Occurrence and diversity of naphthalene dioxygenase genes in soil microbial communities from the Maritime Antarctic

Environmental Microbiology

Volumn 11, Issue 3, 2009, Pages 700-714

  Flocco, Cecilia G ^a,b   Gomes, Newton C M ^c   Mac Cormack, Walter ^d   Smalla, Kornelia ^a  

^a INSTITUTE FOR EPIDEMIOLOGY AND PATHOGEN DIAGNOSTICS   (Germany)

^b Facultad de Ciencias Naturales e Instituto M Lillo   (Argentina)

^c UNIVERSITY OF AVEIRO   (Portugal)

^d INSTITUTO ANTÁRTICO ARGENTINO   (Argentina)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; MULTIENZYME COMPLEX; NAPHTHALENE DIOXYGENASE; OXYGENASE;

ANTARCTICA; ARTICLE; CHEMISTRY; DNA FINGERPRINTING; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PSEUDOMONAS; SEQUENCE HOMOLOGY;

ANTARCTIC REGIONS; DNA FINGERPRINTING; DNA, BACTERIAL; GENETIC VARIATION; MOLECULAR SEQUENCE DATA; MULTIENZYME COMPLEXES; OXYGENASES; PHYLOGENY; POLYMERASE CHAIN REACTION; PSEUDOMONAS; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY; SOIL MICROBIOLOGY;

COLOBANTHUS QUITENSIS; DESCHAMPSIA ANTARCTICA; PSEUDOMONAS; TRACHEOPHYTA;

EID: 61449162196     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2008.01858.x     Document Type: Article

References (58)

