Pseudomonas Fluorescens Phage OBP

''Pseudomonas'' is a genus of Gram-negative, Gammaproteobacteria, belonging to the family Pseudomonadaceae and containing 191 described species. The members of the genus demonstrate a great deal of metabolic diversity and consequently are able to colonize a wide range of niches. 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'' (basonym 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.

Recently, 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-anotation problem has been reported by other analyses as well.

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 Genebank. 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''.

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-positive
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.

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 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.

Although not strictly a plant pathogen, '' 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

Since the mid-1980s, certain members of the genus ''Pseudomonas'' have been applied to cereal seeds or applied directly to soils as a way of preventing the growth or establishment of crop pathogens. This practice is generically referred to as biocontrol. The biocontrol properties of ''P. fluorescens'' and '' P. protegens'' strains (CHA0 or Pf-5 for example) are currently best-understood, although it is not clear exactly how the plant growth-promoting properties of ''P. fluorescens'' are achieved. Theories include: the bacteria might induce systemic resistance in the host plant, so it can better resist attack by a true pathogen; the bacteria might outcompete other (pathogenic) soil microbes, e.g. by siderophores giving a competitive advantage at scavenging for iron; the bacteria might produce compounds antagonistic to other soil microbes, such as phenazine-type antibiotics or hydrogen cyanide. Experimental evidence supports all of these theories.

Other notable ''Pseudomonas'' species with biocontrol properties include '' P. chlororaphis'', which produces a phenazine-type antibiotic active agent against certain fungal plant pathogens, and the closely related species '' P. aurantiaca'', which produces di-2,4-diacetylfluoroglucylmethane, a compound antibiotically active against Gram-positive organisms.

Use as Bioremediation Agents

Some members of the genus are able to metabolise chemical pollutants in the environment, and as a result, can be used for bioremediation. Notable species demonstrated as suitable for use as bioremediation agents include:

* '' P. alcaligenes'', which can degrade polycyclic aromatic hydrocarbons.
* '' P. mendocina'', which is able to degrade toluene.
* '' P. pseudoalcaligenes'', which is able to use cyanide as a nitrogen source.
* '' P. resinovorans'', which can degrade carbazole.
*''P. aeruginosa'', '' P. putida'', ''P. desmolyticum'', and ''P. nitroreducens'' can degrade chlorpyrifos.
* '' P. veronii'', which has been shown to degrade a variety of simple aromatic organic compounds.
* '' P. putida'', which has the ability to degrade organic solvents such as toluene. At least one strain of this bacterium is able to convert morphine in aqueous solution into the stronger and somewhat expensive to manufacture drug hydromorphone (Dilaudid).
* Strain KC of '' P. stutzeri'', which is able to degrade carbon tetrachloride.

Detection of Food Spoilage Agents in Milk

One way of identifying and categorizing multiple bacterial organisms in a sample is to use ribotyping. In ribotyping, differing lengths of chromosomal DNA are isolated from samples containing bacterial species, and digested into fragments. Similar types of fragments from differing organisms are visualized and their lengths compared to each other by Southern blotting or by the much faster method of polymerase chain reaction (PCR). Fragments can then be matched with sequences found on bacterial species. Ribotyping is shown to be a method to isolate bacteria capable of spoilage. Around 51% of ''Pseudomonas'' bacteria found in dairy processing plants are ''P. fluorescens'', with 69% of these isolates possessing proteases, lipases, and lecithinases which contribute to degradation of milk components and subsequent spoilage. Other ''Pseudomonas'' species can possess any one of the proteases, lipases, or lecithinases, or none at all. Similar enzymatic activity is performed by ''Pseudomonas'' of the same ribotype, with each ribotype showing various degrees of milk spoilage and effects on flavour. The number of bacteria affects the intensity of spoilage, with non-enzymatic ''Pseudomonas'' species contributing to spoilage in high number.

