Pseudomonas japonica sp. nov., a novel species that assimilates straight chain alkylphenols

Journal of General and Applied Microbiology

Volumn 54, Issue 1, 2008, Pages 61-69

  Pungrasmi, Wiboonluk ^a,b   Lee, Haeng Seog ^a,c   Yokota, Akira ^a   Ohta, Akinori ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b CHULALONGKORN UNIVERSITY   (Thailand)

^c UNIVERSITY OF FLORIDA   (United States)

Author keywords

Activated sludge; Alkylphenols degrading bacteria; Endocrine disrupter chemicals; Pseudomonas; Pseudomonas japonica sp. nov.

Indexed keywords

ALKYLPHENOL; BACTERIAL DNA; CYTOSINE; DNA 16S; GUANINE; HYDROXY FATTY ACID; PALMITIC ACID; UBIQUINONE; FATTY ACID; PHENOL DERIVATIVE; RNA 16S;

ACTIVATED SLUDGE; ARTICLE; BACTERIAL STRAIN; BACTERIUM ISOLATION; CLADISTICS; CONTROLLED STUDY; DNA CONTENT; DNA DNA HYBRIDIZATION; DNA SEQUENCE; MICROBIAL DEGRADATION; MOLECULAR PHYLOGENY; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PSEUDOMONADACEAE; PSEUDOMONAS; PSEUDOMONAS GRAMINIS; PSEUDOMONAS JAPONICA; PSEUDOMONAS PUTIDA; BACTERIUM IDENTIFICATION; CHEMISTRY; CLASSIFICATION; DNA BASE COMPOSITION; GENETICS; GENOTYPE; ISOLATION AND PURIFICATION; JAPAN; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEIC ACID HYBRIDIZATION; PHENOTYPE; PHYLOGENY; PHYSIOLOGY; SEWAGE; SPECIES DIFFERENCE;

BACTERIA (MICROORGANISMS); PSEUDOMONAS; PSEUDOMONAS GRAMINIS; PSEUDOMONAS JAPONICA; PSEUDOMONAS PUTIDA;

BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; FATTY ACIDS; GENOTYPE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; PHENOLS; PHENOTYPE; PHYLOGENY; PSEUDOMONAS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SEWAGE; SPECIES SPECIFICITY; TOKYO;

EID: 41649117595     PISSN: 00221260     EISSN: 13498037     Source Type: Journal    
DOI: 10.2323/jgam.54.61     Document Type: Article

References (28)

