[8] 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.

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.

[1] The basal group is Magnetococcidae, composed of a large diversity of magnetotactic bacteria only one of which, Magnetococcus marinus, is formally described.

These molecular signatures provide a means to circumscribe the taxonomic groups and to identify and assign new species accurately.

[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.

[1] Magnetococcales Mariprofundales Rickettsiales (including mitochondria[1][27]) "Pelagibacterales" Sphingomonadales Rhodospirillales Rhodothalassiales Iodidimonadales Kordiimonadales Emcibacterales Sneathiellales Hyphomicrobiales Rhodobacterales Micropepsales "Parvularculales" Caulobacterales Spirochaetota Although only a few studies have been reported on natural genetic transformation in the Alphaproteobacteria, this process has been described in Agrobacterium tumefaciens,[28] Methylobacterium organophilum,[29] and Bradyrhizobium japonicum.

[30] 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.