Food spoilage is detrimental to the food industry due to production of volatile compounds from organisms metabolizing the various nutrients found in the food product. Contamination results in health hazards from toxic compound production as well as unpleasant odours and flavours. Electronic nose technology allows fast and continuous measurement of microbial food spoilage by sensing odours produced by these volatile compounds. Electronic nose technology can thus be applied to detect traces of ''Pseudomonas'' milk spoilage and isolate the responsible ''Pseudomonas'' species. The gas sensor consists of a nose portion made of 14 modifiable polymer sensors that can detect specific milk degradation products produced by microorganisms. Sensor data is produced by changes in electric resistance of the 14 polymers when in contact with its target compound, while four sensor parameters can be adjusted to further specify the response. The responses can then be pre-processed by a neural network which can then differentiate between milk spoilage microorganisms such as ''P. fluorescens'' and '' P. aureofaciens''.

Species

''Pseudomonas'' comprises the following species, organized into genomic affinity groups:

''P. aeruginosa'' Group

* ''P. aeruginosa'' (Schroeter 1872) Migula 1900 (Approved Lists 1980)
* '' P. citronellolis'' Seubert 1960 (Approved Lists 1980)
* '' P. delhiensis'' Prakash et al. 2007
* "'' P. denitrificans''" Bergey et al. 1961

* '' P. jinjuensis'' Kwon et al. 2003
* '' P. knackmussii'' Stolz et al. 2007

* '' P. nicosulfuronedens'' Li et al. 2021

* '' P. nitroreducens'' Iizuka and Komagata 1964 (Approved Lists 1980)
* '' P. panipatensis'' Gupta et al. 2008

''P. anguilliseptica'' Group

* '' P. anguilliseptica'' Wakabayashi and Egusa 1972 (Approved Lists 1980)
* '' P. benzenivorans'' Lang et al. 2012
* '' P. borbori'' Vanparys et al. 2006
* '' P. campi'' Timsy et al. 2021
* '' P. cuatrocienegasensis'' Escalante et al. 2009
* '' P. glareae'' Romanenko et al. 2015
* '' P. guineae'' Bozal et al. 2007
* '' P. guryensis'' Kim et al. 2021
* '' P. lalucatii'' Busquets et al. 2021
* '' P. leptonychotis'' Nováková et al. 2020
* '' P. marincola'' Romanenko et al. 2008
* '' P. peli'' Vanparys et al. 2006
* '' P. segitis'' Park et al. 2006
* '' P. taeanensis'' Lee et al. 2010
* '' P. ullengensis'' Kim et al. 2021

''P. fluorescens'' Group

''P. asplenii'' Subgroup

* '' P. agarici'' Young 1970 (Approved Lists 1980)
* '' P. asplenii'' (Ark and Tompkins 1946) Savulescu 1947 (Approved Lists 1980)
* "'' P. batumici''" Kiprianova et al. 2011
* '' P. fuscovaginae'' (ex Tanii et al. 1976) Miyajima et al. 1983
* "'' P. gingeri''" Cutri et al. 1984
* '' P. vanderleydeniana'' Girard et al. 2022

''P. chlororaphis'' Subgroup
* '' P. aurantiaca'' Nakhimovskaya 1948 (Approved Lists 1980)
* '' P. aureofaciens'' Kluyver 1956 (Approved Lists 1980)
* '' P. chlororaphis'' (Guignard and Sauvageau 1894) Bergey et al. 1930 (Approved Lists 1980)
* "'' P. piscium''" (Burr et al. 2010) Chen et al. 2018
''P. corrugata'' Subgroup

* '' P. alvandae'' Girard et al. 2022
* '' P. bijieensis'' Liang et al. 2021
* '' P. brassicacearum'' Achouak et al. 2000
* '' P. canavaninivorans'' Hauth et al. 2022
* '' P. corrugata'' Roberts and Scarlett 1981
* '' P. kilonensis'' Sikorski et al. 2001
* '' P. marvdashtae'' Girard et al. 2022
* '' P. mediterranea'' Catara et al. 2002
* '' P. ogarae'' Garrido-Sanz et al. 2022
* '' P. tehranensis'' Girard et al. 2022
* '' P. thivervalensis'' Achouak et al. 2000
* '' P. viciae'' Zhao et al. 2020
* '' P. zanjanensis'' Girard et al. 2022
* '' P. zarinae'' Girard et al. 2022

