Alphaproteobacteria

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Alphaproteobacteria
Wolbachia.png
Transmission electron micrograph of Wolbachia within an insect cell.
Credit:Public Library of Science / Scott O'Neill
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Domain: Bacteria
Phylum: Pseudomonadota
Class: Alphaproteobacteria
Garrity et al. 2006
Subclasses [1] and Orders [2]
Synonyms [2]
  • CaulobacteriaCavalier-Smith 2020
  • Anoxyphotobacteria(Gibbons and Murray 1978) Murray 1988
  • PhotobacteriaGibbons and Murray 1978 (Approved Lists 1980)
  • AlphabacteriaCavalier-Smith 2002

Alphaproteobacteria is a class of bacteria in the phylum Pseudomonadota (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] [2]

Contents

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]

The Class Alphaproteobacteria is divided into three subclasses Magnetococcidae, Rickettsidae and Caulobacteridae. [1] The basal group is Magnetococcidae , which is composed by a large diversity of magnetotactic bacteria, but only one is described, Magnetococcus marinus . [15] 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. [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]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN). [2] The phylogeny is based on whole-genome analysis. [6] [lower-alpha 1] Subclass names are based on Ferla et al. (2013). [1]


  Bacteria  

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 , [28] Methylobacterium organophilum , [29] and Bradyrhizobium japonicum . [30] 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.

Notes

  1. ↑ Holosporales and Minwuiales are omitted from this phylogenetic tree.

Related Research Articles

<span class="mw-page-title-main">Pseudomonadota</span> Phylum of Gram-negative bacteria

Pseudomonadota is a major phylum of Gram-negative bacteria. Currently, they are considered the predominant phylum within the realm of bacteria. They are naturally found as pathogenic and free-living (non-parasitic) genera. The phylum comprises six classes Acidithiobacilia, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Hydrogenophilia, and Zetaproteobacteria. The Pseudomonadota are widely diverse, with differences in morphology, metabolic processes, relevance to humans, and ecological influence.

The Chloroflexia are a class of bacteria in the phylum Chloroflexota. Chloroflexia are typically filamentous, and can move about through bacterial gliding. It is named after the order Chloroflexales.

<span class="mw-page-title-main">Chlamydiota</span> Phylum of bacteria

The Chlamydiota are a bacterial phylum and class whose members are remarkably diverse, including pathogens of humans and animals, symbionts of ubiquitous protozoa, and marine sediment forms not yet well understood. All of the Chlamydiota that humans have known about for many decades are obligate intracellular bacteria; in 2020 many additional Chlamydiota were discovered in ocean-floor environments, and it is not yet known whether they all have hosts. Historically it was believed that all Chlamydiota had a peptidoglycan-free cell wall, but studies in the 2010s demonstrated a detectable presence of peptidoglycan, as well as other important proteins.

<i>Candidatus Pelagibacter communis</i> Species of bacterium

"Candidatus Pelagibacter", with the single species "Ca. P. communis", was isolated in 2002 and given a specific name, although it has not yet been described as required by the bacteriological code. It is an abundant member of the SAR11 clade in the phylum Alphaproteobacteria. SAR11 members are highly dominant organisms found in both salt and fresh water worldwide and were originally known only from their rRNA genes, first identified in the Sargasso Sea in 1990 by Stephen Giovannoni's laboratory at Oregon State University and later found in oceans worldwide. "Ca. P. communis" and its relatives may be the most abundant organisms in the ocean, and quite possibly the most abundant bacteria in the entire world. It can make up about 25% of all microbial plankton cells, and in the summer they may account for approximately half the cells present in temperate ocean surface water. The total abundance of "Ca. P. communis" and relatives is estimated to be about 2 × 1028 microbes.

<span class="mw-page-title-main">Rickettsiales</span> Order of bacteria

The Rickettsiales, informally called rickettsias, are an order of small Alphaproteobacteria. They are obligate intracellular parasites, and some are notable pathogens, including Rickettsia, which causes a variety of diseases in humans, and Ehrlichia, which causes diseases in livestock. Another genus of well-known Rickettsiales is the Wolbachia, which infect about two-thirds of all arthropods and nearly all filarial nematodes. Genetic studies support the endosymbiotic theory according to which mitochondria and related organelles developed from members of this group.

<span class="mw-page-title-main">Sphingomonadaceae</span> Family of bacteria

Sphingomonadaceae are a gram-negative bacterial family of the Alphaproteobacteria. An important feature is the presence of sphingolipids in the outer membrane of the cell wall. The cells are ovoid or rod-shaped. Others are also pleomorphic, i.e. the cells change the shape over time. Some species from Sphingomonadaceae family are dominant components of biofilms.

<span class="mw-page-title-main">Rickettsiaceae</span> Family of bacteria

The Rickettsiaceae are a family of bacteria. The genus Rickettsia is the most prominent genus within the family. The bacteria that eventually formed the mitochondrion is believed to have originated from this family. Most human pathogens in this family are in genus Rickettsia. They spend part of their lifecycle in the bodies of arthropods such as ticks or lice, and are then transmitted to humans or other mammals by the bite of the arthropod. It contains Gram-negative bacteria, very sensitive to environmental exposure, thus is adapted to obligate intracellular infection. Rickettsia rickettsii is considered the prototypical infectious organism in the group.

