Alphaproteobacteria

''Alphaproteobacteria'' or ''α-proteobacteria'', also called ''α-Purple bacteria'' in earlier literature, is a class of bacteria in the phylum '' Pseudomonadota'' (formerly "Proteobacteria"). The '' Magnetococcales'' and '' Mariprofundales'' are considered basal or sister to the ''Alphaproteobacteria''. The ''Alphaproteobacteria'' are highly diverse and possess few commonalities, but nevertheless share a common ancestor. Like all ''Proteobacteria'', its members are gram-negative, although some of its intracellular parasitic members lack peptidoglycan and are consequently gram variable.

Characteristics

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). A species of technological interest is '' Rhizobium radiobacter'' (formerly ''Agrobacterium tumefaciens''): scientists often use this species to transfer foreign DNA into plant genomes. 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

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, several studies disagree 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. 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. 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''.

Other phylogenetic debates turn on the placement of ''Magnetococcidae'' and the protomitochondrion. There are some debates for the inclusion of ''Magnetococcidae'' in ''Alphaproteobacteria''. For example, an independent proteobacterial class ("''Candidatus'' Etaproteobacteria") for ''Magnetococcidae'' has been proposed. A recent phylogenomic study suggests the placement of the protomitochondrial clade between ''Magnetococcidae'' and all other alphaproteobacterial taxa, 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:
* 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 1983Tuberoidobacter
on: NCBI Taxonomy Browser
* 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). The phylogeny is based on whole-genome analysis. Subclass names are based on Ferla ''et al''. (2013).

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'', '' Methylobacterium organophilum'', and '' Bradyrhizobium japonicum''. 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

References

External links

*

Bacterial (Prokaryotic) Phylogeny Webpage: Alpha Proteobacteria.

{{Taxonbar, from=Q306579

Bacteria classes