''P. fluorescens'' Subgroup

* '' P. allii'' Sawada et al. 2021
* '' P. antarctica'' Reddy et al. 2004
* '' P. asgharzadehiana'' Girard et al. 2022

* '' P. aylmerensis'' corrig. Tchagang et al. 2021
* '' P. azadiae'' Girard et al. 2022
* '' P. azotoformans'' Iizuka and Komagata 1963 (Approved Lists 1980)
* '' P. canadensis'' Tambong et al. 2017
* '' P. carnis'' Lick et al. 2020

* '' P. cedrina'' corrig. Dabboussi et al. 2002
* '' P. costantinii'' Munsch et al. 2002
* '' P. cremoris'' Hofmann et al. 2021
* '' P. cyclaminis'' Sawada et al. 2021
* '' P. edaphica'' Ramírez-Bahena et al. 2019
* '' P. extremaustralis'' López et al. 2010
* '' P. extremorientalis'' Ivanova et al. 2002
* '' P. fildesensis'' Pavlov et al. 2020
* ''P. fluorescens'' Migula 1895 (Approved Lists 1980)
* "'' P. fulgida''" Naureen et al. 2005
* '' P. grimontii'' Baïda et al. 2002
* '' P. haemolytica'' Hofmann et al. 2020
* '' P. kairouanensis'' Oueslati et al. 2020
* '' P. karstica'' Švec et al. 2020
* '' P. khavaziana'' Girard et al. 2022
* '' P. kitaguniensis'' Sawada et al. 2020
* '' P. lactis'' von Neubeck et al. 2017
* '' P. lactucae'' Sawada et al. 2021
* '' P. libanensis'' Dabboussi et al. 1999
* '' P. lurida'' Behrendt et al. 2007
* '' P. marginalis'' (Brown 1918) Stevens 1925 (Approved Lists 1980)
* '' P. nabeulensis'' Oueslati et al. 2020
* '' P. orientalis'' Dabboussi et al. 2002
* '' P. palleroniana'' Gardan et al. 2002
* '' P. panacis'' Park et al. 2005
* '' P. paracarnis'' Lick et al. 2021
* '' P. paralactis'' von Neubeck et al. 2017
* '' P. pisciculturae'' Duman et al. 2021
* '' P. poae'' Behrendt et al. 2003
* '' P. rhodesiae'' Coroler et al. 1997
* '' P. salmasensis'' Girard et al. 2022
* '' P. salomonii'' Gardan et al. 2002
* '' P. simiae'' Vela et al. 2006
* '' P. sivasensis'' Duman et al. 2020
* '' P. spelaei'' Švec et al. 2020
* '' P. synxantha'' (Ehrenberg 1840) Holland 1920 (Approved Lists 1980)
* '' P. tolaasii'' Paine 1919 (Approved Lists 1980)
* '' P. tritici'' Girard et al. 2022
* '' P. trivialis'' Behrendt et al. 2003
* '' P. veronii'' Elomari et al. 1996
* '' P. yamanorum'' Arnau et al. 2015

''P. fragi'' Subgroup

* '' P. bubulae'' Lick et al. 2020
* '' P. deceptionensis'' Carrión et al. 2011
* '' P. endophytica'' Ramírez-Bahena et al. 2015
* '' P. fragi'' (Eichholz 1902) Gruber 1905 (Approved Lists 1980)
* '' P. helleri'' von Neubeck et al. 2016
* '' P. lundensis'' Molin et al. 1986
* '' P. paraversuta'' Lick et al. 2021
* '' P. psychrophila'' Yumoto et al. 2002
* '' P. saxonica'' Hofmann et al. 2020
* '' P. taetrolens'' Haynes 1957 (Approved Lists 1980)
* '' P. versuta'' See-Too et al. 2017
* '' P. weihenstephanensis'' von Neubeck et al. 2016

''P. gessardii'' Subgroup

* '' P. brenneri'' Baïda et al. 2002
* '' P. gessardii'' Verhille et al. 1999
* '' P. meridiana'' Reddy et al. 2004
* '' P. mucidolens'' Levine and Anderson 1932 (Approved Lists 1980)
* '' P. proteolytica'' Reddy et al. 2004
* '' P. shahriarae'' Girard et al. 2022

