Жалпы бактериялар тобы: Pseudomonadota және оның жіктемесі

Phylum of Gram negative bacteria

Pseudomonadota (synonym Proteobacteria) is a major phylum of Gram negative bacteria. Currently, they are considered the predominant phylum within the realm of bacteria. The Pseudomonadota are widely diverse, with differences in morphology, metabolic processes, relevance to humans, and ecological influence. The group was later formally named the 'Proteobacteria' after the Greek god Proteus, who was known to assume many forms. In 2021 the International Committee on Systematics of Prokaryotes designated the synonym Pseudomonadota, and renamed many other prokaryotic phyla as well. The phylum Pseudomonadota encompasses classes Acidithiobacilia, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Hydrogenophilia, and Zetaproteobacteria. Others are free living (non parasitic) and include many of the bacteria responsible for nitrogen fixation. 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. 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). 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. and the National Center for Biotechnology Information (NCBI). The group Pseudomonadota is defined based on ribosomal RNA (rRNA) sequencing, and are divived into several subclasses. These subclasses were regarded as such for many years, but are now treated as various classes of the phylum. These classes are monophyletic. The genus Acidithiobacillus, part of the Gammaproteobacteria until it was transferred to class Acidithiobacillia in 2013, In 2017, the Betaproteobacteria was subject to major revisions and the class Hydrogenophilalia was created to contain the order Hydrogenophilales e. g.:
Acidithiobacillia: Acidithiobacillus, Thermithiobacillus
Alphaproteobacteria: Brucella, Rhizobium, Agrobacterium, Caulobacter, Rickettsia, Wolbachia, etc. Betaproteobacteria: Bordetella, Ralstonia, Neisseria, Nitrosomonas, etc. Gammaproteobacteria: Escherichia, Shigella, Salmonella, Yersinia, Buchnera, Haemophilus, Vibrio, Pseudomonas, Pasteurella, etc. Zetaproteobacteria: Mariprofundus

according to ARB living tree, iTOL, Bergey's and others. 16S rRNA based LTP 12 2021 120 single copy marker proteins based GTDB 08 RS214

Pseudomonadota are a diverse group. Though some species may stain Gram positive or Gram variable in the labortary, they are nominally Gram negative. Their unique outer membrane is mainly composed of lipopolysaccharides, which helps differentiate them from the Gram positive species. Most Pseudomonadota are motile and move using flagella. Many move about using flagella, but some are nonmotile, or rely on bacterial gliding. Pseudomonadota have a wide variety of metabolism types. Most are facultative or obligate anaerobes, chemolithoautotrophs, and 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. Some Alphaproteobacteria can grow at very low levels of nutrients and have unusual morphology within their life cycles. Some form stalks to help with colonization, and form buds during cell division. 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. 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. 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. The Gammaproteobacteria are one of the largest classes in terms of genera, containing approximately 250 validly published names. The bacteria typically use hydrogen gas as an electron donor, but can also use reduced sulfuric compounds. Because of this ability, scientists have begun to use certain species of Hydrogenophilalia to remove sulfides that contaminate industrial wastewater systems. The type order is the Hydrogenophilaceae which contains the genera Thiobacillus, Petrobacter, Sulfuricella, Hydrogenophilus and Tepidiphilus. Currently, no members of this class have been identified as pathogenic. The Zetaproteobacteria are the iron oxidizing neutrophilic chemolithoautotrophs, distributed worldwide in estuaries and marine habitats. The only confirmed type order for this class is the Mariprofundaceae, which does not contain any known pathogenic species.

Studies have suggested Pseudomonadota as a relevant signature of disease in the human gastrointestinal (GI) tract, by operating as a marker for microbiota instability. Classes Betaproteobacteria and Gammaproteobacteria are prevalent within the human oral cavity, and are markers for good oral health. Changes in the oral microbiome are due to endogenous and exogenous factors like host lifestyle, genotype, environment, immune system, and socioeconomic status. Because of this symbiotic relationship, farmers have the ability to increase their crop yields. Increased agricultural output can spark economic growth, contribute to food security, and lead to job creation in rural areas. 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. 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. 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. These bacteria contribute to soil health and fertility, promote natural pest management, and enhance the resilience of crops to environmental stressors.