Dynamic changes in nahAc gene copy numbers during degradation of naphthalene in PAH-contaminated soils

Applied Microbiology and Biotechnology

Volumn 72, Issue 6, 2006, Pages 1322-1329

  Park, Joong Wook ^a   Crowley, David E ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Biodegradation; Biomarker; Environmental monitoring; Microbial ecology; Polycyclic aromatic hydrocarbon; Real time polymerase chain reaction

Indexed keywords

ENVIRONMENTAL MONITORING; MICROBIAL ECOLOGY; REAL-TIME POLYMERASE CHAIN REACTION; SOIL MICROBIAL COMMUNITIES;

BIODEGRADATION; BIOMARKERS; CLONING; ENZYMES; GENETIC ENGINEERING; MICROBIOLOGY; NAPHTHALENE; SOILS;

GENES;

BIOLOGICAL MARKER; DIOXYGENASE; DNA; NAPHTHALENE; POLYCYCLIC AROMATIC HYDROCARBON; PRIMER DNA; SOIL WATER;

BACTERIUM; BIOMARKER; DEGRADATION; DNA; GENE EXPRESSION; NAPHTHALENE; PAH; POLYMERASE CHAIN REACTION; SOIL MICROORGANISM; SOIL POLLUTION;

AMPLICON; ARTICLE; BACTERIAL GENE; BACTERIAL METABOLISM; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; DNA SEQUENCE; GENE NUMBER; GENETIC ANALYSIS; MARKER GENE; METABOLIC RATE; MICROBIAL ACTIVITY; MICROBIAL DEGRADATION; MOLECULAR CLONING; MOLECULAR DYNAMICS; NAHAC GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; REAL TIME POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY; SOIL MICROFLORA; SOIL POLLUTION;

BACTERIA; BACTERIAL PROTEINS; BIODEGRADATION, ENVIRONMENTAL; CLONING, MOLECULAR; DIOXYGENASES; DNA PRIMERS; DNA, BACTERIAL; GENES, BACTERIAL; MULTIENZYME COMPLEXES; NAPHTHALENES; OXYGENASES; POLYCYCLIC HYDROCARBONS, AROMATIC; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; SOIL POLLUTANTS; TIME FACTORS;

BACTERIA (MICROORGANISMS);

EID: 33749853335     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-006-0423-5     Document Type: Article

References (33)

