Proteobacteria

Overview of Proteobacteria

The Proteobacteria are a major group (phylum) of bacteria.

Learning Objectives

Categorize proteobacteria

Key Takeaways

Key Points

  • Proteobacteria include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, and many other notable genera.
  • All proteobacteria are Gram-negative, with an outer membrane mainly composed of lipopolysaccharides.
  • The divisions of the proteobacteria include: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Epsilonproteobacteria and Zetaproteobacteria.

Key Terms

  • Proteobacteria: The Proteobacteria are a major group (phylum) of bacteria. They include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, and many other notable genera. Others are free-living, and include many of the bacteria responsible for nitrogen fixation.
  • pathogens: A pathogen or infectious agent (colloquially known as a germ) is a microorganism (in the widest sense, such as a virus, bacterium, prion, or fungus) that causes disease in its host. The host may be an animal (including humans), a plant, or even another microorganism.
  • Gram-negative: Gram-negative bacteria are bacteria that do not retain crystal violet dye in the Gram staining protocol. In a Gram stain test, a counterstain (commonly safranin) is added after the crystal violet, coloring all Gram-negative bacteria with a red or pink color.

The Proteobacteria are a major group (phylum) of bacteria. They include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, and many other notable genera. Others are free-living, and include many of the bacteria responsible for nitrogen fixation.

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Classification of E. coli: Domain: Bacteria, Kingdom: Eubacteria, Phylum: Proteobacteria, Class: Gammaproteobacteria, Order: Enterobacteriales, Family: Enterobacteriaceae, Genus: Escherichia, Species: E. coli.

In 1987, Carl Woese established this grouping, and informally called it the “purple bacteria and their relatives”. Because of the great diversity of forms found in this group, the Proteobacteria are named after Proteus, a Greek god of the sea, capable of assuming many different shapes, and it is therefore not named after the genus Proteus.

All proteobacteria are Gram-negative, with an outer membrane mainly composed of lipopolysaccharides. Many move about using flagella, but some are nonmotile or rely on bacterial gliding. The last include the myxobacteria, a unique group of bacteria that can aggregate to form multicellular fruiting bodies. There is also a wide variety in the types of metabolism. Most members are facultatively or obligately anaerobic, chemoautotrophs, and heterotrophic, but there are numerous exceptions. A variety of genera, which are not closely related to each other, convert energy from light through photosynthesis. These are called purple bacteria, referring to their mostly reddish pigmentation.

The group is defined primarily in terms of ribosomal RNA (rRNA) sequences. The Proteobacteria are divided into six sections, referred to by the Greek letters alpha through zeta, again based on rRNA sequences. These are often treated as classes. The alpha, beta, delta, epsilon sections are monophyletic, but the Gammaproteobacteria due to the Acidithiobacillus genus is paraphyletic to Betaproteobacteria, according to multigenome alignment studies, which if done correctly are more precise than 16S (note that Mariprofundus ferrooxydans sole member of the Zetaproteobacteria was previously misclassified on NCBI taxonomy). Acidithiobacillus contains 5 species and the sole genus in its order Acidithiobacillales.

The divisions of the proteobacteria were once regarded as subclasses (e.g. α-subclass of the Proteobacteria), but are now regarded as classes (e.g. the Alphaproteobacteria). These classes include: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Epsilonproteobacteria and Zetaproteobacteria.

Alphaproteobacteria

Alphaproteobacteria is a class of Proteobacteria; like all Proteobacteria, they are Gram-negative.

Learning Objectives

Describe the Alphaproteobacteria class of Proteobacteria

Key Takeaways

Key Points

  • The Class Alphaproteobacteria comprises ten orders (viz. Magnetococcales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales, Caulobacterales, Kiloniellales, Kordiimonadales, Parvularculales and Sneathiellales).
  • The Alphaproteobacteria comprise most phototrophic genera, but also several genera metabolising C1-compounds (e.g., Methylobacterium spp.), symbionts of plants (e.g., Rhizobium spp.) and animals, and a group of pathogens, the Rickettsiaceae.
  • Scientists often use Alphaproteobacteria of the genus Agrobacterium to transfer foreign DNA into plant genomes.

Key Terms

  • Alphaproteobacteria: Alphaproteobacteria is a class of Proteobacteria that are Gram-negative.
  • phototroph: An organism that carries out photon capture to acquire energy. They use the energy from light to carry out various cellular metabolic processes.
  • C1-compounds: chemical compounds containing only one carbon atom, for example, methanol.

