簡易檢索 / 詳目顯示

回結果列表
研究生： 邱憲明
Chiu, Hsien-Ming
論文名稱： 利用傳統培養方法和分子生物方法探討油污染土壤的微生物社會結構
Cultivation-Dependent and –Independent Approaches for Determining Microbial Community in Petroleum-Contaminated Soil
指導教授： 曾怡禎
Tseng, I-cheng
學位類別： 碩士
Master
系所名稱： 生物科學與科技學院 - 生物學系
Department of Biology
論文出版年： 2004
畢業學年度： 92
語文別： 中文
論文頁數： 98
中文關鍵詞： 變性梯度凝膠電泳 、功能性基因 、微生物社會結構 、芳香族碳氫化合物
外文關鍵詞： polyphasic approach, microbial community, phylogenetic analysis, aromatic hydrocarbons, DGGE
相關次數： 點閱：170  下載：5 
分享至:
查詢本校圖書館目錄 查詢臺灣博碩士論文知識加值系統 勘誤回報

    • 　　石油組成成分中含有許多會危害自然環境的碳氫化合物，其中的芳香族碳氫化合物是最不易被分解的一類，若其廣泛分布在自然環境中，將會對生物以及人類造成莫大的毒害。因此，找出能有效快速分解此類碳氫化合物的微生物來進行生物復育已被認為是一種必要的趨勢。本研究主要利用傳統培養方法與分子生物方法，分離出本土性的石油碳氫化合物分解菌株和建立本土性石油碳氫化合物分解菌的16S rDNA資料庫，可提供油分解菌之探針設計及實行生物復育之應用。　　　DNA的純度與進行PCR反應是否能順利得到產物有密切相關，本研究測試四種DNA萃取法，結果發現實驗室修飾Miller等人於1999年報導之DNA法及商業套組所萃取之油污土壤和花園土壤DNA皆可順利用來進行PCR反應，而Miller法對於含較高腐植酸的花園土壤則無PCR產物。若於進行PCR反應時，適當的稀釋DNA與添加BSA (bovine serum albumin)則有助於PCR反應。本研究共分離出7株菌株，親源演化分析的結果顯示其中屬於已報導過之石油芳香族碳氫化合物分解菌屬有5株，約佔71%，分離出的油分解菌分別屬於Pseudomonas屬(2株)、Bacillus屬(1株)、Mycobacterium屬(1株)和Acinetobacter屬(1株)。利用16S rDNA選殖分析的方法，建立以苯、甲苯、乙苯、二甲苯等芳香族碳氫化合物為碳源之油污土壤的16S rDNA clone library。結果共得到24個不同的OTU(operational taxonomic unit)，其中9個OTU為已報導過的石油碳氫化合物分解菌屬，分別屬於Pseudomonas屬(30.5%)、Burkholderia屬(24.5%)、Sphingomononas屬(6.0%)、Bacillus屬(2.5%)和Nocardioides屬(0.5%)。由傳統培養與分子生物方法所得到的結果顯示，Pseudomonas屬仍是分布最廣泛且最主要的石油碳氫化合物分解菌屬。此外，本研究自行修飾設計Pseudomonas屬石油碳氫化合物分解菌的功能性基因xylE (catechol 2,3-dioxygenase)引子對與參考Mesarch等人於2000年報導之DEG引子對(degenerate primer)，實際應用於純菌株與環境樣本DNA，結果自行設計之引子對皆可成功得到PCR產物，而DEG引子對應用於環境樣本時則無PCR產物。利用變性梯度凝膠電泳指紋圖譜觀察油污土壤菌群社會結構的變動，結果顯示隨著土壤樣本來源深度不同，其中的菌群社會結構有所差異。在加入BTEX培養一至三星期後，可發現菌群數量減少且產生變動，說明BTEX確實會對微生物的社會結構造成影響。

    　　Petroleum hydrocarbons are the most widespread contaminants in the environment. Several of petroleum aromatic hydrocarbons (PAHs) are known mutagens or carcinogens for human and other organisms and they are difficult to be degraded in the natural environment. Bioremediation is considered an useful method to degrade the PAHs using the PAH-degrading bacteria. In this study, polyphasic approach combined cultivation-dependent with cultivation-independent methods was used to study the microbial communities in petroleum-contaminated soil. A total of 7 strains were isolated and 71% (5 strains) of which were oil-degrading bacteria that belong to Pseudomonas (2 strain)、Bacillus (1 strain)、Mycobacterium (1 strain)、Acinetobacter (1 strain). Phylogenetic analysis of a bacterial 16S rDNA clone library from the petroleum-contaminated soil treated with BTEX as carbon source showed that 9 of 24 OTUs (operational taxonomic units) were the oil-degrading bacteria which belong to Pseudomonas (30.5%)、Burkholderia (24.5%)、Sphingomononas (6.0%)、Bacillus (2.5%) and Nocardioides (0.5%). The results of combined cultivation-dependent with cultivation-independent methods revealed the majority of the oil-degrading bacteria in soil were Pseudomonas. Functional gene (xylE gene；catechol 2,3-dioxygenase) primer was designed in this study could get better and more PCR product from pure bacterium strain and environmental samples than the DEG primers used by Mesarch et al.(2000). The change of the microbial community in petroleum-contaminated soil was investigated by denaturing gel electrophoresis (DGGE) approach. The results indicated that different microbial community structure depended on the soil source and depth. After adding BTEX as carbon source into the petroleum-contaminated soil through one to three weeks, the bacterial number became less and community structure changed. It indicated that BTEX have adverse effects to microbial community structure.

