Novosphingobium naphthalenivorans sp. nov., a naphthalene-degrading bacterium isolated from polychlorinated-dioxin-contaminated environments

Journal of General and Applied Microbiology

Volumn 53, Issue 4, 2007, Pages 221-228

  Zuzuki, Saori ^a   Hiraishi, Akira ^a  

^a TOYOHASHI UNIVERSITY OF TECHNOLOGY   (Japan)

Author keywords

Naphthalene degradation; Novosphingobium naphthalenivorans; Polychlorinated dioxins; Polycyclic aromatic hydrocarbon

Indexed keywords

CARBON; DIOXIN; FATTY ACID; GENOMIC DNA; GLYCOSPHINGOLIPID; NAPHTHALENE; POLYAMINE; POLYCHLORINATED DIBENZOFURAN; POLYCHLORINATED DIOXIN; QUINONE DERIVATIVE; RNA 16S; SPERMIDINE; UBIDECARENONE; UNCLASSIFIED DRUG; NAPHTHALENE DERIVATIVE;

ARTICLE; BACTERIAL GROWTH; BACTERIAL METABOLISM; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; CHEMOTAXONOMY; CONTROLLED STUDY; DNA DNA HYBRIDIZATION; GENETIC SIMILARITY; GRAM NEGATIVE AEROBIC RODS AND COCCI; INCUBATION TIME; MICROBIAL DEGRADATION; MOLECULAR PHYLOGENY; NEW SPECIES; NONHUMAN; NOVOSPHINGOBIUM NAPHTHALENIVORANS; NOVOSPHINGOBIUM PENTAROMATIVORANS; NOVOSPHINGOBIUM SUBARCTICUM; NUCLEOTIDE SEQUENCE; PHENOTYPE; RNA SEQUENCE; SEDIMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SOIL MICROFLORA; SOIL POLLUTION; STRAIN DIFFERENCE; TYPE STRAIN; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY; POLYMERASE CHAIN REACTION; SOIL POLLUTANT; SPHINGOMONADACEAE;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; NOVOSPHINGOBIUM; NOVOSPHINGOBIUM PENTAROMATIVORANS; NOVOSPHINGOBIUM SUBARCTICUM;

BASE SEQUENCE; MOLECULAR SEQUENCE DATA; NAPHTHALENES; PHYLOGENY; POLYMERASE CHAIN REACTION; SOIL MICROBIOLOGY; SOIL POLLUTANTS; SPHINGOMONADACEAE;

EID: 35448988050     PISSN: 00221260     EISSN: 13498037     Source Type: Journal    
DOI: 10.2323/jgam.53.221     Document Type: Article

References (29)

1. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
2. Balkwill, D. L., Drake, G. R., Reeves, R. H., Fredrickson, J. K., White, D. C., Ringelberg, D. B., Chandler, D. P., Romine, M. F., Kennedy, D. W., and Spadoni, C. M. (1997) Taxonomic study of aromatic-degrading bacteria from deep-terrestrial-subsurface sediments and description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterranea sp. nov., and Sphingomonas stygia sp. nov. Int. J. Syst. Bacteriol., 21, 191-201.
3. Barrow, G. I. and Feltham, R. K. A. (1993) Cowan and Steel's Manual for the Identification of Medical Bacteria, 3rd ed., Cambridge University Press.
4. Felsenstein, J. (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39, 783-791.
5. Fujii, K., Satomi, M., Morita, N., Motomura, T., Tanaka, T., and Kikuchi, S. (2003) Novosphingobium tardaugens sp. nov., an oestradiol-degrading bacterium isolated from activated sludge of a sewage treatment plant in Tokyo. Int. J. Syst. Evol. Microbiol., 53, 47-52.
6. Futamata, H., Uchida, T., Yoshida, N., Yonemitsu, Y., and Hiraishi, A. (2004) Distribution of dibenzofuran-degrading bacteria in soils polluted with different levels of polychlorinated dioxins. Microbes Environ., 19, 172-177.
7. Hiraishi, A. (1992) Direct automated sequencing of 16S rDNA amplified by polymerase chain reaction from bacterial cultures without DNA purification. Lett. Appl. Microbiol., 15, 210-213.
8. Hiraishi, A. (2003) Biodiversity of dioxin-degrading microorganisms and potential utilization in bioremediation. Microbes Environ., 18, 105-125.
9. Hiraishi, A., Kaiya, S., Miyakoda, H., and Futamata, H. (2005a) Biotransformation of polychlorinated dioxins and microbial community dynamics in sediment microcosms. Microbes Environ., 20, 227-242.
10. Hiraishi, A., Sakamaki, N., Miyakoda, H., Maruyama, T., Kato, K., and Futamata, H. (2005b) Estimation of "Dehalococcoides" populations in lake sediment contaminated with low levels of polychlorinated dioxins. Microbes Environ., 20, 216-226.
11. Hiraishi, A., Ueda, Y., Ishihara, J., and Mori, T. (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J. Gen. Appl. Microbiol., 42, 457-469.
12. Hiraishi, A., Yonemitsu, Y., Matsushita, M., Shin, Y. K., Kuraishi, H., and Kawahara, K. (2002) Characterization of Porphyrobacter sanguineus sp. nov., an aerobic bacteriochlorophyll-containing bacterium capable of degrading biphenyl and dibenzofuran. Arch. Microbiol., 178, 45-52.
13. Kämpfer, P., Witzenberger, R., Denner, E. B., Busse, H. J., and Neef, A. (2002) Novosphingobium hassiacum sp. nov., a new species isolated from an aerated sewage pond. Syst. Appl. Microbiol., 25, 37-45.
14. Kimura, M. (1980) A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences. J. Mol. Evol., 16, 111-120.
15. Kubota, M., Kawahara, K., Sekiya, K., Uchida, T., Hattori, Y., Futamata, H., and Hiraishi, A. (2005) Nocardioides aromaticivorans sp. nov., a dibenzofuran-degrading bacterium isolated from dioxin-polluted environments. Syst. Appl. Microbiol., 28, 165-174.
16. Leys, N. M. E. J., Ryngaert, A., Bastiaens, L., Verstraete, W., Top, E. M., and Springael, D. (2004) Occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbops. Appl. Environ. Microbiol., 70, 1944-1955.
17. Liu, Z.-P., Wang, B.-J., Liu, Y.-H., and Liu, S.-J. (2005) Novosphingobium taihuense sp. nov., a novel aromatic-compound-degrading bacterium isolated from Taihu Lake, China. Int. J. Syst. Evol. Microbiol., 55, 1229-1232.
18. Marmur, J. (1961) A procedure for the isolation of deoxyribonucleic acid from microorganisms. J. Mol. Biol., 3, 208-218.
19. 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.
20. Pinyakong, O., Habe, H., and Omori, T. (2003) The unique aromatic catabolic genes in sphingomonads degrading polycyclic aromatic hydrocarbons (PAHs). J. Gen. Appl. Microbiol., 49, 1-19.
21. Saitou, N. and Nei, M. (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
22. Sohn, J. H., Kwon, K. K., Kang, J. H., Jung, H. B., and Kim, S. J. (2004) Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. Int. J. Syst. Evol. Microbiol., 54, 1483-1487.
23. Takeuchi, M., Hamana, K., and Hiraishi, A. (2001) Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis on the basis of a phylogenetic and chemotaxonomic analyses. Int. J. Syst. Evol. Microbiol., 51, 1405-1417.
24. Thompson, J. D., Higgins, D. G., and 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.
25. Tiirola, M. A., Busse, H.-J., Kämpfer, P., and Männistö, M. K. (2005) Novosphingobium lentum sp. nov., a psychrotolerant bacterium from a polychlorophenol bioremediation process. Int. J. Syst. Evol. Microbiol., 55, 583-588.
26. 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.
27. Wittich, R.-M. (1998) Degradation of dioxin-like compounds by microorganisms. Appl. Microbiol. Biotechnol., 49, 489-499.
28. T known as a dibenzo-p-dioxin-metabolizer. Int. J. Syst. Evol. Microbiol., 51, 281-292.
29. Yoshida, N., Takahashi, N., and Hiraishi, A. (2005) Phylogenetic characterization of a polychlorinated dioxin-dechlorinating microbial community by use of microcosm studies. Appl. Environ. Microbiol., 71, 4325-4334.