Ecology

Habitat

Depth range based on 1 specimen in 1 taxon.
Water temperature and chemistry ranges based on 1 sample.

Environmental ranges
  Depth range (m): 10 - 10
  Temperature range (°C): 28.991 - 28.991
  Nitrate (umol/L): 0.046 - 0.046
  Salinity (PPS): 34.214 - 34.214
  Oxygen (ml/l): 4.477 - 4.477
  Phosphate (umol/l): 0.113 - 0.113
  Silicate (umol/l): 1.170 - 1.170
 
Note: this information has not been validated. Check this *note*. Your feedback is most welcome.

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Evolution and Systematics

Functional Adaptations

Functional adaptation

Proteins cause ice nucleation: a plant pathogen
 

The cells of Pseudomonas syringae, a plant pathogen, can cause ice nucleation via specific surface proteins.

   
  "P. syringae is one of the few plant pathogens known to be disseminated up into clouds (Jayaweera and Flanagan, 1982; Sands et al., 1982). It is also scrubbed from the air during rain (Constantinidou et al., 1990). Many strains of this bacterium are ice nucleation-active (Lindow, 1983), are known to survive freezing as well as induce freezing, and it has been suggested that they might even have a role in inciting rainfall via their ice nucleation activity (Morris et al., 2004)." (Morris et al. 2007:85)

"Antifreeze proteins (AFPs) inhibit the growth of ice, whereas ice-nucleation proteins (INPs) promote its formation…Although several organisms have been identified as having ice-nucleation activity, the best characterized by biochemical methods are the bacterial INPs. Of these INPs, that of Pseudomonas syringae is often used as a representative protein." (Graether and Jia 2001:1169)
  Learn more about this functional adaptation.
  • Graether, SP; Jia, Z. Modeling Pseudomonas syringae ice-nucleation protein as a b-Helical protein. Biophysical Journal. 80(3): 1169-1173.
  • Morris, C. E.; Kinkel, L. L.; Xiao, K.; Prior, P.; Sands, D. C. 2007. Surprising niche for the plant pathogen Pseudomonas syringae. Infection, Genetics and Evolution. 7(1): 84-92.
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Functional adaptation

Breaking down crude oil: aerobic bacteria
 

The metabolism of Pseudomonas and other aerobic microorganisms is capable of breaking down hydrocarbons in crude oil.

   
  "Both aerobic and anaerobic microorganisms tend to colonise oil pipelines and oil and fuel storage installations. Complex microbial communities consisting of both hydrocarbon oxidizing microorganisms and bacteria using the metabolites of the former form an ecological niche where they thrive." (Yemashova et al. 2007:315)
  Learn more about this functional adaptation.
  • Yemashova NA; Murygina VP; Zhukov DV; Zakharyantz AA; Gladchenko MA; Appanna V; Kalyuzhnyi SV. 2007. Biodeterioration of crude oil and oil derived products: a review. Reviews in Environmental Science and Biotechnology. 6(4): 315-337.
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Wikipedia

Pseudomonas

Pseudomonas is a genus of Gram-negative, aerobic gammaproteobacteria, belonging to the family Pseudomonadaceae containing 191 validly described species.[1] The members of the genus demonstrate a great deal of metabolic diversity, and consequently are able to colonize a wide range of niches.[2] 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.

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,[3][4] the latter statement was later proved incorrect and was due to refractive granules of reserve materials.[5] Despite the vague description, the type species, Pseudomonas pyocyanea (basonym of Pseudomonas aeruginosa), proved the best descriptor.[5]

Classification history[edit]

Like most bacterial genera, the pseudomonad[note 1] 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[5] (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.[6]

Recently, 16S rRNA sequence analysis has redefined the taxonomy of many bacterial species.[7] As a result, the genus Pseudomonas includes strains formerly classified in the genera Chryseomonas and Flavimonas.[8] Other strains previously classified in the genus Pseudomonas are now classified in the genera Burkholderia and Ralstonia.[9][10]

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.[6]

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.[11]

Characteristics[edit]

Members of the genus display these defining characteristics:[12]

Other characteristics that tend to be associated with Pseudomonas species (with some exceptions) include secretion of pyoverdine, a fluorescent yellow-green siderophore[13] under iron-limiting conditions. Certain Pseudomonas species may also produce additional types of siderophore, such as pyocyanin by Pseudomonas aeruginosa[14] and thioquinolobactin by Pseudomonas fluorescens,.[15] 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.