1. Aislabie, J., Balks, M., Astori, N., Stevenson, G. Symons, R. (1999) Polycyclic aromatic hydrocarbons in fuel-oil contaminated soils, Antarctica. Chemosphere 39 : 2201 2207.
2. Aislabie, J.M., Balks, M.R., Foght, J.M. Waterhouse, E.J. (2004) Hydrocarbon spills on Antarctic soils: effects and management. Environ Sci Technol 38 : 1265 1274.
3. Aislabie, J., Saul, D.J. Foght, J.M. (2006) Bioremediation of hydrocarbon-contaminated polar soils. Extremophiles 10 : 171 179.
4. Bouchez, M., Blanchet, D. Vandecasteele, J.P. (1995) Degradation of polycyclic aromatic hydrocarbons by pure strains and by defined strain associations: inhibition phenomena and cometabolism. Appl Microbiol Biotechnol 43 : 156 164.
5. Cerniglia, C.E. (1984) Microbial metabolism of polycyclic aromatic hydrocarbons. Adv Appl Microbiol 30 : 31 71.
6. Cerniglia, C.E., White, G.L. Heflich, R.H. (1985) Fungal metabolism and detoxification of polycyclic aromatic hydrocarbons. Arch Microbiol 143 : 105 110.
7. Chaudhry, Q., Blom-Zandstra, M., Gupta, S. Joner, E.J. (2005) Utilising the synergy between plants and rhizosphere microorganisms to enhance breakdown of organic pollutants in the environment. Environ Sci Pollut Res Int 12 : 34 48.
8. Costa, R., Götz, M., Mrotzek, N., Lottmann, J., Berg, G. Smalla, K. (2006) Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of microbial guilds. FEMS Microbiol Ecol 56 : 236 249.
9. Curtosi, A., Pelletier, E., Vodopivez, C.L. MacCormack, W.P. (2007) Polycyclic aromatic hydrocarbons in soil and surface marine sediment near Jubany Station (Antarctica). Role of permafrost as a low-permeability barrier. Sci Total Environ 383 : 193 204.
10. Debruyn, J.M., Chewning, C.S. Sayler, G.S. (2007) Comparative quantitative prevalence of Mycobacteria and functionally abundant nidA, nahAc and nagAc dioxygenase genes in coal tar contaminated sediments. Environ Sci Technol 41 : 5426 5432.
11. Dennis, J.J. Zylstra, G.J. (2004) Complete sequence and genetic organization of pDTG1, the 83 kilobase naphthalene degradation plasmid from Pseudomonas putida strain NCIB 9816-4. J Mol Biol 341 : 753 768.
12. Dionisi, H.M., Chewning, C.S., Morgan, K.H., Menn, F.M., Easter, J.P. Sayler, G.S. (2004) Abundance of dioxygenase genes similar to Ralstonia sp. strain U2 nagAc is correlated with naphthalene concentrations in coal tar-contaminated freshwater sediments. Appl Environ Microbiol 70 : 3988 3995.
13. Dunbar, J., White, S. Forney, L. (1997) Genetic diversity through the looking glass: effect of enrichment bias. Appl Environ Microbiol 63 : 1326 1331.
14. Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 : 783 791.
15. Ferrero, M., Llobet-Brossa, E., Lalucat, J., Garcia-Valdes, E., Rosselló-Mora, R. Bosch, R. (2002) Coexistence of two distinct copies of naphthalene degradation genes in Pseudomonas strains isolated from the western Mediterranean region. Appl Environ Microbiol 68 : 957 962.
16. Frenot, Y., Chown, S.L., Whinam, J., Selkirk, P.M., Convey, P., Skotnicki, M. Bergstrom, D.M. (2005) Biological invasions in the Antarctic: extent, impacts and implications. Biol Rev Camb Philos Soc 80 : 45 72.
17. Gioia, R., Steinnes, E., Thomas, G.O., Mejier, S.N. Jones, K.C. (2006) Persistent organic pollutants in European background air: derivation of temporal and latitudinal trends. J Environ Monit 8 : 700 710.
18. Gomes, N.C., Kosheleva, I.A., Abraham, W.R. Smalla, K. (2005) Effects of the inoculant strain Pseudomonas putida KT2442 (pNF142) and of naphthalene contamination on the soil bacterial community. FEMS Microbiol Ecol 54 : 21 33.
19. Gomes, N.C., Borges, L.R., Paranhos, R., Pinto, F.N., Krögerrecklenfort, E., Mendonça-Hagler, L.C. Smalla, K. (2007) Diversity of ndo genes in mangrove sediments exposed to different sources of polycyclic aromatic hydrocarbon pollution. Appl Environ Microbiol 73 : 7392 7399.
20. Habe, H. Omori, T. (2003) Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria. Biosci Biotechnol Biochem 67 : 225 243.
21. Heuer, H., Krsek, M., Baker, P., Smalla, K. Wellington, E.M. (1997) Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl Environ Microbiol 63 : 3233 3241.
22. Iqbal, J., Gisclair, D., McMillin, D.J. Portier, R.J. (2007) Aspects of petrochemical pollution in southeastern Louisiana (USA): pre-Katrina background and source characterization. Environ Toxicol Chem 26 : 2001 2009.
23. Jones, D.T., Taylor, W.R. Thornton, J.M. (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8 : 275 282.
24. Karthikeyan, R. Kulakow, P.A. (2003) Soil plant microbe interactions in phytoremediation. Adv Biochem Eng Biotechnol 78 : 51 74.
25. Kauppi, B., Lee, K., Carredano, E., Parales, R.E., Gibson, D.T., Eklund, H. Ramaswamy, S. (1998) Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase. Structure 6 : 571 586.
26. Kowalchuk, G.A., Buma, D.S., de Boer, W., Klinkhamer, P.G. van Veen, J.A. (2002) Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms. Antonie Van Leeuwenhoek 81 : 509 520.
27. Laurie, A.D. Lloyd-Jones, G. (1999) The phn genes of Burkholderia sp. strain RP007 constitute a divergent gene cluster for polycyclic aromatic hydrocarbon catabolism. J Bacteriol 181 : 531 540.
28. Laurie, A.D. Lloyd-Jones, G. (2000) Quantification of phnAc and nahAc in contaminated New Zealand soils by competitive PCR. Appl Environ Microbiol 66 : 1814 1817.
29. Luz, A.P., Pellizari, V.H., Whyte, L.G. Greer, C.W. (2004) A survey of indigenous microbial hydrocarbon degradation genes in soils from Antarctica and Brazil. Can J Microbiol 50 : 323 333.
30. Ma, Y., Wang, L. Shao, Z. (2006) Pseudomonas, the dominant polycyclic aromatic hydrocarbon-degrading bacteria isolated from Antarctic soils and the role of large plasmids in horizontal gene transfer. Environ Microbiol 8 : 455 465.
