行政院環境保護署，「監測井地下水採樣方法」，NIEA W103.53B，94年12月14日環署檢字第0940101385號公告。
行政院環境保護署，2001，飲用水與甲基第三丁基醚相關資料。
杜政榮、李俊福、江亮演，1994，環境學概論，國立空中大學。
柯清水，1992，石油化學概論，正文書局有限公司。
楊金鐘、謝爵安，2000，利用土體加熱/氣提法與蒸氣注入/真空萃取法整治受甲基第三丁基醚與柴油污染土壤之研究，第十五屆廢棄物處理技術研討會論文集，第2-34~2-41頁。
謝昶毅，2003，以PCR-DGGE技術分析石油碳氫化合物污染地下水之微生物相，國立中山大學生物科學學系碩士論文。AFCEE (Air Force Center for Environmental Excellence), 1994. Armstrong Laboratory, and Air Force Institute of Technology, Use of risk-based standards for cleanup of petroleum contaminated soil. Brooks Air Force Base, Texas, U.S.A.
Aksenova, H.W., Raincy, F.A., Janssen, P.H., Zavarzin, G.A., Morgan, H.W., 1992. Spirochaeta thermophila sp. Nov., an obligately anaerobic, polyasccharolytic, extremely thermophilic bacterium. International Journal of Systematic and Evolutionary Microbiology. 42:175-177.
Amann, R.I., Ludwig, W., Schliefer, K.H., 1995. Phylogenetic identication and in situ detection of individual microbial cells without cultivation. Microbiological Reviews. 59:143-169.
Anderson, R.T., Rooney-Varga, J.N., Gaw, C.V., Lovley, D.R., 1998. Anaerobic benzene oxidation in the Fe(III) reduction zone of petroleum-contaminated aquifers. Environmental Science & Technology. 32:1222-1229.
Anderson, R.T., Vrionis, H.A., Ortiz-Bernad, I. & 10 other authors, 2003. Stimulated in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer. Applied and Environmental Microbiology. 69:5884-5891.
Auman, A.J., Speake, C.C., Lidstrom, M.E., 2001. NifH sequences and nitrogen fixation in type I and type II methanotrophs. Applied and Environmental Microbiology 67:4009-4016.
Austin, B., Calomiris, J.J., Walker, J.D., Colwell, R.R., 1977. Numerical taxonomy and ecology of petroleum-degrading bacteria. Applied and Environmental Microbiology. 34:60-68.
Bakermans, C. and Madsen, E.L., 2002. Diversity of 16S rDNA and naphthalene dioxygenase genes from coal-tar-waste-contaminated aquifer waters. Microbial Ecology. 44:95-106.
Baldwin, B.R., Nakatsu, C.H., Nies, L., 2003. Detection and enumeration of aromatic oxygenase genes by multiplex and real-time PCR. Applied and Environmental Microbiology. 69:3350-3358.
Baldwin, B.R., Nakatsu, C.H., Nies, L., 2008. Enumeration of aromatic oxygenase genes to evaluate monitored natural attenuation at gasoline-contaminated sites. Water Research. 42:723-731.
Barbara, T., Wonerow, K., Paschke, K., 1999. DGGE is more sensitive for the detection of somatic point mutations than direct sequencing. BioTechniques. 27:266-268.
Bazylinski, D.A., Dean, A.J., Schuler, D., Phillips, E.J.P., Lovley, D.R., 2000. N2-dependent growth and nitrogenase activity in the metal-metabolizing bacteria, Geobacter and Magnetospirillum species. Environmental Microbiology. 2:266-273.
Bedient, P.B., Rifai, H.S., Newell, C.J., 1999. Ground water contamination –transport and remediation. PTR Prentice-Hall, Inc., New Jersey.
Borden, R.C., Gomez, A.C., Becker, T.M., 1995. Geochemical indicator of natural bioremediation. Ground Water. 33:180-189.
Brakstad, O.G., Bonaunet, K., Nordtug, T., Johansen, O., 2004. Biotransformation and dissolution of petroleum hydrocarbons in natural flowing seawater at low temperature. Biodegradation. 15:337-346.
Brakstad, O.G., Nonstad, I., Faksness, L.G., Brandvik, P.J., 2007. Responses of microbial communities in arctic sea ice after contamination by crude petroleum oil. Microbial Ecology. 55:540-552.
Briée, C., Moreira, D., López-García, P., 2007. Archaeal and bacterial community composition of sediment and plankton from a suboxic freshwater pond. Research in Microbiology. 158:213-227.
Brümmer, I.H.M., Felske, A., Wagner-Döbler, I., 2003. Diversity and seasonal variability of ß-Proteobacteria in biofilms of polluted rivers: analysis by temperature gradient gel electrophoresis and cloning. Applied and Environmental Microbiology. 69:4463-4473.
