Proteobacteria

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Proteobacteria
EscherichiaColi NIAID.jpg
Escherichia coli
Scientific classification Red Pencil Icon.png
Domain: Bacteria
Phylum:Proteobacteria
Stackebrandt et al., 1988, [1] Garrity et al. 2005 [2]
Class

Alphaproteobacteria [3]
Betaproteobacteria [4]
Hydrogenophilalia [4]
Gammaproteobacteria [5]
Acidithiobacillia [5]
Deltaproteobacteria [6]
Epsilonproteobacteria [7]
Oligoflexia [8]

Contents

Proteobacteria is a major phylum of gram-negative bacteria. They include a wide variety of pathogens, such as Escherichia , Salmonella , Vibrio , Helicobacter , Yersinia , Legionellales and many other notable genera. [9] Others are free-living (non-parasitic) and include many of the bacteria responsible for nitrogen fixation.

In biology, a phylum 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 for algae, fungi, and plants accepts the terms as equivalent. Depending on definitions, the animal kingdom Animalia or Metazoa contains approximately 35 phyla, the plant kingdom Plantae contains about 14, and the fungus kingdom Fungi contains about 8 phyla. Current research in phylogenetics is uncovering the relationships between phyla, which are contained in larger clades, like Ecdysozoa and Embryophyta.

Gram-negative bacteria group of bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation

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 wall sandwiched between an inner cytoplasmic cell membrane and a bacterial outer membrane.

In biology, a pathogen, in the oldest and broadest sense, is anything that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ.

Carl Woese established this grouping in 1987, calling it informally the "purple bacteria and their relatives". [10] Because of the great diversity of forms found in this group, it was named after Proteus, a Greek god of the sea capable of assuming many different shapes and is not named after the Proteobacteria genus Proteus . [1] [11]

Carl Woese American microbiologist and biophysicist

Carl Richard Woese was an American microbiologist and biophysicist. Woese is famous for defining the Archaea in 1977 by phylogenetic taxonomy of 16S ribosomal RNA, a technique pioneered by Woese which revolutionized the discipline of microbiology. He was also the originator of the RNA world hypothesis in 1967, although not by that name. He held the Stanley O. Ikenberry Chair and was professor of microbiology at the University of Illinois at Urbana–Champaign.

Proteus Greek mythology

In Greek mythology, Proteus is an early prophetic sea-god or god of rivers and oceanic bodies of water, one of several deities whom Homer calls the "Old Man of the Sea" (halios gerôn). Some who ascribe to him a specific domain call him the god of "elusive sea change", which suggests the constantly changing nature of the sea or the liquid quality of water in general. He can foretell the future, but, in a mytheme familiar to several cultures, will change his shape to avoid having to; he will answer only to someone who is capable of capturing the beast. From this feature of Proteus comes the adjective protean, with the general meaning of "versatile", "mutable", "capable of assuming many forms". "Protean" has positive connotations of flexibility, versatility and adaptability.

<i>Proteus</i> (bacterium) genus of bacteria

Proteus is a genus of Gram-negative Proteobacteria. Proteus bacilli are widely distributed in nature as saprophytes, being found in decomposing animal matter, sewage, manure soil, the mammalian intestine, and human and animal feces. They are opportunistic pathogens, commonly responsible for urinary and septic infections, often nosocomial.

Some Alphaproteobacteria can grow at very low levels of nutrients and have unusual morphology such as stalks and buds. Others include agriculturally important bacteria capable of inducing nitrogen fixation in symbiosis with plants. The type order is the Caulobacterales, comprising stalk-forming bacteria such as Caulobacter .

Alphaproteobacteria class of bacteria

Alphaproteobacteria is a class of bacteria in the phylum Proteobacteria. 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.

The Betaproteobacteria are highly metabolically diverse and contain chemolithoautotrophs, photoautotrophs, and generalist heterotrophs. The type order is the Burkholderiales, comprising an enormous range of metabolic diversity, including opportunistic pathogens.

Betaproteobacteria class of bacteria

Betaproteobacteria are a class of gram-negative bacteria, and one of the eight classes of the phylum Proteobacteria.

