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:	Proteobacteria
Class:	Alphaproteobacteria Garrity et al. 2006
Subclasses
Magnetococcidae Magnetococcales Magnetococcaceae Magnetococcus marinus Bazylinski et al. 2012 Rickettsidae Rickettsiales Anaplasmataceae Midichloriaceae Rickettsiaceae Pelagibacterales (subgroups I–V)[1] Caulobacteridae Holosporales Caulobacterales Caulobacteraceae Parvularculales Parvularculaceae Rhizobiales Aurantimonadaceae Bartonellaceae Beijerinckiaceae Bradyrhizobiaceae Brucellaceae Cohaesibacteraceae Breoghania Gallego et al. 2011[2] Hyphomicrobiaceae Methylobacteriaceae Methylocystaceae Phyllobacteriaceae Rhizobiaceae Rhodobiaceae Xanthobacteraceae Rhizobiales incertae sedis Hartmannibacter Suarez et al. 2014[3] Nordella La Scola et al. 2004[4][5] Rhodobacterales Rhodobacteraceae Rhodospirillales Acetobacteraceae Rhodospirillaceae Geminicoccaceae Geminicoccus Foesel et al. 2008[6] several Rhodospirillales incertae sedis,[7] e. g.: Reyranella massiliensis Pagnier et al. 2011[8] Elioraea tepidiphila Albuquerque et al. 2008 (syn. Ronia tepidophila)[9][10] Sneathiellales Sneathiellaceae Sphingomonadales Erythrobacteraceae Sphingomonadaceae Kiloniellales Kiloniella, Kopriimonas, Rhodovibrio, and Pelagibius[7] Kordiimonadales Kordiimonas and Rhodothalassium[7] Eilatimonas Paramasivam et al. 2013[11] Orders incertae sedis Micropepsales Harbison et al. 2017 Micropepsaceae Rhizomicrobium Ueki et al. 2010[12] Genera incertae sedis Phreatobacter Tóth et al. 2014 emend. Lee et al. 2017 Micavibrio Lambina et al. 1989 [Vibrio] adaptatus and [V.] cyclosites Muir et al. 1990 Furvibacter Lee et al. 2007 Polymorphum gilvum Cai 2010 Subaequorebacter tamlense Lee 2006[13] Tuberoidobacter mutans Nikitin 1983[14][15][16]

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 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     ?Furvibacter ♠ Lee et al. 2007     ?Kopriimonas byunsanensis ♠ Kwon et al. 2005     ?Magnetococcus marinus Bazylinski et al. 2012 (in press)     ?Micavibrio aeruginosavorus ♠ Lambina et al. 1983     ?Polymorphum gilvum ♠ Cai 2010     ?Reyranella massiliensis Pagnier et al. 2011     ?Ronia tepidophila ♠     ?Subaequorebacter tamlense ♠ Lee 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       Rickettsiales       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]
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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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16. Tuberoidobacter, on: NCBI Taxonomy Browser
17. Brenner, Don J.; Krieg, Noel R.; Staley, James T. (July 26, 2005) [1984(Williams & Wilkins)]. George M. Garrity (ed.). The Proteobacteria. Bergey's Manual of Systematic Bacteriology. 2C (2nd ed.). New York: Springer. p. 1388. ISBN 978-0-387-24145-6. British Library no. GBA561951.
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External links

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