Brüggemann, J., Stephen, J.R., Chang Y.J., Macnaughton, S.J., Kowalchuk, G.A., Kline, E., White, D.C., 2000. Competitive PCR-DGGE analysis of bacterial mixtures: an internal standard and an appraisal of template enumeration accuracy. Journal of Microbiological Methods. 40:111-123.
Bruneel, O., Duran, R., Casiot, C., Elbaz-Poulichet, F., Personne´, J.-C., 2006. Diversity of microorganisms in Fe-As-rich acid mine drainage waters of Carnoulès, France. Applied and Environmental Microbiology. 72:551-556.
Cavalca, L., Dell'Amico, E., Andreoni, V., 2004. Intrinsic bioremediability of an aromatic hydrocarbon-polluted groundwater: diversity of bacterial population and toluene monoxygenase genes. Applied Microbiology and Biotechnology. 64:576-587.
Cerniglia, C.E., 1992. Biodegradation of polycyclic aromatic hydrocarbons. Biodegradation. 3: 351-368.
Chen, J.M., Chen, D.Z., Zhong, W.H., Zhang, J.X., Chen, X.A., 2007. Biodegradation of methyl tert-butyl ether by Methylibium petroleiphilum PM1 in poor nutrition solution. Journal of environmental science and health. Part A. 42:2123 -2129.
Coates, J.D., Bhupathiraju, V.K., Achenbach, L.A., McInerney, M.J. Lovley, D.R., 2001. Geobacter hydrogenophilus Geobacter chapellei and Geobacter grbiciae, three new, strictly anaerobic, dissimilatory Fe(III)-reducers. International Journal of Systematic and Evolutionary Microbiology. 51:581-588.
Coppi, M.V., Leang, C., Sandler, S.J., Lovley, D.R., 2001. Development of a genetic system for Geobacter sulfurreducens. Applied and Environmental Microbiology. 67:3180-3187.
Cummings, D.E., Snoeyenbos-West, O.L., Newby, D.T., Niggemyer, A.M., Lovley, D.R., Achenbach, L.A., Rosenzweig, R.F., 2003. Diversity of Geobacteraceae species inhabiting metal-polluted freshwater lake sediments ascertained by 16S rDNA analyses. Microbial Ecology. 46:257-269.
Davidson, J.M., Creek, D.N., 2000. Using the gasoline additive MTBE in forensic environmental investigations. Environmental Forensics. 1:31-36.
Davis, J.W., Odom, J.M., Deweerd, K.A., Stahl, D.A., Fishbain, S.S., West, R.J., Klecka, G.M., DeCarolis, J.G., 2002. Natural attenuation of chlorinated solvents at Area 6, Dover Air Force Base: characterization of microbial community structure. Journal of Contaminant Hydrology. 57:41-59.
Dedysh, S.N., Ricke, P., Liesack, W., 2004. NifH and NifD phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria. Microbiology. 150: 1301-1313.
Duetz, W.A., de Jong, C., Williams, P.A., van Andel, J.G., 1994. Competition in chemostat culture between Pseudomonas strains that use different pathways for the degradation of toluene. Applied and Environmental Microbiology. 60:2858-2863.
Erickson, B.D., and Mondello, F.J., 1992. Nucleotide sequencing and transcriptional mapping of genes encoding biphenyl dioxygenase, a multicomponent polychlorinated-biphenyl-degrading enzyme in Pseudomonas strain LB400. Journal of Bacteriology. 174:2903-2912.
Eweis, J.B., Schroeder, E.D., Chang, D.P.Y., Scow, K.M., 1998. Biodegradation of MTBE in a pilot-scale biofilter. In Wickramanayake G.B. & Hinchee R.E. (ed.), Natural attenuation: Chlorinated and recalcitrant compounds. Battelle Press, Columbus, Ohio.
Fayolle, F., Vandecasteele, J.P., Monot, F., 2001. Microbial degradation and fate in the environment of methyl tert-butyl ether and related fuel oxygenates. Applied Microbiology and Biotechnology. 56:339- 349.
Feris, K.P., Hristova, K., Gebreyesus, B., Mackay, D., Scow, K.M., 2004. A shallow BTEX and MTBE contaminated aquifer supports a diverse microbial community. Microbial Ecology. 48:589-600.
Fiorenza, S. and Hfai, H.S., 2003. Review of MTBE biodegradation and bioremediation. Bioremediation Journal, 7: 1-35.
Fischer, A., Oehm, C., Selle, M., Werner, P., 2005. Biotic and abiotic transformations of methyl tertiary butyl ether (MTBE). Environmental Science and Pollution Research International. 12:381-386.
