Real-Time PCR quantification of PAH-ring hydroxylating dioxygenase (PAH-RHDα) genes from Gram positive and Gram negative bacteria in soil and sediment samples

Journal of Microbiological Methods

Volumn 73, Issue 2, 2008, Pages 148-159

  Cébron, Aurélie ^a   Norini, Marie Paule ^a   Beguiristain, Thierry ^a   Leyval, Corinne ^a  

^a Faculté des Sciences et Technologies   (France)

Author keywords

PAH bacterial degraders; PAH ring hydroxylating dioxygenase alpha subunit (PAH RHD ); Real Time PCR; Sediment; Soil

Indexed keywords

DIOXYGENASE; POLYCYCLIC AROMATIC HYDROCARBON;

AEROBIC METABOLISM; ALCALIGENES; ALLELE; ARHA1 GENE; ARTICLE; BACTERIAL GENE; BPHA1 GENE; BPHAC GENE; BURKHOLDERIA; CONTROLLED STUDY; DNA EXTRACTION; DNTAC GENE; FADA1 GENE; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; HYDROXYLATION; MICROBIAL COMMUNITY; MYCOBACTERIUM; NAGAC GENE; NAHA3 GENE; NAHAC GENE; NARAA GENE; NDOB GENE; NDOC2 GENE; NIDA GENE; NIDA3 GENE; NOCARDIOIDACEAE; NONHUMAN; NUCLEOTIDE SEQUENCE; PAHA3 GENE; PAHAC GENE; PDOA1 GENE; PDOA2 GENE; PHDA GENE; PHNA1 GENE; PHNAC GENE; PRIORITY JOURNAL; PSEUDOMONAS; RALSTONIA; REAL TIME POLYMERASE CHAIN REACTION; RHODOCOCCUS; SEDIMENT; SOIL ANALYSIS; SPHINGOMONAS; TERRABACTER; UNINDEXED SEQUENCE;

BACTERIAL PROTEINS; COLONY COUNT, MICROBIAL; DIOXYGENASES; DNA PRIMERS; DNA, BACTERIAL; GENE DOSAGE; GEOLOGIC SEDIMENTS; GRAM-NEGATIVE BACTERIA; GRAM-POSITIVE BACTERIA; PHYLOGENY; POLYCYCLIC HYDROCARBONS, AROMATIC; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SENSITIVITY AND SPECIFICITY; SEQUENCE HOMOLOGY, AMINO ACID; SOIL MICROBIOLOGY;

ALCALIGENES; BACTERIA (MICROORGANISMS); BURKHOLDERIA; MYCOBACTERIUM; NEGIBACTERIA; NOCARDIOIDES; POLAROMONAS; POSIBACTERIA; PSEUDOMONAS; RALSTONIA; RHODOCOCCUS; SPHINGOMONAS; TERRABACTER;

EID: 42249095068     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2008.01.009     Document Type: Article

References (55)