Alphaproteobacteria is a class of Proteobacteria. Like all Proteobacteria, they are Gram-negative. The Alphaproteobacteria comprise most phototrophic genera, but also several genera metabolising C1-compounds (e.g., Methylobacterium spp.), symbionts of plants (e.g., Rhizobium spp.) and animals, and a group of pathogens, the Rickettsiaceae. In addition, the precursors of the mitochondria of eukaryotic cells are thought to have originated from Rickettsia spp. (See endosymbiotic theory.). Because of their symbiotic properties, scientists often use Alphaproteobacteria of the genus Agrobacterium to transfer foreign DNA into plant genomes, and they also have many other biotechnological properties. Aerobic anoxygenic phototrophic bacteria are alphaproteobacteria, widely distributed marine plankton that may constitute over 10% of the open ocean microbial community.

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Alphaproteobacteria: Transmission electron micrograph of Wolbachia within an insect cell.

The Class Alphaproteobacteria comprises ten orders (viz. Magnetococcales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales, 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 with the exception of Betaproteobacteria and Gammaproteobacteria.

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.

Betaproteobacteria

Betaproteobacteria is a class of Proteobacteria that are all Gram-negative.

Learning Objectives

Evaluate the importance of Betaproteobacteria

Key Takeaways

Key Points

  • The Betaproteobacteria consist of several groups of aerobic or facultative bacteria that are often highly versatile in their degradation capacities.
  • The Betaproteobacteria contain chemolithotrophic genera (e.g., the ammonia-oxidising genus Nitrosomonas) and some phototrophs (members of the genera Rhodocyclus and Rubrivivax).
  • Betaproteobacteria play a role in nitrogen fixation in various types of plants, oxidizing ammonium to produce nitrite- an important chemical for plant function.

Key Terms

  • Betaproteobacteria: Betaproteobacteria is a class of Proteobacteria. Betaproteobacteria are, like all Proteobacteria, Gram-negative.
  • glanders: An infectious disease of horses, mules and donkeys caused by the bacterium Burkholderia, one species of which may be transmitted to humans.
  • melioidosis: An infectious disease caused by a Gram-negative bacterium, Burkholderia pseudomallei, found in soil and water. It is endemic in Southeast Asia and northern Australia. Symptoms may include pain in chest, bones, or joints; cough; skin infections, lung nodules and pneumonia..

Betaproteobacteria is a class of Proteobacteria that are all Gram-negative.

The Betaproteobacteria consist of several groups of aerobic or facultative bacteria that are often highly versatile in their degradation capacities, but also contain chemolithotrophic genera (e.g., the ammonia-oxidising genus Nitrosomonas) and some phototrophs (members of the genera Rhodocyclus and Rubrivivax).

Nitrosomonas is a genus comprising rod shaped chemoautotrophic bacteria. This rare bacteria oxidizes ammonia into nitrite as a metabolic process. Nitrosomonas are useful in treatment of industrial and sewage waste and in the process of bioremediation. They play an important role in the nitrogen cycle by increasing the availability of nitrogen to plants while limiting carbon dioxide fixation.

Betaproteobacteria play a role in nitrogen fixation in various types of plants, oxidizing ammonium to produce nitrite- an important chemical for plant function. Many of them are found in environmental samples, such as waste water or soil. Pathogenic species within this class are the Neisseriaceae (gonorrhea and meningitis) and species of the genus Burkholderia.

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Betaproteobacteria: Burkholderia pseudomallei colonies on a Blood agar plate.

Burkholderia is a genus of proteobacteria probably best known for its pathogenic members: Burkholderia mallei, responsible for glanders, a disease that occurs mostly in horses and related animals; Burkholderia pseudomallei, causative agent of melioidosis; and Burkholderia cepacia, an important pathogen of pulmonary infections in people with cystic fibrosis (CF). The Burkholderia (previously part of Pseudomonas) genus name refers to a group of virtually ubiquitous gram-negative, motile, obligately aerobic rod-shaped bacteria including both animal/human (see above) and plant pathogens as well as some environmentally important species.

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.

Morphologically Unusual Proteobacteria

The two main groups of morphologically unusual proteobacteria include spirillum and prosthecate bacteria.