Heterotroph organism that ingests or absorbs organic carbon (rather than fix carbon from inorganic sources such as carbon dioxide) in order to be able to produce energy and synthesize compounds to maintain its life

A heterotroph is an organism that cannot produce its own food, relying instead on the intake of nutrition from other sources of organic carbon, mainly plant or animal matter. In the food chain, heterotrophs are primary, secondary and tertiary consumers, but not producers. Living organisms that are heterotrophic include all animals and fungi and some bacteria and protists. "Earth’s ocean is estimated to contain a hundred million times more bacteria than there are stars in the universe.The term heterotroph arose in microbiology in 1946 as part of a classification of microorganisms based on their type of nutrition. The term is now used in many fields, such as ecology in describing the food chain.

Burkholderiales order of bacteria

The Burkholderiales are an order of Proteobacteria. Like all Proteobacteria, they are Gram-negative. They include several pathogenic bacteria, including species of Burkholderia, Bordetella, and Ralstonia. They also include Oxalobacter and related genera, which are unusual in using oxalic acid as their source of carbon.. Other well-studied genera include Alcaligenes, Cupriavidus, Achromobacter, Comamonas, Delftia, Massilia, Duganella, Janthinobacterium, Polynucleobacter, non-pathogenic Paraburkholderia, Caballeronia, Polaromonas, Thiomonas, Collimonas, Hydrogenophaga, Sphaerotilus, Variovorax, Acidovorax, Rubrivivax and Rhodoferax, and Herbaspirillum.

The Hydrogenophilalia are obligate thermophiles and include heterotrophs and autotrophs. The type order is the Hydrogenophilales.

The class Hydrogenophilalia in the Bacteria was circumscribed in 2017 when it was demonstrated that the order Hydrogenophilales was distinct from the Betaproteobacteria on the basis of physiology, biochemistry, fatty acid profiles, and phylogenetic analyses on the basis of the 16S rRNA gene and 53 ribosomal protein sequences concatenated using the rMLST platform for multilocus sequence typing.

The Gammaproteobacteria are the largest class in terms of species with validly published names. The type order is the Pseudomonadales, which include the genera Pseudomonas and the nitrogen-fixing Azotobacter .

Gammaproteobacteria class of bacteria

Gammaproteobacteria are a class of bacteria. Several medically, ecologically, and scientifically important groups of bacteria belong to this class. Like all Proteobacteria, the Gammaproteobacteria are Gram-negative.

Pseudomonadales order of bacteria

The Pseudomonadales are an order of Proteobacteria. A few members are opportunistic pathogens, such as species of Pseudomonas, Moraxella, and Acinetobacter, which may cause pneumonia.

<i>Pseudomonas</i> genus of bacteria

Pseudomonas is a genus of Gram-negative, Gammaproteobacteria, belonging to the family Pseudomonadaceae and containing 191 validly described species. The members of the genus demonstrate a great deal of metabolic diversity and consequently are able to colonize a wide range of niches. Their ease of culture in vitro and availability of an increasing number of Pseudomonas strain genome sequences has made the genus an excellent focus for scientific research; the best studied species include P. aeruginosa in its role as an opportunistic human pathogen, the plant pathogen P. syringae, the soil bacterium P. putida, and the plant growth-promoting P. fluorescens.

The Acidithiobacillia contain only sulfur, iron and uranium-oxidising autotrophs. The type order is the Acidithiobacillales, which includes economically important organisms used in the mining industry such as Acidithiobacillus spp.

The Deltaproteobacteria include bacteria that are predators on other bacteria and are important contributors to the anaerobic side of the sulfur cycle. The type order is the Myxococcales, which includes organisms with self-organising abilities such as Myxococcus spp.

The Epsilonproteobacteria are often slender, Gram-negative rods that are helical or curved. The type order is the Campylobacterales, which includes important food pathogens such as Campylobacter spp.

The Oligoflexia are filamentous aerobes. The type order is the Oligoflexales, which contains the genus Oligoflexus .

Characteristics

All "Proteobacteria" are Gram-negative (though some may stain Gram-positive or Gram-variable in practice), with an outer membrane mainly composed of lipopolysaccharides. Many move about using flagella, but some are nonmotile or rely on bacterial gliding. The latter include the myxobacteria, an order of bacteria that can aggregate to form multicellular fruiting bodies. Also, a wide variety in the types of metabolism exists. Most members are facultatively or obligately anaerobic, chemolithoautotrophic, and heterotrophic, but numerous exceptions occur. A variety of genera, which are not closely related to each other, convert energy from light through photosynthesis.