François, A., Mathis, H., Godefroy, D., Piveteau, P., Fayolle, F., Monot, F., 2002. Biodegradation of methyl tert-butyl ether and other fuel oxygenates by a new strain, Mycobacterium austroafricanum IFP 2012. Applied and Environmental Microbiology. 68:2754-2762.
François, A., Garnier, L., Mathis, H., Fayolle, F., Monot, F., 2003. Roles of tert-butyl formate, tert-butyl alcohol and acetone in the regulation of methyl tert-butyl ether degradation by Mycobacterium austroafricanum IFP 2012. Applied Microbiology and Biotechnology. 62:256-262.
Frenzel, P., 2000. Plant-associated methane oxidation in rice fields and wetlands. Advances in Microbial Ecology. 16:85-114.
Focht, D.D., 1994. Microbiological procedures for biodegradation research. In Weaver, R.W. et al. (ed.), Methods of Soil Analysis, Part 2 –Microbiological and Biochemical Properties, Soil Science Society of America, Book Series 5. SSSA, Madison, WS.
Fortin, N.Y. and Deshusses, M.A., 1999. Treatment of methyl tert-butyl ether vapors in biotrickling filters. 1. Reactor startup, steady state performance and culture characteristics. Environmental Science & Technology. 33:2980-2986.
Fortin, N.Y., Morales, M., Nakagawa, Y., Focht, D.D., Deshusses, M.A., 2001. Methyl tert-butyl ether (MTBE) degradation by a microbial consortium. Environmental Microbiology. 3:407-416.
Garnier, P., Auria, R., Magana, M., Revah, S., 1999. Cometabolic biodegradation of methyl t-butyl ether by a soil consortium, In situ bioremediation of petroleum hydrocarbon and other organic compounds. Battelle Publications, Columbus, Ohio.
Geiselbrecht, A.D., Hedlund, B.P., Tichi, M.A., Staley, J.T., 1998. Isolation of marine polycyclic aromatic hydrocarbon (PAH)-degrading Cycloclasticus strains from the Gulf of Mexico and comparison of their PAH degradation ability with that of puget sound Cycloclasticus strains. Applied and Environmental Microbiology. 64:4703-4710.
Gibellini, D., Vitone, F., Cori, F., Placa, M.L., RE, M.C., 2004. Quantitative detection human immunodeficiency virus type 1 (HIV-1) viral load by SYBR green real-time RT-PCR technique in HIV-1 seropositive patients. Journal of Virological Methods. 115: 183-189.
Greated, A., Lambertsen, L., Williams, P.A., Thomas, C.M., 2002. Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida. Environmental Microbiology. 4:856-871.
Guo, C., Sun, W., Harsh, J.B., Ogram, A., 1997. Hybridization analysis of microbial DNA from fuel oil-contaminated and noncontaminated soil. Microbial Ecology. 34:178-187.
Hanson, J.R., Ackerman, C.E., Scow, K.M., 1999. Biodegradation of methyl tert-butyl ether by a bacterial pure culture. Applied and Environmental Microbiology. 65:4788-4792.
Harayama, S. and Kok, M., 1992. Functional and evolutionary relationships among diverse oxygenase. Annual Review of Microbiology. 46:565-601.
Harayama, S. and Rekik, M., 1989. Bacterial aromatic ring-cleavage enzymes are classified into two different gene families. The Journal of Biological Chemistry. 264:15328-15333.
Harwood, C.S. and Canale-Parola, F., 1984. Ecology of spirochete. Annual Review of Microbiology. 38:185-194.
Hatzinger, P.B, McClay, K., Vainberg, S., Tugusheva, M., Condee, C.W., Steffan, R.J., 2001. Biodegradation of methyl tert-butyl ether by a pure bacterial culture. Applied and Environmental Microbiology. 67:5601-5607.
Hedlund, B.P., Geiselbrecht, A.D., Bair, T.J., Staley, J.T., 1999. Polycyclic aromatic hydrocarbon degradation by a new marine bacterium, Neptunomonas naphthovorans gen. nov., sp. nov. Applied and Environmental Microbiology. 65: 251-259.
Heinrich, K., Susanne, K., Roger, W., Pickup, Peter, A., Williams., 1985. Evolutionary conservation of genes coding for meta pathway enzymes within TOL plasmids pWWO and pWW53. Journal of Bacteriology. 164: 887-895.
Hernandez-Perez, G., Fayolle, F., Vandecasteele, J.P., 2001. Biodegradation of ethyl t-butyl ether (ETBE), methyl t-butyl ether (MTBE) and t-amyl methyl ether (TAME) by Gordonia terrae. Applied Microbiology and Biotechnology. 55:117-121.
