DNA recovery and PCR quantification of catechol 2,3-dioxygenase genes from different soil types

Journal of Biotechnology

Volumn 52, Issue 2, 1996, Pages 107-120

  Wikström, Per ^a   Wiklund, Anna ^a   Andersson, Ann Christin ^a   Forsman, Mats ^a  

^a SWEDISH DEFENCE RESEARCH AGENCY   (Sweden)

Author keywords

bioremediation; catechol 2,3 dioxygenase; PAHs; polymerase chain reaction; quantification; soil

Indexed keywords

AROMATIC HYDROCARBONS; BACTERIA; COMPOSITION EFFECTS; CONTAMINATION; ENZYMES; EXTRACTION; GENES; PH EFFECTS; SEDIMENTS; SOIL POLLUTION; SURFACE ACTIVE AGENTS; WATER;

BIOREMEDIATION; POLYCYCLIC AROMATIC HYDROCARBONS; POLYMERASE CHAIN REACTION (PCR); SODIUM DODECYL SULFATE;

DNA;

CATECHOL; OXYGENASE; POLYCYCLIC AROMATIC HYDROCARBON;

ARTICLE; DNA DETERMINATION; GENETIC ANALYSIS; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SOIL MICROFLORA;

CATECHOL 2,3-DIOXYGENASE; DIOXYGENASES; DNA, BACTERIAL; EVALUATION STUDIES; OXYGENASES; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS);

EID: 0030579516     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-1656(96)01635-5     Document Type: Article

References (29)