    中文摘要.............................................................. Ⅰ 英文摘要.............................................................. Ⅱ 誌謝.................................................................. Ⅲ 目錄.................................................................. Ⅳ 表目錄................................................................ Ⅶ 圖目錄................................................................ IX 第一章 前言........................................................... 1 1-1 研究緣起.......................................................... 1 1-2 研究目的.......................................................... 3 1-3 研究架構.......................................................... 4 第二章 文獻回顧....................................................... 5 2-1 芳香碳氫化合物的污染.............................................. 5 2-1-1 芳香族碳氫化合物的來源........................................ 5 2-1-2 石油碳氫化合物的組成.......................................... 6 2-1-3 芳香族碳氫化合物的種類與危害.................................. 7 2-2 芳香族碳氫化合物在環境中的分解.................................... 11 2-2-1 芳香族碳氫化合物的降解路徑.................................... 11 2-2-2 影響芳香族碳氫化合物被分解的因子.............................. 12 2-2-3 分解芳香族碳氫化合物的微生物.................................. 17 2-3 芳香族碳氫化合物分解質體.......................................... 21 2-3-1 芳香族碳氫化合物分解質體的種類................................ 21 2-3-2 芳香族碳氫化合物的分解功能性基因.............................. 23 2-4 分子生物方法應用於微生物生態的研究................................ 27 2-4-1 聚合酵素鏈鎖反應.............................................. 28 2-4-2 變性梯度凝膠電泳.............................................. 28 2-4-3 限制酵素片段長度多型性分析法.................................. 28 2-4-4 螢光原位雜交法................................................ 29 2-5 DNA萃取技術與PCR反應的改良........................................ 29 第三章 材料與方法..................................................... 31 3-1 土壤DNA之萃取..................................................... 31 3-1-1 樣本來源...................................................... 31 3-1-2 油污染分解菌優厚培養與分離.................................... 31 3-2 DNA的萃取方法..................................................... 34 3-3 分析方法.......................................................... 36 3-3-1 聚合酵素鏈鎖反應.............................................. 36 3-3-2 瓊脂膠體電泳.................................................. 36 3-3-3 16S rDNA 分子選殖............................................. 38 3-3-4 變性梯度凝膠電泳.............................................. 38 3-3-5 定序.......................................................... 41 3-3-6 親緣關係的分析................................................ 41 3-3-7 南方轉漬...................................................... 41 3-4 功能性基因引子的設計.............................................. 43 3-4-1 catechol 2,3-dioxygenase引子對的設計.......................... 43 3-4-2 功能性基因引子的測試菌株...................................... 45 3-5 主要儀器.......................................................... 45 第四章 結果與討論..................................................... 