Hino, S., Watanabe, K., Takahashi, N., 1998. Phenol hydroxylase cloned from Ralstonia eutropha strain E2 exhibits novel kinetic properties. Microbiology. 144:1765-1772.
Holben, W.E., 1994. Isolation and purification of bacterial DNA from soil. In Mickelson, S.H. (ed.), Methods of Soil Analysis, Part 2, Soil Society of America. Madison, WI.
Holmes, D.E., Nevin, K.P., Lovley, D.R., 2004. Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov. International Journal of Systematic and Evolutionary Microbiology. 54:1591-1599.
Hyman, M. and O'ReillyK, 1999. Physiological and enzymatic features of MTBE-degrading bacteria. In Alleman B.C. and Leeson A. (ed.), In situ bioremediation of petroleum hydrocarbon and other organic compounds. Battelle, Columbus, Ohio.
Istok, J.D., Senko, J.M., Krumholz, L.R., Watson, D., Bogle, M.A., Peacock, A., Chang, Y.-J., White, D.C., 2004. In situ bioreduction of technetium and uranium in a nitrate-contaminated aquifer. Environmental Science & Technology. 38:468-475.
Jäckel, U., Thummes, K., Kämpfer, P., 2005. Thermophilic methane production and oxidation in compost. FEMS Microbiology Ecology. 52:175-184.
James, K.D., and Williams P.A., 1998. ntn Genes determining the early steps in the divergent catabolism of 4-nitrotoluene and toluene in Pseudomonas sp. strain TW3. Journal of Bacteriology. 180:2043-2049.
Jiménez, N., Viñas, M., Bayona, J.M., Albaiges, J., Solanas, A.M., 2007. The Prestige oil spill: bacterial community dynamics during a field biostimulation assay. Applied Microbiology and Biotechnology. 77:935-945.
Johnson, E.L., Smith, C.A., O'Reilly, K.T., Hyman, M.R., 2004. Induction of methyl tertiary butyl ether (MTBE)-oxidizing activity in Mycobacterium vaccae JOB5 by MTBE. Applied and Environmental Microbiology. 70: 1023-1030.
Joseph, P.J. and Joseph, A., 2008. Microbial enhanced separation of oil from a petroleum refinery sludge. Journal of Hazardous Materials. [Epub ahead of print]
Joynt, J., Bischoff, M., Turco, R., Konopka, A., Nakatsu, C.H., 2006. Microbial community analysis of soils contaminated with lead, chromium and petroleum hydrocarbons. Microbial Ecology. 51:209-219.
Juck, D., Charles, T., Whyte, L.G., Greer, C.W., 2000. Polyphasic microbial community analysis of petroleum hydrocarbon-contaminated soils from two northern Canadian. FEMS Microbiology Ecology. 33:241-249.
Kao, C.M. and Borden, R.C., 1997. Site specific variability in BTEX biodegradation under denitrifying conditions. Ground Water. 35:305-311.
Kao, C.M. and Prosser, J., 1999. Intrinsic bioremediation of trichloroethene and chlorobenzene: field and laboratory studies. Journal of Hazardous Materials. 69:67-79.
Kao, C.M. and Wang, C.C., 2000. Control of BTEX migration by intrinsic bioremediation at a gasoline spill site. Water Research. 34:3413-3423.
Kao, C.M., Chen, S.C., Liu, J.K., Wang, Y.S., 2001. Application of microbial enumeration technique to evaluate the occurrence of natural bioremediation. Water Research. 35:1951-1960.
Kao, C.M., Huang, W.Y., Chang, L.J., Chien, H.Y., Hou, F., 2005. Application of monitored natural attenuation to remediate a petroleum-hydrocarbon spill site. Water Science and Technology. 53: 321-328.
Kasai, Y., Kishira, H., Syutsubo, K., Harayama, S., 2001. Molecular detection of marine bacterial populations on beaches contaminated by the Nakhodka tanker oil-spill accident. Environmental Microbiology. 3:246-255.
Katsivela, E., Moore, E.R.B., Kalogerakis, N., 2003a. Biodegradation of aliphatic and aromatic hydrocarbons: specificity among bacteria isolated from refinery waste sludge. Water, Air, and Soil Pollution: Focus. 3:103-115.
Katsivela, E., Maroukli, D., Moore, E.R.B., Weller, R., Heuer, H., Pieper, D., Kalogerakis, N., 2003b. Degradation of petroleum hydrocarbons by a newly isolated Alcaligenes species and monitoring of its relative abundance in landfarming sites. Proceedings of the Second European Bioremediation Conference. Chania, Greece.