1. nd ed. Benjamin Cummings, Redwood City, CA.
2. Bartilson, M. and Shingler, V. (1989) Nucleotide sequences and expression of the catechol 2,3-dioxygenase-encoding gene of phenol-catabolizing Pseudomonas CF600. Gene. 85, 233-238.
3. Bertani, G. (1951) Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J. Bacteriol. 62, 293-300.
4. Cerniglia, C. and Heitkamp M. (1989) Microbial degradation of polycyclic aromatic hydrocarbons (PAH) in the aquatic environment. In: Varanasi U. (ed.), Metabolism of Polycyclic Aromatic Hydrocarbons in the Aquatic Environment, CRC Press, Boca raton, Florida. p. 41-68.
5. Cesarone, C.F., Bolognesi C. and Santi L. (1979) Improved microfluorometric DNA determination in biological material using 33258 Hoechst. Anal. Biochem. 100, 188-197.
6. Dagley, S. (1986) Biochemistry of aromatic hydrocarbon degradation in pseudomonads. In: Sokatch J.R. (Ed.), The Bacteria, Vol X, The Biology of Pseudomonas. Academic Press, London, pp. 527-556.
7. Dorch, M. and Stackebrandt, E. (1992) Some modifications in the procedure of direct sequencing of PCR amplified 16S rDNA. J. Microbiol. Methods. 16, 271-279.
8. Emerson, W.W, Foster, B.C. and Oades, J.M. (1986) Organo-mineral complexes in relation to soil aggregation and structure. In: Huang P.M and Schnitzer M. (Eds.), Interactions of soil minerals with natural organics and microbes. Soil Science Society of America, Madison, Wisconsin, USA. p. 521-545.
9. Emteryd, O. (1989) Chemical and physical analysis of inorganic nutrients in plant, soil, water and air. Swedish University of Agricultural Sciences, Department of Forest Site Research, Umeå, Sweden.
10. Erb, R.W. and Wagner-Döbler, I. (1993) Detection of polychlorinated biphenyl degradation genes in polluted sediments by direct DNA extraction and polymerase chain reaction. Appl. Environ. Microbiol. 59, 4065-4073.
11. FAO (1981) FAO/Unesco Soil Map of the World, Revised Legends. Vol. V, Europe, FAO/Unesco, Rome, pp 172-173.
12. Forsman, M., Nyrén, A., Sjöstedt, A., Sjökvist, L. and Sandström, G. (1995) Identification of Francisella tularensis in natural waters by PCR. FEMS Microbiol. Ecol. 16, 83-92.
13. Franklin, F.C., Bagdasarian, H.M., Bagdasarian, M.M. and Timmis, K.N. (1981) Molecular and functional analysis of the TOL plasmid pWW0 from Pseudomonas putida and cloning of genes for the entire regulated aromatic ring meta cleavage pathway. Proc. Natl. Acad. Sci. USA 78, 7458-7462.
14. Herrick, J.B., Madsen, E.L., Bratt, C.A. and Ghiorse, W.C. (1993) Polymerase chain reaction amplification of naphtalene catabolic and 16S rDNA sequences from indigenous sediment bacteria. Appl. Environ. Microbiol. 59, 687-694.
15. Jin, C-F., Mata, M. and Fink, D.J. (1994) Rapid construction of deleted DNA fragments for use as internal standards in competitive PCR. PCR Methods Applic. 3, 253-255.
16. Lorenz, G.M. and Wackernagel W. (1994) Bacterial gene transfer by genetic transformation in the environment. Microbiol. Rev. 58, 563-602.
17. Nakai, C., Hori, K., Kagamiyama, H., Nakazawa, T. and Nozaki, M. (1983) Purification, subunit structure, and partial amino sequence of metapyrocatechase. J. Biol. Chem. 258, 2916-2922.
18. Sambrook, J., Fritch, E.F. and Maniatis, T. (1989) Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
19. Selenska-Pobell, S. (1995). Direct and simultaneous extraction of DNA and RNA from soil. In: Akkermans, A.D.L., van Elsas, J.D. and de Bruijn, F.J. (Eds.), Molecular Microbial Ecology Manual. Kluwer, Dordrecht, section 1.5.1.
20. Swedish Environmental Protection Agency. (1990) Sampling and methods for analyses of sludge. Report 3829.
21. Torsvik, T. (1995) Cell extraction method. In: Akkermans, A.D.L., van Elsas, J.D. and de Bruijn F.J. (Eds.), Molecular Microbial Ecology Manual. Kluwer, Dordrecht, section 1.3.1.
22. Tsai, Y-L. and Olson, B.H. (1991) Rapid method for extraction of DNA from soil and sediments. Appl. Environ. Microbiol. 57, 1070-1074.
23. van Elsas, J.D. and Smalla K. (1995) Extraction of microbial community DNA from soils. In: Akkermans, A.D.L., van Elsas, J.D. and de Bruijn F.J. (Eds.), Molecular Microbial Ecology Manual. Kluwer, Dordrecht, section 1.3.3.
24. Wang, R-F., Luneau A., Cao W-W. and Cerniglia C.E. (1996) PCR detection of polycyclic aromatic hydrocarbon-degrading mycobacteria. Environ. Sci. Technol. 30, 307-311.
25. Williams, A.P. and Sayers, J.P. (1994) The evolution of pathways for aromatic hydrocarbon oxidation in Pseudomonas. Biodegradation. 5, 195-217.
26. Wood, T., Bormann F.H. and Voigt G. K. (1984) Phosphorous cycling in a northern hardwood forest: Biological and chemical control. Science 223, 391-393.
27. Yen, K-M. and Gunsalius, I.C.G. (1982) Plasmid gene organization: Naphtalene/salicylate oxidation. Proc. Natl. Acad. Sci. USA 79, 874-878.
28. Yvonne, R.B., Sadowsky M.J., Ellis L. B.M., Que L. Jr. and Wackett L.P. (1995) A manganese-dependent dioxygenase from Arthrobacter globiformis CM-2 belongs to the major extradiol dioxygenase family. J. Bacteriol. 177, 1225-1232.
29. Zhou, J., Bruns M.A. and Tiedje J.M. (1996) DNA recovery from soils of diverse composition. Appl. Environ. Microbiol 62, 316-322.