31. Martins, C.C., Bícego, M.C., Taniguchi, S. Montone, R.C. (2004) Aliphatic and polycyclic aromatic hydrocarbons in surface sediments in Admiralty Bay, King George Island, Antarctica. Antarctic Sci 16 : 117 122.
32. Mazzera, D., Hayes, T., Lowenthal, D. Zielinska, B. (1999) Quantification of polycyclic aromatic hydrocarbons in soil at McMurdo Station, Antarctica. Sci Total Environ 229 : 65 71.
33. van der Meer, J.R., Werlen, C., Nishino, S.F. Spain, J.C. (1998) Evolution of a pathway for chlorobenzene metabolism leads to natural attenuation in contaminated groundwater. Appl Environ Microbiol 64 : 4185 4193.
34. Nam, J.W., Nojiri, H., Yoshida, T., Habe, H., Yamane, H. Omori, T. (2001) New classification system for oxygenase components involved in ring-hydroxylating oxygenations. Biosci Biotechnol Biochem 65 : 254 263.
35. Newby, D.T., Gentry, T.J. Pepper, I.L. (2000) Comparison of 2,4-dichlorophenoxyacetic acid degradation and plasmid transfer in soil resulting from bioaugmentation with two different pJP4 donors. Appl Environ Microbiol 66 : 3399 3407.
36. Ni Chadhain, S.M., Norman, R.S., Pesce, K.V., Kukor, J.J. Zylstra, G.J. (2006) Microbial dioxygenase gene population shifts during polycyclic aromatic hydrocarbon biodegradation. Appl Environ Microbiol 72 : 4078 4087.
37. Rosselló, R. (1992). Universitat de les Illes Balears, PhD Thesis. Palma de Mallorca, Spain.
38. Ruberto, L.A.M., Vázquez, S. MacCormack, W.P. (2003) Polycyclic aromatic hydrocarbons in fuel-oil contaminated soils, Antarctica. Int Biodeterioration Biodegradation 52 : 125.
39. Ruberto, L.A.M., Vázquez, S. MacCormack, W.P. (2008) Bacteriology of extremely cold soils exposed to hydrocarbon pollution. In Microbiology of Extreme Soils. Dion, P. Shekhar Nautiyal, C. (eds). Berlin, Heidelberg, Germany : Springer-Verlag, pp. 247 274.
40. Saitou, N. Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 : 406 425.
41. Shaw, L.J. Burns, R.G. (2004) Enhanced mineralization of [U-(14)C]2,4-dichlorophenoxyacetic acid in soil from the rhizosphere of Trifolium pratense. Appl Environ Microbiol 70 : 4766 4774.
42. Shuttleworth, K.L. Cerniglia, C.E. (1995) Environmental aspects of PAH biodegradation. Appl Biochem Biotechnol 54 : 291 302.
43. Siciliano, S.D., Germida, J.J., Banks, K. Greer, C.W. (2003) Changes in microbial community composition and function during a polyaromatic hydrocarbon phytoremediation field trial. Appl Environ Microbiol 69 : 483 489.
44. Skupinska, K., Misiewicz, I. Kasprzycka-Guttman, T. (2004) Polycyclic aromatic hydrocarbons: physicochemical properties, environmental appearance and impact on living organisms. Acta Pol Pharm 61 : 233 240.
45. Smalla, K., Wieland, G., Buchner, A., Zock, A., Parzy, J., Kaiser, S., et al. (2001) Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microbiol 67 : 4742 4751.
46. Sota, M., Yano, H., Ono, A., Miyazaki, R., Ishii, H., Genka, H., et al. (2006) Genomic and functional analysis of the IncP-9 naphthalene-catabolic plasmid NAH7 and its transposon Tn4655 suggests catabolic gene spread by a tyrosine recombinase. J Bacteriol 188 : 4057 4067.
47. Stallwood, B., Shears, J., Williams, P.A. Hughes, K.A. (2005) Low temperature bioremediation of oil-contaminated soil using biostimulation and bioaugmentation with a Pseudomonas sp. from maritime Antarctica. J Appl Microbiol 99 : 794 802.
48. Takai, K. Horikoshi, K. (2000) Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes. Appl Environ Microbiol 66 : 5066 5072.
49. Tamura, K., Dudley, J., Nei, M. Kumar, S. (2007) Mega4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24 : 1596 1599.
50. Vandermeer, K.D. Daugulis, A.J. (2007) Enhanced degradation of a mixture of polycyclic aromatic hydrocarbons by a defined microbial consortium in a two-phase partitioning bioreactor. Biodegradation 18 : 211 221.
51. Vinas, M., Sabate, J., Espuny, M.J. Solanas, A.M. (2005) Bacterial community dynamics and polycyclic aromatic hydrocarbon degradation during bioremediation of heavily creosote-contaminated soil. Appl Environ Microbiol 71 : 7008 7018.
52. Wilson, M.S., Herrick, J.B., Jeon, C.O., Hinman, D.E. Madsen, E.L. (2003) Horizontal transfer of phnAc dioxygenase genes within one of two phenotypically and genotypically distinctive naphthalene-degrading guilds from adjacent soil environments. Appl Environ Microbiol 69 : 2172 2181.
53. Yen, K.M. Gunsalus, I.C. (1982) Plasmid gene organization: naphthalene/salicylate oxidation. Proc Natl Acad Sci USA 79 : 874 878.
54. Yergeau, E., Newsham, K.K., Pearce, D.A. Kowalchuk, G.A. (2007a) Patterns of bacterial diversity across a range of Antarctic terrestrial habitats. Environ Microbiol 9 : 2670 2682.
55. Yergeau, E., Bokhorst, S.H., Uiskes, A.H.L., Boschker, H.T.S., Aerts, R. Kowalchuk, G.A. (2007b) Size and structure of bacterial, fungal and nematode communities along an Antarctic environmental gradient. FEMS Microbiol Ecol 59 : 436 451.
56. Zhang, S., Zhang, W., Wang, K., Shen, Y., Hu, L. Wang, X. (2008) Concentration, distribution and source apportionment of atmospheric polycyclic aromatic hydrocarbons in the southeast suburb of Beijing, China. Environ Monit Assess (in press): doi:10.1007/s10661-008-0261-2.
57. Zhou, H.W., Guo, C.L., Wong, Y.S. Tam, N.F. (2006) Genetic diversity of dioxygenase genes in polycyclic aromatic hydrocarbon-degrading bacteria isolated from mangrove sediments. FEMS Microbiol Lett 262 : 148 157.
58. Zocca, C., Di, G.S., Visentini, F. Vallini, G. (2004) Biodiversity amongst cultivable polycyclic aromatic hydrocarbon-transforming bacteria isolated from an abandoned industrial site. FEMS Microbiol Lett 238 : 375 382.