SEARCH

SEARCH BY CITATION

References

  • Atlas RM & Cerniglia CE (1995) Bioremediation of petroleum pollutants: diversity and environmental aspects of hydrocarbon biodegradation. BioScience 45: 332338.
  • Ayoubi PJ & Harker AR (1998) Whole-cell kinetics of trichloroethylene degradation by phenol hydroxylase in a Ralstonia eutropha JMP134 derivative. Appl Environ Microbiol 64: 43534356.
  • Baldwin BR, Nakatsu CH & Nies L (2003) Detection and enumeration of aromatic oxygenase genes by multiplex and real-time PCR. Appl Environ Microbiol 69: 33503358.
  • Barker JF, Patrick GC & Major D (1987) Natural attenuation of aromatic hydrocarbons in a shallow sand aquifer. Ground Water Monit Rev 7: 6471.
  • Bertoni G, Martino M, Galli E & Barbieri P (1998) Analysis of the gene cluster encoding toluene/o-xylene monooxygenase from Pseudomonas stutzeri OX1. Appl Environ Microbiol 64: 36263632.
  • Burlage RS, Hooper SW & Sayler GS (1989) The TOL (pWWO) catabolic plasmid. Appl Environ Microbiol 55: 13231328.
  • Byrne AM, Kukor JJ & Olsen RH (1995) Sequence analysis of the gene cluster encoding toluene 3-monooxygenase from Pseudomonas pickettii PKO1. Gene 154: 6570.
  • Cavalca L, Dell'Amico E & Andreoni V (2003) Intrinsic bioremediability of an aromatic hydrocarbon-polluted groundwater: diversity of bacterial population and toluene monooxygenase genes. Appl Microbiol Biotechnol 64: 576587.
  • Duarte GF, Rosado AS, Seldin L, de Araujo W & van Elsas JD (2001) Analysis of bacterial community structure in sulfurous-oil-containing soils and detection of species carrying dibenzothiophene desulfurization (dsz) genes. Appl Environ Microbiol 67: 10521062.
  • El-Fantroussi S, Mahillon J, Naveau H & Agathos SN (1997) Introduction and PCR detection of Desulfomonile tiedjei in soil slurry microcosms. Biodegradation 8: 125133.
  • Fjellbirkeland A, Torsvik V & Øvreas L (2001) Methanotrophic diversity in an agricultural soil as evaluated by denaturing gradient gel electrophoresis profiles of pmoA, mxaF and 16S rDNA sequences. Antonie Van Leeuwenhoek 79: 209217.
  • Futamata H, Harayama S & Watanabe K (2001a) Diversity in kinetics of trichloroethylene-degrading bacteria. Appl Microbiol Biotechnol 55: 248253.
  • Futamata H, Harayama S & Watanabe K (2001b) Group-specific monitoring of phenol hydroxylase genes for a functional assessment of phenol-stimulated trichloroethylene bioremediation. Appl Environ Microbiol 67: 46714677.
  • Guo C, Suo W, Harsh JB & Ogram A (1997) Hybridization analysis of microbial DNA from fuel oil-contaminated and noncontaminated soil. Microb Ecol 34: 178187.
  • Henckel T, Friedrich M & Conrad R (1999) Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase. Appl Environ Microbiol 65: 19801990.
  • Hendrickx B, Dejonghe W, Boënne W, et al. (2005a) Dynamics of an oligotrophic community during contact with a BTEX contaminated groundwater plume: an in situ microcosm study. Appl Environ Microbiol 71: 38153825.
  • Hendrickx B, Junca H, Vosahlova J, et al. (2005b) Alternative primer sets for PCR detection of genotypes involved in bacterial aerobic BTEX degradation: distribution of the genes in BTEX degrading isolates and in subsurface soils of a BTEX contaminated industrial site. J Microbiol Methods, in press.
  • Johnson GR & Olsen RH (1997) Multiple pathways for toluene degradation in Burkholderia sp. strain JS150. Appl Environ Microbiol 63: 40474052.
  • Junca H & Pieper DH (2003a) Amplified functional DNA restriction analysis to determine catechol 2,3-dioxygenase gene diversity in soil bacteria. J Microbiol Meth 55: 697708.
  • Junca H & Pieper DH (2003b) Functional gene diversity analysis in BTEX contaminated soils by means of PCR-SSCP DNA fingerprinting: comparative diversity assessment against bacterial isolates and PCR-DNA clone libraries. Environ Microbiol 6: 95110.
  • Kahng H-Y, Malinverni JC, Majko MM & Kukor JJ (2001) Genetic and functional analysis of the tbc operons for catabolism of alkyl- and chloroaromatic compounds in Burkholderia sp. strain JS150. Appl Environ Microbiol 67: 48054816.
  • Keil H, Lebens MR & Williams PA (1985) TOL plasmid pWW15 contains two nonhomologous, independently regulated catechol 2,3-dioxygenase genes. J Bacteriol 163: 248255.
  • Kim E & Zylstra GJ (1999) Functional analysis of genes involved in biphenyl, naphthalene, phenanthrene, and m-xylene degradation by Sphingomonas yanoikuyae B1. J Ind Microbiol Biotechnol 23: 294302.