1. Ajithkumar, B., Ajithkumar, V. P., and Iriye, R. (2003) Degradation of 4-amylphenol and 4-hexylphenol by a new activated sludge isolate of Pseudomonas veronii and proposal for a new subspecies status. Res. Microbiol., 154, 17-23.
2. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) Basic logical alignment search tool. J. Mol. Biol., 215, 403-410.
3. Anzai, Y., Kim, H., Park, J. Y., Wakabayashi, H., and Oyaizu, H. (2000) Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int. J. Syst. Evol. Microbiol., 50, 1563-1589.
4. Behrendt, U., Ulrich, A., Schumann, P., Erler, W., Burghardt, J., and Seyfarth, W. (1999) A taxonomic study of bacteria isolated from grasses: A proposed new species Pseudomonas graminis sp. nov. Int. J. Syst. Evol. Microbiol., 49, 297-308.
5. Ezaki, T., Hashimoto, Y., and Yabuuchi, E. (1989) Fluorometric deoxyribonucleic acid hybridization in microdilution 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. (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39, 783-791.
7. Fujii, K., Urano, N., Ushio, H., Satomi, M., and Kimura, S. (2001) Sphingomonas cloacae sp. nov., a nonylphenol-degrading bacterium isolated from wastewater of a sewage- treatment plant in Tokyo. Int. J. Syst. Evol. Microbiol., 51, 603-610.
8. Gibson, D. T. and Subramanian, V. (1984) Microbial Degradation of Organic Compounds, ed. by Gibson, D. T., Dekker, New York, pp. 181-252.
9. Hucker, G. J. and Conn, H. J. (1923) Methods of Gram Staining. Technical Bulletin 129, New York State Agricultural Experiment Station, Ithaca.
10. King, E. O., Ward, M. K., and Raney, D. E. (1954) Two simple media for the demonstration of pyocyanin and fluorescin. J. Lab. Clin. Med., 44, 474-477.
11. Marmur, J. (1961) A procedure for isolation of deoxyribonucleic acid from microorganisms. J. Mol. Biol., 3, 208-218.
12. Mesbah, M., Premachandran, U., and Whitman, W. B. (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high performance liquid chromatography. Int. J. Syst., Bacteriol., 39, 159-167.
13. Moore, E. R. B., Mua, M., Amscheidt, A., Bottger, E. C., Hutson, R. A., Collins, M. D., Van der Peer, Y., De Wachter, R., and Timmis, K. N. (1996) The determination and comparison of the 16S rRNA gene sequences of species of the genus Pseudomonas (sensu stricto) and estimation of the natural, intrageneric relationship. Syst. Appl. Microbiol., 19, 478-492.
14. Omori, T., Monno, L., Saiki, Y., and Komada, T. (1992) Desulfulrization of dibenzothiophene by Corynebacterium sp. strain SY1. Appl. Environ. Microbiol., 58, 911-915.
15. Oyaizu, H. and Komagata, K. (1983) Grouping of Pseudomonas species on the basis of the cellular fatty acid composition and the quinone system with special reference to the existence of 3-hydroxy fatty acids. J. Gen. Appl. Microbiol., 29, 17-40.
16. AL (nom. cons. opin. 5, jud. comm. 1952, 237). In Bergey's Manual of Systematic Bacteriology 1, ed. by Krieg, N. R. and Holt, J. G, Williams & Wilkins, Baltimore, pp. 141-199.
17. Rudling, L. and Solyom, P. (1974) The investigation of biodegradability of branched nonyl phenol ethoxylates. Water Res., 8, 115-119.
18. Saito, H. and Miura, K. (1963) Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim. Biophys. Acta, 72, 619-629.
19. Saitou, N. and Nei, M. (1987) The neighbor-joining method: A new method for reconstructing phylogenetic tree. Mol. Biol. Evol., 4, 406-425.
20. Stackebrandt, E. and Goebel, B. M. (1994) Taxonomio note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol., 44, 846-849.
21. Thompson, J. D., Higgins, D. G., and Gibson, J. J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
22. Tamaoka, J. and Komagata, K. (1984) Determination of DNA base composition by reverse-phase high-performance liquid chromatography. FEMS Microbiol. Lett., 25, 125-128.
23. Vallini, G., Frassinetti, S., and Scorzetti, G. (1997) Candida aquaetextoris sp. nov., a new species yeast occurring in sludge from textile industry wastewater treatment plant in Tuscany, Italy. Int. J. Syst. Bacteriol., 47, 336-340.
24. Wayne, L. G., Brenner, D. J., Colwell, R. R., and 9 other authors (1987) International committee on systematic bacteriology, report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol., 37, 463-464.
25. Weisburg, W. G., Barns, S. M., Pelletier, D. A., and Lane, D. J. (1991) 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol., 173, 697-703.
26. Yamada, Y. and Kuraishi, I. (1982) Ubiquinone and menaquinone. In Biseibutsu no Kagakubunrui Jikkenhou, ed. by Komagata, K., Gakkai Shuppan Center, Tokyo, pp. 143-155 (in Japanese).
27. Yamada, Y., Takinami-Nakamura, H., Tahara, Y., Oyaizu, H., and Komagata, K. (1982) The ubiquinone systems in the strain of Pseudomonas species. J. Gen. Appl. Microbiol., 28, 7-12.
28. Yamamoto, S., Kasai, H., Arnold, D. L., Jackson, R. W., Vivian, A., and Harakama, S. (2001) Phylogenic of the genus Pseudomonas: Intragenetic structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology, 146, 2385-2394.