Diversity of hydrocarbon-degrading Klebsiella strains isolated from hydrocarbon-contaminated estuaries

Journal of Applied Microbiology

Volumn 106, Issue 4, 2009, Pages 1304-1314

  Rodrigues, D F ^a,b   Sakata, S K ^b   Comasseto, J V ^b   Bicego M C ^b   Pellizari, V H ^b  

^a Yale University   (United States)

^b UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Biodegradation; BOX PCR; Catabolic genes; Estuary; Hydrocarbon; Klebsiella

Indexed keywords

BACTERIA; ESTUARIES; GENES; NAPHTHALENE; RNA; SEWAGE;

16S RRNA GENE SEQUENCING; BOX-PCR; CATABOLIC GENES; CONTAMINATED SEDIMENT; ESTUARY SYSTEM; HYDROCARBON COMPOUNDS; HYDROCARBON DEGRADATION; KLEBSIELLA; KLEBSIELLA ORNITHINOLYTICA; KLEBSIELLA PNEUMONIAE;

BIODEGRADATION;

BACTERIAL DNA; HYDROCARBON; NAPHTHALENE; NONANE; OIL; PARA XYLENE; RNA 16S; TOLUENE;

ALKENE; BACTERIUM; BIODEGRADATION; CATABOLISM; ESTUARINE POLLUTION; ESTUARINE SEDIMENT; GENE EXPRESSION; MICROBIAL COMMUNITY; OIL; POLYMERASE CHAIN REACTION; RNA; SEDIMENT POLLUTION; SEWAGE; SPECIES DIVERSITY;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM ISOLATION; BIODEGRADATION; BRAZIL; CATABOLISM; CONTROLLED STUDY; ESTUARY; GENE AMPLIFICATION; GENETIC POLYMORPHISM; GENOMICS; KLEBSIELLA; KLEBSIELLA PNEUMONIAE; MICROBIAL DIVERSITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA SEQUENCE; SEA POLLUTION; SEDIMENT;

EID: 62149140465     PISSN: 13645072     EISSN: 13652672     Source Type: Journal    
DOI: 10.1111/j.1365-2672.2008.04097.x     Document Type: Article

References (65)

