Proteobacteria

Novosphingobium sp., from MiDAS. Scale bar = 5 µm.

Belongs within: Gracilicutes.
Contains: Chromatibacteria, Rickettsiales, Rhodospirillales, Rhodobacteraceae, Rhizobiales.

The Proteobacteria are a diverse clade of bacteria united by molecular data.

Alpha bacteria
Published 8 October 2015
Two budding individuals of Caulobacter crescentus, from the US Dept of Energy.

From about the 1980s onwards, the increasing application of molecular data (particularly the sequences of ribosomal RNA genes) to bacterial phylogeny meant that what had previously been an intractable mass of diversity began to emerge into some sort of order. One of the major new groups of bacteria to be recognised in this way was the Proteobacteria, a hyperdiverse array that includes many of those bacteria of direct significance to ourselves. Within this bacterial supergroup, the phylogeneticists also resolved five major subgroups that, in the absence of any more obvious markers, they labelled alphabetically: the alpha, beta, gamma, delta and epsilon Proteobacteria. Eventually these convenient labels would become formalised, and it is with the group known as the Alphaproteobacteria that I am concerned today.

Like the other proteobacterial lineages, the Alphaproteobacteria are diverse in features and habits. To the best of my knowledge, no uniting characteristic has yet been identified for members of this group other than their shared ribosomal heritage. Many of the Alphaproteobacteria are associated with anoxic habitats. Many are at least facultatively photosynthetic, obtaining energy from sunlight by means of bacteriochlorophyll a and/or carotenoids; these factors give such bacteria a purple coloration. Other Alphaproteobacteria are intracellular parasites of eukaryotes, including a number that are of medical significance to humans.

Culture of vinegar bacteria Acetobacter aceti, copyright Эрг.

A recent study of Alphaproteobacteria ribosomal phylogeny by Ferla et al. (2013) recognised three major lineages within the group which they dubbed the Magnetococcidae, Rickettsidae and Caulobacteridae. The Caulobacteridae include the greater number of the named free-living Alphaproteobacteria: both of the orders covered in earlier posts, for instance, belong to this lineage. Detailed coverage of the various members of Caulobacteridae would fill a book, so I’ll just mention some highlights. The earlier post on Rhodospirillales mentioned the family Acetobacteraceae, but one important detail I neglected to mention was that many members of this family obtain their energy by oxidising ethanol to acetic acid: these are the bacteria responsible for producing ethanol. Also potentially belonging to the Rhodospirillales is Sporospirillum, a candidate genus of enormous bacteria that have been found in the intestines of tadpoles. Individuals of Sporospirillum reach up to one-tenth of a millimetre in length, potentially large enough to be observed with a standard dissecting microscope, though they are only up to 5 µm in width. Because Sporospirillum have never been cultured or studied from a molecular perspective, their relationships remain uncertain: they may alternatively belong to the Spirillaceae, a family of the Betaproteobacteria (Brenner et al. 2005).

Also belonging to the Caulobacteridae are the Caulobacterales. As recognised by Ferla et al. (2013), this order contains two families, the Caulobacteraceae and Hyphomonadaceae. Many (but not all) of the members of these families have a distinctive life cycle, in which a previously motile individual loses its flagellum and grows an elongate stalk. This now-immotile individual then produces a motile offspring by budding at one end. The manner of budding differs between the two families: in the Caulobacteraceae, the stalk functions as an attachment to the substrate and the offspring buds from the unattached end of the cell, but in the Hyphomonadaceae the stalk is not an attachment organ and the offspring buds from the end of the stalk. Similar modes of growth and budding are found in other families of the Caulobacteridae, such as the Hyphomicrobiaceae in the Rhizobiales.

TEM view of Magnetococcus marinus, showing the line of magnetic particles (magnetosomes).

The other subclasses of the Alphaproteobacteria are smaller than the Caulobacteridae in terms of numbers of named species, but this may reflect our low appreciation of bacterial diversity more than environmental reality. The Magnetococcidae are represented by only a single named species, Magnetococcus marinus. This is an aquatic chemolithoautotroph, obtaining energy from sulphur compounds. Cells of Magnetococcus contain a row of magnetic particles that the bacterium uses to orient itself. Though only one species of magnetococcid has been named to date, environmental DNA samples indicate that many more await description (Bazylinski et al. 2013).

The ciliate Paramecium, infected with Holospora (in the swollen nucleus in the lower part of the photo). Photo from here.

