Alphaproteobacteria

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 includes (as an extinct member) 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).[7] A species of technological interest is Rhizobium radiobacter (formerly Agrobacterium tumefaciens): scientists often use this species to transfer foreign DNA into plant genomes.[19] 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.

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-richness between members of several orders.[7] 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.[20][21][22] However, several studies disagree.[7][23][24][25]

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.[7]

The Class Alphaproteobacteria is divided into three subclasses Magnetococcidae, Rickettsidae and Caulobacteridae.[7] The basal group is Magnetococcidae, which is composed by a large diversity of magnetotactic bacteria, but only one is described, Magnetococcus marinus.[26] 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.[27] 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.[28][29]

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [18] and National Center for Biotechnology Information (NCBI)[30] and the phylogeny is based on 16S rRNA-based LTP release 106 by 'The All-Species Living Tree' Project [31]

Notes:
♠ Strains found at the National Center for Biotechnology Information (NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LSPN).

Aquaspirillum is now regarded to belong to Betaproteobacteria. A newer tree based on 16S and 23S rRNA (and other data) is given by Ferla et al. (2013) as follows:

An updated phylogeny of the alphaproteobacteria was published in which the position of the Mitochondria is not clear yet. [32]

Although only a few studies have been reported on natural genetic transformation in the Alphaproteobacteria, this process has been described in Agrobacterium tumefaciens,[33] Methylobacterium organophilum,[34] and Bradyrhizobium japonicum.[35] 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.

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