"Proteobacteria" are associated with the imbalance of microbiota of the lower reproductive tract of women. These species are associated with inflammation. [12] "Proteobacteria" are part of a normal, healthy placental microbiome. [13]

Taxonomy

Phylogeny of "Proteobacteria"

Acidobacteria

Deltaproteobacteria

Epsilonproteobacteria

Alphaproteobacteria

Zetaproteobacteria

Gammaproteobacteria

Betaproteobacteria

Phylogeny of the "Proteobacteria" according to ARB living tree, iTOL, Bergey's and others

The group is defined primarily in terms of ribosomal RNA (rRNA) sequences. The "Proteobacteria" are divided into six classes with validly published names, referred to by the Greek letters alpha through epsilon and the Acidithiobacillia and Oligoflexia. These were previously regarded as subclasses of the phylum, but they are now treated as classes. These classes are monophyletic. [14] [15] [16] The genus Acidithiobacillus , part of the Gammaproteobacteria until it was transferred to class Acidithiobacillia in 2013, [17] was previously regarded as paraphyletic to the Betaproteobacteria according to multigenome alignment studies. [18] In 2017, the Betaproteobacteria was subject to major revisions and the class Hydrogenophilalia was created to contain the order Hydrogenophilales [19]

Proteobacterial classes with validly published names include some prominent genera: [20] e.g.:

Transformation

Transformation, a process in which genetic material passes from bacterium to another, [21] has been reported in at least 30 species of "Proteobacteria" distributed in the classes alpha, beta, gamma and epsilon. [22] The best-studied "Proteobacteria" with respect to natural genetic transformation are the medically important human pathogens Neisseria gonorrhoeae (class beta), Haemophilus influenzae (class gamma) and Helicobacter pylori (class epsilon). [23] 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. In pathogenic "Proteobacteria", transformation appears to serve as a DNA repair process that protects the pathogen's DNA from attack by their host's phagocytic defenses that employ oxidative free radicals. [23]

Notes

    Related Research Articles

    Nitrosomonadales order of bacteria

    The Nitrosomonadales are an order of the class Betaproteobacteria in the phylum "Proteobacteria". Like all members of their class, they are Gram-negative.

    The Rhodocyclaceae are a family of gram-negative bacteria. They are given their own order in the beta subgroup of Proteobacteria, and include many genera previously assigned to the family Pseudomonadaceae.

    Rhizobiales order of bacteria

    The Rhizobiales are an order of Gram-negative Alphaproteobacteria.

    Rhodocyclales order of bacteria

    The Rhodocyclales are an order of the class Betaproteobacteria in the phylum "Proteobacteria". Following a major reclassification of the class in 2017, the previously monofamilial order was split into three families:

    Comamonadaceae family of bacteria

    The Comamonadaceae are a family of the Betaproteobacteria. Like all Proteobacteria, they are Gram-negative. They are aerobic and most of the species are motile via flagella. The cells are curved rod-shaped.

    The Hydrogenophilaceae are a family of the Hydrogenophilalia, with two genera – Hydrogenophilus and Tepidiphilus. Like all "Proteobacteria", they are Gram-negative. All known species are thermophilic, growing around 50 °C and using molecular hydrogen or organic molecules as their source of electrons to support growth - some species are autotrophs.

    Thiobacillus is a genus of Gram-negative Betaproteobacteria. Thiobacilus thioparus is the type species of the genus, and the type strain thereof is the StarkeyT strain, isolated by Robert Starkey in the 1930s from a field at Rutgers University in the United States of America. While over 30 "species" have been named in this genus since it was defined by Martinus Beijerinck in 1904, most names were never validly or effectively published. The remainder were either reclassified into Paracoccus, Starkeya ; Sulfuriferula, Annwoodia, Thiomonas ; Halothiobacillus, Guyparkeria, or Thermithiobacillus or Acidithiobacillus. The very loosely defined "species" Thiobacillus trautweinii was where sulfur oxidising heterotrophs and chemolithoheterotrophs were assigned in the 1910-1960s era, most of which were probably Pseudomonas species. Many species named in this genus were never deposited in service collections and have been lost.

    <i>Methylobacterium</i> genus of bacteria

    The Methylobacteria are a genus of Rhizobiales.

    Aminobacter aminovorans is a Gram-negative soil bacteria.

    Thauera is a genus of Gram-negative bacteria in the family Zoogloeaceae of the order Rhodocyclales of the Betaproteobacteria. The genus is named for the German microbiologist Rudolf Thauer. Most species of this genus are motile by flagella and are mostly rod-shaped. The species occur in wet soil and polluted freshwater.

    Spirillaceae family of bacteria

    Spirillaceae is a family in the order Nitrosomonadales in the class Betaproteobacteria of the bacteria.