The named members of the Rickettsidae are mostly placed in the order Rickettsiales, an assemblage of intracellular parasites of eukaryotes. This order contains two families, the Rickettsiaceae and Anaplasmataceae; a third family, the Holosporaceae, that contains intracellular endosymbionts of large protozoans such as Paramecium and Acanthamoeba, was found by Ferla et al. (2013) to be potentially closer to the Caulobacteridae than the Rickettsidae. Members of the Rickettsiales of significance to humans include those causing such diseases as typhus or spotted fever. The Anaplasmataceae also includes the genus Wolbachia which has come under the spotlight in recent years for the significance that its effects on reproductive compatibility may have for the evolution of insects.

The only free-living bacterium associated with the Rickettsidae to date is the marine Pelagibacter ubique but, again, environmental DNA samples suggest that this is merely a representative of a larger undescribed group, commonly referred to as the ‘SAR11’ clade. Indeed, Pelagibacter and its relatives may be the most numerous organisms on the entire planet, making up about a third of the planktonic cells in the surface layers of the world’s oceans (Morris et al. 2002). Even by bacterial standards, Pelagibacter cells are small, and it has one of the smallest known genomes for any free-living organisms.

Stained sample of Pelagibacter ubique, copyright Thomas Lankiewicz & Matthew Cottrell.

There is one final important subgroup of the alphaproteobacterial lineage that I haven’t mentioned yet: us. At some point in the distant past, a member of the Alphaproteobacteria developed a close and personal relationship with another micro-organism, either a member of the Archaea or a close relative thereof. Phylogenetic studies indicate that this early alphaproteobacterium was probably a close relative of the Rickettsiales. Over time, this relationship became ever closer, until the one became inseparable from the other. Together, these two microbes were to give rise to the eukaryotes, with the alphaproteobacteria becoming transformed into the mitochondria of a eukaryote cell. From the perspective of descent, then, we are all Alphaproteobacteria.

Systematics of Proteobacteria
<==Proteobacteria [Athiorhodaceae, Hydrogenophilaceae, Hydrogenophilales, Rhodobacteria, Thiobacteria]
| i. s.: Epulopiscium fishelsoniC-S02, PHK96
|--+--Mariprofundus [Mariprofundaceae, Mariprofundales, Zetaproteobacteria]WK13
| | |--M. ferrooxydansWK13
| | `--M. micoguttaCD21
| `--+--ChromatibacteriaMK03
| `--Acidithiobacillales [Acidithiobacillia]WK13
| |--Thermithiobacillus [Thermithiobacillaceae]WK13
| | `--*T. tepidariusWK13
| `--Acidithiobacillus Kelly & Wood 2000 [Acidithiobacillaceae]WK13
| | i. s.: A. albertensisWK13 [=Thiobacillus albertensisKT03]
| |--+--A. caldus [=Thiobacillus caldus]KT03
| | `--‘A. cuprithermicus’KT03
| `--+--*A. thiooxidansWK13[=Thiobacillus thiooxidansKT03; incl. T. concretivoransRK92]
| `--+--A. ferrivorans Hallberg et al. 2010VP WK13, IJSEM10
| `--A. ferrooxidansKT03 [=Thiobacillus ferrooxidansKT03; incl. Ferrobacillus ferrooxidansRK92]
`--+--MagnetococcusLB05 [MagnetococcalesCD21, Magnetococcia]
`--Alphaproteobacteria [Alphabacteria]MK03
| i. s.: Acidisphaera rubrifaciensI01
| Silicobacter pomeroyiMO08
| Terasakiella Satomi, Kimura et al. 2002SK02
| `--*T. pusilla (Terasaki) Satomi, Kimura et al. 2002 [=Oceanospirillum pusillum Terasaki 1973]SK02
|--RickettsialesLB05
`--+--RhodospirillalesLB05
|--Granulibacter bethesdensisWK13
`--+--+--+--RhodobacteraceaeLB05
| | `--Parvularcula bermudensisWK13
| `--+--RhizobialesLB05
| `--PseudovibrioWK13
`--Sphingomonadaceae [Sphingomonadales]GH01
| i. s.: Sandaracinobacter sibiricusGH01, I01 [=Erythromicrobium sibiricumI01]
| Zymomonas mobilisGH01, GP03
|--+--‘Citromicrobium bathyomarinum’RS03
| |--ErythromicrobiumRS03
| | |--E. ezovicumI01
| | |--E. hydrolyticumI01
| | `--E. ramosumRS03
| |--ErythrobacterRS03
| | |--‘E. citreus’RS03
| | |--E. litoralisRS03
| | `--E. longusRS03
| `--PorphyrobacterRS03
| |--P. cryptus Rainey, Silva et al. 2003RS03
| |--P. neustonensisRS03
| `--P. tepidariusRS03
`--+--Erythromonas ursincolaRS03 [=Erythromicrobium ursincolaI01]
`--+--SphingomonasUTO03
| |--S. alaskensisMN03
| |--S. aquatilis Lee et al. 2001JC08
| |--S. koreensis Lee et al. 2001JC08
| |--‘Blastobacter’ natatorius [=Blastomonas natatoria]DT03
| |--S. paucimobilisUTO03
| |--S. pruniKN02
| |--S. taejonensis Lee et al. 2001JC08
| `--S. trueperiUTO03
`--+--SphingobiumUTO03
| |--S. yanoikuyae (Yabuuchi et al. 1990) Takeuchi et al. 2001UTO03, JC08
| `--+--+--S. amiense Ushiba, Takahara & Ohta 2003UTO03
| | `--‘Sphingomonas’ cloacae Fujii et al. 2001UTO03, JC08
| `--+--S. herbicidovorans (Zipper et al. 1997) Takeuchi et al. 2001UTO03, JC08
| `--+--S. chlorophenolicum (Nohynek et al. 1996) Takeuchi et al. 2001UTO03, JC08
| `--+--‘Sphingomonas agrestis’UTO03
| `--‘Sphingomonas’ chungbukensisUTO03
`--+--SphingopyxisUTO03
| |--S. macrogoltabida (Takeuchi et al. 1993) Takeuchi et al. 2001UTO03, JC08
| `--S. terrae (Takeuchi et al. 1993) Takeuchi et al. 2001UTO03, JC08
`--NovosphingobiumUTO03
| i. s.: N. hassiacumFS03
|--N. stygiumFS03
`--+--N. tardaugens Fujii, Satomi et al. 2003FS03
`--+--+--N. aromaticivoransUTO03
| `--N. subterraneumFS03
`--+--N. capsulatum (Leifson 1962) Takeuchi et al. 2001UTO03, JC08
`--+--N. rosaFS03
`--N. subarcticum (Nohynek et al. 1996) Takeuchi et al. 2001FS03, JC08