Biofilm formation[edit]

All species and strains of Pseudomonas have historically been classified as strict aerobes. Exceptions to this classification have recently been discovered in Pseudomonas biofilms.[16] 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.[17] 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.

Pseudomonas species have the ability to metabolize a variety of nutrients. Combined with the ability to form biofilms, they are, thus, able to survive in a variety of unexpected places. For example, they have been found in areas where pharmaceuticals are prepared. A simple carbon source, such as soap residue or cap liner-adhesives is a suitable place for them to thrive. Other unlikely places where they have been found include antiseptics, such as quaternary ammonium compounds, and bottled mineral water.

Antibiotic resistance[edit]

Being Gram-negative bacteria, 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.[17] 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.[18] 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.,[19]) 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 may be important in the response of P. aeruginosa populations to antibiotic treatment.[6]

Taxonomy[edit]

The studies on the taxonomy of this complicated genus groped their way in the dark while following the classical procedures developed for the description and identification of the organisms involved in sanitary bacteriology during the first decades of the 20th century. This situation sharply changed with the proposal to introduce as the central criterion the similarities in the composition and sequences of macromolecular components of the ribosomal RNA. The new methodology clearly showed the genus Pseudomonas, as classically defined, consists of a conglomerate of genera that could clearly be separated into five so-called rRNA homology groups. Moreover, the taxonomic studies suggested an approach that might prove useful in taxonomic studies of all other prokaryotic groups. A few decades after the proposal of the new genus Pseudomonas by Migula in 1894, the accumulation of species names assigned to the genus reached alarming proportions. The number of species in the current list has contracted more than 90%. In fact, this approximated reduction may be even more dramatic if one considers the present list contains many new names; i.e., relatively few names of the original list survived in the process. The new methodology and the inclusion of approaches based on the studies of conservative macromolecules other than rRNA components constitutes an effective prescription that helped to reduce Pseudomonas nomenclatural hypertrophy to a manageable size.[6]

Pathogenicity[edit]

Animal pathogens[edit]

Main article: Pseudomonas infection

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)[citation needed]. 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.[20]

Plant pathogens[edit]

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.[21] Similarly, P. agarici can cause drippy gill in cultivated mushrooms.[22]

Use as biocontrol agents[edit]

Since the mid-1980s, certain members of the Pseudomonas genus 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.[23]

Other notable Pseudomonas species with biocontrol properties include P. chlororaphis, which produces a phenazine-type antibiotic active agent against certain fungal plant pathogens,[24] and the closely related species P. aurantiaca, which produces di-2,4-diacetylfluoroglucylmethane, a compound antibiotically active against Gram-positive organisms.[25]

Use as bioremediation agents[edit]

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:

Food spoilage agents[edit]

As a result of their metabolic diversity, ability to grow at low temperatures, and ubiquitous nature, many Pseudomonas species can cause food spoilage. Notable examples include dairy spoilage by P. fragi,[34] mustiness in eggs caused by P. taetrolens and P. mudicolens,[35] and P. lundensis, which causes spoilage of milk, cheese, meat, and fish.[36]

Species previously classified in the genus[edit]

Recently, 16S rRNA sequence analysis redefined the taxonomy of many bacterial species previously classified as being in the Pseudomonas genus.[7] Species that moved from the Pseudomonas genus are listed below; clicking on a species will show its new classification. The term 'pseudomonad' does not apply strictly to just the Pseudomonas genus, 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. butanovorae, P. caryophylli, P. cattleyae, P. cepacia, P. cocovenenans, P. delafieldii, P. facilis, P. flava, P. gladioli, P. glathei, P. glumae, P. graminis, P. huttiensis, P. indigofera, P. lanceolata, P. lemoignei, P. mallei, P. mephitica, P. mixta, P. palleronii, P. phenazinium, P. pickettii, P. plantarii, P. pseudoflava, P. 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. beteli, 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. halodurans, P. halophila, P. iners, P. marina, P. nautica, P. nigrifaciens, P. pavonacea,[37] P. piscicida, P. stanieri.