Learning Objectives

Compare the two main groups of morphologically unusual proteobacteria

Key Takeaways

Key Points

  • Spirillum in microbiology refers to a bacterium with a cell body that twists like a spiral.
  • Prosthecate bacteria are a non-phylogenetically related group of Gram-negative bacteria that possess appendages, termed prosthecae.
  • Caulobacter is an important model organism for studying the regulation of the cell cycle, asymmetric cell division, and cellular differentiation.

Key Terms

  • spirillum: Any of various aerobic bacteria of the genus Spirillum, having an elongated spiral form and bearing a tuft of flagella.
  • morphologically: In biology, morphology is a branch of bioscience dealing with the study of the form and structure of organisms and their specific structural features.
  • prosthecate: Prosthecate bacteria are a non-phylogenetically related group of Gram-negative bacteria that possess appendages, termed prosthecae. These cellular appendages are neither pili nor flagella, as they are extensions of the cellular membrane and contain cytosol. One notable group of prosthecates is the genus Caulobacter.

Two main groups of morphologically unusual proteobacteria include spirillum and prosthecate bacteria.

Spirillum in microbiology refers to a bacterium with a cell body that twists like a spiral. It is a genus comprising elongated forms with clusters of flagellae at both poles. Spirillium usually live in stagnant water rich in organic matter. They are twisted and aerobic, and are highly flexible, like a spring.

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Spirillum: Spirillum in microbiology refers to a bacterium with a cell body that twists like a spiral.

Prosthecate bacteria are a non-phylogenetically related group of Gram-negative bacteria that possess appendages, termed prosthecae. These cellular appendages are neither pili nor flagella, as they are extensions of the cellular membrane and contain cytosol.

Prosthecates are generally chemoorganotrophic aerobes that can grow in nutrient-poor habitats, being able to survive at nutrient levels on the order of parts-per-million – for which reason they are often found in aquatic habitats. These bacteria will attach to surfaces with their prosthecae, allowing a greater surface area with which to take up nutrients (and release waste products). Some prosthecates will grow in nutrient-poor soils as aerobic heterotrophs.

Caulobacter: An Important Model Organism

One notable group of prosthecates is the genus Caulobacter crescentus, a Gram-negative, oligotrophic bacterium widely distributed in fresh water lakes and streams. Caulobacter is an important model organism for studying the regulation of the cell cycle, asymmetric cell division, and cellular differentiation. Caulobacter daughter cells have two very different forms. One daughter is a mobile “swarmer” cell that has a single flagellum at one cell pole that provides swimming motility for chemotaxis. The other daughter, called the “stalked” cell, has a tubular stalk structure protruding from one pole that has an adhesive holdfast material on its end, with which the stalked cell can adhere to surfaces. Swarmer cells differentiate into stalked cells after a short period of motility. Chromosome replication and cell division only occurs in the stalked cell stage. The second word of its name (crescentus) refers to the fact that it forms a crescent shape; crescentin is a protein that imparts this shape.

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Caulobacter crescentus: Caulobacter daughter cells have two very different forms. One daughter is a mobile “swarmer” cell that has a single flagellum at one cell pole that provides swimming motility for chemotaxis. The other daughter, called the “stalked” cell has a tubular stalk structure protruding from one pole that has an adhesive holdfast material on its end, with which the stalked cell can adhere to surfaces. Swarmer cells differentiate into stalked cells after a short period of motility.

Gammaproteobacteria

Gammaproteobacteria is a class of several medically, ecologically and scientifically important groups of bacteria.

Learning Objectives

Classify Gammaproteobacteria

Key Takeaways

Key Points

  • Gammaproteobacteria include an exceeding number of important pathogens, e.g. Salmonella, Yersinia, Vibrio, Pseudomonas aeruginosa.
  • Like all Proteobacteria, the Gammaproteobacteria are Gram-negative.
  • Some Gammaproteobacteria are methane oxidizers, and many of them are in symbiosis with geothermic ocean vent dwelling animals.

Key Terms

  • symbiosis: A close, prolonged association between two or more organisms of different species, regardless of benefit to the members.
  • pathogens: A pathogen or infectious agent (colloquially known as a germ) is a microorganism (in the widest sense, such as a virus, bacterium, prion, or fungus) that causes disease in its host. The host may be an animal (including humans), a plant, or even another microorganism.
  • Gammaproteobacteria: Gammaproteobacteria is a class of several medically, ecologically and scientifically important groups of bacteria, such as the Enterobacteriaceae (Escherichia coli), Vibrionaceae and Pseudomonadaceae. Like all Proteobacteria, the Gammaproteobacteria are Gram-negative.

