Anoxyphotobacteria (Gibbons and Murray 1978) Murray 1988
Photobacteria Gibbons and Murray 1978 (Approved Lists 1980)
Alphabacteria Cavalier-Smith 2002
Alphaproteobacteria is a
class of
bacteria in the
phylumPseudomonadota (formerly "Proteobacteria").[4] The Magnetococcales and Mariprofundales are considered basal or sister to the Alphaproteobacteria.[5][6] 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.[4][3]
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).[1][7] A species of technological interest is Rhizobium radiobacter (formerly Agrobacterium tumefaciens): scientists often use this species to transfer foreign DNA into plant genomes.[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.
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.[1] Specifically, Pelagibacterales, Rickettsiales and Holosporales contain species with AT-rich genomes.[jargon] It has been argued that it could be a case of
convergent evolution that would result in an artefactual clustering.[9][10][11] However, several studies disagree.[1][12][13][14]
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.[1]
Comparative analyses of the
sequenced genomes have also led to discovery of many
conservedinsertion-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]
^Chilton MD, Drummond MH, Merio DJ, Sciaky D, Montoya AL, Gordon MP, Nester EW (June 1977). "Stable incorporation of plasmid DNA into higher plant cells: the molecular basis of crown gall tumorigenesis". Cell. 11 (2): 263–71.
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10.1016/0092-8674(77)90043-5.
PMID890735.
S2CID7533482.
^Bazylinski DA, Williams TJ, Lefèvre CT, Berg RJ, Zhang CL, Bowser SS, Dean AJ, Beveridge TJ (2012). "Magnetococcus marinus gen. nov., sp. nov., a marine, magnetotactic bacterium that represents a novel lineage (Magnetococcaceae fam. nov.; Magnetococcales ord. nov.) at the base of the Alphaproteobacteria". Int J Syst Evol Microbiol. 63 (Pt 3): 801–808.
doi:
10.1099/ijs.0.038927-0.
PMID22581902.
^Gupta RS (2005). "Protein signatures distinctive of alpha proteobacteria and its subgroups and a model for alpha-proteobacterial evolution". Critical Reviews in Microbiology. 31 (2): 101–35.
doi:
10.1080/10408410590922393.
PMID15986834.
S2CID30170035.
^Gupta RS, Sneath PH (January 2007). "Application of the character compatibility approach to generalized molecular sequence data: branching order of the proteobacterial subdivisions". Journal of Molecular Evolution. 64 (1): 90–100.
Bibcode:
2007JMolE..64...90G.
doi:
10.1007/s00239-006-0082-2.
PMID17160641.
S2CID32775450.
^Ji B, Zhang SD, Zhang WJ, Rouy Z, Alberto F, Santini CL, et al. (March 2017). "The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of Proteobacteria". Environmental Microbiology. 19 (3): 1103–1119.
doi:
10.1111/1462-2920.13637.
PMID27902881.
S2CID32324511.