alphaproteobacteria

Alphaproteobacteria 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 and some of its intracellular parasitic members lack peptidoglycan and are consequently gram variable.

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). 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

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. Specifically, ''Pelagibacterales'', ''Rickettsiales'' and ''Holosporales'' contain species with AT-rich genomes. It has been argued that it could be a case of convergent evolution that would result in an artefactual clustering. However, several studies disagree.

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.

The Class ''Alphaproteobacteria'' is divided into three subclasses ''Magnetococcidae'', ''Rickettsidae'' and ''Caulobacteridae''. The basal group is ''Magnetococcidae'', which is composed by a large diversity of magnetotactic bacteria, but only one is described, ''Magnetococcus marinus''. 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. 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''.

The phylogeny of Alphaproteobacteria has constantly been revisited and updated. There are some debates for the inclusion of ''Magnetococcidae'' in Alphaproteobacteria. For example, an independent proteobacterial class (''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