1. Altshul, S.F., Gish, W., Miller, W., Mayers, E.W. Lipman, D.J. (1990) Basic local alignment search tool. J Mol Biol 215, 403 410.
2. Barberio, C. Fani, R. (1998) Biodiversity of an Acinetobacter population isolated from activated sludge. Res Microbiol 149, 665 673.
3. Bellinaso Mde, L., Henriques, J.A., Gaylarde, C.C. Greer, C.W. (2004) Genes similar to naphthalene dioxygenase genes in trifluralin-degrading bacteria. Pest Manag Sci 60, 474 478.
4. Bhattacharya, D., Sarma, P.M., Krishnan, S., Mishra, S. Lal, B. (2003) Evaluation of genetic diversity among Pseudomonas citronellolis strains isolated from oily sludge-contaminated sites. Appl Environ Microbiol 69, 1435 1441.
5. Bícego, M.C., Taniguchi, S., Yogui, G.T., Montone, R.C., Moreira da Silva, D.A., Lourenco, R.A., de Castro Martins, C., Sasaki, S.T. et al. (2006) Assessment of contamination by polychlorinated biphenyls and aliphatic and aromatic hydrocarbons in sediments of the Santos and Sao Vicente Estuary System, Sao Paulo, Brazil. Mar Pollut Bull 52, 1804 1816.
6. Braga, E.S., Bonetti, C.V.D.H., Burone, L. Filho, J.B. (2000) Eutrophication and bacterial pollution caused by industrial and domestic wastes at the Baixada Santista Estuarine System - Brazil. Mar Pollut Bull 40, 165 173.
7. Brisse, S., Grimont, F. Grimont, P.A.D. (2006) The genus Klebsiella. In The Prokaryotes ed. Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H. Stackebrandt, E. pp. 159 196. New York : Springer Science & Business Media, LLC.
8. Burns, K., Ehrhardt, M.G., Macpheferson, J., Tierney, J. Kananen, G. (1990) Organic and trace metal contaminants in sediments, seawater and organisms from two Bermuda Harbours. J Exp Mar Biol Ecol 138, 9 34.
9. Caccamo, D., Di Cello, F., Fani, R., Gugliandolo, C. Maugeri, T.L. (1999) Polyphasic approach to the characterization of marine luminous bacteria. Res Microbiol 150, 221 230.
10. Cha, J.Y., Kim, H.S., Cho, Y.S., Lee, Y.C. Choi, Y.L. (2000) Characterization of crude oil degradation by Klebsiella sp. KCL-2 isolated from sea water. Korean J Life Sci 10, 300 306.
11. Chen, J., Wong, M.H., Wong, Y.S. Tam, N.F. (2008) Multi-factors on biodegradation kinetics of polycyclic aromatic hydrocarbons (PAHs) by Sphingomonas sp. a bacterial strain isolated from mangrove sediment. Mar Pollut Bull 57, 695 702.
12. Desoete, G. (1983) On the construction of optimal phylogenetic trees. Z Naturforsch [C] 38, 156 158.
13. Diaz, E., Ferrandez, A., Prieto, M.A. Garcia, J.L. (2001) Biodegradation of aromatic compounds by Escherichia coli. Microbiol Mol Biol Rev 65, 523 569.
14. Eden, P.A., Schmidt, T.M., Blakemore, R.P. Pace, N.R. (1991) Phylogenetic analysis of Aquaspirillum magnetotacticum using polymerase chain reaction-amplified 16S rRNA-specific DNA. Int J Syst Bacteriol 41, 324 325.
15. Ehrhardt, M.G. Burns, K. (1993) Hydrocarbons and related photooxidation products in Saudi Arabian Gulf coastal waters and hydrocarbons in underlying sediments and bioindicator bivalves. Mar Pollut Bull 11, 187 197.
16. Fukuda, K., Nagata, S. Taniguchi, H. (2002) Isolation and characterization of dibenzofuran-degrading bacteria. FEMS Microbiol Lett 208, 179 185.
17. Furukawa, K., Matsumura, F. Tonomura, K. (1978) Alcaligenes and Acinetobacter strains capable of degrading polychlorinated biphenyls. Agric Biol Chem 42, 543 548.
18. Grant, D.J. (1967) Kinetic aspects of the growth of Klebsiella aerogenes with some benzenoid carbon sources. J Gen Microbiol 46, 213 224.
19. Head, I.M., Jones, D.M. Roling, W.F. (2006) Marine microorganisms make a meal of oil. Nat Rev Microbiol 4, 173 182.
20. Herman, L. Heyndrickx, M. (2000) The presence of intragenically located REP-like elements in Bacillus sporothermodurans is sufficient for REP-PCR typing. Res Microbiol 151, 255 261.
21. Irvine, V.A., Kulakov, L.A. Larkin, M.J. (2000) The diversity of extradiol dioxygenase (edo) genes in cresol degrading rhodococci from a creosote-contaminated site that express a wide range of degradative abilities. Antonie Van Leeuwenhoek 78, 341 352.
22. Kanaly, R.A. Harayama, S. (2000) Biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons by bacteria. J Bacteriol 182, 2059 2067.