''P. jessenii'' Subgroup

* '' P. azerbaijanoccidentalis'' corrig. Girard et al. 2022

* '' P. azerbaijanorientalis'' corrig. Girard et al. 2022
* '' P. izuensis'' Lu et al. 2020
* '' P. jessenii'' Verhille et al. 1999
* '' P. laurylsulfatiphila'' corrig. Furmanczyk et al. 2019
* '' P. laurylsulfativorans'' corrig. Furmanczyk et al. 2019

* '' P. mohnii'' Cámara et al. 2007
* '' P. moorei'' Cámara et al. 2007
* '' P. reinekei'' Cámara et al. 2007
* '' P. umsongensis'' Kwon et al. 2003
* '' P. vancouverensis'' Mohn et al. 1999

''P. koreensis'' Subgroup

* '' P. allokribbensis'' Morimoto et al. 2021
* '' P. anatoliensis'' Duman et al. 2021
* '' P. atacamensis'' Poblete-Morales et al. 2021
* '' P. atagonensis'' corrig. Morimoto et al. 2020

* '' P. baetica'' López et al. 2012
* "'' P. bananamidigenes''" Girard et al. 2021
* "'' P. botevensis''" Girard et al. 2021
* "'' P. crudilactis''" Schlusselhuber et al. 2021
* '' P. ekonensis'' Girard et al. 2022
* '' P. glycinae'' Jia et al. 2021
* '' P. gozinkensis'' Morimoto et al. 2021
* '' P. granadensis'' Pascual et al. 2015
* '' P. hamedanensis'' Girard et al. 2022
* '' P. helmanticensis'' Ramírez-Bahena et al. 2014
* '' P. iranensis'' Girard et al. 2022
* '' P. iridis'' Duman et al. 2021
* '' P. khorasanensis'' Girard et al. 2022
* '' P. koreensis'' Kwon et al. 2003
* "'' P. kribbensis''" Chang et al. 2016
* '' P. monsensis'' Girard et al. 2022
* '' P. moraviensis'' Tvrzová et al. 2006
* '' P. neuropathica'' Duman et al. 2021
* '' P. siliginis'' Girard et al. 2022
* '' P. tensinigenes'' Girard et al. 2022
* '' P. triticicola'' Girard et al. 2022
* '' P. zeae'' Girard et al. 2022

''P. mandelii'' Subgroup

* '' P. arsenicoxydans'' Campos et al. 2011
* '' P. farris'' Girard et al. 2022
* '' P. frederiksbergensis'' Andersen et al. 2000
* "'' P. gregormendelii''" Kosina et al. 2016
* '' P. lini'' Delorme et al. 2002
* '' P. mandelii'' Verhille et al. 1999
* '' P. migulae'' Verhille et al. 1999
* '' P. mucoides'' Duman et al. 2021
* '' P. piscicola'' Duman et al. 2021
* '' P. prosekii'' Kosina et al. 2014
* '' P. silesiensis'' Kaminski et al. 2018

''P. protegens'' Subgroup

* "'' P. aestus''" Vasconcellos et al. 2017
* '' P. piscis'' Liu et al. 2020
* '' P. protegens'' Ramette et al. 2012
* '' P. saponiphila'' Lang et al. 2012
* "'' P. sessilinigenes''" Girard et al. 2021

''incertae sedis''

* "'' P. blatchfordae''" Blatchford and Schuster 1980
* '' P. kielensis'' Gieschler et al. 2021

''P. linyingensis'' Group

* '' P. guangdongensis'' Yang et al. 2013
* '' P. linyingensis'' He et al. 2015
* "'' P. oryzae''" Yu et al. 2013
* '' P. sagittaria'' Lin et al. 2013

''P. lutea'' Group

* '' P. abietaniphila'' Mohn et al. 1999
* '' P. bohemica'' Saati-Santamaría et al. 2018
* '' P. graminis'' Behrendt et al. 1999
* '' P. lutea'' Peix et al. 2004

