Pseudomonas

From Palaeos

The two main sources used in the tree below were Kwon et al. (2003) and Peix et al. (2003). Both of these papers supply a phylogenetic tree with a large number of species of Pseudomonas - both of them with most branches extremely poorly supported (one cannot and should not take any branch seriously that has a bootstrap support of only 3%!) and in significant conflict with one another. Both of them resolve the species above Pseudomonas cremoricolorata in the tree below as basal to the remaining species (though Peix et al. did not include any of the species from P. alcaligenes to P. pseudoalcaligenes), and both support P. cremoricolorata to P. plecoglossicida as a clade. Beyond these two points, disagreement is total.

As such, I have selected Peix et al. (2003) as the main backbone of the tree. The authors of this paper claim to have used maximum parsimony and maximum likelihood as well as neighbour joining in constructing their tree, while Kwon et al. (2003) used neighbour joining only. However, it is not clear in the former paper which was the primary calculation method reflected in the final tree, so my selection should ultimately be regarded as arbitrary and probably best ignored. As occurs far too often with bacterial phylogeny, no result is to be regarded as particularly trustworthy.

<==Pseudomonas Migula 1894
   |  i. s.: P. aureofaciens
   |         P. cannabina
   |         P. cedrella
   |         P. chitinolytica
   |         P. denitrificans
   |         P. elongata
   |         P. halophila
   |         P. hibiscicola
   |         P. iners
   |         P. mallei
   |         P. paucimobilis
   |         P. pickettii
   |         P. pseudomallei
   |         P. psychrophila Yumoto, Kusano et al. 2002VP
   |         P. putrefaciens
   |         P. saccharophila
   |         P. tremae
   |--P. balearica
   `--+--+--P. stutzeri
      |  `--+--*P. aeruginosa
      |     `--P. resinovorans
      `--+--+--P. pertucinogena
         |  `--P. anguilliseptica
         `--+--+--P. luteola
            |  `--P. oleovorans
            `--+--+--P. alcaligenes
               |  `--+--P. nitroreducens
               |     `--+--P. citrinellolis
               |        `--P. jinjuensis Kwon, Kim et al. 2003
               `--+--+--+--P. flavescens
                  |  |  `--P. straminea
                  |  `--+--P. alcaliphila
                  |     |--P. mendocina
                  |     `--P. pseudoalcaligenes
                  `--+--+--P. cremoricolorata Uchino, Shida et al. 2002VP
                     |  `--+--P. putida [incl. Arthrobacter siderocapsulatus]
                     |     `--+--+--P. fulva
                     |        |  `--P. parafulva Uchino, Shida et al. 2002VP
                     |        `--+--P. oryzihabitans
                     |           `--+--P. monteilii
                     |              `--P. plecoglossicida
                     `--+--+--P. agarici
                        |  `--+--P. asplenii
                        |     `--P. fuscovaginae
                        `--+--+--P. umsongensis Kwon, Kim et al. 2003
                           |  `--+--P. graminis
                           |     `--P. rhizosphaerae Peix, Rivas et al. 2003
                           `--+--+--P. jessenii
                              |  `--+--P. koreensis Kwon, Kim et al. 2003
                              |     `--‘P. pavonaceae’
                              `--+--P. migulae
                                 `--+--+--+--P. brassicacearum
                                    |  |  |--P. corrugata
                                    |  |  `--+--P. kilonensis
                                    |  |     `--P. thivervalensis
                                    |  `--+--+--P. lini
                                    |     |  `--+--P. frederiksbergensis
                                    |     |     `--P. mandelii
                                    |     `--+--+--+--P. cichorii
                                    |        |  |  `--+--P. avellanae
                                    |        |  |     `--P. viridiflava
                                    |        |  `--+--+--P. amygdali
                                    |        |     |  `--P. savastanoi
                                    |        |     `--+--P. caricapapayae
                                    |        |        `--P. syringae
                                    |        `--+--+--P. aurantiaca
                                    |           |  `--P. chlororaphis
                                    |           `--+--P. taetrolens
                                    |              `--+--P. lundensis
                                    |                 `--P. fragi
                                    `--+--+--P. constantinii
                                       |  `--P. tolaasii
                                       `--+--+--P. veronii
                                          |  `--+--P. poae
                                          |     `--P. trivialis
                                          `--+--+--P. extremorientalis
                                             |  `--+--P. marginalis
                                             |     `--+--P. grimontii
                                             |        `--P. rhodesiae
                                             `--+--P. fluorescens
                                                `--+--P. orientalis
                                                   `--+--+--P. cedrina
                                                      |  `--‘P. fulgida’
                                                      `--+--P. azotoformans
                                                         `--+--P. gessardii
                                                            |--P. libanensis
                                                            `--+--P. mucidolens
                                                               `--P. synxantha

