Pseudomonadota

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Pseudomonadota
Escherichia coli
Scientific classification Edit this classification
Domain: Bacteria
Phylum: Pseudomonadota
Garrity et al. 2021[1]
Classes
Synonyms

Pseudomonadota (synonym Proteobacteria) is a major phylum of Gram-negative bacteria.[10] Currently, they are considered the predominant phylum within the realm of bacteria.[11] They are naturally found as pathogenic and free-living (non-parasitic) genera.[11] The phylum comprises six classes Acidithiobacilia, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Hydrogenophilia, and Zetaproteobacteria.[11] The Pseudomonadota are widely diverse, with differences in morphology, metabolic processes, relevance to humans, and ecological influence.[11]

Classification

American microbiologist Carl Woese established this grouping in 1987, calling it informally the "purple bacteria and their relatives".[12] The group was later formally named the 'Proteobacteria' after the Greek god Proteus, who was known to assume many forms.[13] In 2021 the International Committee on Systematics of Prokaryotes designated the synonym Pseudomonadota, and renamed many other prokaryotic phyla as well.[1] This renaming of several prokaryote phyla in 2021, including Pseudomonadota, remains controversial among microbiologists, many of whom continue to use the earlier name Proteobacteria, of long standing in the literature.[14] The phylum Pseudomonadota encompasses classes Acidithiobacilia, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Hydrogenophilia, and Zetaproteobacteria.[11] The phylum includes a wide variety of pathogenic genera, such as Escherichia, Salmonella, Vibrio, Yersinia, Legionella, and many others.[15] Others are free-living (non-parasitic) and include many of the bacteria responsible for nitrogen fixation.[16]

Previously, the Pseudomonadota phylum included two additional classes, namely Deltaproteobacteria and

Desulfobacterota (encompassing Thermodesulfobacteria), Myxococcota, and Bdellovibrionota (comprising Oligoflexia).[17]

The class

chemolithotrophic primary producers and its metabolic prowess in deep-sea hydrothermal vent ecosystems.[18] Noteworthy pathogenic genera within this class include Campylobacter, Helicobacter, and Arcobacter. Analysis of phylogenetic tree topology and genetic markers revealed the direct divergence of Epsilonproteobacteria from the Pseudomonadota phylum.[18] Limited outgroup data and low bootstrap values support these discoveries. Despite further investigations, consensus has not been reached regarding the monophyletic nature of Epsilonproteobacteria within Proteobacteria, prompting researchers to propose its taxonomic separation from the phylum. The proposed reclassification of the name Epsilonproteobacteria is Campylobacterota.[18]

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)[19] and the National Center for Biotechnology Information (NCBI).[20]

The group Pseudomonadota is defined based on

Hydrogenophilales[4]

Pseudomonadota classes with validly published names include some prominent genera:[25] e.g.:

according to ARB living tree, iTOL, Bergey's and others. 16S rRNA based
LTP_12_2021[26][27][28]
 120 single copy marker proteins based GTDB 08-RS214[29][30][31]

"

Caulobacteria" (Alphaproteobacteria
)

"Mariprofundia" (Zetaproteobacteria)

"Magnetococcia"

"Pseudomonadia"

clade 1

"Foliamicales"

clade 3

Immundisolibacterales

clade 5

"Acidithiobacillidae" (Acidithiobacillia)

"Neisseriidae" (

Hydrogenophilalia
)

"Pseudomonadidae" (Gammaproteobacteria)

Characteristics

Pseudomonadota are a diverse group. Though some species may stain Gram-positive or Gram-variable in the labortary, they are nominally

bacterial gliding.[33]

Pseudomonadota have a wide variety of

heterotrophs, though numerous exceptions exist. A variety of distantly related genera within the Pseudomonadota, obtain their energy from light through conventional photosynthesis or anoxygenic photosynthesis.[33]

The Acidithiobacillia contain only sulfur, iron, and uranium-oxidizing autotrophs. The type order is the Acidithiobacillaceae, which includes five different Acidthiobacillus species used in the mining industry. In particular, these microbes assist with the process of bioleaching, which involves microbes assisting in metal extraction from mining waste that typically extraction methods cannot remove.[34]

Some

mitochondria of eukaryotes are thought to be descendants of an alphaproteobacterium.[36]

The

opportunistic pathogens. These pathogens are primary for both humans and animals, such as the horse pathogen Burkholderia mallei, and Burkholderia cepacia which causes reparatory tract infections in people with cystic fibrosis.[37]