''P. massiliensis'' Group

* "'' P. massiliensis''" Bardet et al. 2018
* '' P. typographi'' Peral-Aranega et al. 2021

''P. oleovorans'' Group

* '' P. alcaliphila'' Yumoto et al. 2001

* "'' P. chaetocerotis''" Girard et al.
* '' P. chengduensis'' Tao et al. 2014
* '' P. composti'' Gibello et al. 2011
* '' P. guguanensis'' Liu et al. 2013
* '' P. hydrolytica'' Zhou et al. 2020
* "'' P. indoloxydans''" Manickam et al. 2008
* '' P. khazarica'' Tarhriz et al. 2020
* '' P. mendocina'' Palleroni 1970 (Approved Lists 1980)
* '' P. oleovorans'' Lee and Chandler 1941 (Approved Lists 1980)

* "'' P. sediminis''" Behera et al. 2018
* "'' P. sihuiensis''" Wu et al. 2014
* '' P. toyotomiensis'' Hirota et al. 2011

''P. oryzihabitans'' Group

* '' P. asuensis'' Reddy and Garcia-Pichel 2015
* '' P. duriflava'' Liu et al. 2008
* '' P. luteola'' Kodama et al. 1985
* '' P. oryzihabitans'' Kodama et al. 1985

* '' P. rhizoryzae'' Wang et al. 2020

''P. pohangensis'' Group

* '' P. mangrovi'' Ye et al. 2019
* '' P. pohangensis'' Weon et al. 2006

''P. putida'' Group

* '' P. akappageensis'' corrig. Morimoto et al. 2020

* '' P. alkylphenolica'' Mulet et al. 2015
* '' P. alloputida'' Keshavarz-Tohid et al. 2020
* '' P. anuradhapurensis'' Girard et al. 2022
* '' P. arcuscaelestis'' Mulet et al. 2021
* '' P. asiatica'' Tohya et al. 2019
* '' P. brassicae'' Sawada et al. 2020
* "'' P. capeferrum''" Berendsen et al. 2015
* '' P. cremoricolorata'' Uchino et al. 2002
* '' P. defluvii'' Qin et al. 2020
* '' P. donghuensis'' Gao et al. 2015
* '' P. entomophila'' Mulet et al. 2012
* '' P. fakonensis'' Girard et al. 2022
* '' P. farsensis'' Girard et al. 2022
* '' P. fulva'' Iizuka and Komagata 1963 (Approved Lists 1980)
* '' P. guariconensis'' Toro et al. 2013
* '' P. huaxiensis'' Qin et al. 2019
* "'' P. hunanensis''" Gao et al. 2014
* "'' P. hutmensis''" Xiang et al. 2019
* '' P. inefficax'' Keshavarz-Tohid et al. 2019
* '' P. japonica'' Pungrasmi et al. 2008
* '' P. juntendi'' Tohya et al. 2019
* '' P. kermanshahensis'' Girard et al. 2022
* '' P. kurunegalensis'' Girard et al. 2022
* '' P. laurentiana'' Wright et al. 2019
* '' P. maumuensis'' Girard et al. 2022
* '' P. monteilii'' Elomari et al. 1997
* '' P. mosselii'' Dabboussi et al. 2002
* '' P. muyukensis'' Girard et al. 2022
* '' P. oryzicola'' Girard et al. 2022
* "'' P. oryziphila''" Yang et al. 2021
* '' P. palmensis'' Gutierrez-Albanchez et al. 2022
* '' P. parafulva'' Uchino et al. 2002
* '' P. peradeniyensis'' Girard et al. 2022
* '' P. persica'' Keshavarz-Tohid et al. 2020
* '' P. plecoglossicida'' Nishimori et al. 2000
* '' P. promysalinigenes'' Girard et al. 2022
* '' P. putida'' (Trevisan 1889) Migula 1895 (Approved Lists 1980)
* "'' P. pyomelaminifaciens''" Chakraborty et al.
* "'' P. qingdaonensis''" Wang et al. 2019
* '' P. reidholzensis'' Frasson et al. 2017
* '' P. shirazensis'' Girard et al. 2022
* '' P. shirazica'' Keshavarz-Tohid et al. 2020
* '' P. sichuanensis'' Qin et al. 2019
* '' P. soli'' Pascual et al. 2015
* '' P. taiwanensis'' Wang et al. 2010
* '' P. tructae'' Oh et al. 2019
* '' P. urmiensis'' Girard et al. 2022
* "'' P. vlassakiae''" Girard et al. 2021
* '' P. vranovensis'' Tvrzová et al. 2006
* '' P. wadenswilerensis'' Frasson et al. 2017
* "'' P. wayambapalatensis''" Girard et al. 2021
* '' P. xantholysinigenes'' Girard et al. 2022

