Novel alkane hydroxylase gene (alkB) diversity in sediments associated with hydrocarbon seeps in the Timor Sea, Australia

Applied and Environmental Microbiology

Volumn 75, Issue 23, 2009, Pages 7391-7398

  Wasmund, Kenneth ^a,b   Burns, Kathryn A ^a   Kurtböke, D Ipek ^b   Bourne, David G ^a  

^a AUSTRALIAN INSTITUTE OF MARINE SCIENCE   (Australia)

^b UNIVERSITY OF THE SUNSHINE COAST   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ALKANE HYDROXYLASE; AUSTRALIA; BIO-INDICATORS; BIODEGRADATION POTENTIALS; CHEMICAL COMPONENT; CLONE LIBRARY; CONTINENTAL SHELVES; CONTINENTAL SLOPE; COPY NUMBER; DEEP WATER; GAMMAPROTEOBACTERIA; GAS CHROMATOGRAPHY-MASS SPECTROMETRY TECHNIQUES; GENE COPY NUMBER; GEOCHEMICAL ANALYSIS; HYDROCARBON SEEPS; LOW LEVEL; PETROLEUM HYDROCARBONS; PROTEIN SEQUENCES; REAL-TIME PCR ASSAY; SEDIMENT SAMPLES; SEQUENCE DIVERSITY; SEQUENCE IDENTITY; SHALLOW WATERS; TIMOR SEA;

AIR POLLUTION CONTROL; ANALYTICAL GEOCHEMISTRY; BIOCHEMISTRY; CHROMATOGRAPHIC ANALYSIS; CLONING; DEGRADATION; GAS CHROMATOGRAPHY; GENES; MASS SPECTROMETRY; MICROBIOLOGY; ORGANIC COMPOUNDS; PARAFFINS; PETROLEUM CHEMISTRY; PROTEINS; SEDIMENTOLOGY; SEEPAGE;

BIODEGRADATION;

ALKANE HYDROXYLASE; HYDROCARBON; OXYGENASE; UNCLASSIFIED DRUG;

ALKANE; BACTERIUM; BIODEGRADATION; BIOINDICATOR; CRUDE OIL; ECOSYSTEM RESPONSE; GENE EXPRESSION; HYDROCARBON SEEP; MARINE SEDIMENT; SEEPAGE; SPECIES DIVERSITY;

AMINO ACID SEQUENCE; ARTICLE; AUSTRALIA; BIOREMEDIATION; CLONE; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; ENZYME LOCALIZATION; GAMMAPROTEOBACTERIA; GENE TARGETING; GENETIC ASSOCIATION; GENETIC CORRELATION; GENETIC IDENTIFICATION; GENETIC VARIABILITY; GEOCHEMISTRY; MASS FRAGMENTOGRAPHY; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; SEA; SEDIMENT; SEQUENCE ANALYSIS; WATER SAMPLING;

ALKANE 1-MONOOXYGENASE; AUSTRALIA; CLUSTER ANALYSIS; COLONY COUNT, MICROBIAL; GAMMAPROTEOBACTERIA; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; GENETIC VARIATION; GEOLOGIC SEDIMENTS; HYDROCARBONS; METAGENOME; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; SEAWATER; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID;

INDIAN OCEAN; TIMOR SEA;

GAMMAPROTEOBACTERIA;

EID: 72949106034     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01370-09     Document Type: Article

References (45)