1. Achour A.R., Bauda P., and Billard P. Diversity of arsenite transporter genes from arsenic-resistant soil bacteria. Res. Microbiol. 158 (2007) 128-137
2. Baldwin B.R., Nakatsu C.H., and Nies L. Detection and enumeration of aromatic oxygenase genes by multiplex and real-time PCR. Appl. Environ. Microbiol. 69 (2003) 3350-3358
3. Bastiaens L., Springael D., Wattiau P., Harms H., DeWachter R., Verachtert H., and Diels L. Isolation of adherent Polycyclic Aromatic Hydrocarbon (PAH)-degrading bacteria using PAH-sorbing carriers. Appl. Environ. Microbiol. 66 (2000) 1834-1843
4. Beller H.R., Kane S.R., Legler T.C., and Alvarez P.J.J. A Real-Time Polymerase Chain Reaction method for monitoring anaerobic, hydrocarbon-degrading bacteria based on a catabolic gene. Environ. Sci. Technol. 36 (2002) 3977-3984
5. Brezna B., Khan A.A., and Cerniglia C.E. Molecular characterization of dioxygenases from polycyclic aromatic hydrocarbon-degrading Mycobacterium spp. FEMS Microbiol. Lett. 223 (2003) 177-183
6. Cerniglia C.E. Biodegradation of polycyclic aromatic hydrocarbons. Biodegradation 3 (1992) 351-368
7. Chadhain S.M., Norman R.S., Pesce K.V., Kukor J.J., and Zylstra G.J. Microbial dioxygenase gene population shifts during polycyclic aromatic hydrocarbon biodegradation. Appl. Environ. Microbiol. 72 (2006) 4078-4087
8. Corgié S.C., Beguiristain T., and Leyval C. Spatial distribution of bacterial communities and phenanthrene degradation in the rhizosphere of Lolium perenne L. Appl. Environ. Microbiol. 70 (2004) 3552-3557
9. Dionisi H., Chewning C., Morgan K., Menn F., Easter J., and Sayler G. 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 (2004) 3988-3995
10. Felske A., Akkermans A.D.L., and De Vos W.M. Quantification of 16 S rRNAs in complex bacterial communities by multiple competitive reverse transcription-PCR in temperature gradient gel electrophoresis fingerprints. Appl. Environ. Microbiol. 64 (1998) 4581-4587
11. Ferrero M., Llobet-Brossa E., Lalucat J., Garcia-Valdes E., Rossello-Mora R., and Bosch R. Coexistence of two distinct copies of naphthalene degradation genes in Pseudomonas strains isolated from the western Mediterranean region. Appl. Environ. Microbiol. 68 (2002) 957-962
12. Feselstein J. PHYLIP-phylogeny inference package (version 3.2). Cladistics 5 (1989) 164-166
13. Goyal A.K., and Zylstra G.J. Molecular cloning of novel genes for polycyclic aromatic hydrocarbon degradation from Comamonas testosteroni GZ39. Appl. Environ. Microbiol. 62 (1996) 230-236
14. Habe H., and Omori T. Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria. Biosci. Biotechnol. Biochem. 67 (2003) 225-243
15. Hamann C., Hegemann J., and Hildebrandt A. Detection of polycyclic aromatic hydrocarbon degradation genes in different soil bacteria by polymerase chain reaction and DNA hybridization. FEMS Micriobiol. Let. 173 (1999) 255-263
16. Jeon C.O., Park M., Ro H.S., Park W., and Madsen E.L. The naphthalene catabolic (nag) genes of Polaromonas naphthalenivorans CJ2: evolutionary implications for two gene clusters and novel regulatory control. Appl. Environ. Microbiol. 72 (2006) 1086-1095
17. Johnsen A.R., and Karlson U. Evaluation of bacterial strategies to promote the bioavailability of polycyclic aromatic hydrocarbons. Appl. Microbiol. Biotechnol. 63 (2004) 452-459
18. Johnsen A.R., and Karlson U. PAH degradation capacity of soil microbial communities-does it depend on PAH exposure?. Microb. Ecol. 50 (2005) 488-495
19. Johnsen A.R., De Lipthay J.R., Reichenberg F., Sorensen S.J., Andersen O., Christensen P., Binderup M.L., Jacobsen C., et al. Biodegradation, bioaccessibility, and genotoxicity of diffuse Polycyclic Aromatic Hydrocarbon (PAH) pollution at a motorway site. Environ. Sci. Technol. 40 (2006) 3293-3298