The Gammaproteobacteria are one of the largest classes in terms of genera, containing approximately 250 validly published names.[24] The type order is the Pseudomonadales, which include the genera Pseudomonas and the nitrogen-fixing Azotobacter, along with many others. Besides being a well-known pathogenic genera, Pseudomonas is also capable of biodegradation of certain materials, like cellulose.[35]

The

Hydrogenophilaceae which contains the genera Thiobacillus, Petrobacter, Sulfuricella, Hydrogenophilus and Tepidiphilus. Currently, no members of this class have been identified as pathogenic.[39]

The

Mariprofundaceae, which does not contain any known pathogenic species.[41]

Transformation

Transformation, a process in which genetic material passes from one bacterium to another,[42] has been reported in at least 30 species of Pseudomonadota distributed in the classes alpha, beta, and gamma.[43] The best-studied Pseudomonadota with respect to natural genetic transformation are the medically important human pathogens Neisseria gonorrhoeae (class beta), and Haemophilus influenzae (class gamma).[44] 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 Pseudomonadota, 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.[44]

Habitat

Due to the distinctive nature of each of the six classes of Pseudomonadota, this phylum occupies a multitude of habitats. These include:

  • Human oral cavity[45]
  • Microbial mats in the deep sea[46]
  • Marine sediments[7]
  • Thermal sulfur springs[47]
  • Agricultural soil[47]
  • Hydrothermal vents[48]
  • Stem nodules of legumes[11]
  • Within aphids as endosymbionts[11]
  • Gastrointestinal tract of warm-blooded species[11]
  • Brackish, estuary waters[11]
  • Microbiomes of shrimp and mollusks[11]
  • Human vaginal tract[10]
  • Potato rhizosphere microbiome[49]

Significance

Human Health

Studies have suggested Pseudomonadota as a relevant signature of disease in the human

nonalcoholic fatty liver disease (NAFLD), wherein patients with NAFLD having a higher abundance of Gammproteobacteria than patients without the disease.[51]

Classes Betaproteobacteria and Gammaproteobacteria are prevalent within the human oral cavity, and are markers for good oral health.

saturated fatty acid (SAF) content, achieved through poor diet, has been correlated to increased abundance of Betaproteobacteria in the oral cavity.[52]

Economic Value

Pseudomonadota bacteria have a symbiotic or mutualistic association with plant roots, an example being in the rhizomes of potato plants.[53] Because of this symbiotic relationship, farmers have the ability to increase their crop yields.[53] Healthier root systems can lead to better nutrient uptake, improved water retention, increased resistance to diseases and pests, and ultimately higher crop yields per acre.[54] Increased agricultural output can spark economic growth, contribute to food security, and lead to job creation in rural areas.[55]

As briefly mentioned in previous sections, members of Pseudomonadota have vast metabolic abilities that allow them to utilize and produce a variety of compounds. Bioleaching, done by various Thiobacillus species, are a primary example of this.[56] Any iron and sulfur oxidizing species has the potential to uncover metals and low-grade ores that conventional mining techniques were unable to extract. At present, they are most often used for recovering copper and uranium, but researchers are looking to expand this field in the future. The downside of this method is that the bacteria produce acidic byproducts that end up in acid mine drainage. Bioleaching has significant economic promise if it can be controlled and not cause any further harm to the environment.[34]

Ecological Impact

Pseudomonadota are microbes commonly found within soil systems.[53] Microbes play a crucial role in the surrounding ecosystem by performing functions such as nutrient cycling, carbon dioxide fixation, decomposition, and nitrogen fixation.[57] Pseudomonadota can be described as phototrophs, heterotrophs, and lithotrophs. As heterotrophs (examples Pseudomonas and Xanthomonas) these bacteria are effective in breaking down organic matter, contributing to nutrient cycling.[57] Additionally, photolithotrophs within the phylum are able to perform photosynthesis using sulfide or elemental sulfur as electron donors, which enables them to participate in carbon fixation and oxygen production even in anaerobic conditions.[57] These Pseudomonadota bacteria are also considered copiotrophic organisms, meaning they can be found in environments with high nutrient availability.[57] These environments have ample sources of carbon and other nutrients, environments like fertile soils, compost, and sewage. These copiotrophic bacteria are able to enhance soil health by performing nutrient cycling and waste decomposition.[57]

Because this phylum are able to form a symbiotic relationship with plant roots, incorporating Pseudomonadota into agricultural practices aligns with principles of sustainable farming.[58][53] These bacteria contribute to soil health and fertility, promote natural pest management, and enhance the resilience of crops to environmental stressors.[58]

See also

References

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External links

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