1. Altschul, S. F., T. L. Madden, A. A. Schaeffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Avigan, J., and B. Blumer. 1968. On the origin of pristane in marine organisms. J. Lipid Res. 9:350-352.
3. Burns, K. A., and S. Codi. 1999. Non-volatile hydrocarbon chemistry studies around a production platform on Australia's northwest shelf. Estuarine Coastal Shelf Sci. 46:853-876.
4. Burns, K. A., J. K. Volkman, J. Cavanagh, and J. Brinkman. 2003. Lipids as biomarkers for carbon cycling on the Northwest Shelf of Australia: results from a sediment trap study. Mar. Chem. 80:103-128.
5. Caruso, G., R. Denaro, M. Genovese, L. Giuliano, M. Mancuso, and M. M. Yakimov. 2004. New methodological strategies for detecting bacterial indicators. Chem. Ecol. 20:167-181.
6. Cébron, A., M.-P. Norini, T. Beguiristain, and C. Leyval. 2008. Real-time PCR quantification of PAH-ring hydroxylating dioxygenase (PAH-RHDa) genes from gram positive and gram negative bacteria in soil and sediment samples. J. Microbiol. Methods 73:148-159.
7. Chao, A. 1984. Nonparametric estimation of the number of classes in a population. Scand. J. Stat. 11:265-270.
8. Coates, J. D., J. Woodward, J. Allen, P. Philp, and D. R. Lovley. 1997. Anaerobic degradation of polycyclic aromatic hydrocarbons and alkanes in petroleum-contaminated marine harbor sediments. Appl. Environ. Microbiol. 63:3589-3593.
9. Dionisi, H. M., C. S. Chewning, K. H. Morgan, F.-M. Menn, J. P. Easter, and G. S. Sayler. 2004. Abundance of dioxygenase genes similar to Ralstonia sp. strain U2 nagAc is correlated with naphthalene concentrations in coal tarcontaminated freshwater sediments. Appl. Environ. Microbiol. 70:3988-3995.
10. Dumont, M. G., S. M. Radajewski, I. R. McDonald, and J. C. Murrell. 2006. Identification of a complete methane monooxygenase operon from soil by combining stable isotope probing and metagenomic analysis. Environ. Microbiol. 8:1240-1250.
11. Felsenstein, J. 1989. PHYLIP-phylogeny inference package. Cladistics 5:164-166.
12. Hara, A., S. Baik, K. Syutsubo, N. Misawa, T. H. M. Smits, J. B. van Beilen, and S. Harayama. 2004. Cloning and functional analysis of alkB genes in Alcanivorax borkumensis SK2. Environ. Microbiol. 6:191-197.
13. Harayama, S., Y. Kasai, and A. Hara. 2004. Microbial communities in oilcontaminated seawater. Curr. Opin. Biotechnol. 15:205-214.
14. Head, I. M., D. M. Jones, and W. F. M. Roling. 2006. Marine microorganisms make a meal of oil. Nature 4:173-182.
15. Heck, K. L., G. V. Belle, and D. Simberloff. 1975. Explicit calculation of the rarefaction diversity measurement and the determination of sufficient sample size. Ecology 56:1459-1461.
16. Heiss-Blanquet, S., Y. Benoit, C. Marechaux, and F. Monot. 2005. Assessing the role of alkane hydroxylase genotypes in environmental samples by competitive PCR. J. Appl. Microbiol. 99:1392-1403.
17. Johnsen, A. R., J. R. De Lipthay, F. Reichenberg, S. J. Sorensen, O. Andersen, P. Christensen, M. L. Binderup, and C. Jacobsen. 2006. Biodegradation, bioaccessibility, and genotoxicity of diffuse polycyclic aromatic hydrocarbon (PAH) pollution at a motorway site. Environ. Sci. Technol. 40: 3293-3298.
18. Kimura, M. 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge, United Kingdom.
19. Kloos, K., J. C. Munch, and M. Schloter. 2006. A new method for the detection of alkane-monooxygenase homologous genes (alkB) in soils based on PCR-hybridization. J. Microbiol. Methods 66:486-496.
20. Kuhn, E., G. S. Bellicanta, and V. H. Pellizari. 2009. New alk genes detected in Antarctic marine sediments. Environ. Microbiol. 11:669-673.
21. Leahy, J. G., and R. R. Colwell. 1990. Microbial degradation of hydrocarbons in the environment. Microbiol. Rev. 54:305-315.
22. Maeng, J. H., Y. Sakai, Y. Tani, and N. Kato. 1996. Isolation and characterization of a novel oxygenase that catalyzes the first step of n-alkane oxidation in Acinetobacter sp. strain M-1. J. Bacteriol. 178:3695-3700.
23. Magurran, A. E. 1988. Ecological diversity and its measurement. Princeton University Press, Princeton, NJ.