20. Johnsen A.R., Schmidt S., Hybholt T.K., Henriksen S., Jacobsen C.S., and Andersen O. Strong impact on the Polycyclic Aromatic Hydrocarbon (PAH)-degrading community of a PAH-polluted soil but marginal effect on PAH degradation when priming with bioremediated soil dominated by Mycobacteria. Appl. Environ. Microbiol. 73 (2007) 1474-1480
21. Joner E.J., Corgié S.C., Amellal N., and Leyval C. Nutritional constraints to degradation of polycyclic aromatic hydrocarbons in a simulated rhizosphere. Soil Biol. Biochem. 34 (2002) 859-864
22. Joubert A.V.P., Lucas L., Garrido F., Joulian C., and Jauzein M. Effect of temperature, gas phase composition, pH and microbial activity on As, Zn, Pb and Cd mobility in selected soils in the Ebro and Meuse Basins in the context of global change. Environ. Pollut. 148 (2007) 749-758
23. Juhasz A.L., and Naidu R. Bioremediation of high molecular weight polycyclic aromatic hydrocarbons: a review of the microbial degradation of benzo[a]pyrene. Int. Biodeterior. Biodegrad. 45 (2000) 57-88
24. Kauppi B., Lee K., Carredano E., Parales R., Gibson D., Eklund H., and Ramaswamy S. Structure of an aromatic-ring-hydroxylating dioxygenasenaphthalene 1,2-dioxygenase. Structure 6 (1998) 571-586
25. Kanaly R.A., and Harayama S. Biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons by bacteria. J. Bacteriol. 182 (2000) 2059-2067
26. Khan A.A., Wang R.F., Cao W.W., Doerge D.R., Wennerstrom D., and Cerniglia C.E. Molecular cloning, nucleotide sequence, and expression of genes encoding a polycyclic aromatic ring dioxygenase from Mycobacterium sp. strain PYR-1. Appl. Environ. Microbiol. 67 (2001) 3577-3585
27. Kim S.J., Kweon O., Freeman J.P., Jones R.C., Adjei M.D., Jhoo J.W., Edmondson R.D., and Cerniglia C.E. Molecular cloning and expression of genes encoding a novel dioxygenase involved in low- and high-molecular-weight polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1. Appl. Environ. Microbiol. 72 (2006) 1045-1054
28. Klappenbach J.A., Dunbar J.M., and Schmidt T.M. rRNA operon copy number reflects ecological strategies of bacteria. Appl. Environ. Microbiol. 66 (2000) 1328-1333
29. Kolb S., Knief C., Dunfield P.F., and Conrad R. Abundance and activity of uncultured methanotrophic bacteria involved in the consumption of atmospheric methane in two forest soils. Environ. Microbiol. 7 (2005) 1150-1161
30. Krivobok S., Kuony S., Meyer C., Louwagie M., Willison J.C., and Jouanneau Y. Identification of pyrene-induced proteins in Mycobacterium sp. strain 6PY1: evidence for two ring-hydroxylating dioxygenases. J. Bacteriol. 185 (2003) 3828-3841
31. Larkin M.J., Allen C.C., Kulakov L.A., and Lipscomb D.A. Purification and characterization of a novel naphthalene dioxygenase from Rhodococcus sp. strain NCIMB12038. J. Bacteriol. 181 (1999) 6200-6204
32. Laurie A.D., and Lloyd-Jones G. The phn genes of Burkholderia sp. strain RP007 constitute a divergent gene cluster for polycyclic aromatic hydrocarbon catabolism. J. Bacteriol. 181 (1999) 531-540
33. Laurie A.D., and Lloyd-Jones G. Quantification of phnAc and nahAc in contaminated New Zealand soils by competitive PCR. Appl. Environ. Microbiol. 66 (2000) 1814-1817
34. Leys N.M., Ryngaert A., Bastiaens L., Wattiau P., Top E.M., Verstraete W., and Springael D. Occurrence and community composition of fast growing Mycobacterium in soils contaminated with polycyclic aromatic hydrocarbons. FEMS Microbiol. Ecol. 51 (2005) 375-388
35. Lloyd-Jones G., Laurie A.D., Hunter D.W.F., and Fraser R. Analysis of catabolic genes for naphthalene and phenanthrene degradation in contaminated New Zealand soils. FEMS Microbiol. Ecol. 29 (1999) 69-79
36. Lopez-Gutiérrez J.C., Henry S., Hallet S., Martin-Laurent F., Catroux G., and Philippot L. Quantification of a novel group of nitrate-reducing bacteria in the environment by real-time PCR. J. Microbiol. Meth. 57 (2004) 399-407
