Pseudomonadota

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Pseudomonadota
Escherichia coli
Scientific classification Edit this classification
Domain: Bacteria
Phylum: Pseudomonadota
Garrity et al. 2021[1]
Classes
Synonyms
  • "Proteobacteria" Stackebrandt et al. 1988[6]
  • "Proteobacteria" Gray and Herwig 1996[7]
  • "Proteobacteria" Garrity et al. 2005[8]
  • "Proteobacteria" Cavalier-Smith 2002[9]
  • Alphaproteobacteraeota Oren et al. 2015
  • "Alphaproteobacteriota" Whitman et al. 2018
  • "Caulobacterota" corrig. Garrity et al. 2021
  • "Neoprotei" Pelletier 2012
  • Rhodobacteria Cavalier-Smith 2002

Pseudomonadota (synonym Proteobacteria) is a major phylum of Gram-negative bacteria.[10] At present, 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.[12] The Pseudomonadota are widely diverse, with differences in morphology, metabolic processes, relevance to humans, and ecological influence.[11]

Classification[edit]

The 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.[13] The phylum Pseudomonadota encompasses classes Acidithiobacilia, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Hydrogenophilia, and Zetaproteobacteria.[14] 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.

Carl Woese established this grouping in 1987, calling it informally the "purple bacteria and their relatives".[16] Because of the great diversity of forms found in this group, it was later informally named Proteobacteria, after Proteus, a Greek god of the sea capable of assuming many different shapes (not after the Proteobacteria genus Proteus).[6][17] In 2021 the International Committee on Systematics of Prokaryotes designated the synonym Pseudomonadota.[1]

Previously, the Pseudomonadota phylum included two additional classes, namely Deltaproteobacteria and Oligoflexia. However, further investigation into the phylogeny of these taxa through genomic marker analysis demonstrated their separation from the Pseudomonadota phylum.[18] Deltaproteobacteria has been identified as a diverse taxonomic unit, leading to a proposal for its reclassification into distinct phyla: Desulfobacterota (encompassing Thermodesulfobacteria), Myxococcota, and Bdellovibrionota (comprising Oligoflexia).[18]

The class Epsilonprotobacteria was additionally identified within the Pseudomonadota phylum. This class is characterized by its significance as chemolithotrophic primary producers and its metabolic prowess in deep-sea hydrothermal vent ecosystems.[19] Noteworthy pathogenic genera within this class include Campylobacter, Helicobacter, and Arcobacter. Analysis of phylogenetic tree topology and genetic markers revealed the direct divergence of Epsilonprotobacteria from the Pseudomonadota phylum.[19] 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 Epsilonprotobacteria is Campylobacterota.[19]

Characteristics[edit]

Pseudomonadota are a diverse group. Though some species may stain Gram-positive or Gram-variable in the laboratory, they are nominally Gram-negative. Their unique outer membrane is mainly composed of lipopolysaccharides, which helps differentiate them from the Gram-positive species[20]. Most Pseudomonadota are motile and move using flagella. Many move about using flagella, but some are nonmotile, or rely on bacterial gliding.[21]

Pseudomonadota have a wide variety of metabolism types. Most 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 conventional photosynthesis or anoxygenic photosynthesis.[citation needed]

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. The mitochondria of eukaryotes are thought to be descendants of an alphaproteobacterium.[22]

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.[citation needed]

The Gammaproteobacteria are one of the largest classes in terms of genera, containing approximately 250 validly published names[23]. The type order is the Pseudomonadales, which include the genera Pseudomonas and the nitrogen-fixing Azotobacter.[citation needed]

The Zetaproteobacteria are iron-oxidizing neutrophilic chemolithoautotrophs, distributed worldwide in estuaries and marine habitats. The type order is the Mariprofundales.[citation needed]

The Hydrogenophilalia are thermophilic chemoheterotrophs and autotrophs. The bacteria typically use hydrogen gas as an electron donor. The type order is the Hydrogenophilales which contains two genera, Hydrogenophilus and Tepidiphilus.[24]

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.[citation needed]

