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International Journal of Systematic and Evolutionary Microbiology, Vol 50, 1563-1589, Copyright © 2000 by Society for General Microbiology

Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence

Y Anzai, H Kim, JY Park, H Wakabayashi and H Oyaizu
Nippon Roche Research Center, Kamakura, Kanagawa 247-8530, Japan

The broad and vague phenotypic definition allowed the genus Pseudomonas to become a dumping ground for incompletely characterized polarly flagellated, Gram-negative, rod-shaped, aerobic bacteria, and a large number of species have been accommodated in the genus Pseudomonas. The 16S rRNA sequences of 128 valid and invalid Pseudomonas species, which included almost valid species of the genus Pseudomonas listed in the Approved Lists of Bacterial Names, were obtained: sequences of 59 species were determined and those of 69 species were obtained from the GenBank/EMBL/DDBJ databases. These sequences were compared with the sequences of other species of the Proteobacteria. Fifty-seven valid or invalid species including Pseudomonas aeruginosa (type species of the genus Pseudomonas Migula 1894) belonged to the genus Pseudomonas (sensu stricto). Seven subclusters were formed in the cluster of the genus Pseudomonas (sensu stricto), and the resulting clusters conformed well to the rRNA--DNA hybridization study by 54>Palleroni (1984). The other species did not belong to the genus Pseudomonas (sensu stricto) and were related to other genera, which were placed in four subclasses of the Proteobacteria (alpha, beta, gamma and gamma-beta subclasses). Twenty-six examined species, which were not included in the cluster of the Pseudomonas (sensu stricto) and have not been transferred to other genera as yet, are listed alphabetically: 'Pseudomonas abikonensis', Pseudomonas antimicrobica, Pseudomonas beijerinckii, Pseudomonas beteli, Pseudomonas boreopolis, 'Pseudomonas butanovora', Pseudomonas carboxydohydrogena, Pseudomonas cissicola, Pseudomonas doudoroffii, Pseudomonas echinoides, Pseudomonas elongata, Pseudomonas flectens, Pseudomonas geniculata, Pseudomonas halophila, Pseudomonas hibiscicola, Pseudomonas huttiensis, Pseudomonas iners, Pseudomonas lanceolata, Pseudomonas lemoignei, Pseudomonas mephitica, Pseudomonas pictorum, Pseudomonas saccharophila, Pseudomonas spinosa, Pseudomonas stanier, Pseudomonas syzygii and Pseudomonas woodsii. The phylogenetic affiliations of these 26 pseudomonads species are shown.


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J.-H. Yoon, K. H. Kang, T.-K. Oh, and Y.-H. Park
Erythrobacter aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea
Int J Syst Evol Microbiol, November 1, 2004; 54(6): 1981 - 1985.
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 Int. J. Syst. Evol. Microbiol.Home page
L. Ding and A. Yokota
Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. nov.
Int J Syst Evol Microbiol, November 1, 2004; 54(6): 2223 - 2230.
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 Int. J. Syst. Evol. Microbiol.Home page
J.-H. Yoon, M.-H. Lee, and T.-K. Oh
Porphyrobacter donghaensis sp. nov., isolated from sea water of the East Sea in Korea
Int J Syst Evol Microbiol, November 1, 2004; 54(6): 2231 - 2235.
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 Int. J. Syst. Evol. Microbiol.Home page
J.-H. Yoon, S.-H. Yeo, I.-G. Kim, and T.-K. Oh
Shewanella marisflavi sp. nov. and Shewanella aquimarina sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea
Int J Syst Evol Microbiol, November 1, 2004; 54(6): 2347 - 2352.
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 Appl. Environ. Microbiol.Home page
B. S. Weir, S. J. Turner, W. B. Silvester, D.-C. Park, and J. M. Young
Unexpectedly Diverse Mesorhizobium Strains and Rhizobium leguminosarum Nodulate Native Legume Genera of New Zealand, while Introduced Legume Weeds Are Nodulated by Bradyrhizobium Species
Appl. Envir. Microbiol., October 1, 2004; 70(10): 5980 - 5987.