*Type species of generic name indicated

References

Bazylinski, D. A., T. J. Williams, C. T. Lefèvre, R. J. Berg, C. L. Zhang, S. S. Bowser, A. J. Dean & T. J. Beveridge. 2013. Magnetococcus marinus gen. nov., sp. nov., a marine, magnetotactic bacterium that represents a novel lineage (Magnetococcaceae fam. nov., Magnetococcales ord. nov.) at the base of the Alphaproteobacteria. International Journal of Systematic and Evolutionary Microbiology 63: 801–808.

Brenner, D. J., N. R. Krieg & J. T. Staley. 2005. Bergey’s Manual of Systematic Bacteriology 2nd ed. vol. 2 pt C. The Alpha-, Beta-, Delta-, and Epsilonproteobacteria. Springer.

[C-S02] Cavalier-Smith, T. 2002. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. International Journal of Systematic and Evolutionary Microbiology 52: 7–76.

[CD21] Coleman, G. A., A. A. Davín, T. A. Mahendrarajah, L. L. Szánthó, A. Spang, P. Hugenholtz, G. J. Szöllősi & T. A. Williams. 2021. A rooted phylogeny resolves early bacterial evolution. Science 372: 588.

[DT03] Doronina, N. V., & Y. A. Trotsenko. 2003. Reclassification of ‘Blastobacter viscosus’ 7d and ‘Blastobacter aminooxidans’ 14a as Xanthobacter viscosus sp. nov. and Xanthobacter aminoxidans sp. nov. International Journal of Systematic and Evolutionary Microbiology 53: 179–182.

Ferla, M. P., J. C. Thrash, S. J. Giovannoni & W. M. Patrick. 2013. New rRNA gene-based phylogenies of the Alphaproteobacteria provide perspective on major groups, mitochondrial ancestry and phylogenetic instability. PLoS One 8 (12): e83383. doi:10.1371/journal.pone.0083383.

[FS03] Fujii, K., M. Satomi, N. Morita, T. Motomura, T. Tanaka & S. Kikuchi. 2003. Novosphingobium tardaugens sp. nov., an oestradiol-degrading bacterium isolated from activated sludge of a sewage treatment plant in Tokyo. International Journal of Systematic and Evolutionary Microbiology 53: 47–52.

[GH01] Garrity, G. M., & J. G. Holt. 2001. The road map to the Manual. In: Boone, D. R., R. W. Castenholz & G. M. Garrity (eds) Bergey’s Manual of Systematic Bacteriology 2nd ed. vol. 1. The Archaea and the Deeply Branching and Phototrophic Bacteria pp. 119–166. Springer.

[GP03] Gupta, R. S., M. Pereira, C. Chandrasekara & V. Johari. 2003. Molecular signatures in protein sequences that are characteristic of cyanobacteria and plastid homologues. International Journal of Systematic and Evolutionary Microbiology 53: 1833–1842.

[IJSEM10] IJSEM. 2010. Validation list no. 132. List of new names and new combinations previously effectively, but not validly, published. International Journal of Systematic and Evolutionary Microbiology 60: 469–472.

