Alphaproteobacteria

Alphaproteobacteria is a class of bacteria in the phylum Proteobacteria (See also bacterial taxonomy).[17] Its members 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.[17][18]

Alphaproteobacteria
Transmission electron micrograph of Wolbachia within an insect cell.
Credit:Public Library of Science / Scott O'Neill
Scientific classification
Domain:
Bacteria
Phylum:
Class:
Alphaproteobacteria

Garrity et al. 2006
subclasses

Characteristics

The Alphaproteobacteria is 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.

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-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]

Phylogeny

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]

?Aquaspirillum polymorphum(Williams and Rittenberg 1957) Hylemon et al. 1973

?FurvibacterLee et al. 2007

?Kopriimonas byunsanensisKwon et al. 2005

?Magnetococcus marinus Bazylinski et al. 2012 (in press)

?Micavibrio aeruginosavorusLambina et al. 1983

?Polymorphum gilvumCai 2010

?Reyranella massiliensis Pagnier et al. 2011

?Ronia tepidophila

?Subaequorebacter tamlenseLee 2006

?Tuberoidobacter mutans

?Vibrio adaptatus Muir et al. 1990

?Vibrio cyclosites Muir et al. 1990

Rhodovibrio

Rhodospirillaceae 2

Tistrella

Rhodospirillaceae 3

Rhodospirillaceae 4

Defluviicoccus vanus Maszenan et al. 2005

Elioraea tepidiphila Albuquerque et al. 2008

Acetobacteraceae

Rickettsiales [incl. Mitochondrion]

Sneathiella

Sphingomonadaceae [incl. Erythrobacteraceae, Caulobacter leidyi, Asticcacaulis]

Rhodothalassium salexigens (Drews 1982) Imhoff et al. 1998

Kordiimonas

Rhodospirillaceae 1 [incl. Roseospirillum parvum, Kiloniella laminariae, Terasakiella pusilla]

Rhizobiales [incl. Caulobacteraceae, Rhodobacteraceae, Parvularcula]

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:

Schematic ribosomal RNA phylogeny of Alphaproteobacteria
  Magnetococcidae  

  Magnetococcus marinus

  Caulobacteridae  

  Rhodospirillales, Sphingomonadales,
  Rhodobacteraceae, Rhizobiales, etc.

  Holosporales

  Rickettsidae  
  Pelagibacterales  
  Pelagibacteraceae  

  Pelagibacter

  Subgroups Ib, II, IIIa, IIIb, IV and V

  Proto-mitochondria

  Anaplasmataceae  

  Ehrlichia

  Anaplasma

  Wolbachia

  Neorickettsia

  Midichloriaceae  

  Midichloria

  Rickettsiaceae  

  Rickettsia

  Orientia

The cladogram of Rickettsidae has been inferred by Ferla et al. [7] from the comparison of 16S + 23S ribosomal RNA sequences.

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,[32] Methylobacterium organophilum,[33] and Bradyrhizobium japonicum.[34] 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.

References

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  2. Breoghania, on: NCBI Taxonomy Browser
  3. Hartmannibacter, on: NCBI Taxonomy Browser
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  5. Nordella, on: NCBI Taxonomy Browser]
  6. Geminicoccus, on: NCBI Taxonomy Browser
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  8. Reyranella, on: NCBI Taxonomy Browser
  9. Elioraea tepidiphila (SPECIES), on: UniProt Taxonomy
  10. Elioraea tepidiphila, on: NCBI Taxonomy Broeser
  11. Eilatimonas, on: NCBI Taxonomy Browser
  12. Rhizomicrobium, on: NCBI Taxonomy Browser
  13. Subaequorebacter, on: NCBI Taxonomy Browser
  14. Advances in Microbial Physiology, Vol. 24, Academic Press, 1983-07-12,ISBN 0-12-027724-7 , p. 111
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