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 Appl. Environ. Microbiol.Home page
F. Rezzonico, G. Defago, and Y. Moenne-Loccoz
Comparison of ATPase-Encoding Type III Secretion System hrcN Genes in Biocontrol Fluorescent Pseudomonads and in Phytopathogenic Proteobacteria
Appl. Envir. Microbiol., September 1, 2004; 70(9): 5119 - 5131.
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 Int. J. Syst. Evol. Microbiol.Home page
E. P. Ivanova, N. M. Gorshkova, N. V. Zhukova, A. M. Lysenko, E. A. Zelepuga, N. G. Prokof'eva, V. V. Mikhailov, D. V. Nicolau, and R. Christen
Characterization of Pseudoalteromonas distincta-like sea-water isolates and description of Pseudoalteromonas aliena sp. nov.
Int J Syst Evol Microbiol, September 1, 2004; 54(5): 1431 - 1437.
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 Int. J. Syst. Evol. Microbiol.Home page
J.-H. Yoon, I.-G. Kim, T.-K. Oh, and Y.-H. Park
Microbulbifer maritimus sp. nov., isolated from an intertidal sediment from the Yellow Sea, Korea
Int J Syst Evol Microbiol, July 1, 2004; 54(4): 1111 - 1116.
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 Int. J. Syst. Evol. Microbiol.Home page
G. S. N. Reddy, G. I. Matsumoto, P. Schumann, E. Stackebrandt, and S. Shivaji
Psychrophilic pseudomonads from Antarctica: Pseudomonas antarctica sp. nov., Pseudomonas meridiana sp. nov. and Pseudomonas proteolytica sp. nov.
Int J Syst Evol Microbiol, May 1, 2004; 54(3): 713 - 719.
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 Int. J. Syst. Evol. Microbiol.Home page
A. Peix, R. Rivas, I. Santa-Regina, P. F. Mateos, E. Martinez-Molina, C. Rodriguez-Barrueco, and E. Velazquez
Pseudomonas lutea sp. nov., a novel phosphate-solubilizing bacterium isolated from the rhizosphere of grasses
Int J Syst Evol Microbiol, May 1, 2004; 54(3): 847 - 850.
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 J. Clin. Microbiol.Home page
T. Spilker, T. Coenye, P. Vandamme, and J. J. LiPuma
PCR-Based Assay for Differentiation of Pseudomonas aeruginosa from Other Pseudomonas Species Recovered from Cystic Fibrosis Patients
J. Clin. Microbiol., May 1, 2004; 42(5): 2074 - 2079.
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 Appl. Environ. Microbiol.Home page
L. Lagace, M. Pitre, M. Jacques, and D. Roy
Identification of the Bacterial Community of Maple Sap by Using Amplified Ribosomal DNA (rDNA) Restriction Analysis and rDNA Sequencing
Appl. Envir. Microbiol., April 1, 2004; 70(4): 2052 - 2060.
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 Int. J. Syst. Evol. Microbiol.Home page
M. Vaneechoutte, P. Kampfer, T. De Baere, E. Falsen, and G. Verschraegen
Wautersia gen. nov., a novel genus accommodating the phylogenetic lineage including Ralstonia eutropha and related species, and proposal of Ralstonia [Pseudomonas] syzygii (Roberts et al. 1990) comb. nov.
Int J Syst Evol Microbiol, March 1, 2004; 54(2): 317 - 327.
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 Int. J. Syst. Evol. Microbiol.Home page
J.-H. Yoon, K. H. Kang, T.-K. Oh, and Y.-H. Park
Shewanella gaetbuli sp. nov., a slight halophile isolated from a tidal flat in Korea
Int J Syst Evol Microbiol, March 1, 2004; 54(2): 487 - 491.