[I01] Imhoff, J. F. 2001. The anoxygenic phototrophic purple bacteria. In: Boone, D. R., R. W. Castenholz & G. M. Garrity (eds) Bergey’s Manual of Systematic Bacteriology 2nd ed. vol. 1. The Archaea and the Deeply Branching and Phototrophic Bacteria pp. 631–637. Springer.

[JC08] Judicial Commission of the International Committee on Systematics of Prokaryotes. 2008. Status of strains that contravene Rules 27 (3) and 30 of the International Code of Nomenclature of Bacteria. Opinion 81. International Journal of Systematic and Evolutionary Microbiology 58: 1755–1763.

[KN02] Kämpfer, P., A. Neef, M. S. Salkinoja-Salonen & H.-J. Busse. 2002. Chelatobacter heintzii (Auling et al. 1993) is a later subjective synonym of Aminobacter aminovorans (Urakami et al. 1992). International Journal of Systematic and Evolutionary Microbiology 52: 835–839.

[KT03] Karavaiko, G. I., T. P. Turova, T. F. Kondrat’eva, A. M. Lysenko, T. V. Kolganova, S. N. Ageeva, L. M. Muntyan & T. A. Pivovarova. 2003. Phylogenetic heterogeneity of the species Acidithiobacillus thiooxidans. International Journal of Systematic and Evolutionary Microbiology 53: 113–119.

[LB05] Lang, B. F., H. Brinkmann, L. B. Koski, M. Fujishima, H.-D. Görtz & G. Burger. 2005. On the origin of mitochondria and Rickettsia-related eukaryotic endosymbionts. Japanese Journal of Protozoology 38 (2): 171–183.

[MN03] Moffitt, M. C., & B. A. Neilan. 2003. Evolutionary affiliations within the superfamily of ketosynthases reflect complex pathway associations. Journal of Molecular Evolution 56: 446–457.

[MO08] Moore, R. B., M. Oborník, J. Janouškovec, T. Chrudimský, M. Vancová, D. H. Green, S. W. Wright, N. W. Davies, C. J. S. Bolch, K. Heimann, J. Šlapeta, O. Hoegh-Guldberg, J. M. Logsdon Jr. & D. A. Carter. 2008. A photosynthetic alveolate closely related to apicomplexan parasites. Nature 451: 959–963.

[MK03] Mori, K., H. Kim, T. Kakegawa & S. Hanada. 2003. A novel lineage of sulfate-reducing microorganisms: Thermodesulfobiaceae fam. nov., Thermodesulfobium narugense, gen. nov., sp. nov., a new thermophilic isolate from a hot spring. Extremophiles 7: 283–290.

Morris, R. M., M. S. Rappé, S. A. Connon, K. L. Vergin, W. A. Siebold, C. A. Carlson & S. J. Giovannoni. 2002. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420: 806–810.

[PHK96] Prescott, L. M., J. P. Harley & D. A. Klein. 1996. Microbiology 3rd ed. Wm. C. Brown Publishers: Dubuque (Iowa).

[RS03] Rainey, F. A., J. Silva, M. F. Nobre, M. T. Silva & M. S. da Costa. 2003. Porphyrobacter cryptus sp. nov., a novel slightly thermophilic, aerobic, bacteriochlorophyll a-containing species. International Journal of Systematic and Evolutionary Microbiology 53: 35–41.

[RK92] Robertson, L. A., & J. G. Kuenen. 1992. The colorless sulfur bacteria. In: Balows, A., H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer (eds) The Prokaryotes: A handbook on the biology of bacteria: Ecophysiology, isolation, identification, applications 2nd ed. vol. 1 pp. 385–413. Springer-Verlag: New York.

[SK02] Satomi, M., B. Kimura, T. Hamada, S. Harayama & T. Fujii. 2002. Phylogenetic study of the genus Oceanospirillum based on 16S rRNA and gyrB genes: Emended description of the genus Oceanospirillum, description of Pseudospirillum gen. nov., Oceanobacter gen. nov. and Terasakiella gen. nov. and transfer of Oceanospirillum jannaschii and Pseudomonas stanieri to Marinobacterium as Marinobacterium jannaschii comb. nov. and Marinobacterium stanieri comb. nov. International Journal of Systematic and Evolutionary Microbiology 52: 739–747.

[UTO03] Ushiba, Y., Y. Takahara & H. Ohta. 2003. Sphingobium amiense sp. nov., a novel nonylphenol-degrading bacterium isolated from a river sediment. International Journal of Systematic and Evolutionary Microbiology 53: 2045–2048.

[WK13] Williams, K. P., & D. P. Kelly. 2013. Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria. International Journal of Systematic and Evolutionary Microbiology 63 (8): 2901–2906.

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