Pseudomonas toyotomiensis sp. nov., a psychrotolerant facultative alkaliphile that utilizes hydrocarbons

International Journal of Systematic and Evolutionary Microbiology

Volumn 61, Issue 8, 2011, Pages 1842-1848

  Hirota, Kikue ^a   Yamahira, Keiko ^a,b   Nakajima, Kenji ^a   Nodasaka, Yoshinobu ^c   Okuyama, Hidetoshi ^c   Yumoto, Isao ^a,c  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b ROM Co Ltd   (Japan)

^c HOKKAIDO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CASEIN; DNA; FATTY ACID; GELATIN; HYDROCARBON; QUINONE DERIVATIVE; RIBOSOME RNA; STARCH; UBIQUINONE 9; UNCLASSIFIED DRUG; WATER;

ARTICLE; BACTERIAL FLAGELLUM; BACTERIAL STRAIN; BACTERIUM ISOLATION; CELL; DNA DNA HYBRIDIZATION; GENE SEQUENCE; HYDROLYSIS; JAPAN; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PSEUDOMONAS; PSEUDOMONAS ALCALIPHILA; PSEUDOMONAS OLEOVORANS; PSEUDOMONAS TOYOTOMIENSIS; SOIL; THERMAL SPRING; UNINDEXED SEQUENCE;

ALKALIES; DNA, BACTERIAL; DNA, RIBOSOMAL; GEOLOGIC SEDIMENTS; HOT SPRINGS; HYDROCARBONS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PSEUDOMONAS; RNA, RIBOSOMAL, 16S;

NEGIBACTERIA; PSEUDOMONAS; PSEUDOMONAS ALCALIPHILA; PSEUDOMONAS OLEOVORANS;

EID: 79961044161     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.024612-0     Document Type: Article

References (28)

1. Ait Tayeb, L., Ageron, E., Grimont, F. & Grimont, P. A. D. (2005). Molecular phylogeny of the genus Pseudomonas based on rpoB sequences and application for the identification of isolates. Res Microbiol 156, 763-773.
2. Anzai, Y., Kim, H., Park, J.-Y., Wakabayashi, H. & Oyaizu, H. (2000). Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int J Syst Evol Microbiol 50, 1563-1589.
3. Barrow, G. I. & Feltham, R. K. A. (editors) (1993). Cowan and Steel's Manual for the Identification of Medical Bacteria, 3rd edn. Cambridge: Cambridge University Press.
4. Boulton, C. A. & Ratledge, C. (1984). The physiology of hydrocarbon utilizing microorganisms. In Enzyme and Fermentation Biotechnology, pp. 11-77. Edited by A. Wiseman. New York: Wiley.
5. Ezaki, T., Hashimoto, Y. & Yabuuchi, E. (1989). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in micro-dilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39, 224-229.
6. Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368-376.
7. Fitch, W. M. (1971). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20, 406-416.
8. Hugh, R. & Leifson, E. (1953). The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various gram negative bacteria. J Bacteriol 66, 24-26.
9. Kersters, K., Ludwig, W., Vancanneyt, M., De Vos, P., Gillis, M. & Schleifer, K.-H. (1996). Recent changes in the classification of pseudomonads: an overview. Syst Appl Microbiol 19, 465-477.
10. Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111-120.
11. Kiska, D. L. & Gilligan, P. H. (1999). Pseudomonas. In Manual of Clinical Microbiology, 7th edn, pp. 517-525. Edited by P. R. Murray, E. J. Baron & M. A. Pfaller. Washington, DC: American Society for Microbiology.
12. Marmur, J. (1961). A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3, 208-218.
13. Moore, E. R. B., Mau, M., Arnscheidt, A., Bottger, E. C., Hutson, R. A., Collins, M. D., van de Peer, Y., de Wachter, R. & Timmis, K. T. (1996). The determination and comparison of the 16S rDNA gene sequence of species of the genus Pseudomonas (sensu stricto) and estimation of the natural genetic relationships. Syst Appl Microbiol 19, 478-492.
14. Mulet, M., Lalucat, J. & Garcia-Valdes, E. (2010). DNA sequence-based analysis of the Pseudomonas species. Environ Microbiol 12, 1513-1530.
15. AL (Nom. cons. Opin. 5, Jud. Comm. 1952, 237). In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 141-199. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins.
16. Palleroni, N. J. (1993). Pseudomonas classification. A new case history in the taxonomy of gram-negative bacteria. Antonie van Leeuwenhoek 64, 231-251.
17. Park, Y.-D., Yi, H., Baik, K. S., Seong, C. N., Bae, K. S., Moon, E. Y. & Chun, J. (2006). Pseudomonas segetis sp. nov., isolated from soil. Int J Syst Evol Microbiol 56, 2593-2595.
18. T. Curr Microbiol 60, 294-300.
19. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
20. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
21. Tamaoka, J. & Komagata, K. (1984). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25, 125-128.
22. Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007). MEGA4: molecular evolutionary genetic analysis (MEGA) software version 4.0. Mol Biol Evol 24, 1596-1599.
23. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680.
24. Yamahira, K., Hirota, K., Nakajima, K., Morita, N., Nodasaka, Y. & Yumoto, I. (2008). Acinetobacter sp. strain Ths, a novel psychrotolerant and alkalitolerant bacterium that utilizes hydrocarbon. Extremophiles 12, 729-734.
25. Yamamoto, S. & Harayama, S. (1995). PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol 61, 1104-1109.
26. Yamamoto, S., Kasai, H., Arnold, D. L., Jackson, R. W., Vivian, A. & Harayama, S. (2000). Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology 146, 2385-2394.
27. Yumoto, I., Yamazaki, K., Hishinuma, M., Nodasaka, Y., Suemori, A., Nakajima, K., Inoue, N. & Kawasaki, K. (2001). Pseudo-monas alcaliphila sp. nov., a novel facultatively psychrophilic alkaliphile isolated from seawater. Int J Syst Evol Microbiol 51, 349-355.
28. Yumoto, I., Nakamura, A., Iwata, H., Kojima, K., Kusumoto, K., Nodasaka, Y. & Matsuyama, H. (2002). Dietzia psychralcaliphila sp. nov., a novel, facultatively psychrophilic alkaliphile that grows on hydrocarbons. Int J Syst Evol Microbiol 52, 85-90.