Pseudomonas is a genus of gram-negative bacteria belonging to the family Pseudomonadaceae in the class Gammaproteobacteria. The 348 members of the genus Partial citation, see Parte et al., 2020 for project reference demonstrate a great deal of metabolic diversity and consequently are able to colonize a wide range of niches and hosts. 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, P. lini, P. migulae, and P. graminis.
Because of their widespread occurrence in water and plant seeds such as dicots, the pseudomonads were observed early in the history of microbiology. The generic name Pseudomonas created for these organisms was defined in rather vague terms by Walter Migula in 1894 and 1900 as a genus of Gram-negative, rod-shaped, and polar-flagellated bacteria with some sporulating species.Migula, W. (1894) Über ein neues System der Bakterien. Arb Bakteriol Inst Karlsruhe 1: 235–238.Migula, W. (1900) System der Bakterien, Vol. 2. Jena, Germany: Gustav Fischer. The latter statement was later proved incorrect and was due to refractive granules of reserve materials. Despite the vague description, the type species, Pseudomonas pyocyanea (basionym of Pseudomonas aeruginosa), proved the best descriptor.
Classification history Like most bacterial genera, the pseudomonad last common ancestor lived hundreds of millions of years ago. They were initially classified at the end of the 19th century when first identified by Walter Migula. The etymology of the name was not specified at the time and first appeared in the seventh edition of Bergey's Manual of Systematic Bacteriology (the main authority in bacterial nomenclature) as Greek pseudes (ψευδής) "false" and -monas (μονάς/μονάδος) "a single unit", which can mean false unit; however, Migula possibly intended it as false Monas, a nanoflagellated protist (subsequently, the term "monad" was used in the early history of microbiology to denote unicellular organisms). Soon, other species matching Migula's somewhat vague original description were isolated from many natural niches and, at the time, many were assigned to the genus. However, many strains have since been reclassified, based on more recent methodology and use of approaches involving studies of conservative macromolecules.
16S rRNA sequence analysis has redefined the taxonomy of many bacterial species. As a result, the genus Pseudomonas includes strains formerly classified in the genera Chryseomonas and Flavimonas. Other strains previously classified in the genus Pseudomonas are now classified in the genera Burkholderia and Ralstonia.
In 2020, a phylogenomic analysis of 494 complete Pseudomonas genomes identified two well-defined species (P. aeruginosa and P. chlororaphis) and four wider phylogenetic groups (P. fluorescens, P. stutzeri, P. syringae, P. putida) with a sufficient number of available proteomes. The four wider evolutionary groups include more than one species, based on species definition by the Average Nucleotide Identity levels. In addition, the phylogenomic analysis identified several strains that were mis-annotated to the wrong species or evolutionary group. This mis-annotation problem has been reported by other analyses as well. In 2021, a broad phylogenomic analysis on this genus led to the reorganization of the species included in Pseudomonas, leading to the creation of several new genera to accommodate some of them.
Genomics In 2000, the complete genome sequence of a Pseudomonas species was determined; more recently, the sequence of other strains has been determined, including P. aeruginosa strains PAO1 (2000), P. putida KT2440 (2002), P. protegens Pf-5 (2005), P. syringae pathovar tomato DC3000 (2003), P. syringae pathovar syringae B728a (2005), P. syringae pathovar phaseolica 1448A (2005), P. fluorescens Pf0-1, and P. entomophila L48.
By 2016, more than 400 strains of Pseudomonas had been sequenced. Sequencing the genomes of hundreds of strains revealed highly divergent species within the genus. In fact, many genomes of Pseudomonas share only 50–60% of their genes, e.g. P. aeruginosa and P. putida share only 2971 proteins out of 5350 (or ~55%).
By 2020, more than 500 complete Pseudomonas genomes were available in NCBI GenBank. A phylogenomic analysis utilized 494 complete proteomes and identified 297 core orthologues, shared by all strains. This set of core orthologues at the genus level was enriched for proteins involved in metabolism, translation, and transcription and was utilized for generating a phylogenomic tree of the entire genus, to delineate the relationships among the Pseudomonas major evolutionary groups. In addition, group-specific core proteins were identified for most evolutionary groups, meaning that they were present in all members of the specific group, but absent in other pseudomonads. For example, several P. aeruginosa-specific core proteins were identified that are known to play an important role in this species' pathogenicity, such as CntL, CntM, PlcB, Acp1, MucE, SrfA, Tse1, Tsi2, Tse3, and EsrC.
In 2021, a comparative genomic study with more than 3000 Pseudomonas genomes helped to discover genes and functions related with the environmental adaptation of these bacteria.