* '' P. xanthosomatis'' corrig. Girard et al. 2022

''P. resinovorans'' Group

* '' P. furukawaii'' Kimura et al. 2018
* '' P. lalkuanensis'' Thorat et al. 2020
* '' P. mangiferae'' Anurat et al. 2019
* '' P. otitidis'' Clark et al. 2006
* '' P. resinovorans'' Delaporte et al. 1961 (Approved Lists 1980)

''P. rhizosphaerae'' Group

* '' P. baltica'' Gieschler et al. 2021
* '' P. coleopterorum'' Menéndez et al. 2015
* "'' P. eucalypticola''" Liu et al. 2021
* '' P. rhizosphaerae'' Peix et al. 2003

''P. straminea'' Group

* '' P. argentinensis'' Peix et al. 2005
* '' P. daroniae'' Bueno-Gonzalez et al. 2019
* '' P. dryadis'' Bueno-Gonzalez et al. 2019
* '' P. flavescens'' Hildebrand et al. 1994
* '' P. punonensis'' Ramos et al. 2013
* '' P. seleniipraecipitans'' corrig. Hunter and Manter 2011

* '' P. straminea'' corrig. Iizuka and Komagata 1963 (Approved Lists 1980)

''P. stutzeri'' Group

* '' P. azotifigens'' Hatayama et al. 2005
* '' P. balearica'' Bennasar et al. 1996
* '' P. chloritidismutans'' Wolterink et al. 2002
* '' P. kirkiae'' Bueno-Gonzalez et al. 2020

* '' P. nitrititolerans'' Peng et al. 2019
* '' P. nosocomialis'' Mulet et al. 2019

* "'' P. saudiphocaensis''" Azhar et al. 2017
* "'' P. songnenensis''" Zhang et al. 2015
* '' P. stutzeri'' (Lehmann and Neumann 1896) Sijderius 1946 (Approved Lists 1980)
* '' P. urumqiensis'' Zou et al. 2019
* '' P. xanthomarina'' Romanenko et al. 2005
* '' P. zhaodongensis'' Zhang et al. 2015

''P. syringae'' Group

* "'' P. alliivorans''" Zhao et al. 2021
* '' P. amygdali'' Psallidas and Panagopoulos 1975 (Approved Lists 1980)
* '' P. asturiensis'' González et al. 2013
* '' P. avellanae'' Janse et al. 1997
* '' P. cannabina'' (ex Šutič and Dowson 1959) Gardan et al. 1999
* '' P. capsici'' Zhao et al. 2021
* '' P. caricapapayae'' Robbs 1956 (Approved Lists 1980)
* '' P. caspiana'' Busquets et al. 2017
* '' P. cerasi'' Kałuzna et al. 2017
* '' P. cichorii'' (Swingle 1925) Stapp 1928 (Approved Lists 1980)
* '' P. congelans'' Behrendt et al. 2003
* "'' P. coronafaciens''" (Elliott 1920) Stevens 1958

* '' P. ficuserectae'' Goto 1983
* '' P. floridensis'' Timilsina et al. 2018
* "'' P. foliumensis''" Tambong et al. 2021
* "'' P. helianthi''" Elasri et al. 2001
* '' P. meliae'' Ogimi 1981
* '' P. ovata'' Rao et al. 2021