δ proteobacteria: P. formicans.

Bacteriophage[edit]

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

See also[edit]

Footnotes[edit]

  1. ^ To aid in the flow of the prose in English, genus names can be "trivialised" to form a vernacular name to refer to a member of the genus: for the genus Pseudomonas it is "pseudomonad" (plural: "pseudomonads"), a variant on the non-nominative cases in the Greek declension of monas, monada.[41] For historical reasons, members of several genera that were formerly classified as Pseudomonas species can be referred to as pseudomonads, while the term "fluorescent pseudomonad" refers strictly to current members of the genus Pseudomonas, as these produce pyoverdin, a fluorescent siderophore.[2] The latter term, fluorescent pseudomonad, is distinct from the term P. fluorescens group, which is used to distinguish a subset of members of the Pseudomonas sensu stricto and not as a whole.

References[edit]

  1. ^ Pseudomonas entry in LPSN [Euzéby, J.P. (1997). "List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet". Int J Syst Bacteriol 47 (2): 590–2. doi:10.1099/00207713-47-2-590. ISSN 0020-7713. PMID 9103655. ]
  2. ^ a b Madigan M; Martinko J, ed. (2005). Brock Biology of Microorganisms (11th ed.). Prentice Hall. ISBN 0-13-144329-1. 
  3. ^ Migula, W. (1894) Über ein neues System der Bakterien. Arb Bakteriol Inst Karlsruhe 1: 235–328.
  4. ^ Migula, W. (1900) System der Bakterien, Vol. 2. Jena, Germany: Gustav Fischer.
  5. ^ a b c Palleroni, N. J. (2010). "The Pseudomonas Story". Environmental Microbiology 12 (6): 1377–1383. doi:10.1111/j.1462-2920.2009.02041.x. PMID 20553550.  edit
  6. ^ a b c d Cornelis P (editor) (2008). Pseudomonas: Genomics and Molecular Biology (1st ed.). Caister Academic Press. ISBN 1-904455-19-0. 
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  8. ^ Anzai, Y; Kudo, Y; Oyaizu, H (1997). "The phylogeny of the genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera". Int J Syst Bacteriol 47 (2): 249–251. doi:10.1099/00207713-47-2-249. PMID 9103607. 
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  25. ^ Esipov; Adanin, VM; Baskunov, BP; Kiprianova, EA; Garagulia, AD (1975). "New antibiotically active fluoroglucide from Pseudomonas aurantiaca". Antibiotiki 20 (12): 1077–81. PMID 1225181. 
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  28. ^ Huertas MJ; Luque-Almagro VM; Martínez-Luque M; Blasco, R.; Moreno-Vivián, C.; Castillo, F.; Roldán, M.-D. (2006). "Cyanide metabolism of Pseudomonas pseudoalcaligenes CECT5344: role of siderophores". Biochem. Soc. Trans. 34 (Pt 1): 152–5. doi:10.1042/BST0340152. PMID 16417508. 
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  32. ^ Marqués S, Ramos JL (1993). "Transcriptional control of the Pseudomonas putida TOL plasmid catabolic pathways". Mol. Microbiol. 9 (5): 923–929. doi:10.1111/j.1365-2958.1993.tb01222.x. PMID 7934920. 
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  35. ^ Levine, M, and Anderson, DQ (Apr 1932). "Two New Species of Bacteria Causing Mustiness in Eggs". J Bacteriol 23 (4): 337–47. PMC 533329. PMID 16559557. 
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  41. ^ Buchanan, R. E. (1955). "Taxonomy". Annual Review of Microbiology 9: 1–20. doi:10.1146/annurev.mi.09.100155.000245. PMID 13259458.  edit
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