The following species were mentioned in Sneath et al. (1981). They may or may not correspond to taxa validated after 1985:

Pre-1985 taxa: Pseudomonas acidovorans
               P. alliicola
               P. caryophylli
               P. gladioli [incl. P. marginata]
               P. maltophilia
               P. multivorans
               P. vesicularis

* Type species of genus indicated

References

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Gorshkova, N. M., E. P. Ivanova, A. F. Sergeev, N. V. Zhukova, Y. Alexeeva, J. P. Wright, D. V. Nicolau, V. V. Mikhailov & R. Christen. 2003. Marinobacter excellens sp. nov., isolated from sediments of the Sea of Japan. International Journal of Systematic and Evolutionary Microbiology 53: 2073-2078.

IJSEM. 2002. Validation list no. 85: Validation of publication of new names and new combinations previously effectively published outside the IJSEM. International Journal of Systematic and Evolutionary Microbiology 52: 685-690.

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Kerry, B. R., & W. M. Hominick. 2002. Biological control. In The Biology of Nematodes (D. L. Lee, ed.) pp. 483-509. Taylor & Francis: Florence (Kentucky).

Kwon, S. W., J. S. Kim, I. C. Park, S. H. Yoon, D. H. Park, C. K. Lim & S. J. Go. 2003. Pseudomonas koreensis sp. nov., Pseudomonas umsongensis sp. nov. and Pseudomonas jinjuensis sp. nov., novel species from farm soils in Korea. International Journal of Systematic and Evolutionary Microbiology 53: 21-27.

Mignucci-Giannoni, A. A., & D. K. Odell. 2001. Tropical and subtropical records of hooded seals (Cystophora cristata) dispel the myth of extant Caribbean monk seals (Monachus tropicalis). Bulletin of Marine Science 68 (1): 47-58.

Notomista, E. A. Lahm, A. Di Donato & A. Tramontano. 2003. Evolution of bacterial and archaeal multicomponent monooxygenases. Journal of Molecular Evolution 56: 435-445.

Peix, A., R. Rivas, P. F. Mateos, E. Martínez-Molina, C. Rodríguez-Barrueco & E. Velázquez. 2003. Pseudomonas rhizosphaerae sp. nov., a novel species that actively solubilizes phosphate in vitro. International Journal of Systematic and Evolutionary Microbiology 53: 2067-2072.

Prescott, L. M., J. P. Harley & D. A. Klein. 1996. Microbiology (3rd ed.) Wm. C. Brown Publishers: Dubuque (Iowa).

Sneath, P. H. A., M. Stevens & M. J. Sackin. 1981. Numerical taxonomy of Pseudomonas based on published records of substrate utilization. Antonie van Leeuwenhoek 47: 423-448.

Storms, V., L. A. Devriese, R. Coopman, P. Schumann, F. Vyncke & M. Gillis. 2003. Arthrobacter gandavensis sp. nov., for strains of veterinary origin. International Journal of Systematic and Evolutionary Microbiology 53: 1881-1884.

Tepfer, D., A. Goldmann, N. Pamboukdjian, M. Maille, A. Lepingle, D. Chevalier, J. Dénarié & C. Rosenberg. 1988. A plasmid of Rhizobium meliloti 41 encodes catabolism of two compounds from root exudate of Calystegium sepium. Journal of Bacteriology 170 (3): 1153-1161.

Zeng, R., R. Zhang, J. Zhao & N. Lin. 2003. Cold-active serine alkaline protease from the psychrophilic bacterium Pseudomonas strain DY-A: Enzyme purification and characterization. Extremophiles 7: 335-337.

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CKT061212