1. Agency for Toxic Substances and Disease Registry (ATSDR) (1996) Polycyclic aromatic hydrocarbons (PAHs), ToxFAQs (http://www.atsdr.cdc.gov/). CAS # 130498-29-2
2. Ahn Y, Sanseverino J, Sayler GS (1999) Analyses of polycyclic aromatic hydrocarbon-degrading bacteria isolated from contaminated soils. Biodegradation 10:149-157
3. Baelum J, Henriksen T, Hansen HC, Jacobsen CS (2006) Degradation of 4-chloro-2-methylphenoxyacetic acid in top- and subsoil is quantitatively linked to the class III tfdA gene. Appl Environ Microbiol 72:1476-1486
4. Baldwin BR, Nakatsu CH, Nies L (2003) Detection and enumeration of aromatic oxygenase genes by multiplex and real-time PCR. Appl Environ Microbiol 69:3350-3358
5. Beller HR, Kane SR, Legler TC, Alvarez PJ (2002) A real-time polymerase chain reaction method for monitoring anaerobic, hydrocarbon-degrading bacteria based on a catabolic gene. Environ Sci Technol 36:3977-3984
6. Cerniglia CE (1984) Microbial metabolism of polycyclic aromatic hydro-carbons. Adv Appl Microbiol 30:31-71
7. Cerniglia CE (1992) Biodegradation of polycyclic aromatic hydrocarbons. Biodegradation 3:351-368
8. Chandler DP, Brockman FJ (1996) Estimating biodegradative gene numbers at a Jp-5 contaminated site using PCR. Appl Biochem Biotech 57:971-982
9. Cuny P, Faucet J, Acquaviva M, Bertrand JC, Gilewicz M (1999) Enhanced biodegradation of phenanthrene by a marine bacterium in presence of a synthetic surfactant. Lett Appl Microbiol 29:242-245
10. Davies JI, Evans WC (1964) Oxidative metabolism of naphthalene by soil pseudomonads: the ring-fission mechanism. Biochem J 91:251-261
11. Diaz E, Prieto MA (2000) Bacterial promoters triggering biodegradation of aromatic pollutants. Curr Opin Biotechnol 11:467-475
12. Duodu S, Bhuvaneswari TV, Gudmundsson J, Svenning MM (2005) Symbiotic and saprophytic survival of three unmarked Rhizobium leguminosarum biovar trifolii strains introduced into the field. Environ Microbiol 7:1049-1058
13. Eaton RW, Chapman PJ (1992) Bacterial metabolism of naphthalene: construction and use of recombinant bacteria to study ring cleavage of 1,2-dihydroxynaphthalene and subsequent reactions. J Bacteriol 174:7542-7554
14. Ensley BD, Haigler BE (1990) Naphthalene dioxygenase from Pseudomonas NCIB9816. Methods Enzymol 188:46-52
15. Ensley BD, Gibson DT, Laborede A (1982) Oxidation of naphthalene by a multicomponent enzyme system from Pseudomonas sp. strain NCIB9816. J Bacteriol 149:948-954
16. Habe H, Omori T (2003) Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria. Biosci Biotechnol Biochem 67:225-243
17. Hall M, Grover PL (1990) Polycyclic aromatic hydrocarbons: metabolism, activation, and tumor initiation. Springer, Berlin Heidelberg New York, pp 327-372
18. Hamann C, Hegemann J, Hildebrandt A (1999) Detection of polycyclic aromatic hydrocarbon degrading genes in different soil bacteria by polymerase chain reaction and DNA hybridization. FEMS Microbiol Lett 173:255-263
19. Herrick JB, Stuart-Keil KG, Ghiorse WC, Madsen EL (1997) Natural horizontal transfer of a naphthalene dioxygenase gene between bacteria native to a coal tar-contaminated field site. Appl Environ Microbiol 63:2330-2337
20. Kolb S, Knief C, Stubner S, Conrad R (2003) Quantitative detection of methanotrophs in soil by novel pmoA-targeted real-time PCR assays. Appl Environ Microbiol 69:2423-2429
21. Laurie AD, Lloyd-Jones G (2000) Quantification of phnAc and nahAc in contaminated New Zealand soils by competitive PCR. Appl Environ Microbiol 66:1814-1817
22. Lloyd-Jones G, Laurie AD, Hunter DWF, Fraser R (1999) Analysis of catabolic genes for naphthalene and phenanthrene degradation in contaminated New Zealand soils. FEMS Microbiol Ecol 29:69-79
23. Mason JR, Cammack R (1992) The electron-transport proteins of hydroxylating bacterial dioxygenases. Annu Rev Microbiol 46:277-305
24. Mavrodi DV, Kovalenko NP, Sokolov SL, Parfenyuk VG, Kosheleva IA, Boromin AM (2003) Identification of the key genes of naphthalene catabolism in soil DNA. Microbiology 72:597-604
25. Moser R, Stahl U (2001) Insight into the genetic diversity of initial dioxygenase from PAH-degrading bacteria. Appl Microbiol Biotechnol 55:609-618
26. Nakatsu CH, Carmosini N, Baldwin B, Beasley F, Kourtev P, Konopka A (2005) Soil microbial community responses to additions of organic carbon substrates and heavy metals (Pb and Cr). Appl Environ Microbiol 71:7679-7689
27. National Research Council (1983) Polycyclic aromatic hydrocarbons; evaluation of sources and effects. National Academic, Washington, D.C.
28. Okano Y, Hristova KR, Leutenegger CM, Jackson LE, Denison RF, Gebreyesus B, Lebauer D, Scow KM (2004) Application of real-time PCR to study effects of ammonium on population size of ammonia-oxidizing bacteria in soil. Appl Environ Microbiol 70:1008-1016
29. Parales RE (2003) The role of active-site residues in naphthalene dioxygenase. J Ind Microbiol Biotechnol 30:271-278
30. Sanseverino J, Applegate BM, King JMH, Sayler GS (1993) Plasmid-mediated mineralization of naphthalene, phenanthrene, and anthracene. Appl Microbiol Biotechnol 59:1931-1937
31. Simon MJ, Osslund TS, Saunders R, Ensley BD, Suggs S, Harcourt A, Suen W, Cruden DL, Gibson DT, Zylstra GJ (1993) Sequences of genes encoding naphthalene dioxygenase in Pseudomonas putida strains G7 and NCIB 9816-4. Gene 127:31-37
32. Stuart-Keil KG, Hohnstock AM, Drees KP, Herrick JB, Madsen EL (1998) Plasmids responsible for horizontal transfer of naphthalene catabolism genes between bacteria at a coal tar-contaminated site are homologous to pDTG1 from Pseudomonas putida NCIB 9816-4. Appl Environ Microbiol 64:3633-3640
33. Wilson MS, Bakermans C, Madsen EL (1999) In situ, real-time catabolic gene expression: extraction and characterization of naphthalene dioxygenase mRNA transcript from ground water. Appl Environ Microbiol 65:80-87