23. Kasai, Y., Kishira, H., Sasaki, T., Syutsubo, K., Watanabe, K. Harayama, S. (2002) Predominant growth of Alcanivorax strains in oil-contaminated and nutrient-supplemented sea water. Environ Microbiol 4, 141 147.
24. Kerr, R.P. Capone, D.G. (1988) The effect of salinity on the microbial mineralization of two polycyclic aromatic hydrocarbons in estuarine sediments. Mar Environ Res 26, 181 198.
25. Kim, H.Y. Song, H.G. (2005) Purification and characterization of NAD(P)H-dependent nitroreductase I from Klebsiella sp. C1 and enzymatic transformation of 2,4,6-trinitrotoluene. Appl Microbiol Biotechnol 68, 766 773.
26. Kim, W., Song, M.O., Song, W., Kim, K.J., Chung, S.I., Choi, C.S. Park, Y.H. (2003) Comparison of 16S rDNA analysis and rep-PCR genomic fingerprinting for molecular identification of Yersinia pseudotuberculosis. Antonie Van Leeuwenhoek 83, 125 133.
27. Kurkela, S., Lehvaslaiho, H., Palva, T. Teeri, T. (1988) Cloning, nucleotide sequence and characterization of genes encoding naphthalene dioxygenase of Pseudomonas putida strain NCIB9816. Gene 73, 355 362.
28. Lamparelli, M.C., Costa, M.P., Prosperi, V.A., Bevilacqua, J.E., Araujo, R.P.A., Eysink, G.G.J. Pompeia, S. (2001) Santos and Sao Vicente Estuary Systems. Sao Paulo, Brazil : CETESB Technical Report.
29. Lane, C.D.J. (1991) 16S/23S rRNA sequencing. In Nucleic Acids Techniques in Bacterial Systematics ed. Stackebrant, E. Goodfellov, M., pp. 115 148. Chichester, UK : Wiley.
30. Leahy, J.G. Colwell, R.R. (1990) Microbial degradation of hydrocarbons in the environment. Microbiol Rev 54, 305 315.
31. Leys, N.M., Ryngaert, A., Bastiaens, L., Verstraete, W., Top, E.M. Springael, D. (2004) Occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons. Appl Environ Microbiol 70, 1944 1955.
32. Leys, N.M., Ryngaert, A., Bastiaens, L., Wattiau, P., Top, E.M., Verstraete, W. Springael, D. (2005) Occurrence and community composition of fast-growing Mycobacterium in soils contaminated with polycyclic aromatic hydrocarbons. FEMS Microbiol Ecol 51, 375 388.
33. Mac Rae, I.C. Cameron, A.J. (1985) Bacterial reduction of fensulfothion and its hydrolysis product 4-methylsulfinyl phenol. Appl Environ Microbiol 49, 236 237.
34. Maher, W.A. Aislabie, J. (1992) Polycyclic aromatic hydrocarbons in nearshore marine sediments of Australia. Sci Total Environ 112, 143 164.
35. McBride, K.E., Kenny, J.W. Stalker, D.M. (1986) Metabolism of the herbicide bromoxynil by Klebsiella pneumoniae subsp. ozaenae. Appl Environ Microbiol 52, 325 330.
36. Mileva, A., Sapundzhiev, T. Beschkov, V. (2008) Modeling 1,2-dichloroethane biodegradation by Klebsiella oxytoca va 8391 immobilized on granulated activated carbon. Bioprocess Biosyst Eng 31, 75 85.
37. Mosqueda, G., Ramos-Gonzalez, M.I. Ramos, J.L. (1999) Toluene metabolism by the solvent-tolerant Pseudomonas putida DOT-T1 strain, and its role in solvent impermeabilization. Gene 232, 69 76.
38. Nair, D., Fernandez-Acero, F.J., Garcia-Luque, E., Riba, I. Del Valls, T.A. (2008) Isolation and characterization of naphthalene-degrading bacteria from sediments of Cadiz area (SW Spain). Environ Toxicol 23, 576 582.
39. Nakai, C., Kagamiyama, H., Nozaki, M., Nakamura, T., Inoue, S., Ebina, Y. Nakazawa, A. (1983) Complete nucleotide sequence of the metapyrocatechase gene on the TOL plasmid of Pseudomonas putida mt-2. J Biol Chem 258, 2923 2928.
40. Olsen, G.J., Matsuda, H., Hagstrom, R. Overbeek, R. (1994) fastDNAml - a tool for construction of phylogenetic trees of DNA-sequences using maximum-likelihood. Comput Appl Biosci 10, 41 48.
41. Pellizari, V.H., Bezborodnikov, S., Quensen, J.F., III. Tiedje, J.M. (1996) Evaluation of strains isolated by growth on naphthalene and biphenyl for hybridization of genes to dioxygenase probes and polychlorinated biphenyl-degrading ability. Appl Environ Microbiol 62, 2053 2058.
42. Rademaker, J.L.W., Louws, F.J. Bruijn, F.J. (1998) Characterisation of diversity of ecologically important microbes by rep-PCR fingerprinting. In Molecular Microbial Ecology Manual, Supplement, 3rd edn. ed. Akkermans, A.D.L., van Elsas, J.D. Bruijn, F.J. pp. 1 26. Dordrecht, the Netherlands : Kluwer Academic Publishers.
43. Roy, S., Hens, D., Biswas, D., Biswas, D. Kumar, R. (2002) Survey of petroleum-degrading bacteria in coastal waters of Sunderban Biosphere. World J Microbiol Biotechnol 18, 575 581.