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 Appl. Environ. Microbiol.Home page
A. F. Meyer, D. A. Lipson, A. P. Martin, C. W. Schadt, and S. K. Schmidt
Molecular and Metabolic Characterization of Cold-Tolerant Alpine Soil Pseudomonas Sensu Stricto
Appl. Envir. Microbiol., January 1, 2004; 70(1): 483 - 489.
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 Int. J. Syst. Evol. Microbiol.Home page
A. Peix, R. Rivas, P. F. Mateos, E. Martinez-Molina, C. Rodriguez-Barrueco, and E. Velazquez
Pseudomonas rhizosphaerae sp. nov., a novel species that actively solubilizes phosphate in vitro
Int J Syst Evol Microbiol, November 1, 2003; 53(6): 2067 - 2072.
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 Appl. Environ. Microbiol.Home page
J. J. Huang, J.-I. Han, L.-H. Zhang, and J. R. Leadbetter
Utilization of Acyl-Homoserine Lactone Quorum Signals for Growth by a Soil Pseudomonad and Pseudomonas aeruginosa PAO1
Appl. Envir. Microbiol., October 1, 2003; 69(10): 5941 - 5949.
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 Int. J. Syst. Evol. Microbiol.Home page
J.-H. Yoon, H. Kim, K. H. Kang, T.-K. Oh, and Y.-H. Park
Transfer of Pseudomonas elongata Humm 1946 to the genus Microbulbifer as Microbulbifer elongatus comb. nov.
Int J Syst Evol Microbiol, September 1, 2003; 53(5): 1357 - 1361.
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 Int. J. Syst. Evol. Microbiol.Home page
U. Behrendt, A. Ulrich, and P. Schumann
Fluorescent pseudomonads associated with the phyllosphere of grasses; Pseudomonas trivialis sp. nov., Pseudomonas poae sp. nov. and Pseudomonas congelans sp. nov.
Int J Syst Evol Microbiol, September 1, 2003; 53(5): 1461 - 1469.
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 Int. J. Syst. Evol. Microbiol.Home page
J.-H. Yoon, I.-G. Kim, K. H. Kang, T.-K. Oh, and Y.-H. Park
Alteromonas marina sp. nov., isolated from sea water of the East Sea in Korea
Int J Syst Evol Microbiol, September 1, 2003; 53(5): 1625 - 1630.
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 Int. J. Syst. Evol. Microbiol.Home page
T. Coenye, J. Goris, P. De Vos, P. Vandamme, and J. J. LiPuma
Classification of Ralstonia pickettii-like isolates from the environment and clinical samples as Ralstonia insidiosa sp. nov.
Int J Syst Evol Microbiol, July 1, 2003; 53(4): 1075 - 1080.
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 Int. J. Syst. Evol. Microbiol.Home page
J.-H. Yoon, H. Kim, I.-G. Kim, K. H. Kang, and Y.-H. Park
Erythrobacter flavus sp. nov., a slight halophile from the East Sea in Korea
Int J Syst Evol Microbiol, July 1, 2003; 53(4): 1169 - 1174.
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 Int. J. Syst. Evol. Microbiol.Home page
M. M. Yakimov, L. Giuliano, G. Gentile, E. Crisafi, T. N. Chernikova, W.-R. Abraham, H. Lunsdorf, K. N. Timmis, and P. N. Golyshin
Oleispira antarctica gen. nov., sp. nov., a novel hydrocarbonoclastic marine bacterium isolated from Antarctic coastal sea water
Int J Syst Evol Microbiol, May 1, 2003; 53(3): 779 - 785.
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 Int. J. Syst. Evol. Microbiol.Home page
M. M. Yakimov, H. Lunsdorf, and P. N. Golyshin
Thermoleophilum album and Thermoleophilum minutum are culturable representatives of group 2 of the Rubrobacteridae (Actinobacteria)
Int J Syst Evol Microbiol, March 1, 2003; 53(2): 377 - 380.