37. Marlowe E.M., Wang J.M., Pepper I.L., and Maier R.M. Application of a Reverse Transcription-PCR assay to monitor regulation of the catabolic nahAc gene during phenanthrene degradation. Biodegradation. 13 (2002) 251-260
38. Nyyssönen M., Piskonen R., and Itävaara M. A targeted Real-Time PCR assay for studying naphthalene degradation in the environment. Microb. Ecol. 52 (2006) 533-543
39. Park J.W., and Crowley D.E. Dynamic changes in nahAc gene copy numbers during degradation of naphthalene in PAH-contaminated soils. Appl. Microbiol. Biotechnol. 72 (2006) 1322-1329
40. Porteous L.A., Seidler R.J., and Watrud L.S. An improved method for purifying DNA from soil for polymerase chain reaction amplification and molecular ecology applications. Mol. Ecol. 6 (1997) 787-791
41. Romine M.F., Stillwell L.C., Wong K.K., Thurston S.J., Sisk E.C., Sensen C., Gaasterland T., Fredrikson J.K., and Saffer J.D. Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199. J. Bacteriol. 181 (1999) 1585-1602
42. Rose T.M., Schultz E.R., Henikoff J.G., Pietrokovski S., McCallum C.M., and Henikoff S. Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly-related sequences. Nucleic Acids Research 26 (1998) 1628-1635
43. Saito A., Iwabuchi T., and Harayama S. Characterization of genes for enzymes involved in the phenanthrene degradation in Nocardioides sp. KP7. Chemosphere 38 (1999) 1331-1337
44. Sanger F., Coulson A.R., Hong G.F., Hill D.F., and Peterson G.B. Nucleotide sequence of bacteriophage λ DNA. Mol. Biol. 162 (1982) 729-733
45. Simon M.J., Osslund T.D., Saunders R., Ensley B.D., Suggs S., Harcourt A., Suen W.C., Cruden D.L., Gibson D.T., and Zylstra G.J. Sequences of genes encoding naphthalene dioxygenase in Pseudomonas putida strains G7 and NCIB 9816-4. Gene. 127 (1993) 31-37
46. Smith C.J., Nedwell D.B., Dong L.F., and Osborn A.M. Evaluation of quantitative polymerase chain reaction based approaches for determining gene copy and gene transcript numbers in environmental samples. Environ. Microbiol. 8 (2006) 804-815
47. Stapleton R., and Sayler G. Assessment of the microbiological potential for the natural attenuation of petroleum hydrocarbons in a shallow aquifer system. Microb. Ecol. 36 (1998) 349-361
48. Stubner S. Enumeration of 16 S rDNA of Desulfotomaculum lineage 1 in rice field soil by real-time PCR with SybrGreen detection. J. Microbiol. Methods 50 (2002) 155-164
49. Suzuki M.T., Taylor L.T., and DeLong E.F. Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5'-nuclease assays. Appl. Environ. Microbiol. 66 (2000) 4605-4614
50. 14C-naphthalene mineralization potential in petroleum hydrocarbon-contaminated oxic soil layers. FEMS Microbiol. Ecol. 51 (2004) 99-107
51. Uyttebroek M., Breugelmans P., Janssen M., Wattiau P., Joffe B., Karlson U., Ortega-Calvo J.J., Bastiaens L., Ryngaert A., Hausner M., and Springael D. Distribution of the Mycobacterium community and polycyclic aromatic hydrocarbons (PAHs) among different size fractions of a long term PAH-contaminated soil. Environ. Microbiol. 8 (2006) 836-847
52. Widada J., Nojiri H., Kasuga K., Yoshida T., Habe H., and Omori T. Molecular detection and diversity of polycyclic aromatic hydrocarbon-degrading bacteria isolated from geographically diverse sites. Appl. Microbiol. Biotechnol. 58 (2002) 202-209
53. Wilson M.S., Bakermans C., and Madsen E.L. In situ, real-time catabolic gene expression: extraction and characterization of naphthalene dioxygenase mRNA transcripts from groundwater. Appl. Environ. Microbiol. 65 (1999) 80-87
54. Zhou H.W., Guo C.L., Wong Y.S., and Tam N.F.Y. Genetic diversity of dioxygenase genes in polycyclic aromatic hydrocarbon-degrading bacteria isolated from mangrove sediments. FEMS Microbiol Lett. 262 (2006) 148-157
55. Zhou, H.W., Luan, T.G., Zou, F., Tam, N.F., in press. Different bacterial groups for biodegradation of three- and four-ring PAHs isolated from a Hong Kong mangrove sediment. J. Hazard. Mater.