Katsoyiannis, I.A. and Zouboulis, A.I., 2004. Biological treatment of Mn(II) and Fe(II) containing groundwater: kinetic considerations and product characterization. Water Research. 38:1922-1932.
Kharoune, M., Kharoune, L., Lebault, J.M., Pauss, A., 2002. Aerobic degradation of ethyl-tert-butyl ether by a microbial consortium: selection and evaluation of biodegradation ability. Environmental Toxicology and Chemistry. 21:2052-2058.
Kimbara, K., Hashimoto, T., Fukuda, M., Koana, T., Takagi, M., Oishi, M., Yano, K., 1989. Cloning and sequencing of two tandem genes involved in degradation of 2,3-dihydroxybiphenyl to benzoic acid in the polychlorinated biphenyl-degrading soil bacterium Pseudomonas sp. strain KKS102. Journal of Bacteriology. 171:2740-2747.
Kimura, N., Nishi, A., Goto, M. Furukawa, K., 1997. Functional analyses of a variety of chimeric dioxygenases constructed from two biphenyl dioxygenases that are similar structurally but different functionally. Journal of Bacteriology. 179:3936-3943.
Knief, C. and Dunfield, P.F., 2005. Response and adaptation of different methanotrophic bacteria to low methane mixing ratios. Environmental Microbiology. 7:1307-1317.
Knief, C., Kolb, S., Bodelier, P.L., Lipski, A., Dunfield, P.F., 2006. The active methanotrophic community in hydromorphic soils changes in response to changing methane concentration. Environmental Microbiology. 8:321-333.
Labbe, D., Margesin, R., Schinner, F., Whyte, L.G., Greer, C.W., 2007. Comparative phylogenetic analysis of microbial communities in pristine and hydrocarbon-contaminated Alpine soils. FEMS Microbiology Ecology. 59:466-475.
Lapara, T.M., Nakatsu, C.H., Pantea, L.M., 2002. Stability of the bacterial communities supported by a seven-stage biological process treating pharmaceutical wastewater as revealed by PCR-DGGE. Water Research. 36: 638-646.
Lau, P.C.K., Bergeron, H., Labbe, D., Wang, Y., Brousseau, R., Gibson, D.T., 1994. Sequence and expression of the todGIH genes involved in the last three steps of toluene degradation by Pseudomonas putida F1. Gene. 146:7-13.
Leahy, J.G. and Olsen, R.H., 1997. Kinetics of toluene degradation by toluene-oxidizing bacteria as a function of oxygen concentration, and the effect of nitrate. FEMS Microbiology Ecology. 23:23-30.
Leander, M., Vallaeys, T., Fulthorpe, R.R., 1998. Primers for amplification and determination of the chloro- and dichloro-catechol 1,2-dioxygenases family. Canadian Journal of Microbiology.
Lin, C.W., Cheng, Y.W., Tsai, S.L., 2007. Influences of metals on kinetics of methyl tert-butyl ether biodegradation by Ochrobactrum cytisi. Chemosphere. 69:1485-1491.
Liu, C.Y., Speitel, G.E., Georgiou, G., 2001. Kinetics of methyl t-butyl ether cometabolism at low concentrations by pure cultures of butane-degrading bacteria. Applied and Environmental Microbiology. 67:2197-2201.
Lovley, D.R., Giovannoni, S.J., Champine, W., Phillips, E.J.P., Gorby, Goodwin, Y.A., 1993. Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals. Archives of Microbiology. 159:336-344.
Lovley, D.R., Holmes, D.E., Nevin, K.P., 2004. Dissimilatory Fe(III) and Mn(IV) reduction. Advances in Microbial Physiology. 49:219-286.
Ma, Y. and Herson, D.S., 1996. NCBI database direct submission. Biology. University of Delaware, Newark, DE, 19716, USA.
Magot, M., Fardeau, M.L., Arnauld, O., Lanau, C., Ollivier, B., Thomas, P., Patel, B.K., 1997. Spirochaeta smaragdinae sp. nov., a new mesophilic strictly anaerobic spirochete from an oil field. FEMS Microbiology Letters. 155:185-191.
Mezey, P.G., Zimpel, Z., Warburton, P., Walker, P.D., Irvine, D.G., Huang, X.D., Dixon, D.G., Greenberg, B.M., 1998. Use of quantitative shape-activity relationships to model the photoinduced toxicity of polycyclic aromatic hydrocarbons: Electron density shape features accurately predict toxicity. Environmental Toxicology and Chemistry. 17:1207-1215.
Mo, K., Lora, C.O., Wanken, A.E., Javanmardian M., Yang, X., Kulpa C.F., 1997. Biodergradation of methyl t-butyl ether by pure bacterial cultures. Applied Microbiology and Biotechnology. 47:69-72.
