Alphaproteobacteria is a
class
Class or The Class may refer to:
Common uses not otherwise categorized
* Class (biology), a taxonomic rank
* Class (knowledge representation), a collection of individuals or objects
* Class (philosophy), an analytical concept used differently ...
of
bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...
in the
phylum
In biology, a phylum (; plural: phyla) is a level of classification or taxonomic rank below kingdom and above class. Traditionally, in botany the term division has been used instead of phylum, although the International Code of Nomenclature ...
Pseudomonadota
Pseudomonadota (synonym Proteobacteria) is a major phylum of Gram-negative bacteria. The renaming of phyla in 2021 remains controversial among microbiologists, many of whom continue to use the earlier names of long standing in the literature. Th ...
(formerly Proteobacteria).
The
Magnetococcales and
Mariprofundales
''Mariprofundus ferrooxydans'' is a neutrophilic, chemolithotrophic, Gram-negative bacterium which can grow by oxidising ferrous to ferric iron. It is one of the few members of the class Zetaproteobacteria in the phylum Pseudomonadota. It is ty ...
are considered basal or sister to the Alphaproteobacteria.
The Alphaproteobacteria are highly diverse and possess few commonalities, but nevertheless share a common ancestor. Like all ''Proteobacteria'', its members are
gram-negative
Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wa ...
and some of its intracellular parasitic members lack
peptidoglycan
Peptidoglycan or murein is a unique large macromolecule, a polysaccharide, consisting of sugars and amino acids that forms a mesh-like peptidoglycan layer outside the plasma membrane, the rigid cell wall (murein sacculus) characteristic of most ba ...
and are consequently gram variable.
[
]
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
''Rhizobium'' is a genus of Gram-negative soil bacteria that fix nitrogen. ''Rhizobium'' species form an endosymbiotic nitrogen-fixing association with roots of (primarily) legumes and other flowering plants.
The bacteria colonize plant cells ...
'' spp.), endosymbiont
An ''endosymbiont'' or ''endobiont'' is any organism that lives within the body or cells of another organism most often, though not always, in a mutualistic relationship.
(The term endosymbiosis is from the Greek: ἔνδον ''endon'' "within ...
s of arthropods (''Wolbachia
''Wolbachia'' is a genus of intracellular bacteria that infects mainly arthropod species, including a high proportion of insects, and also some nematodes. It is one of the most common parasitic microbes, and is possibly the most common reproducti ...
'') and intracellular pathogen
In biology, a pathogen ( el, πάθος, "suffering", "passion" and , "producer of") in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a g ...
s (''e.g. Rickettsia
''Rickettsia'' is a genus of nonmotile, gram-negative, nonspore-forming, highly pleomorphic bacteria that may occur in the forms of cocci (0.1 μm in diameter), bacilli (1–4 μm long), or threads (up to about 10 μm long). The term "ricke ...
''). Moreover, the class is sister to the protomitochondrion
The proto-mitochondrion is the hypothetical ancestral bacterial endosymbiont from which all mitochondria in eukaryotes are thought to descend, after an episode of symbiogenesis which created the aerobic eukaryotes.
Phylogeny
The phylogenetic ...
, the bacterium that was engulfed by the eukaryotic ancestor and gave rise to the mitochondria
A mitochondrion (; ) is an organelle found in the cells of most Eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is used ...
, which are organelles in eukaryotic cells (See endosymbiotic theory
Symbiogenesis (endosymbiotic theory, or serial endosymbiotic theory,) is the leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms. The theory holds that mitochondria, plastids such as chloroplasts, and possib ...
).Rhizobium radiobacter
''Agrobacterium radiobacter'' (more commonly known as ''Agrobacterium tumefaciens'') is the causal agent of crown gall disease (the formation of tumours) in over 140 species of eudicots. It is a rod-shaped, Gram-negative soil bacterium. Sympto ...
'' (formerly ''Agrobacterium tumefaciens''): scientists often use this species to transfer foreign DNA into plant genomes. Aerobic anoxygenic phototrophic bacteria Aerobic anoxygenic phototrophic bacteria (AAPBs) are Alphaproteobacteria and Gammaproteobacteria that are obligate aerobes that capture energy from light by anoxygenic photosynthesis. Anoxygenic photosynthesis is the phototrophic process where light ...