* '' P. savastanoi'' (Janse 1982) Gardan et al. 1992
* '' P. syringae'' van Hall 1902 (Approved Lists 1980)
* "'' P. tomato''" Gardan et al. 1999
* '' P. tremae'' Gardan et al. 1999
* "'' P. triticumensis''" Tambong et al. 2021
* '' P. viridiflava'' (Burkholder 1930) Dowson 1939 (Approved Lists 1980)

'' incertae sedis''

* "'' P. acephalitica''" Tapia-Paniagua et al. 2014
* "'' P. acidophila''" Imada et al. 1981
* " ''Ca.'' P. adelgestsugas" von Dohlen et al. 2013

* '' P. alcaligenes'' Monias 1928 (Approved Lists 1980)
* "'' P. alginovora''" Boyen et al. 1990
* "'' P. alkanolytica''" Nakao and Kuno 1972
* "'' P. amyloderamosa''" Norrman and Wober 1975
* "'' P. andersonii''" Han et al. 2001
* "'' P. bathycetes''" Quigley and Colwell 1968

* "'' P. borealis''" Wilson et al. 2006

* '' P. cavernae'' Zhu et al. 2022
* '' P. cavernicola'' Zhu et al. 2022
* "'' P. cellulosa''" Andrews et al. 2000
* "'' P. clemancea''" Rahman et al. 2010
* "'' P. coenobios''" ZoBell and Upham 1944

* "'' P. diazotrophicus''" Watanabe et al. 1987
* "'' P. diterpeniphila''" Morgan and Wyndham 2002
* "'' P. elodea''" Fialho et al. 1991
* "'' P. excibis''" Steinhaus
* '' P. flexibilis'' (Hespell 1977) Shin et al. 2016

* '' P. fluvialis'' Sudan et al. 2018

* '' P. gelidicola'' Kadota 1951 (Approved Lists 1980)
* "'' P. guezennei''" Simon-Colin et al. 2008
* "'' P. halodenitrificans''" Alonso et al. 2001
* "'' P. halodurans''" Cuhel et al. 1981
* "'' P. halosaccharolytica''" Ohno et al. 1976
* "'' P. halosensibilis''" Zou and Cai 1994

* "'' P. hydrogenothermophila''" Goto et al. 1978
* "'' P. hydrogenovora''" Igarashi et al. 1980
* '' P. indica'' Pandey et al. 2002

* "'' P. jinanensis''" Cai et al. 1989
* '' P. kuykendallii'' Hunter and Manter 2012

* "'' P. lopnurensis''" Mamtimin et al. 2021
* "'' P. lubricans''" Rehman et al. 2010
* '' P. matsuisoli'' Lin et al. 2015
* "'' P. melophthora'' Allen and Riker 1932
* "'' P. mesoacidophila''" Kintaka et al. 1981
* "'' P. multiresinovorans''" Hernandez et al. 2008

* "'' P. perolens''" Szybalski 1950

* '' P. pharmacofabricae'' corrig. Yu et al. 2019

* "'' P. pratensis''" Zhang et al. 2021

* '' P. quercus'' Li et al. 2021
* "'' P. raguenesii''" Simon-Colin et al. 2009
* "'' P. reactans''" Preece and Wong 1982
* "'' P. reptilivora''" Caldwell and Ryerson 1940
* "'' P. rhizophila''" Hassen et al. 2018
* "'' P. rhizovicinus''" He et al. 2021
* "''P. rubescens''" Pivnick 1955

* '' P. schmalbachii'' Shelomi et al. 2021
* "'' P. septica''" Bergey et al. 1930
* '' P. sesami'' Madhaiyan et al. 2017

* "'' P. siderocapsa''" Falamin and Pinevich 2006

* "'' P. suis''" Woods 1930
* "'' P. tamsuii''" Liang et al. 2015
* '' P. tarimensis'' Anwar et al. 2017
* "'' P. teessidea''" Rahman et al. 2010
* "'' P. thermocarboxydovorans''" Lyons et al. 1984
* '' P. thermotolerans'' Manaia and Moore 2002
* '' P. tianjinensis'' Chen et al. 2018
* '' P. tohonis'' Yamada et al. 2021
* "'' P. turbinellae''" Sreenivasan 1956
* '' P. turukhanskensis'' Korshunova et al. 2016
* "'' P. tuticorinensis''" Sreenivasan 1956
* "'' P. wenzhouensis''" Zhang et al. 2021

