmid = 21957463 | pmc = 3177885 | doi = 10.1371/journal.pone.0024857 | doi-access = free | bibcode = 2011PLoSO...624857G }} {{open access}}{{cite journal | vauthors = Thrash JC, Boyd A, Huggett MJ, Grote J, Carini P, Yoder RJ, Robbertse B, Spatafora JW, Rappé MS, Giovannoni SJ | display-authors = 6 | title = Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade | journal = Scientific Reports | volume = 1 | pages = 13 | year = 2011 | pmid = 22355532 | pmc = 3216501 | doi = 10.1038/srep00013 | bibcode = 2011NatSR...1...13T }}{{cite journal | vauthors = Williams KP, Sobral BW, Dickerman AW | title = A robust species tree for the alphaproteobacteria | journal = Journal of Bacteriology | volume = 189 | issue = 13 | pages = 4578–86 | date = July 2007 | pmid = 17483224 | pmc = 1913456 | doi = 10.1128/JB.00269-07 }} and no consensus has been reached.

Furthermore, the GC-content of ribosomal RNA, the traditional phylogenetic marker for prokaryotes, does not correlate well with the GC-content of the genome. For example, members of the Holosporales have a much higher ribosomal GC-content than members of the Pelagibacterales and Rickettsiales, though they are more closely related to species with high genomic GC-contents than to members of the latter two orders.

Alphaproteobacteria are divided into three subclasses, Magnetococcidae, Rickettsidae, and Caulobacteridae. The basal group is Magnetococcidae, composed of a large diversity of magnetotactic bacteria only one of which, Magnetococcus marinus, is formally described.{{cite journal | vauthors = Bazylinski DA, Williams TJ, Lefèvre CT, Berg RJ, Zhang CL, Bowser SS, Dean AJ, Beveridge TJ | year = 2012 | title = 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 | journal = Int J Syst Evol Microbiol | volume = 63| issue = Pt 3 | pages = 801–808| doi = 10.1099/ijs.0.038927-0 | pmid = 22581902 }} 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 revealed 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 a means to circumscribe the taxonomic groups and to identify and assign new species accurately.{{cite journal | vauthors = Gupta RS | title = Protein signatures distinctive of alpha proteobacteria and its subgroups and a model for alpha-proteobacterial evolution | journal = Critical Reviews in Microbiology | volume = 31 | issue = 2 | pages = 101–35 | year = 2005 | pmid = 15986834 | doi = 10.1080/10408410590922393 | s2cid = 30170035 }} 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.{{cite journal | vauthors = Gupta RS | title = The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes | journal = FEMS Microbiology Reviews | volume = 24 | issue = 4 | pages = 367–402 | date = October 2000 | pmid = 10978543 | doi = 10.1111/j.1574-6976.2000.tb00547.x | doi-access = free }}{{cite journal | vauthors = Gupta RS, Sneath PH | title = Application of the character compatibility approach to generalized molecular sequence data: branching order of the proteobacterial subdivisions | journal = Journal of Molecular Evolution | volume = 64 | issue = 1 | pages = 90–100 | date = January 2007 | pmid = 17160641 | doi = 10.1007/s00239-006-0082-2 | s2cid = 32775450 | bibcode = 2007JMolE..64...90G }}

Other phylogenetic debates turn on the placement of Magnetococcidae and the protomitochondrion.{{cite journal | vauthors = Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M | display-authors = 6 | title = Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of 'Alphaproteobacteria' | journal = Frontiers in Microbiology | volume = 11 | pages = 468 | date = 2020-04-07 | pmid = 32373076 | pmc = 7179689 | doi = 10.3389/fmicb.2020.00468 | doi-access = free }}{{cite journal | vauthors = Muñoz-Gómez SA, Hess S, Burger G, Lang BF, Susko E, Slamovits CH, Roger AJ | title = An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins | journal = eLife | volume = 8 | pages = e42535 | date = February 2019 | pmid = 30789345 | doi = 10.7554/eLife.42535 | veditors = Rokas A, Wittkopp PJ, Irisarri I | pmc = 6447387 | doi-access = free }} There are some debates for the inclusion of Magnetococcidae in Alphaproteobacteria. For example, an independent proteobacterial class ("Candidatus Etaproteobacteria") for Magnetococcidae has been proposed.{{cite journal | vauthors = Ji B, Zhang SD, Zhang WJ, Rouy Z, Alberto F, Santini CL, Mangenot S, Gagnot S, Philippe N, Pradel N, Zhang L, Tempel S, Li Y, Médigue C, Henrissat B, Coutinho PM, Barbe V, Talla E, Wu LF | display-authors = 6 | title = The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of Proteobacteria | journal = Environmental Microbiology | volume = 19 | issue = 3 | pages = 1103–1119 | date = March 2017 | pmid = 27902881 | doi = 10.1111/1462-2920.13637 | bibcode = 2017EnvMi..19.1103J | s2cid = 32324511 }}{{cite journal | vauthors = Lin W, Zhang W, Zhao X, Roberts AP, Paterson GA, Bazylinski DA, Pan Y | title = Genomic expansion of magnetotactic bacteria reveals an early common origin of magnetotaxis with lineage-specific evolution | journal = The ISME Journal | volume = 12 | issue = 6 | pages = 1508–1519 | date = June 2018 | pmid = 29581530 | pmc = 5955933 | doi = 10.1038/s41396-018-0098-9 | bibcode = 2018ISMEJ..12.1508L }} A recent phylogenomic study suggests the placement of the protomitochondrial clade between Magnetococcidae and all other alphaproteobacterial taxa,{{cite journal | vauthors = Martijn J, Vosseberg J, Guy L, Offre P, Ettema TJ | title = Deep mitochondrial origin outside the sampled alphaproteobacteria | journal = Nature | volume = 557 | issue = 7703 | pages = 101–105 | date = May 2018 | pmid = 29695865 | doi = 10.1038/s41586-018-0059-5 | bibcode = 2018Natur.557..101M | s2cid = 13740626 | doi-access = free }} 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.