24. McKew, B. A., F. Coulon, M. M. Yakimov, R. Denaro, M. Genovese, C. M. Smith, M. Osborn, K. N. Timmis, and T. J. McGenity. 2007. Efficacy of intervention strategies for bioremediation of crude oil in marine systems and effects on indigenous hydrocarbonoclastic bacteria. Environ. Microbiol. 9:1562-1571.
25. Mikolasch, A., E. Hammer, and F. Schauer. 2003. Synthesis of imidazol-2-yl amino acids by using cells from alkane-oxidizing bacteria. Appl. Environ. Microbiol. 69:1670-1679.
26. Mirallesa, G., V. Grossia, M. Acquavivaa, R. Duranb, J. C. Bertranda, and P. Cunya. 2007. Alkane biodegradation and dynamics of phylogenetic subgroups of sulfate-reducing bacteria in an anoxic coastal marine sediment artificially contaminated with oil. Chemosphere 68:1327-1334.
27. O'Brien, G. W., K. Glenn, G. Lawrence, A. Wlliams, M. Webster, S. Burns, and R. Cowley. 2002. Influence of hydrocarbon migration and seepage on benthic communities in the Timor Sea. APPEA J. 42:225-240.
28. Pearson, A., J. S. Seewald, and T. I. Eglinton. 2005. Bacterial incorporation of relict carbon in the hydrothermal environment of Guaymas Basin. Geochim. Cosmochim. Acta 69:5477-5486.
29. Rehm, H. J., and I. Reiff. 1981. Mechanisms and occurrence of microbial oxidation of long-chain alkanes. Adv. Biochem. Eng. 19:175-215.
30. Saitou, N., and M. Nei. 1987. The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
31. Schloss, P. D., and J. Handelsman. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71:1501-1506.
32. Shannon, C. E., and W. Weaver. 1963. The mathematical theory of communication. University of Illinois Press, Urbana.
33. Siciliano, S. D., N. Fortin, A. Mihoc, G. Wisse, S. Labelle, D. Beaumier, D. Ouellette, R. Roy, L. G. Whyte, M. K. Banks, P. Schwab, K. Lee, and C. W. Greer. 2001. Selection of specific endophytic bacterial genotypes by plants in response to soil contamination. Appl. Environ. Microbiol. 67:2469-2475.
34. Sikkema, J., J. A. M. de Bont, and B. Poolman. 1995. Mechanisms of membrane toxicity of hydrocarbons. Microbiol. Rev. 59:201-222.
35. Smits, T. H. M., M. Röthlisberger, B. Witholt, and J. B. van Beilen. 1999. Molecular screening for alkane hydroxylase genes in gram-negative and gram-positive strains. Environ. Microbiol. 1:307-317.
36. Stapleton, R. D., and G. S. Sayler. 1998. Assessment of the microbiological potential for the natural attenuation of petroleum hydrocarbons in a shallow aquifer system. Microb. Ecol. 36:349-361.
37. Steichen, D. J., S. J. Holbrook, and C. W. Osenberg. 1996. Distribution and abundance of benthic and demersal macrofauna within a natural hydrocarbon seep. Mar. Ecol. Prog. Ser. 138:71-82.
38. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1994. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 22:4673-4680.
39. Throne-Holst, M., A. Wentzel, T. E. Ellingsen, H.-K. Kotlar, and S. B. Zotchev. 2007. Identification of novel genes involved in long-chain n-alkane degradation by Acinetobacter sp. strain DSM 17874. Appl. Environ. Microbiol. 73:3327-3332.
40. van Beilen, J. B., and E. G. Funhoff. 2007. Alkane hydroxylases involved in microbial alkane degradation. Appl. Microbiol. Biotechnol. 74:13-21.
41. van Beilen, J. B., and E. G. Funhoff. 2005. Expanding the alkane oxygenase toolbox: new enzymes and applications. Curr. Opin. Biotechnol. 16:308-314.
42. van Beilen, J. B., T. H. M. Smits, F. F. Roos, T. Brunner, S. B. Balada, M. Röthlisberger, and B. Witholt. 2005. Identification of an amino acid position that determines the substrate range of integral membrane alkane hydroxylases. J. Bacteriol. 187:85-91.
43. Whyte, L. G., A. Schultz, J. B. van Beilen, A. P. Luz, V. Pellizari, and D. Labbe. 2002. Prevalence of alkane monooxygenase genes in Arctic and Antarctic hydrocarbon-contaminated and pristine soils. FEMS Microbiol. Ecol. 41:141-150.
44. Widdel, F., and R. Rabus. 2001. Anaerobic biodegradation of saturated and aromatic hydrocarbons. Curr. Opin. Biotechnol. 12:259-276.
45. Zhou, J., M. A. Bruns, and J. M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:316-322.