Alphaproteobacteria

Alphaproteobacteria
Transmission electron micrograph of Public Library of Science / Scott O'Neill
Scientific classification
Domain:	Bacteria
Phylum:	Pseudomonadota
Class:	Alphaproteobacteria Garrity et al. 2006
Subclasses[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 Trüper 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

Alphaproteobacteria is a

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 ("Candidatus 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
  • 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. 1990

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