The following taxa have been assigned to the Alphaproteobacteria, but have not been assigned to one or more intervening taxonomic ranks:{{cite web| vauthors = Euzéby JP, Parte AC |url=https://lpsn.dsmz.de/family/alphaproteobacteria-no-family |title=Alphaproteobacteria, not assigned to a family |access-date=June 7, 2021 |publisher=List of Prokaryotic names with Standing in Nomenclature (LPSN)}}

• 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{{cite book | title = Advances in Microbial Physiology | volume = 24 | publisher = Academic Press | date = 1983 | isbn = 0-12-027724-7 | page = 111 | url = https://books.google.com/books?id=VCLiX0d-I4IC | vauthors = Rose AH, Tempest DW, Morris JG }}[https://www.uniprot.org/taxonomy/131 Tuberoidobacter], on: IniProt Taxonomy[https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=131 Tuberoidobacter], on: NCBI Taxonomy Browser
• Species not assigned to a genus
• Vibrio adaptatus Muir et al. 1990
• Vibrio cyclosites Muir et al. 1990

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN). The phylogeny is based on whole-genome analysis.{{cite journal | vauthors = Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M | display-authors = 6 | title = Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of 'Alphaproteobacteria' | journal = Frontiers in Microbiology | volume = 11 | pages = 468 | date = 7 April 2020 | pmid = 32373076 | pmc = 7179689 | doi = 10.3389/fmicb.2020.00468 | doi-access = free }}{{efn|Holosporales and Minwuiales are omitted from this phylogenetic tree.}} Subclass names are based on Ferla et al. (2013).

{{Clade

| style=font-size:75%;line-height:75%

|label1=Bacteria

|1={{clade

|label1=Alphaproteobacteria

|1={{clade

|1={{clade

|1=Magnetococcales

|2=Mariprofundales

}}

|2={{clade

|label1=Rickettsidae

|1={{clade

|1=Rickettsiales (including mitochondria{{cite journal | vauthors = Roger AJ, Muñoz-Gómez SA, Kamikawa R | title = The Origin and Diversification of Mitochondria | journal = Current Biology | volume = 27 | issue = 21 | pages = R1177–R1192 | date = November 2017 | pmid = 29112874 | doi = 10.1016/j.cub.2017.09.015 | doi-access = free | bibcode = 2017CBio...27R1177R }})

|2="Pelagibacterales"

}}

|label2=Caulobacteridae

|2={{clade

|1=Sphingomonadales

|2={{clade

|1=Rhodospirillales

|2={{clade

|1={{clade

|1={{clade

|1={{clade

|1=Rhodothalassiales

|2=Iodidimonadales

}}

|2=Kordiimonadales

}}

|2={{clade

|1=Emcibacterales

|2=Sneathiellales

}}

}}

|2={{clade

|1=Hyphomicrobiales

|2={{clade

|1={{clade

|1=Rhodobacterales

|2=Micropepsales

}}

|2={{clade

|1="Parvularculales"

|2=Caulobacterales

}}

}}

}}

}}

}}

}}

}}

}}

|label2=(outgroup)

|2=Spirochaetota

}}

}}

Although only a few studies have been reported on natural genetic transformation in the Alphaproteobacteria, this process has been described in Agrobacterium tumefaciens,{{cite journal | vauthors = Demanèche S, Kay E, Gourbière F, Simonet P | title = Natural transformation of Pseudomonas fluorescens and Agrobacterium tumefaciens in soil | journal = Applied and Environmental Microbiology | volume = 67 | issue = 6 | pages = 2617–21 | date = June 2001 | pmid = 11375171 | pmc = 92915 | doi = 10.1128/AEM.67.6.2617-2621.2001 | bibcode = 2001ApEnM..67.2617D }} Methylobacterium organophilum,{{cite journal | vauthors = O'Connor M, Wopat A, Hanson RS | title = Genetic transformation in Methylobacterium organophilum | journal = Journal of General Microbiology | volume = 98 | issue = 1 | pages = 265–72 | date = January 1977 | pmid = 401866 | doi = 10.1099/00221287-98-1-265 | doi-access = free }} and Bradyrhizobium japonicum.{{cite journal | vauthors = Raina JL, Modi VV | title = Deoxyribonucleate binding and transformation in Rhizobium jpaonicum | journal = Journal of Bacteriology | volume = 111 | issue = 2 | pages = 356–60 | date = August 1972 | pmid = 4538250 | pmc = 251290 | doi = 10.1128/jb.111.2.356-360.1972 }} 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.

{{notelist}}

{{Reflist|2}}

• {{MeshName|Alphaproteobacteria}}
• [http://www.bacterialphylogeny.info/groupspecific/alphaproteo/alpha.html Bacterial (Prokaryotic) Phylogeny Webpage: Alpha Proteobacteria.] {{Webarchive|url=https://web.archive.org/web/20100510232929/http://www.bacterialphylogeny.info/groupspecific/alphaproteo/alpha.html |date=2010-05-10 }}

{{Bacteria classification}}

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Category:Bacteria classes