Alphaproteobacteria

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 Rickettsidae Rickettsiales Anaplasmataceae Midichloriaceae Rickettsiaceae Pelagibacterales (subgroups I–V) Caulobacteridae Holosporales Caulobacterales Caulobacteraceae Parvularculales Parvularculaceae Rhizobiales Aurantimonadaceae Bartonellaceae Beijerinckiaceae Bradyrhizobiaceae Brucellaceae Cohaesibacteraceae Hyphomicrobiaceae Methylobacteriaceae Methylocystaceae Phyllobacteriaceae Rhizobiaceae Rhodobiaceae Xanthobacteraceae Rhodobacterales Rhodobacteraceae Rhodospirillales Acetobacteraceae Rhodospirillaceae several unclassified Rhodospirillales Sneathiellales Sneathiellaceae Sphingomonadales Erythrobacteraceae Sphingomonadaceae Kiloniellales Kiloniella, Kopriimonas, Rhodovibrio, and Pelagibius Kordiimonadales Kordiimonas and Rhodothalassium

Alphaproteobacteria is a class of bacteria in the phylum Proteobacteria (See also bacterial taxonomy). Its members are highly diverse and possess few commonalities, but nevertheless share a common ancestor. Like most members of the Proteobacteria, most of its members are Gram-negative and some of its intracellular parasitic members lack peptidoglycan and are consequently gram variable.

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). A species of technological interest is Rhizobium radiobacter (formerly Agrobacterium tumefaciens): scientists often use this species to transfer foreign DNA into plant genomes. Aerobic anoxygenic phototrophic bacteria, such as Pelagibacter ubique, are alphaproteobacteria that are a widely distributed marine plankton that 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. This issue stems form the large difference in gene content (e.g. genome streamlining in Pelagibacter ubique) and the large difference in GC-richness between members of several order. Specifically,Pelagibacterales, Rickettsiales and Holosporales contains 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. However, several studies disagree,. Furthermore, it has been found that the GC-content of ribosomal RNA, the traditional phylogenetic marker, little reflects the GC-content of the genome: for example, members of the Holosporales have a much higher ribosomal GC-content than members of the Pelagibacterales and Rickettsiales, which have similarly low genomic GC-content, because they are more closely related to species with high genomic GC-contents than to members of the latter two orders

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

Phylogeny

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

?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 & Streptomyces longisporoflavus]

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)

External links

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