Characteristics Members of the genus display these defining characteristics: Rod-shaped Gram-negative Flagellum one or more, providing motility Aerobic Non-spore forming Catalase-positive Oxidase-variable Other characteristics that tend to be associated with Pseudomonas species (with some exceptions) include secretion of pyoverdine, a fluorescent yellow-green siderophore under iron-limiting conditions. Certain Pseudomonas species may also produce additional types of siderophore, such as pyocyanin by Pseudomonas aeruginosa and thioquinolobactin by Pseudomonas fluorescens. Pseudomonas species also typically give a positive result to the oxidase test, the absence of gas formation from glucose, glucose is oxidised in oxidation/fermentation test using Hugh and Leifson O/F test, beta hemolytic (on blood agar), indole negative, methyl red negative, Voges–Proskauer test negative, and citrate positive.
Pseudomonas may be the most common nucleator of ice crystals in clouds, thereby being of utmost importance to the formation of snow and rain around the world.
The genus Pseudomonas is recognized for its remarkable metabolic diversity, enabling it to thrive in a wide range of environments. These bacteria produce a vast array of secondary metabolites, including antibiotics, siderophores, and biosurfactants, which contribute to their ecological versatility and biotechnological potential.
Biofilm formation All species and strains of Pseudomonas have historically been classified as strict aerobes. Exceptions to this classification have recently been discovered in Pseudomonas biofilms. A significant number of cells can produce exopolysaccharides associated with biofilm formation. Secretion of exopolysaccharides such as alginate makes it difficult for pseudomonads to be phagocytosed by mammalian white blood cells. Exopolysaccharide production also contributes to surface-colonising biofilms that are difficult to remove from food preparation surfaces. Growth of pseudomonads on spoiling foods can generate a "fruity" odor.
Antibiotic resistance Most Pseudomonas spp. are naturally resistant to penicillin and the majority of related beta-lactam antibiotics, but a number are sensitive to piperacillin, imipenem, ticarcillin, or ciprofloxacin. Aminoglycosides such as tobramycin, gentamicin, and amikacin are other choices for therapy.
This ability to thrive in harsh conditions is a result of their hardy cell walls that contain proteins known as porins. Their resistance to most antibiotics is attributed to efflux pumps, which pump out some antibiotics before they are able to act.
Pseudomonas aeruginosa is increasingly recognized as an emerging opportunistic pathogen of clinical relevance. One of its most worrying characteristics is its low antibiotic susceptibility. This low susceptibility is attributable to a concerted action of multidrug efflux pumps with chromosomally encoded antibiotic resistance genes (e.g., mexAB-oprM, mexXY, etc.) and the low permeability of the bacterial cellular envelopes. Besides intrinsic resistance, P. aeruginosa easily develops acquired resistance either by mutation in chromosomally encoded genes or by the horizontal gene transfer of antibiotic resistance determinants. Development of multidrug resistance by P. aeruginosa isolates requires several different genetic events that include acquisition of different mutations and/or horizontal transfer of antibiotic resistance genes. Hypermutation favours the selection of mutation-driven antibiotic resistance in P. aeruginosa strains producing chronic infections, whereas the clustering of several different antibiotic resistance genes in integrons favours the concerted acquisition of antibiotic resistance determinants. Some recent studies have shown phenotypic resistance associated to biofilm formation or to the emergence of small-colony-variants, which may be important in the response of P. aeruginosa populations to antibiotic treatment.
Sensitivity to gallium Although gallium has no natural function in biology, gallium ions interact with cellular processes in a manner similar to iron(III). When gallium ions are mistakenly taken up in place of iron(III) by bacteria such as Pseudomonas, the ions interfere with respiration, and the bacteria die. This happens because iron is redox-active, allowing the transfer of electrons during respiration, while gallium is redox-inactive.
Pathogenicity
Animal pathogens
Infectious species include P. aeruginosa, P. oryzihabitans, and P. plecoglossicida. P. aeruginosa flourishes in hospital environments, and is a particular problem in this environment, since it is the second-most common infection in hospitalized patients (nosocomial infections). This pathogenesis may in part be due to the proteins secreted by P. aeruginosa. The bacterium possesses a wide range of secretion systems, which export numerous proteins relevant to the pathogenesis of clinical strains. Intriguingly, several genes involved in the pathogenesis of P. aeruginosa, such as CntL, CntM, PlcB, Acp1, MucE, SrfA, Tse1, Tsi2, Tse3, and EsrC are core group-specific, meaning that they are shared by the vast majority of P. aeruginosa strains, but they are not present in other Pseudomonads.
Plant pathogens
P. syringae is a prolific plant pathogen. It exists as over 50 different pathovars, many of which demonstrate a high degree of host-plant specificity. Numerous other Pseudomonas species can act as plant pathogens, notably all of the other members of the P. syringae subgroup, but P. syringae is the most widespread and best-studied.
Fungus pathogens
P. tolaasii can be a major agricultural problem, as it can cause bacterial blotch of cultivated mushrooms. Similarly, P. agarici can cause drippy gill in cultivated mushrooms.
Use as biocontrol agents