Mohanty, S.R., Bodelier, P.L., Conrad, R., 2007. Effect of temperature on composition of the methanotrophic community in rice field and forest soil. FEMS Microbiology Ecology. 62:24-31.
Motta, F.C., Rosado, A.S., Siqueira, M.M., 2006. Comparison between denaturing gradient gel electrophoresis and phylogenetic analysis for characterization of A/H3N2 influenza samples detected during the 1999-2004 epidemics in Brazil. Journal of Virological Methods. 135:76-82.
Müller, R.H., Rohwerder, T., Harms1, H., 2008. Degradation of fuel oxygenates and their main intermediates by Aquincola tertiaricarbonis L108. Microbiology. 154:1414-1421.
Murrell, J.C. and Dalton, H., 1983. Nitrogen fixation in obligate methanotrophs. Journal of General Microbiology. 129:3481-3486.
Muyzer, G., 1999. DGGE/TGGE a method for identifying genes from natural ecosystems. Current Opinion in Microbiology. 2:317-322.
Muyzer, G. and Smalla, K., 1998. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek. 73:127-141.
Muyzer, G., Waal, E.C., de., A. G., 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology. 59:659-700.
Nakagawa, T., Sato, S., Yamamoto, Y., Fukui, M., 2002. Successive changes in community structure of an ethylbenzene-degrading sulfate-reducing consortium. Water Research. 36:2813-2823.
Ng, L.C., Shingler, V., Sze,C.C., Poh, C.L., 1994. Cloning and sequences of the first eight genes of the chromosomally encoded (methyl) phenol degradation pathway from Pseudomonas putida P35X. Gene. 151:29-36.
Noll, M., Frenzel, P., Conrad, R., 2008. Selective stimulation of type I methanotrophs in a rice paddy soil by urea fertilization revealed by RNA-based stable isotope probing. FEMS Microbiology Ecology. 65:125-132.
Nordlund, I., Powlowski, J., Shingler, V., 1990. Complete nucleotide sequence and polypeptide analysis of multicomponent hydroxylase from Pseudomonas sp. strain CF600. Journal of Bacteriology. 172:6826-6833.
Ogino, A., Koshikawa, H., Nakahara, T., Uchiyama, H., 2001. Succession of microbial communities during a biostimulation process as evaluated by DGGE and clone library analyses. Journal of Applied Microbiology. 91:625-635.
Okeke, B.C. and Frankenberger, W.T. Jr., 2003. Biodegradation of methyl tertiary butyl ether (MTBE) by a bacterial enrichment consortia and its monoculture isolates. Microbiological Research. 158:99-106.
Øvrea°s, L., Forney, L., Daae, F.D., Torsvik, V., 1997. Distribution of bacterioplancton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Applied and Environmental Microbiology. 63:3367-3373.
Patel, B.K.C., Morgan, H.W., Daniel, R.M., 1985. Thermophilic anaerobic spirochetes in New Zealand hot spring. FEMS Microbiology Letters. 26:101-106.
Polymenakou, P.N., Bertilsson, S., Tselepides, A., Stephanou, E.G., 2005. Bacterial community composition in different sediments from the Eastern Mediterranean Sea: a comparison of four 16S ribosomal DNA clone libraries. Microbial Ecology. 50:447-462.
Potter, T.L. and Simmons, K.E., 1998. Total petroleum hydrocarbon criteria working group, volume 2: Composition of petroleum mixtures. Amherst Scientific Press, Amherst, MA.
Pruden, A., Sedran, M.A., Suidan, M.T., Venosa, A.D., 2005. Anaerobic biodegradation of methyl tert-butyl ether under iron-reducing conditions in batch and continuous-flow cultures. Water Environment Research. 77:297-303.
Pruden, A., Suidan, M.T., Venosa, A.D., Wilson, G.J., 2001. Biodegradation of methyl tert-butyl ether under various substrate conditions. Environmental Science & Technology. 35:4235-4241.
Randall, J.C., Philip B.B., Raymond C.L., 1992. Groundwater Remediation. Lancaster, USA.
Ranjard, L., Poly, F., Nazaret, S., 2000. Monitoring complex bacterial communities using culture-independent molecular techniques: application to soil environment. Research in Microbiology. 151:167-177.
Reeburgh, W.S., Whalen, S.C., Alperin, M.J., 1993. The role of methylotrophy in the global methane budget. In Murrell J.C. & Kelly D.P. (ed.), Microbial Growth on C-1 Compounds. Intercept, Andover.