Gammaproteobacteria is a class of several medically, ecologically and scientifically important groups of bacteria, such as the Enterobacteriaceae ( Escherichia coli ), Vibrionaceae and Pseudomonadaceae. Like all Proteobacteria, the Gammaproteobacteria are Gram-negative.

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Gammaproteobacteria: Transmission electron microsope image of Vibrio choleraethat has been negatively stained. Vibrio choleraeis the bacteria responsible for the gastroinestinal disease cholera. In order to get the disease cholera, the bacteria must be able to colonize in the small intestine and a critical factor necessary for this colonization is the toxin-co-regulated pilus(TCP). 0395 is a wild type strain, showing the normal bundling of toxin-co-regulated pilus(TCP). Wild-type pili are clearly visible as 7 nm fibres that form bundles @ 0.2Ð0.3 µm wide and 3Ð6 µm long.

The Gammaproteobacteria comprise several medically and scientifically important groups of bacteria, such as the Enterobacteriaceae, Vibrionaceae and Pseudomonadaceae. A number of important pathogens belongs to this class, e.g. Salmonella spp. (enteritis and typhoid fever), Yersinia pestis (plague), Vibrio cholerae (cholera), Pseudomonas aeruginosa (lung infections in hospitalized or cystic fibrosis patients), and Escherichia coli (food poisoning).

The Enterobacteriaceae is a large family of Gram-negative bacteria that includes, along with many harmless symbionts, many of the more familiar pathogens, such as Salmonella, Escherichia coli, Yersinia pestis, Klebsiella and Shigella. Other disease-causing bacteria in this family include Proteus, Enterobacter, Serratia, and Citrobacter. This family is the only representative in the order Enterobacteriales of the class Gammaproteobacteria in the phylum Proteobacteria. Phylogenetically, in the Enterobacteriales, several peptidoglycan-less insect endosymbionts form a sister clade to the Enterobacteriaceae, but since they are not validly described, this group is not officially a taxon; examples of these species are Sodalis, Buchnera, Wigglesworthia, Baumannia and Blochmannia. Members of the Enterobacteriaceae can be trivially referred to as enterobacteria, as several members live in the intestines of animals. In fact, the etymology of the family is enterobacterium with the suffix to designate a family (aceae) — not after the genus Enterobacter (which would be “Enterobacteraceae”)— and the type genus is Escherichia.

Members of Chromatium are photosynthetic and oxidize hydrogen sulfide instead of water, producing sulfur as excrement. Some Gammaproteobacteria are methane oxidizers, and many of them are in symbiosis with geothermic ocean vent dwelling animals.

The Deltaproteobacteria

Deltaproteobacteria is a class of Proteobacteria that are Gram-negative.

Learning Objectives

Review the Deltaproteobacteria class of Proteobacteria

Key Takeaways

Key Points

  • The Deltaproteobacteria comprise a branch of predominantly aerobic genera.
  • Deltaproteobacteria include the fruiting-body-forming Myxobacteria which release myxospores in unfavorable environments.
  • Deltaproteobacteria include a branch of strictly anaerobic genera, which contains most of the known sulfate- (Desulfovibrio, Desulfobacter, Desulfococcus, Desulfonema, etc. ) and sulfur-reducing bacteria (e.g. Desulfuromonas spp. ).

Key Terms

  • aerobic: Living or occurring only in the presence of oxygen.
  • Deltaproteobacteria: Deltaproteobacteria is a class of Proteobacteria. All species of this group are, like all Proteobacteria, Gram-negative.
  • Gram-negative: Gram-negative bacteria are bacteria that do not retain crystal violet dye in the Gram staining protocol. In a Gram stain test, a counterstain (commonly safranin) is added after the crystal violet, coloring all Gram-negative bacteria with a red or pink color.

Deltaproteobacteria is a class of Proteobacteria. All species of this group are, like all Proteobacteria, Gram-negative.