<span class="mw-page-title-main">Ehrlichiaceae</span> Family of bacteria

The Ehrlichiaceae are a family of bacteria, included in the order Rickettsiales.

The Holosporaceae are a family of bacteria. The member Holospora is an intracellular parasite found in the unicellular protozoa Paramecium.

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.

"Candidatus Midichloria" is a candidatus genus of Gram-negative, non-endospore-forming bacteria, with a bacillus shape around 0.45 μm in diameter and 1.2 μm in length. First described in 2004 with the temporary name IricES1, "Candidatus Midichloria" species are symbionts of several species of hard ticks. They live in the cells of the ovary of the females of this tick species. These bacteria have been observed in the mitochondria of the host cells, a trait that has never been described in any other symbiont of animals.

<span class="mw-page-title-main">Gracilicutes</span> Infrakingdom of bacteria

Gracilicutes is a clade in bacterial phylogeny.

<span class="mw-page-title-main">Pelagibacterales</span> Order of bacteria

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 quarter and a half of all prokaryotic cells in the ocean.

Nitrospirota is a phylum of bacteria. It includes multiple genera, such as Nitrospira, the largest. The first member of this phylum, Nitrospira marina, was discovered in 1985. The second member, Nitrospira moscoviensis, was discovered in 1995.

<span class="mw-page-title-main">Bacterial phyla</span> Phyla or divisions of the domain Bacteria

Bacterial phyla constitute the major lineages of the domain Bacteria. While the exact definition of a bacterial phylum is debated, a popular definition is that a bacterial phylum is a monophyletic lineage of bacteria whose 16S rRNA genes share a pairwise sequence identity of ~75% or less with those of the members of other bacterial phyla.

There are several models of the Branching order of bacterial phyla, one of these was proposed in 1987 paper by Carl Woese.

Nanohaloarchaea is a clade of diminutive archaea with small genomes and limited metabolic capabilities, belonging to the DPANN archaea. They are ubiquitous in hypersaline habitats, which they share with the extremely halophilic haloarchaea.

The Pelagibacteraceae are a family in the Alphaproteobacteria composed of free-living marine bacteria.

The Magnetococcales were an order of Alphaproteobacteria, but now the mitochondria are considered as sister to the alphaproteobactera, together forming the sister the marineproteo1 group, together forming the sister to Magnetococcidae.

<span class="mw-page-title-main">Asgard (archaea)</span> Proposed superphylum of archaea

Asgard or Asgardarchaeota is a proposed superphylum consisting of a group of archaea that contain eukaryotic signature proteins. It appears that the eukaryotes, the domain that contains the animals, plants, and fungi, emerged within the Asgard, in a branch containing the Heimdallarchaeota. This supports the two-domain system of classification over the three-domain system.

References

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  2. 1 2 3 4 Euzéby JP, Parte AC. "Alphaproteobacteria". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved May 31, 2021.
  3. ↑ Grote J, Thrash JC, Huggett MJ, Landry ZC, Carini P, Giovannoni SJ, Rappé MS (2012). "Streamlining and core genome conservation among highly divergent members of the SAR11 clade". mBio. 3 (5): e00252-12. doi:10.1128/mBio.00252-12. PMC   3448164 . PMID   22991429.
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  6. 1 2 Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, et al. (7 April 2020). "Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of 'Alphaproteobacteria'". Frontiers in Microbiology. 11: 468. doi: 10.3389/fmicb.2020.00468 . PMC   7179689 . PMID   32373076.
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  10. ↑ Viklund J, Ettema TJ, Andersson SG (February 2012). "Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade". Molecular Biology and Evolution. 29 (2): 599–615. doi:10.1093/molbev/msr203. PMID   21900598.
  11. ↑ Viklund J, Martijn J, Ettema TJ, Andersson SG (2013). "Comparative and phylogenomic evidence that the alphaproteobacterium HIMB59 is not a member of the oceanic SAR11 clade". PLOS ONE. 8 (11): e78858. Bibcode:2013PLoSO...878858V. doi: 10.1371/journal.pone.0078858 . PMC   3815206 . PMID   24223857. Open Access logo PLoS transparent.svg
  12. ↑ Georgiades K, Madoui MA, Le P, Robert C, Raoult D (2011). "Phylogenomic analysis of Odyssella thessalonicensis fortifies the common origin of Rickettsiales, Pelagibacter ubique and Reclimonas americana mitochondrion". PLOS ONE. 6 (9): e24857. Bibcode:2011PLoSO...624857G. doi: 10.1371/journal.pone.0024857 . PMC   3177885 . PMID   21957463. Open Access logo PLoS transparent.svg
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  16. ↑ 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. PMID   15986834. S2CID   30170035.
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  19. ↑ Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, et al. (2020-04-07). "Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of 'Alphaproteobacteria'". Frontiers in Microbiology. 11: 468. doi: 10.3389/fmicb.2020.00468 . PMC   7179689 . PMID   32373076.
  20. ↑ Muñoz-Gómez SA, Hess S, Burger G, Lang BF, Susko E, Slamovits CH, Roger AJ (February 2019). Rokas A, Wittkopp PJ, Irisarri I (eds.). "An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins". eLife. 8: e42535. doi: 10.7554/eLife.42535 . PMC   6447387 . PMID   30789345.
  21. ↑ 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. PMID   27902881. S2CID   32324511.
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