Röling, W.F., van Breukelen, B.M., Braster, M., Lin, B., van Verseveld, H.W., 2002. Relationships between microbial community structure and hydrochemistry in a landfill leachate-polluted aquifer. Applied and Environmental Microbiology. 67:4619-4629.
Rollins, B.D. and Colwell, R.R., 1986. Viable but nonculturable stage of Campylobacter jejuni and its role in survival in the natural aquatic environment. Applied and Environmental Microbiology. 52:531-538.
Rooney-Varga, J.N., Anderson, R.T., Fraga, J.L., Ringelberg, D., Lovley, D.R., 1999. Microbial communities associated with anaerobic benzene degradation in a petroleum-contaminated aquifer. Applied and Environmental Microbiology. 65: 3056-3063.
Rozsak, D.B. and Colwell, R.R., 1987. Survival strategies of bactera in the natural environment. Microbiological Reviews. 51:365-379.
Saitou, N. and Nei, M., 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution. 4:406-425.
Salanitro, J.P., Diaz, L.A., Williams, M.P., Wisniewski, H.L., 1994. Isolation of a bacterial culture that degrades methyl t-butyl ether. Applied and Environmental Microbiology. 60:2593-2596.
Schmidt, T.C., Schirmer, M., Weiß, H., Haderlein, S.B., 2004. Microbial degradation of methyl tert-butyl ether and tert-butyl alcohol in the subsurface. Journal of Contaminant Hydrology. 70:173-203.
Schroder, I., Johnson, E., de Vries, S., 2003. Microbial ferric iron reductases. FEMS Microbiology Reviews. 27:427-447.
Schwaiger, M., Cassinotti, P., 2003. Development of a quantitative real-time RT-PCR assay with internal control for the laboratory detection of tick borne encephalitis virus (TBEV) RNA. Journal of Clinical Virology. 27: 136-145.
Sekiguchi, H., Watanabe, M., Nakahara, T., Xu, B., Uchiyama, H., 2002. Succession of bacterial community structure along the Changjiang River determined by denaturing gradient gel electrophoresis and clone library analysis. Applied and Environmental Microbiology. 68:5142-5150.
Shaw, J.P. and Harayama, S., 1992. Purification and characterisation of the NADH: acceptor reductase component of xylene monooxygenase encoded by the TOL plasmid pWW0 of Pseudomonas putida mt-2. European Journal of Biochemistry. 209:51-61.
Simon, M.J., Osslund, T.D., Saunders, R., Ensley, B.D., Suggs, S., Harcourt, A.A., Suen, W.-C., Cruden, D.L., Gibson, D.T., Zylstra, G.J., 1993. Sequences of genes encoding naphthalene dioxygenase in Pseudomonas putida strain G7 and NCIB 9816-4. Gene. 127:31-37.
Smalla, K., Wieland, G., Buchner, A., Zock, A., Parzy, J., Kaiser, S., Roskot, N., Heuer, H., Berg, G., 2001. Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Applied and Environmental Microbiology. 67:4742-4751.
Smith, C.A. and Hyman, M.R., 2004. Oxidation of methyl tert-butyl ether by alkane hydroxylase in dicyclopropylketone-induced and n-octane-grown Pseudomonas putida GPo1. Applied and Environmental Microbiology. 70:4544-4550.
Smith, C.A., and O’Reilly, K.T., 2003. Characterization of the initial reactions during the cometabolic oxidation of methyl teri-butyl ether by propane-grown Mycobacteriurn vaccae JOB5. Applied and Environmental Microbiology. 69: 796-804.
Smith, M.R., 1990. The biodegradation of aromatic hydrocarbons by bacteria. Biodegradation. 1:191-206.
Sogaard, E.G., Aruna, R., Abraham-Peskir, J., Bender, K.C., 2001. Conditions for biological precipitation of iron by Gallionella ferruginea in a slightly polluted ground water. Applied Geochemistry. 16:1129-1137.
Steffan, R.J., Mc Clay, K., Vainberg, S., Condee, C.W., Zhang, D., 1997. Biodegradation of the gasoline oxygenates methyl tert-butyl ether, ethyl tert-butyl ether and tert-amyl methyl ether by propane-oxidizing bacteria. Applied and Environmental Microbiology. 63:4216-4222.
Stralis-Pavese, N., Sessitsch, A., Weilharter, A., Reichenauer, T., Riesing, J., Csontos, J., Murrell, J.C., Bodrossy, L., 2004. Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers. Environmental Microbiology. 6:347-363.
Suen, W.-C. and Gibson, D.T., 1993. Isolation and preliminary characterization of the subunits of the terminal component of naphthalene dioxygenase from Pseudomonas putida NCIB 9816-4. Journal of Bacteriology. 175:5877-5881.