44. Saitou, N. Nei, M. (1987) The neighbor-joining method - a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406 425.
45. Sakata, S.K., Taniguchi, S., Rodrigues, D.F., Urano, M.E., Wandermuren, M.N., Pellizari, V.H. Comasseto, J.V. (2004) Development of a static headspace gas chromatographic/mass spectrometric method to analyze the level of volatile contaminants biodegradation. J Chromatogr A 1048, 67 71.
46. Sarma, P.M., Bhattacharya, D., Krishnan, S. Lal, B. (2004a) Assessment of intra-species diversity among strains of Acinetobacter baumannii isolated from sites contaminated with petroleum hydrocarbons. Can J Microbiol 50, 405 414.
47. Sarma, P.M., Bhattacharya, D., Krishnan, S. Lal, B. (2004b) Degradation of polycyclic aromatic hydrocarbons by a newly discovered enteric bacterium, Leclercia adecarboxylata. Appl Environ Microbiol 70, 3163 3166.
48. Seurinck, S., Verstraete, W. Siciliano, S.D. (2003) Use of 16S-23S rRNA intergenic spacer region PCR and repetitive extragenic palindromic PCR analyses of Escherichia coli isolates to identify nonpoint fecal sources. Appl Environ Microbiol 69, 4942 4950.
49. Shiaris, M.P. (1989) Seasonal biotransformation of naphthalene, phenanthrene, and benzo[a]pyrene in surficial estuarine sediments. Appl Environ Microbiol 55, 1391 1399.
50. Sikorski, J., Rossello-Mora, R. Lorenz, M.G. (1999) Analysis of genotypic diversity and relationships among Pseudomonas stutzeri strains by PCR-based genomic fingerprinting and multilocus enzyme electrophoresis. Syst Appl Microbiol 22, 393 402.
51. Siripattanakul, S., Wirojanagud, W., McEvoy, J. Khan, E. (2007) Characterization of Novel Atrazine-Degrading Mixed Culture. Bethesda, MD : NCBI.
52. Smits, T.H., Röthlisberger, M., Witholt, B. van Beilen, J.B. (1999) Molecular screening for alkane hydroxylase genes in Gram-negative and Gram-positive strains. Environ. Microbiol 1, 307 317.
53. Survery, S., Ahmad, S., Subhan, S.A., Ajaz, M. Rasool, S.A. (2004) Hydrocarbon degrading bacteria from Pakistani soil: isolation, identification, screening and genetical studies. Pak J Biol Sci 7, 1518 1522.
54. Tonso, N.L., Matheson, V.G. Holben, W.E. (1995) Polyphasic characterization of a suite of bacterial isolates capable of degrading 2,4-D. Microb Ecol 30, 1 2.
55. Trejo-Hernandez, M.R., Ortiz, A., Okoh, A.I., Morales, D. Quintero, R. (2007) Biodegradation of heavy crude oil Maya using spent compost and sugar cane bagasse wastes. Chemosphere 68, 848 855.
56. Vangnai, A.S. Petchkroh, W. (2007) Biodegradation of 4-chloroaniline by bacteria enriched from soil. FEMS Microbiol Lett 268, 209 216.
57. Versalovic, J., Schneider, M., de Bruijn, F.J. Lupski, J.R. (1994) Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol Cell biol 5, 25 40.
58. Ward, D.M. Brock, T.D. (1978) Hydrocarbon biodegradation in hypersaline environments. Appl Environ Microbiol 35, 353 359.
59. Whyte, L.G., Greer, C.W. Inniss, W.E. (1996) Assessment of the biodegradation potential of psychrotrophic microorganisms. Can J Microbiol 42, 99 106.
60. Whyte, L.G., Bourbonniere, L. Greer, C.W. (1997) Biodegradation of petroleum hydrocarbons by psychrotrophic Pseudomonas strains possessing both alkane (alk) and naphthalene (nah) catabolic pathways. Appl Environ Microbiol 63, 3719 3723.
61. Whyte, L.G., Smits, T.H., Labbe, D., Witholt, B., Greer, C.W. van Beilen, J.B. (2002) Gene cloning and characterization of multiple alkane hydroxylase systems in Rhodococcus strains Q15 and NRRL B-16531. Appl Environ Microbiol 68, 5933 5942.
62. Wright, A. Olsen, R.H. (1994) Self-mobilization and organization of the genes encoding the toluene metabolic pathway of Pseudomonas mendocina KR1. Appl Environ Microbiol 60, 235 242.
63. Yakubu, M.B. (2007) Biodegradation of Lagoma crude oil using pig dung. Afr J Biotechnol 6, 2821 2825.
64. Yoo, J.S., Kim, H.S., Chung, S.H., Lee, Y.C., Cho, Y.S. Choi, Y.L. (2001) Characterization of the small cryptic plasmid, pGD2, of Klebsiella sp. KCL-2. J Biochem Mol Biol 34, 584 589.
65. Zylstra, G.J. Gibson, D.T. (1989) Toluene degradation by Pseudomonas putida F1. Nucleotide sequence of the todC1C2BADE genes and their expression in Escherichia coli. J Biol Chem 264, 14940 14946.