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 Int. J. Syst. Evol. Microbiol.Home page
D. R. Humphry, G. W. Black, and S. P. Cummings
Reclassification of 'Pseudomonas fluorescens subsp. cellulosa' NCIMB 10462 (Ueda et al. 1952) as Cellvibrio japonicus sp. nov. and revival of Cellvibrio vulgaris sp. nov., nom. rev. and Cellvibrio fulvus sp. nov., nom. rev.
Int J Syst Evol Microbiol, March 1, 2003; 53(2): 393 - 400.
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 Int. J. Syst. Evol. Microbiol.Home page
J.-H. Yoon, D.-Y. Shin, I.-G. Kim, K. H. Kang, and Y.-H. Park
Marinobacter litoralis sp. nov., a moderately halophilic bacterium isolated from sea water from the East Sea in Korea
Int J Syst Evol Microbiol, March 1, 2003; 53(2): 563 - 568.
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 Int. J. Syst. Evol. Microbiol.Home page
S. W. Kwon, J. S. Kim, I. C. Park, S. H. Yoon, D. H. Park, C. K. Lim, and S. J. Go
Pseudomonas koreensis sp. nov., Pseudomonas umsongensis sp. nov. and Pseudomonas jinjuensis sp. nov., novel species from farm soils in Korea
Int J Syst Evol Microbiol, January 1, 2003; 53(1): 21 - 27.
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 Int. J. Syst. Evol. Microbiol.Home page
J.-H. Yoon, I.-G. Kim, D.-Y. Shin, K. H. Kang, and Y.-H. Park
Microbulbifersalipaludis sp. nov., a moderate halophile isolated from a Korean salt marsh
Int J Syst Evol Microbiol, January 1, 2003; 53(1): 53 - 57.
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 MicrobiologyHome page
M. K. Sluis, L. A. Sayavedra-Soto, and D. J. Arp
Molecular analysis of the soluble butane monooxygenase from 'Pseudomonas butanovora'
Microbiology, November 1, 2002; 148(11): 3617 - 3629.
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 Appl. Environ. Microbiol.Home page
J.-M. Meyer, V. A. Geoffroy, N. Baida, L. Gardan, D. Izard, P. Lemanceau, W. Achouak, and N. J. Palleroni
Siderophore Typing, a Powerful Tool for the Identification of Fluorescent and Nonfluorescent Pseudomonads
Appl. Envir. Microbiol., June 1, 2002; 68(6): 2745 - 2753.
[Abstract] [Full Text] [PDF]

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 J. Clin. Microbiol.Home page
T. Coenye, J. Goris, T. Spilker, P. Vandamme, and J. J. LiPuma
Characterization of Unusual Bacteria Isolated from Respiratory Secretions of Cystic Fibrosis Patients and Description of Inquilinus limosus gen. nov., sp. nov.
J. Clin. Microbiol., June 1, 2002; 40(6): 2062 - 2069.
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 J. Bacteriol.Home page
A. S. Vangnai, D. J. Arp, and L. A. Sayavedra-Soto
Two Distinct Alcohol Dehydrogenases Participate in Butane Metabolism by Pseudomonas butanovora
J. Bacteriol., April 1, 2002; 184(7): 1916 - 1924.
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 Appl. Environ. Microbiol.Home page
R. L. Meyer, L. H. Larsen, and N. P. Revsbech
Microscale Biosensor for Measurement of Volatile Fatty Acids in Anoxic Environments
Appl. Envir. Microbiol., March 1, 2002; 68(3): 1204 - 1210.
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 Appl. Environ. Microbiol.Home page
M. Yamasaki, Y. Matsushita, M. Namura, H. Nyunoya, and Y. Katayama
Genetic and Immunochemical Characterization of Thiocyanate-Degrading Bacteria in Lake Water
Appl. Envir. Microbiol., February 1, 2002; 68(2): 942 - 946.
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