47 4-1 分子生物技術操作.................................................. 47 4-1-1 土壤DNA萃取方法的比較......................................... 47 4-1-2 PCR分析技術................................................... 47 4-2 利用分子生物技術分析油污土壤的菌群結構............................ 53 4-2-1 以BTEX為基質的油污土壤之選殖分析.............................. 53 4-2-2 DGGE快速篩選.................................................. 53 4-2-3 親緣演化分析.................................................. 57 4-3 本土性油污分解菌株的分離.......................................... 60 4-3-1 油污分解菌的分離.............................................. 60 4-3-2 親緣演化分析.................................................. 60 4-4 芳香族碳氫化合物分解質體之功能性基因的分析........................ 65 4-4-1 PCR反應引子鍊合溫度測試....................................... 65 4-4-1-1 DEG-F和DEG-R引子.......................................... 65 4-4-1-2 xylE-F1和xylE-R1引子...................................... 65 4-4-1-3 xylE-F2和xylE-R2引子...................................... 66 4-4-1-4 xylE-F1和xylE-R2引子...................................... 66 4-4-2 功能性基因引子的純菌測試分析.................................. 70 4-4-2-1 DEG-F和DEG-R引子的純菌測試................................ 70 4-4-2-2 xylE-F1和xylE-R1引子的純菌測試............................ 70 4-4-2-3 xylE-F2和xylE-R2引子的純菌測試............................ 70 4-4-2-4 xylE-F1和xylE-R2引子的純菌測試............................ 71 4-4-3功能性基因引子的環境樣本測試分析…............................. 74 4-4-3-1 DEG-F和DEG-R引子的環境樣本測試............................ 74 4-4-3-2 xylE-F1和xylE-R1引子的環境樣本測試........................ 75 4-4-3-3 xylE-F2和xylE-R2引子的環境樣本測試........................ 75 4-4-3-4 xylE-F1和xylE-R2引子的環境樣本測試........................ 75 4-4-4 油污染環境土壤樣本的南方轉漬分析.............................. 78 4-5 以分子生物方法探討油污染土壤的菌群結構變化........................ 79 4-5-1 以BTEX為基質優厚培養期間菌群結構的變化........................ 79 第五章 結論與建議..................................................... 82 5-1 結論.............................................................. 82 5-2 建議.............................................................. 83 第六章 參考文獻....................................................... 85

    李孟哲。2002。純菌株對於多環芳香烴碳氫化合物-萘、菲分解能力之研究。國立中興大學環境工程學系碩士論文。
    吳春生。2002。以生物曝氣法整治受地下儲槽洩漏之石化系有機污染物模場研究。國立中山大學碩士論文。
    林居慶。1999。乳化菌之篩選及其特性之研究。國立台灣大學碩士論文。
    林美鳳。2000。建立苯環化合物分解菌中苯環加氧與切割酶之基因偵測法。國立中央大學生命科學研究所碩士論文。
    高櫻芬。2001。高屏溪河口與近岸海域沉積物中石油衍生性有機化合物
    及重金屬含量分析研究。國立中山大學海洋環境及工程學系碩士論文。
    張碧芬、袁紹英。1999。多環芳香族碳氫化合物(PAHs)之環境流布及生物分解。http://www.niea.gov.tw/analysis/publish/month/22/3-1.htm
    游宗霖。2003。以純化菌種Candida viswanathii 處理海水中柴油多環芳香烴之研究。國立中山大學海洋環境及工程學系碩士論文。
    鄭竹逸。1997。萘分解菌對於芳香族碳氫化合物的分解與菌種基本特性之研究。國立成功大學生物學研究所碩士論文。
    簡青紅。2003。利用傳統培養方法和分子生物方法探討厭氧生物產氫反應槽的微生物社會結構。國立成功大學生物學研究所碩士論文。
    Abe, A., A. Inoue, R. Usami, K. Moriya, and K. Horikoshi. 1995. Degradation of polyaromatic hydrocarbons by organic solvent-tolerant bacteria from deep sea. Bioscience and Biotechnology of Biochemistry. 59:1154-1156.
    Altschul, S. F., W. Gish, W. Miller, E. Myers, and D. J. Lipman. 1990. Basic local alignment serach tool. Journal of Molecular Biology. 215: 403-410.
    Alvarez, P. J. J., and T. M. Vogel. 1991. Substrate interactions of benzene, toluene, and para-xylene during microbial degradation by pure cultures and mixculture quifer. Applied and Environmental Microbiology. 57:2981-2985.