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Deltaproteobacteria: Desulfovibrio vulgaris

The Deltaproteobacteria comprise a branch of predominantly aerobic genera, the fruiting-body-forming Myxobacteria that release myxospores in unfavorable environments. It is a branch of strictly anaerobic genera, which contains most of the known sulfate- (Desulfovibrio, Desulfobacter, Desulfococcus, Desulfonema, etc. ) and sulfur-reducing bacteria (e.g. Desulfuromonas spp.) alongside several other anaerobic bacteria with different physiology (e.g. ferric iron-reducing Geobacter spp. and syntrophic Pelobacter and Syntrophus spp.). A pathogenic intracellular Deltaproteobacteria has recently been identified.

The myxobacteria (“slime bacteria”) are a group of bacteria that predominantly live in the soil and feed on insoluble organic substances. The myxobacteria have very large genomes, relative to other bacteria, e.g. 9–10 million nucleotides. Sorangium cellulosum has the largest known (as of 2008) bacterial genome, at 13.0 million nucleotides. Myxobacteria are included among the delta group of proteobacteria, a large taxon of Gram-negative forms.

Myxobacteria can move actively by gliding. They typically travel in swarms (also known as wolf packs), containing many cells kept together by intercellular molecular signals. Individuals benefit from aggregation as it allows accumulation of extracellular enzymes which are used to digest food. This in turn increases feeding efficiency. Myxobacteria produce a number of biomedically and industrially useful chemicals, such as antibiotics. They export those chemicals outside of the cell.

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.

Epsilonproteobacteria

Epsilonproteobacteria is a class of Proteobacteria that are Gram-negative.

Learning Objectives

Identify the characteristics of Epsilonproteobacteria

Key Takeaways

Key Points

  • The Epsilonproteobacteria consist of few known genera, mainly the curved to spirilloid Wolinella spp., Helicobacter spp., and Campylobacter spp.
  • Most of the known species inhabit the digestive tract of animals and serve as symbionts (Wolinella spp. in cows) or pathogens (Helicobacter spp. in the stomach, Campylobacter spp. in the duodenum).
  • There have also been numerous environmental sequences of Epsilonproteobacteria recovered from hydrothermal vents and cold seep habitats.

Key Terms

  • Gram-negative: Gram-negative bacteria are bacteria that do not retain crystal violet dye in the Gram staining protocol. In a Gram stain test, a counterstain (commonly safranin) is added after the crystal violet, coloring all Gram-negative bacteria with a red or pink color.
  • symbionts: Symbiosis is close and often long-term interaction between two or more different biological species.
  • Epsilonproteobacteria: Epsilonproteobacteria is a class of Proteobacteria. All species of this class are, like all Proteobacteria, gram-negative.

Epsilonproteobacteria is a class of Proteobacteria. All species of this class are, like all Proteobacteria, Gram-negative.

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Epsilonproteobacteria: Campylobacter bacteria are the number-one cause of food-related gastrointestinal illness in the United States. To learn more about this pathogen, ARS scientists are sequencing multiple Campylobacter genomes. This scanning electron microscope image shows the characteristic spiral, or corkscrew, shape of C. jejuni cells and related structures.

The Epsilonproteobacteria consist of few known genera, mainly the curved to spirilloid Wolinella spp., Helicobacter spp., and Campylobacter spp. Most of the known species inhabit the digestive tract of animals and serve as symbionts (Wolinella spp. in cows) or pathogens (Helicobacter spp. in the stomach, Campylobacter spp. in the duodenum).

There have also been numerous environmental sequences of Epsilonproteobacteria recovered from hydrothermal vents and cold seep habitats. A member of the class Epsilonproteobacteria occurs as an endosymbiont in the large gills of the deep water sea snail Alviniconcha hessleri.

Often the epsilonproteobacteria living in hydrothermal deep sea-vents exhibit chemolithotrophic features, and they are able to meet their energy needs by reducing or oxidixing chemical compounds.

Helicobacter is a genus of Gram-negative bacteria possessing a characteristic helix shape. They were initially considered to be members of the Campylobacter genus, but since 1989 they have been grouped in their own genus. The Helicobacter genus belongs to the class Epsilonproteobacteria, order Campylobacterales, family Helicobacteraceae and already has more than 35 species.

Some species have been found living in the lining of the upper gastrointestinal tract, as well as the liver of mammals and some birds. The most widely known species of the genus is H. pylori which infects up to 50% of the human population. Some strains of this bacterium are pathogenic to humans as it is strongly associated with peptic ulcers, chronic gastritis, duodenitis, and stomach cancer. It also serves as the type species of the genus.