    Dechloromonas is a genus in the phylum Proteobacteria (Bacteria).

    Azoarcus is a genus of nitrogen-fixing bacteria. Species in this genus are usually found in contaminated water, as they are involved in the degradation of some contaminants, commonly inhabiting soil. These bacteria have also been found growing in the endophytic compartment of some rice species and other grasses. The genus is within the family Zoogloeaceae in the Rhodocyclales of the Betaproteobacteria.

    Azonexus is a genus of gram-negative, non-spore-forming, highly motile bacteria that is the type genus of the family Azonexaceae which is in the order Rhodocyclales of the class Betaproteobacteria.

    Azovibrio is a genus of bacteria from the order Rhodocyclales which belongs to the class of Betaproteobacteria, but the family to which it belongs is uncertain since it falls in between the Zoogloeaceae and the Rhodocyclaceae. Up to now there is only on species known.

    <i>Zoogloea</i> genus of bacteria

    Zoogloea is a genus of gram-negative, aerobic, rod-shaped bacteria from the family of Zoogloeaceae in the Rhodocyclales of the class Betaproteobacteria.

    The genus Annwoodia was named in 2017 to circumscribe an organism previously described as a member of the genus Thiobacillus, Thiobacillus aquaesulis - the type and only species is Annwoodia aquaesulis, which was isolated from the geothermal waters of the Roman Baths in the city of Bath in the United Kingdom by Ann P. Wood and Donovan P. Kelly of the University of Warwick - the genus was subsequently named to honour Wood's contribution to microbiology. The genus falls within the family Thiobacillaceae along with Thiobacillus and Sulfuritortus, both of which comprise autotrophic organisms dependent on thiosulfate, other sulfur oxyanions and sulfide as electron donors for chemolithoheterotrophic growth. Whilst Annwoodia spp. and Sulfuritortus spp. are thermophilic, Thiobacillus spp. are mesophilic.

    Nevskia is a Gram negative, strictly aerobic and motile genus of bacteria from the family Xanthomonadaceae.

    The Hahellaceae are a family of Proteobacteria in the order of Oceanospirillales.