* '' P. xionganensis'' Zhao et al. 2020

* '' P. yangonensis'' Tohya et al. 2020

Species previously classified in the genus

Recently, 16S rRNA sequence analysis redefined the taxonomy of many bacterial species previously classified as being in the genus ''Pseudomonas''. Species removed from ''Pseudomonas'' are listed below; clicking on a species will show its new classification. The term 'pseudomonad' does not apply strictly to just the genus ''Pseudomonas'', and can be used to also include previous members such as the genera '' Burkholderia'' and '' Ralstonia''.

α proteobacteria: '' P. abikonensis'', '' P. aminovorans'', '' P. azotocolligans'', '' P. carboxydohydrogena'', '' P. carboxidovorans'', '' P. compransoris'', '' P. diminuta'', '' P. echinoides'', '' P. extorquens'', '' P. lindneri'', '' P. mesophilica'', '' P. paucimobilis'', '' P. radiora'', '' P. rhodos'', '' P. riboflavina'', '' P. rosea'', '' P. vesicularis''.

β proteobacteria: '' P. acidovorans'', '' P. alliicola'', '' P. antimicrobica'', '' P. avenae'', '' P. butanovora'', '' P. caryophylli'', '' P. cattleyae'', '' P. cepacia'', '' P. cocovenenans'', '' P. delafieldii'', '' P. facilis'', '' P. flava'', '' P. gladioli'', '' P. glathei'', '' P. glumae'', '' P. huttiensis'', '' P. indigofera'', '' P. lanceolata'', '' P. lemoignei'', ''B. mallei'', '' P. mephitica'', '' P. mixta'', '' P. palleronii'', '' P. phenazinium'', '' P. pickettii'', '' P. plantarii'', '' P. pseudoflava'', '' B. pseudomallei'', '' P. pyrrocinia'', '' P. rubrilineans'', '' P. rubrisubalbicans'', '' P. saccharophila'', '' P. solanacearum'', '' P. spinosa'', '' P. syzygii'', '' P. taeniospiralis'', '' P. terrigena'', '' P. testosteroni''.

γ-β proteobacteria: '' P. boreopolis'', '' P. cissicola'', '' P. geniculata'', '' P. hibiscicola'', '' P. maltophilia'', '' P. pictorum''.

γ proteobacteria: '' P. beijerinckii'', '' P. diminuta'', '' P. doudoroffii'', ''P. elongata'', '' P. flectens'', '' P. marinus'', '' P. halophila'', '' P. iners'', ''P. marina'', '' P. nautica'', '' P. nigrifaciens'', '' P. pavonacea'', '' P. piscicida'', '' P. stanieri''.

δ proteobacteria: '' P. formicans''.

Phylogenetics

The following relationships between genomic affinity groups have been determined by phylogenetic analysis:

Bacteriophages

There are a number of bacteriophages that infect ''Pseudomonas'', e.g.

* ''Pseudomonas'' phage Φ6
* ''Pseudomonas'' phage ΦCTX
* ''Pseudomonas aeruginosa'' phage EL
* ''Pseudomonas aeruginosa'' phage ΦKMV (a Phikmvvirus)
* ''Pseudomonas aeruginosa'' phage LKD16 (a Phikmvvirus)
* ''Pseudomonas aeruginosa'' phage LKA1 (a Phikmvvirus)
* ''Pseudomonas aeruginosa'' phage LUZ19 (a Phikmvvirus)
* ''Pseudomonas aeruginosa'' phage ΦKZ
* ''Pseudomonas putida'' phage gh-1

See also

* Culture collection for a list of culture collections

Footnotes

References

External links

General

Pseudomonas at origin of world's rain and snow



''Pseudomonas'' genome database


* Fluorescent Pseudomona

{{portal bar, Biology

Pseudomonadales
Bacteria genera
Psychrophiles
Gram-negative bacteria
Pathogenic bacteria