Transformation[edit]

Transformation, a process in which genetic material passes from one bacterium to another,[25] has been reported in at least 30 species of Pseudomonadota distributed in the classes alpha, beta, and gamma.[26] 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).[27] 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.[27]

Taxonomy[edit]

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)[28] and the National Center for Biotechnology Information (NCBI).[29]

The group is defined primarily in terms of ribosomal RNA (rRNA) sequences. The Pseudomonadota are divided into several classes. These were previously regarded as subclasses of the phylum, but they are now treated as classes. These classes are monophyletic.[30][31][32] The genus Acidithiobacillus, part of the Gammaproteobacteria until it was transferred to class Acidithiobacillia in 2013,[2] was previously regarded as paraphyletic to the Betaproteobacteria according to multigenome alignment studies.[33] In 2017, the Betaproteobacteria was subject to major revisions and the class Hydrogenophilalia was created to contain the order Hydrogenophilales[4]

Pseudomonadota classes with validly published names include some prominent genera:[34] e.g.:

according to ARB living tree, iTOL, Bergey's and others. 16S rRNA based LTP_12_2021[35][36][37] 120 single copy marker proteins based GTDB 08-RS214[38][39][40]

"Caulobacteria" (Alphaproteobacteria)

"Mariprofundia" (Zetaproteobacteria)

"Magnetococcia"

"Pseudomonadia"

clade 1

"Foliamicales"

clade 3

Immundisolibacterales

clade 5

"Acidithiobacillidae" (Acidithiobacillia)

"Neisseriidae" (Betaproteobacteria & nested Hydrogenophilalia)

"Pseudomonadidae" (Gammaproteobacteria)

Habitat[edit]

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[41]
  • Microbial mats in the deep sea[42]
  • Marine sediments[43]
  • Thermal sulfur springs[44]
  • Agricultural soil[44]
  • Hydrothermal vents[45]
  • Stem nodules of legumes[46]
  • Within aphids as endosymbionts[46]
  • Gastrointestinal tract of warm-blooded species[46]
  • Brackish, estuary waters[46]
  • Microbiomes of shrimp and mollusks[46]
  • Human vaginal tract[10]

Significance[edit]

Human Health[edit]

Studies have suggested Pseudomonadota as a relevant signature of disease in the human gastrointestinal (GI) tract, by operating as a marker for microbiota instability.[10] The human gut microbiome consists mainly of four phyla: Firmicutes, Bacteroidetes, Actinobacteria, and Pseudomonadota.[10] Microorganism gut colonization is dynamic from birth to death, with stabilization at the first few years of life, to higher diversity in adults, to reduced diversity in the elderly.[10] The gut microbiome conducts processes like nutrient synthesis, chemical metabolism, and the formation of the gut barrier.[10] Additionally, the gut microbiome facilitates host interactions with its surrounding environment through regulation of nutrient absorption and bacterial intake. In 16s rRNA and metagenome sequencing studies, Proteobacteria have been identified as bacteria that prompts endotoxemia (an inflammatory gut response) and metabolic disorders in human GI tracts.[10] An example in Lambeth et al. found increased bacterial count in patients with type 2 diabetes (T2DM) in comparison to patients with pre-diabetes or other control groups.[47] Another study by Michail et al. showed a correlation of microbial composition in children with and without nonalcoholic fatty liver disease (NAFLD), wherein patients with NAFLD having a higher abundance of Gammproteobacteria than patients without the disease.[48]

Classes Betaproteobacteria and Gammaproteobacteria are prevalent within the human oral cavity, and are markers for good oral health.[41] The oral microbiome consists of 11 habitats, including the tongue dorsum, hard palate, tonsils, throat, saliva, and more.[49] Changes in the oral microbiome are due to endogenous and exogenous factors like host lifestyle, genotype, environment, immune system, and socioeconomic status.[49] Considering diet as a factor, high saturated fatty acid (SAF) content, achieved through poor diet, has been correlated to increased abundance of Betaproteobacteria in the oral cavity.[49]

See also[edit]

References[edit]

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External links[edit]

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