    References

    1. 1 2 Stackebrandt, E.; Murray, R. G. E.; Truper, H. G. (1988). "Proteobacteria classis nov., a Name for the Phylogenetic Taxon That Includes the "Purple Bacteria and Their Relatives"". International Journal of Systematic Bacteriology. 38 (3): 321–325. doi:10.1099/00207713-38-3-321.
    2. Garrity, G. M., Bell, J. A. & Lilburn, T. (2005). Phylum XIV. Proteobacteria phyl. nov. In: Bergey’s Manual of Systematic Bacteriology, 2nd edn, vol. 2 (The Proteobacteria), part B (The Gammaproteobacteria), p. 1. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
    3. Garrity GM, Bell JA, Lilburn T (2005). "Class I. Alphaproteobacteria class. nov.". In Brenner DJ, Krieg NR, Staley JT, Garrity GM. Bergey's Manual of Systematic Bacteriology Volume 2: The Proteobacteria Part C (The Alpha-, Beta-, Delta- and Epsilonproteobacteria (2nd ed.). Springer. p. 1. doi:10.1002/9781118960608.cbm00041. ISBN   9781118960608.
    4. 1 2 Boden R, Hutt LP, Rae AW (2017). "Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov., transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the "Proteobacteria", and four new families within the orders Nitrosomonadales and Rhodocyclales". International Journal of Systematic and Evolutionary Microbiology. 67 (5): 1191–1205. doi:10.1099/ijsem.0.001927. PMID   28581923.
    5. 1 2 Williams KP, Kelly DP (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: 2901–2906. doi:10.1099/ijs.0.049270-0. PMID   23334881.
    6. Kuever J, Rainey FA, Widdel F (2005). "Class IV. Deltaproteobacteria class. nov.". In Brenner DJ, Krieg NR, Staley JT, Garrity GM. Bergey's Manual of Systematic Bacteriology Volume 2: The Proteobacteria Part C (The Alpha-, Beta-, Delta- and Epsilonproteobacteria (2nd ed.). Springer. p. 922. doi:10.1002/9781118960608.cbm00043. ISBN   9781118960608.
    7. Garrity GM, Bell JA, Lilburn T (2005). "Class V. Epsilonproteobacteria class. nov.". In Brenner DJ, Krieg NR, Staley JT, Garrity GM. Bergey's Manual of Systematic Bacteriology Volume 2: The Proteobacteria Part C (The Alpha-, Beta-, Delta- and Epsilonproteobacteria (2nd ed.). Springer. p. 1145. doi:10.1002/9781118960608.cbm00044. ISBN   9781118960608.
    8. Nakai R, Nishijima M, Tazato N, Handa Y, Karray F, Sayadi S, Isoda H, Naganuma T (2014). "Oligoflexus tunisiensis gen. nov., sp. nov., a Gram-negative, aerobic, filamentous bacterium of a novel proteobacterial lineage, and description of Oligoflexaceae fam. nov., Oligoflexales ord. nov. and Oligoflexia classis nov". International Journal of Systematic and Evolutionary Microbiology. 64 (Pt 10): 3353–3359. doi:10.1099/ijs.0.060798-0. PMC   4179278 . PMID   25013226.CS1 maint: Uses authors parameter (link)
    9. Madigan, M. and J. Martinko. (eds.) (2005). Brock Biology of Microorganisms (11th ed.). Prentice Hall. ISBN   978-0-13-144329-7.CS1 maint: Extra text: authors list (link)
    10. Woese, CR (1987). "Bacterial evolution". Microbiological Reviews. 51 (2): 221–71. PMC   373105 . PMID   2439888.
    11. "Proteobacteria". Discover Life: Tree of Life. Retrieved 2007-02-09.
    12. Bennett, John (2015). Mandell, Douglas, and Bennett's principles and practice of infectious diseases. Philadelphia, PA: Elsevier/Saunders. ISBN   9781455748013; Access provided by the University of Pittsburgh
    13. Mor, Gil; Kwon, Ja-Young (2015). "Trophoblast-microbiome interaction: a new paradigm on immune regulation". American Journal of Obstetrics and Gynecology. 213 (4): S131–S137. doi:10.1016/j.ajog.2015.06.039. ISSN   0002-9378. PMID   26428492.
    14. Noel R. Krieg; Don J. Brenner; James T. Staley (2005). Bergey's Manual of Systematic Bacteriology: The Proteobacteria. Springer. ISBN   978-0-387-95040-2.
    15. Ciccarelli, FD; Doerks, T; Von Mering, C; Creevey, CJ; Snel, B; Bork, P (2006). "Toward automatic reconstruction of a highly resolved tree of life". Science. 311 (5765): 1283–7. CiteSeerX   10.1.1.381.9514 . doi:10.1126/science.1123061. PMID   16513982.
    16. Yarza, P; Ludwig, W; Euzéby, J; Amann, R; Schleifer, KH; Glöckner, FO; Rosselló-Móra, R (2010). "Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses". Systematic and Applied Microbiology. 33 (6): 291–9. doi:10.1016/j.syapm.2010.08.001. PMID   20817437..
    17. Williams, KP; Kelly, DP (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 (Pt 8): 2901–6. doi:10.1099/ijs.0.049270-0. PMID   23334881.
    18. Williams, K. P.; Gillespie, J. J.; Sobral, B. W. S.; Nordberg, E. K.; Snyder, E. E.; Shallom, J. M.; Dickerman, A. W. (2010). "Phylogeny of Gammaproteobacteria". Journal of Bacteriology. 192 (9): 2305–14. doi:10.1128/JB.01480-09. PMC   2863478 . PMID   20207755.
    19. Boden, R.; Hutt, L. P.; Rae, A. W. (2017). "Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov., transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the Proteobacteria, and four new families within the orders Nitrosomonadales and Rhodocyclales". International Journal of Systematic and Evolutionary Microbiology. 67 (5): 1191–1205. doi:10.1099/ijsem.0.001927. PMID   28581923.
    20. Interactive Tree of Life
    21. Johnston C, Martin B, Fichant G, Polard P, Claverys JP (2014). "Bacterial transformation: distribution, shared mechanisms and divergent control". Nat. Rev. Microbiol. 12 (3): 181–96. doi:10.1038/nrmicro3199. PMID   24509783.
    22. Johnsborg O, Eldholm V, Håvarstein LS (2007). "Natural genetic transformation: prevalence, mechanisms and function". Res. Microbiol. 158 (10): 767–78. doi:10.1016/j.resmic.2007.09.004. PMID   17997281.
    23. 1 2 Michod RE, Bernstein H, Nedelcu AM (2008). "Adaptive value of sex in microbial pathogens". Infect. Genet. Evol. 8 (3): 267–85. doi:10.1016/j.meegid.2008.01.002. PMID   18295550.