    Amann, R. I., W. Ludwig, and K. H. Schliefer. 1995. Phylogenetic identication and in situ detection of individual microbial cells without cultivation. Microbiological Reviews. Mar.: 143-169.
    Anton, A. I., Martinez-Murcia, A. J., and Rodriguez-Valera, F. 1998. Sequence diversity in the 16S–23S intergenic spacer region (ISR) of the rRNA operons in pepresentatives of the Escherichia coli ECOR collection. Journal of molecular evolution. 47. 62-72.
    Arai, H., Ohishi, T., Chang, M. Y., and Kudo, T. 2000. Arrangement and regulation of the genes for meta-pathway enzymes required for degradation of phenol in Comamonas testosteroni TA441. Microbiology. 146: 1707-1715.
    Arenghi, F. L., Berlanda, D., Galli, E., Sello, G., and Barbieri, P. 2001. Organization and regulation of meta cleavage pathway genes for toluene and o-xylene derivative degradation in Pseudomonas stutzeri OX1. Applied and Environmental Microbiology. 67: 3304-3308.
    Arvin, E., B. K. Jensen, and A. T. Gundersen. 1989. Substrate interactions during aerobic biodegradation of benzene. Applied and Environmental Microbiology. 55: 3221-3225.
    Ashok, B. T., S. Saxena, and J. Musarrat. 1995. Isoation and characterization of four polycyclic aromatic hydrocarbon degrading bacteria from soil near an oil refinery. Letters in Applied Microbiology. 21: 246-248.
    Banat, I. M. 1995. Biosurfactants production and possible uses in microbial enhanced oil recovery and oil pollution remediation: A review. Bioresource Technology. 51: 1-12.
    Barnsley, E. A. 1976. Role and regulation of the ortho and meta pathways of catechol metabolism in Pseudomonads metabolizing naphthalene and salicylate. Journal of Bacteriology. 125: 404-408.
    Barnsley, E. A. 1983. Bacterial oxidation of naphthalene and phenanthrene. Journal of Bacteriology. 153: 1069-1071.
    Bauer, J. E., and D. G. Capone. 1985. Degradation and mineralization of the polycyclic aromatic hydrocarbons anthracene and naphthalene in intertidal marine sediments. Applied and Environmental Microbiology. 50: 81-90.
    Bauer, J. E., and D. G. Capone. 1988. Effect of co-occuring aromatic hydrocarbons on degradation of individual polycyclic aromatic hydrocarbons in marine sediment slurries. Applied and Environmental Microbiology. 54: 1649-1655.
    Bergery, D. H., Holt, J. G., Krieg, N. R. 1984. Bergery manual of systematic bacteriology. First printing. 1: 214-219.
    Bindu, Joshi, and Satish, Walia. 1996. PCR amplification of catechol 2,3-dioxygenase gene sequences from naturally occurring hydrocarbon degrading bacteria isolated from petroleum hydrocarbon contaminated groundwater. FEMS Microbiology Ecology. 19. 5-15.
    Biodegradative Strain Database (BSD). http://bsd.cme.msu.edu/bsd/index.html
    Braid, M. D., Daniels, L. M., and Kitts, C. L. 2003. Removal of PCR inhibitors from soil DNA by chemical flocculation. Journal of Microbiological Methods. 52: 389-393.
    Brezna, B., Khan, A. A., and Cerniglia, C. E. 2003. Molecular characterization of dioxygenases from polycyclic aromatic hydrocarbon-degrading Mycobacterium spp. FEMS Microbiology Letters. 223: 177-183.
    Brosius, J., T. J. Dull, D. D. Sleeter, and H. F. Noller. 1981. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. Journal of Molecular Biology. 148: 107-127.
    Budzinski, H., I. Jones, J. Bellocq, C. Pierard and P. Garrigues. 1997. Evaluation of sediment contamination by polycyclic aromatic hydrocarbons in the gironde estuary” Marine Chemistry. 58: 85-97.
    Carrington, B., Lowe, A., Shaw, L. E., and Williams, P. A. 1994. The lower pathway operon for benzoate catabolism in biphenyl-utilizing Pseudomonas sp. strain IC and the nucleotide sequence of the bphE gene for catechol 2,3-dioxygenase. Microbiology. 140: 499-508.