  • Kimura M (1980) A simple model for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111120.
  • Kitayama A, Suzuki E, Kawakami Y & Nagamune T (1996) Gene organization and low regiospecificity in aromatic-ring hydroxylation of a benzene monooxygenase of Pseudomonas aeruginosa JI104. J Ferment Bioeng 82: 421425.
  • Kok RG, Young DM & Ornston LN (1999) Phenotypic expression of PCR-generated random mutations in a Pseudomonas putida gene after its introduction into an Acinetobacter chromosome by natural transformation. Appl Environ Microbiol 65: 16751680.
  • Kowalchuk GA, Naoumenko ZS, Derikx PJL, Felske A, Stephen JR & Arkhipchenko IA (1999) Molecular analysis of ammonia oxidizing bacteria of the beta subdivision of the class Proteobacteria in compost and composted materials. Appl Environ Microbiol 65: 396403.
  • Kukor JJ & Olsen RH (1996) Catechol 2,3-dioxygenase functional in oxygen-limited (hypoxic) environments. Appl Environ Microbiol 62: 17281740.
  • Leys NM, Ryngaert A, Bastiaens L, Wattiau P, Top EM, Verstraete W & Springael D (2005) Occurrence and diversity of fast-growing Mycobacterium species in soils contaminated with polycyclic aromatic hydrocarbons (PAHs). FEMS Microbiol Ecol 51: 375388.
  • Lovley DR (2001) Bioremediation. Anaerobes to rescue. Science 293: 14441446.
  • Ma Y & Herson DS (2000) The catechol 2,3-dioxygenase gene and toluene monooxygenase genes from Burkholderia sp. AA1, an isolate capable of degrading aliphatic hydrocarbons and toluene. J Ind Microbiol Biotechnol 25: 127131.
  • Mergeay M, Nies DH, Schlegel HG, Gerits J, Charles P & Van Gijsegem F (1985) Alcaligenes eutrophus CH34 is a facultative chemolithotroph with plasmid-bound resistance to heavy metals. J Bacteriol 162: 328334.
  • Muyzer G, de Waal EC & Uitterlinden A (1993) Profiling of complex microbial populations using denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 695700.
  • Ogram A, Sun W, Brockman FJ & Frederickson JK (1995) Isolation and characterization of RNA from low-biomass deep-subsurface sediments. Appl Environ Microbiol 61: 763768.
  • Ramos JL, Duque E, Gallegos MT, Godoy P, Ramos-Gonzaléz MI, Terwan W & Segura A (2002) Mechanisms of solvent tolerance in Gram-negative bacteria. Annu Rev Microbiol 56: 743768.
  • Rosado AS, Duarte GF, Seldin L & van Elsas JD (1998) Genetic diversity of nifH gene sequences in Paenibacillus azotofixans strains and soil samples analyzed by denaturing gradient gel electrophoresis of PCR-amplified gene fragments. Appl Environ Microbiol 64: 27702779.
  • Saitou N & Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406425.
  • Sambrook J, Fritsch EF & Maniatis T (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
  • Shields MS, Reagin MJ, Gerger RR, Campbell R & Somerville C (1995) TOM, a new aromatic degradative plasmid from Burkholderia (Pseudomonas) cepacia G4. Appl Environ Microbiol 61: 13521356.
  • Sinigalliano CD, Kuhn DN & Jones RD (1995) Amplification of the amoA gene from diverse species of ammonium-oxidizing bacteria and from an indigenous bacterial population from seawater. Appl Environ Microbiol 61: 27022706.
  • Swoboda-Colberg NG (1995) Chemical contamination of the environment: sources, types and fate of synthetic organic chemicals. Microbial transformations and degradation of toxic organic chemicals (YoungLY & CernigliaCE, eds), pp. 2774. Wiley-Liss Inc., New York, NY, USA.
  • Vanbroekhoven K, Ryngaert A, Wattiau P, De Mot R & Springael D (2004) Acinetobacter diversity in environmental samples assessed by 16S rRNA gene PCR–DGGE fingerprinting. FEMS Microbiol Ecol 50: 3750.
  • Watanabe K, Teramoto M & Harayama S (2002) Stable augmentation of activated sludge with foreign catabolic genes harboured by an indigenous dominant bacterium. Environ Microbiol 4: 577583.
  • Wawer C, Jetten MSM & Muyzer G (1997) Genetic diversity and expression of the [NiFe] hydrogenase large-subunit gene of Desulfovibrio spp. in environmental samples. Appl Environ Microbiol 63: 43604369.
  • Yen K-M, Karl MR, Blatt LM, Simon MJ, Winter RB, Fausset PR, Lu HS, Harcourt AA & Chen KK (1991) Cloning and characterization of a Pseudomonas putida KR1 gene cluster encoding toluene-4-monooxygenase. J Bacteriol 173: 53155327.
  • Zylstra GJ & Gibson DT (1989) Toluene degradation by Pseudomonas putida F1. Nucleotide sequence of the todC1C2BADE genes and their expression in Escherichia coli. J Biol Chem 264: 1494014946.