Biodegradation

, Volume 16, Issue 5, pp 393–402 | Cite as

Isolation and characterization of phenanthrene-degrading Sphingomonas paucimobilis strain ZX4

  • Ying Xia
  • Hang Min
  • Gang Rao
  • Zhen-mei Lv
  • Ji Liu
  • Yang-fang Ye
  • Xue-jun Duan
Article

Abstract

Phenanthrene-degrading bacterium strain ZX4 was isolated from an oil-contaminated soil, and identified as Sphingomonaspaucimobilis based on 16S rDNA sequence, cellular fatty acid composition, mol% G + C and Biolog-GN tests. Besides phenanthrene, strain ZX4 could also utilize naphthalene, fluorene and other aromatic compounds. The growth on salicylic acid and catechol showed that the strain degraded phenanthrene via salicylate pathway, while the assay of catechol 2, 3-dioxygenase revealed catechol could be metabolized through meta-cleavage pathway. Three genes, including two of meta-cleavage operon genes and one of GST encoding gene were obtained. The order of genes arrangement was similar to S-type meta-pathway operons. The phylogenetic trees based on 16S rDNA sequence and meta-pathway gene both revealed that strain ZX4 is clustered with strains from genus Sphingomonas.

Keywords

16S rDNA meta-cleavage operon genes phenanthrene degradation phylogenetic analysis 