    Cerniglia, C. E. 1982. Aromatic hydrocarbons: metabolism by bacteria, fungi, and algae. Review of Biochemical Toxicology. 3: 321-361.
    Cerniglia, C. E. 1984. Microbial metabolism of polycyclic aromatic hydrocarbons. Adv. Applied of Microbiology. 30: 31-71.
    Cerniglia, C.E. and Heitkamp, M.A. 1989. Microbial degradation of polycyclic aromatic hydrocarbons (PAH) in the aquatic environment. In: Metabolism of Polycyclic Aromatic Hydrocarbons in the Aquatic Environment (U. Varanasi Ed.), 41-68, CRC press, Boca Raton, FL.
    Cerniglia, C. E. 1992. Biodegradation of polycyclic aromatic hydrocarbons. Biodegradation. 3: 351-368.
    Chang, M. K., T. C. Voice, and C. S. Criddle. 1992. Kinetics of competitive inhibition and cometabolism in the biodegradation of benzene, toluene, and p-xylene by two Pseudomonas isolates. Biotechnology and Bioengineering. 41: 1057-1065.
    Chen, C. C., Teng, L. J., and Chang, T. C. 2004. Identification of Clinically Relevant Viridans Group Streptococci by Sequence Analysis of the 16S-23S Ribosomal DNA Spacer Region. Journal of Clinical Microbiology. 42. 2651-2657.
    Cheung, Pui-Yi , and Kinkle K. B. 2001. Mycobacterium diversity and pyrene mineralization in petroleum-contaminated soils. Applied and Environmental Microbiology. 67. 2222-2229.
    Churchill, S. A., Harper, J. P., and Churchill, P. F. 1999. Isolation and characterization of a Mycobacterium species capable of degrading three- and four-ring aromatic and aliphatic hydrocarbons. Applied and Environmental Microbiology. 65: 549-552.
    Daniel, A. Kunz, and Peter, J. Chapman. 1981. Isolation and characterization of spontaneously occurring TOL plasmid mutants of Pseudomonas putida HS1. Journal of Bacteriology. 146. 952-964.
    Downing, R., and P. Broda. 1979. A cleavage map of TOL plasmid of Pseudomonas putida mt-2. Molecular general Genetic. 177: 189-191.
    Duffner, F. M., Kirchner, U., Bauer, M. P., and Muller, R. 2000. Phenol/cresol degradation by the thermophilic Bacillus thermoglucosidasius A7: cloning and sequence analysis of five genes involved in the pathway. Gene. 256: 215-221.
    Eaton, R. W., and P. J. Chapman. 1992. Bacterial metabolism of naphthalene： construction and use of recombinant bacteria to study ring cleavage of 1,2-dihydroxynaphthalene and subsequent reactions. Journal of Bacteriology. 174: 7542-7554.
    Edwards, E. A., Wills, L. E., Reinhard, M., and Grbic-Galic, D. 1992. Anaerobic degradation of toluene and xylene by aquifer microorganisms under sulfate-reducing conditions. Applied and Environmental Microbiology. 58: 794-800.
    EPA. 1989. IRIS substance file. Office of Health and Environment Assessment, U.S. Environmental Protection Agency, Washington,DC.
    Evans, F. F., Seldin, L., Sebastian, G.V., Kjelleberg, S., Holmstrom, C., and Rosado, A. S. 2004. Influence of petroleum contamination and biostimulation treatment on the diversity of Pseudomonas spp. In soil microcosms as evaluated by 16S rRNA based-PCR and DGGE. Letters in Applied Microbiology. 38. 93-98.
    Evans, W. C., H. N. Fernley, and E. Griffiths. 1965. Oxidative metabolism of phenanthrene and anthracene by soil Pseudomonads. Biochemical Journal. 95: 819-831.
    Fernandes, M. B.,M-A. Sicre and J. Tronczynski. 1997. Polyaromatic hydrocarbon (PAH) distribution in the Seine river and its estuary. Marine Pollution Bulletin. 34: 857-867.
    Ferris, M. J., G. Muyzer, and D. M. Ward. 1996. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populaitons inhabiting a hot spring microbial mat community. Applied and Environmental Microbiology. 62: 340-346.