Suen, W.-C., Haigler, B.E., Spain, J.C., 1996. 2,4-Dinitrotoluene dioxygenase from Burkholderia sp. strain DNT: similarity to naphthalene dioxygenase. Journal of Bacteriology. 178:4926-4934.
Sylvestre, M., Sirois, M., Hurtubise, Y., Bergeron, J., Ahmad, D., Shareck, F., Barriault, D., Guillemette, I., Juteau, J.M., 1996. Sequencing of Comamonas testosteroni strain B-356-biphenyl/chlorobiphenyl dioxygenase genes: evolutionary relationships among Gram-negative bacterial biphenyl dioxygenases. Gene. 174:195-202.
Tan, H.M., Tang, H.Y., Joannou, C.J., Abdel-Wahab, N.H., Mason, J.R., 1993. The Pseudomonas putida ML2 plasmid-encoded genes for benzene dioxygenase are unusual in codon usage and low in G+C content. Gene. 130:33-39.
Tchawa, Y.M., Dunfield, P.F., Ricke, P., Heyer, J., Liesack,W., 2003. Wide distribution of a novel pmoA-like gene copy among type II methanotrophs, and its expression in Methylocystis strain SC2. Applied and Environmental Microbiology. 69:5593-5602.
Wang, Y., Garnon, J., Labbe, D., Bergeron, H., Lau, P.C.K., 1995. Sequence and expression of the bpdC1C2BADE genes involved in the initial steps of biphenyl/chlorobiphenyl degradation by Rhodococcus sp. M5. Gene. 164:117-122.
Watanabe, K., Watanabe, K., Kodama, Y., Syutsubo, K., Harayma, S., 2000. Molecular characterization of bacterial populations in petroleum-Contaminated groundwater discharged from underground crude oil storage cavities. Applied and Environmental Microbiology. 66:4803-4809.
Watanabe, K., Kodama, Y., Harayama, S., 2001. Design and evaluation of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting. Journal of Microbiological Methods. 44:253-262.
Werlen, C., Kohler, H.P., van der Meer, J.R., 1996. The broad substrate chlorobenzene dioxygenase and cis-chlorobenzene dihydrodiol dehydrogenase of Pseudomonas sp. strain P51 are linked evolutionarily to the enzymes for benzene and toluene degradation. The Journal of Biological Chemistry. 271:4009-4016.
Wilkinson, S.G., 1988. Gram-negative bacteria. In Ratledge C. and Wilkinson S.G. (ed.), Microbial lipids. Academic Press, London, England.
Yeh, W.K., Gibson, D.T., Liu, T.-N., 1977. Toluene dioxygenase: A multicomponent enzyme system. Biochemical and Biophysical Research Communications. 78:401-410.
Yen, K. M. and Karl, M.R., 1992. Identification of a new gene, tmo F, in the Pseudomonas mendocina KR1 gene cluster encoding toluene-4-monooxygenase. Journal of Bacteriology. 174:7253-7261.
Yoshida, N., Yagi, K., Sato, D., Watanabe, N., Kuroishi, T., Nishimoto, K., Yanagida, A., Katsuragi, T., Kanagawa, T., Kurane, R., Tani, Y., 2005. Bacterial communities in petroleum oil in stockpiles. Journal of Bioscience and Bioengineering. 99:143-149.
Yu, C.P., Ahuja, R.G., Sayler, Chu, K.H., 2005. Quantitative molecular assay for fingerprinting microbial communities of wastewater and estrogen-degrading consortia. Applied and Environmental Microbiology. 71:1433-1444.
Zaitsev, G.M., Uotila, J.S., Häggblom, M.M., 2007. Biodegradation of methyl tert-butyl ether by cold-adapted mixed and pure bacterial cultures. Applied Microbiology and Biotechnology. 74:1092-1102.
Zhang, R.L., Huang, G.Q., Lian, J.Y., Li, X.G., 2007. Degradation of MTBE and TBA by a new isolate from MTBE-contaminated soil. Journal of Environmental Sciences (China). 19:1120-1124.
Zhong, W.H., Chen, J.M., Lu, Z., Chen, D.Z., Chen, X., 2007. Aerobic degradation of methyl tert-butyl ether by a Proteobacteria strain in a closed culture system. Journal of Environmental Sciences (China). 19:18-22.
Zylstra, G.J., 1994. Molecular analysis of aromatic hydrocarbon degradation. In Seymour J.G. (ed.), Molecular environmental biology. Lewis Publishers, Boca Raton.
Zylstra, G.J. and Gibson, D.T., 1989. Toluene degradation by Pseudomonas putida F1: nucleotide sequence of the todC1C2BADE genes and their expression in E. coli. The Journal of Biological Chemistry. 264:14940-14946.