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References

  1. Balashova, NV, Kosheleva, IA, Golovchenko, NP, Boronin, AM 1999Phenanthrene metabolism by Pseudomonas and Burkholderia strainsProcess. Biochem.35291296Google Scholar
  2. Balashova, NV, Stolz, A, Knackmuss, HJ, Kosheleva, IA, Naumov, AV, Boronin, AM 2001Purification and characterization of a salicylate hydroxylase involved in 1-hydroxy-2 -naphthoic acid hydroxylation from the naphthalene and phenanthrene-degrading bacterial strain Pseudomonas putida BS202-P1Biodegradation12179188Google Scholar
  3. Cerniglia, CE 1992Biodegradation of polycyclic aromatic hydrocarbonsBiodegradation3351368Google Scholar
  4. Dagher, F, Deziel, E, Lirette, P, Paquette, G, Bisaillon, J-G, Villemur, R 1997Comparative study of five polycyclic aromatic hydrocarbon degrading bacterial strains isolated from contaminated soilsCan. J. Microbiol.43368377CrossRefGoogle Scholar
  5. Dean-Ross, D, Moody, J, Cerniglia, CE 2002Utilization of mixtures of polycyclic aromatic hydrocarbons by bacteria isolated from contaminated sedimentFEMS. Microbiol. Ecol.4117Google Scholar
  6. Diaz, E, Timmis, KN 1995Identification of functional residues in a 2-hydroxymuconic semialdehyde hydrolaseJ. boil. chem.27064036411Google Scholar
  7. Doddamani, HP, Ninnekar, HZ 2000Biodegradation of phenanthrene by a Bacillus speciesCurr. Microbiol.411114Google Scholar
  8. Dong, XZ, Cai, MY 2001Manual of General Bacteria Systemic IdentificationScience PressBeijing180182Google Scholar
  9. Furukawa, K, Miyazaki, T 1986Cloning of a gene cluster encoding biphenyl and chlorobiphenyl degradation in Pseudomonas pseudoalcaligenesJ. Bacteriol.166392398Google Scholar
  10. Goyal, AK, Zylstra, GJ 1996Molecualr cloning of novel genes for polycyclic aromatic hydrocarbon degradation from Comamonas testosteroni GZ39Appl. Environ. Microbiol.62230236Google Scholar
  11. Harayama, S 1997Polycyclic aromatic hydrocarbon bioremediation designCurr. Opin. Biotechnol.8268273Google Scholar
  12. Kim, E, Zylstra, GJ 1995Molecular and biochemical characterization of two meta-cleavage dioxygenases involved in biphenyl and m-xylene degradation by Beijerinckia spstrain B1. J. Bacteriol.17730953103Google Scholar
  13. Laurie, AL, Lloyd-Jones, G 1999aThe phn genes of Burkholderia spstrain RP007 constitute a divergent genes cluster for polycylic aromatic hydrocarbon catabolism. J. bacteriol.181531540Google Scholar
  14. Laurie, AD, Lloyd-Jones, G 1999bConserved and hybrid meta-cleavage operons from PAH-degrading Burkholeria RP007Biochem. Biophy. Res. Comm.262308314Google Scholar
  15. Lloyd-Jones, G, Lau, PC 1997Glutathione S-transferase-encoding gene as a potential probe for environmental bacteria isolates capable of degrading polycyclic aromatic hydrocarbonsAppl. Environ. Microbiol6332863290Google Scholar
  16. Masai, E, Shinohara, S, Hara, H, Nishikawa, S, Katayama, Y, Fukuda, M 1999Genetic and biochemical characterization of a 2-pyrone-4, 6-dicarboxylic acid hydrolase involved in the protocatechuate 4,5-cleavage pathway of Sphingomonas paucimobilis SYK-6J. Bacteriol.1815562Google Scholar
  17. Meyer, S, Moser, R, Neef, A, Stahl, U, Kampfer, P 1999Differential detection of key enzymes of polyaromatic-hydrocarbon-degrading bacteria using PCR and gene probesMicrobiology14517311741CrossRefGoogle Scholar
  18. Miyauchi, K, Suh, SK, Nagata, Y, Takagi, M 1998Cloning and sequencing of a 2,5-dichlorohydroquinone reductive dehalogenase gene whose product is involved in degradation of gamma-hexachlorocyclohexane by Sphingomonas paucimobilisJ. Bacteriol.18013541359Google Scholar
  19. Nalin, R, Simonies, P, Vogel, TM, Normand, P 1999Rhodanobacter lindaniclasticus gen. nov., sp. nov., a lindane-degrading bacteriumInt. J. Syst. Bacteriol.491923Google Scholar
  20. Nohynek, LJ, Nurmiaho-Lassila, EL, Suhonen, EL, Busse, HJ, Mohammadi, M, Hantula, J, Rainey, F, Salkinoja-Salonen, MS 1996Description of chlorophenol-degrading Pseudomonas sp. strains KF1T, KF3, and NKF1 as a new species the genus of Sphingomonas, Sphingomonas subarctica sp. novInt. J. Syst. Bacteriol.4610421055CrossRefGoogle Scholar
  21. Pinyakong, O, Habe, H, Omori, T 2003The unique aromatic catabolic genes in Sphingomonads degrading polycyclic aromatic hydrocarbons (PAHs)J. Gen. Appl. Microbiol.49119Google Scholar
  22. Saito, A, Iwabuchi, T, Harayama, SA 2000novel phenanthrene dioxygenase from Nocardioides sp. strain KP7: Expression in Escherichia coilJ. bacterial.18221342141Google Scholar
  23. Sambrook, J, Fritsch, EF, Maniatis, T 1990Molecular cloning: A laboratory manualCold Spring Harbour Laboratory pressNew YorkGoogle Scholar
  24. Shin, HJ, Kim, SJ, Kim, YC 1997Sequence analysis of the phnD gene encoding 2-hydroxymuconic semialdehyde hydrolase in Pseudomonas sp. strain DJ77Biochem. Biophy. Res. Comm.232288291Google Scholar
  25. Tian, L, Ma, p, Zhong, JJ 2002Kinetics and key enzymes activities of phenanthrene degradation by Pseudomonas mendocinaProcess. Biochem.3714311437Google Scholar
  26. Vuilleumier, S, Pagni, M 2002The elusive roles of bacterial glutathione S-transferases: new lesson from genomesAppl. Microbiol. Biotechnol.58138146Google Scholar
  27. Yabuuchi, E, Yano, I, Oyaizu, H, Hashimoto, Y, Ezaki, T, Yamamoto, H 1990Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus SphingomonasMicrobiol. Immunol.3499119Google Scholar

Copyright information

© Springer 2005

Authors and Affiliations

  • Ying Xia
    • 1
    • 2
  • Hang Min
    • 1
  • Gang Rao
    • 3
  • Zhen-mei Lv
    • 1
  • Ji Liu
    • 1
  • Yang-fang Ye
    • 1
  • Xue-jun Duan
    • 1
  1. 1.College of Life SciencesZhejiang UniversityHangzhouChina
  2. 2.Microbiology InstituteChinese Academy of SciencesBeijingChina
  3. 3.State Intellectual Property Office of P.R. ChinaBeijingChina

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