, 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
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological s ...
of the orders
Order, ORDER or Orders may refer to:
* Categorization, the process in which ideas and objects are recognized, differentiated, and understood
* Heterarchy, a system of organization wherein the elements have the potential to be ranked a number of ...
, especially for the location of the ''Pelagibacterales
The Pelagibacterales are an order in the Alphaproteobacteria composed of free-living marine bacteria that make up roughly one in three cells at the ocean's surface. Overall, members of the ''Pelagibacterales'' are estimated to make up between a q ...
'', but overall there is some consensus. The discord stems from the large difference in gene content (''e.g.'' genome streamlining Genomic streamlining is a theory in evolutionary biology and microbial ecology that suggests that there is a reproductive benefit to prokaryotes having a smaller genome size with less non-coding DNA and fewer non-essential genes. There is a lot o ...
in ''Pelagibacter ubique'') and the large difference in GC-content
In molecular biology and genetics, GC-content (or guanine-cytosine content) is the percentage of nitrogenous bases in a DNA or RNA molecule that are either guanine (G) or cytosine (C). This measure indicates the proportion of G and C bases out ...
between members of several orders.convergent evolution
Convergent evolution is the independent evolution of similar features in species of different periods or epochs in time. Convergent evolution creates analogous structures that have similar form or function but were not present in the last com ...
that would result in an artefactual clustering. However, several studies disagree.ribosomal RNA
Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from riboso ...
(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
The Pelagibacterales are an order in the Alphaproteobacteria composed of free-living marine bacteria that make up roughly one in three cells at the ocean's surface. Overall, members of the ''Pelagibacterales'' are estimated to make up between a q ...
'' and '' Rickettsiales'', even though they are more closely related to species with high genomic GC-contents than to members of the latter two orders.magnetotactic bacteria
Magnetotactic bacteria (or MTB) are a polyphyletic group of bacteria that orient themselves along the magnetic field lines of Earth's magnetic field. Discovered in 1963 by Salvatore Bellini and rediscovered in 1975 by Richard Blakemore, this ...
, 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 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. 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''.
The phylogeny of Alphaproteobacteria has constantly been revisited and updated. There are some debates for the inclusion of ''Magnetococcidae'' in Alphaproteobacteria. For example, an independent proteobacterial class (''Etaproteobacteria'') for ''Magnetococcidae'' has been proposed. A recent phylogenomic study suggests the placement of the protomitochondrial clade between ''Magnetococcidae'' and all other alphaproteobacterial taxa,
''Incertae Sedis''
The following taxa have been assigned to the Alphaproteobacteria, but have not been assigned to one or more intervening taxonomic ranks:
on: NCBI Taxonomy Browser
* Species not assigned to a genus
** ''
Vibrio adaptatus''
Muir ''et al''. 1990
** ''
Vibrio cyclosites''
Muir ''et al''. 1990
Phylogeny
The currently accepted taxonomy is based on the
List of Prokaryotic names with Standing in Nomenclature
List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the nomenclature, naming and Taxonomy (biology), taxonomy of prokaryotes, following the taxonomy requirements and rulings of the In ...
(LPSN).
[ The phylogeny is based on whole-genome analysis.]
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
''Agrobacterium radiobacter'' (more commonly known as ''Agrobacterium tumefaciens'') is the causal agent of crown gall disease (the formation of tumours) in over 140 species of eudicots. It is a rod-shaped, Gram-negative soil bacterium. Symptom ...
'',Bradyrhizobium japonicum
''Bradyrhizobium japonicum'' is a species of legume- root nodulating, microsymbiotic nitrogen-fixing bacteria. The species is one of many Gram-negative, rod-shaped bacteria commonly referred to as rhizobia. Within that broad classification, w ...
''.DNA transfer
In molecular biology and genetics, transformation is the genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material from its surroundings through the cell membrane(s). For transformation to ...
from one bacterial cell to another through the intervening medium, and the integration of the donor sequence into the recipient genome by homologous recombination
Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids (usually DNA as in cellular organisms but may ...
.
Notes
References
External links
*
Bacterial (Prokaryotic) Phylogeny Webpage: Alpha Proteobacteria.
{{Taxonbar, from=Q306579
Bacteria classes