    Frackman, S., G. Kobs, D. Simpson, and Doug Promega Corporation. 1998. Betaine and DMSO: enhancing agents for PCR. Promega Notes Number 65: 27.
    Fredrickson, J. K., F. J. Brockman, D. J. Workman, S. W. Li, and T. O. Stevens. 1991. Isolation and characterization of a subsurface bacterium capable of growth on toluene, naphthalene, ad other aromatic compounds. Applied and Environmental Microbiology. 57: 796-803.
    Fredrickson, J. K., D. L. Balkwill, G. R. Deake, and M. F. Romine. 1995. Aromatic-degrading Sphingomonas isolates from the deep subsurface. Applied and Environmental Microbiology. 61: 1917-1922.
    Garcia-Valdes, E., E. Cozar, R. Rotger, J. Lalucat, and J. Ursing. 1988. New naphthalene-degrading marine Pseudomonas strains. Applied and Environmental Microbiology. 54: 2478-2485.
    Gary, M. K. and David T. Gibson. 1981. Inhibition of Catechol 2,3-Dioxygenase from Pseudomonas putida by 3-Chlorocatechol. Applied and Environmental Microbiology. 41: 1159-1165.
    Grund, E., B. Denecke, and R. Eichenlaub. 1992. Naphthalene degradation via salicylate and gentisate by Rhodococcus sp. strain B4. Applied and Environmental Microbiology. 58: 1874-1877.
    Harayama, S., Lehrbach, P. R., and Timmis, K. N. 1984. Transposon mutagenesis analysis of meta-cleavage pathway operon genes of the TOL plasmid of Pseudomonas putida mt-2. Journal of Bacteriology. 160: 251-5.
    Heinrich, K., Susanne, K., Roger, W. Pickup, and 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.
    Heitkamp, M. A., J. P. Freeman, and C. E. Cerrniglia. 1987. Naphthalene biodegradation in environmental microbiology estimates of degradation rates and characterization of metabolites. Applied and Environmental Microbiology. 53: 129-136.
    Heitkamp, M. A., and C. E. Cerrniglia. 1988. Mineralization of polycyclic aromatic hydrocarbons by a bacterium isolation from sediment below an oil field. Applied and Environmental Microbiology. 54: 1612-1614.
    Heitkamp, M. A., W. Franklin, and C. E. Cerrniglia. 1988. Microbial metabolism of polycyclic aromatic hydrocarbons：isolation and characterization of a pyrene-degrading bacterium. Applied and Environmental Microbiology. 54: 2549-2555.
    Heuer, H., M. Drsek, P. Baker, K. Smalla, and E. M. H. Wellington. 1997. Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Applied and Environmental Microbiology. 63: 3233-3241.
    Higuchi, R. 1989. Simple and rapid preparation of samples for PCR, p.31-38. In H. A. Erlich (ed.), PCR technology: principles and applications for DNA amplification. Stockton Press, New York.
    Houghton, J.E., Brown, T.M., Appel, A.J., Hughes, E.J. and Ornston, L.N. 1995. Discontinuities in the evolution of Pseudomonas putida cat genes. Journal of Bacteriology. 177: 401–412.
    Hubert, H. Attaway, and Michael, G. Schmidt. 2002. Tandem biodegradation of BTEX components by two Pseudomonas sp. Current Microbiology. 45: 30-36.
    Hughes, E. J., and Bayly, R. C. 1983. Control of catechol meta-cleavage pathway in Alcaligenes eutrophus. Journal of Bacteriology. 154:1363-70.
    Hughes, E. J., R. C. Bayly, and R. A. Skurray. 1984. Characterization of a TOL-like plasmid from Alcaligenes eutrophus that controls expression if a chromosomallu encoded p-cresol pathway. Journal of Bacteriology. 158: 73-78.
    Innis, M. A., and D. H. Gelfand. 1990. Optimization of PCRs. In: PCR protocols: A guide in methods and applications. Edited by Inns M. A., Gelfand D. H., Sninsky J. J. and White T. J. Academic Press, INC, pp: 3-12.
    Inoue, A., M. Yamamoto, and K. Horikoshi. 1991. Pseudomonas putida which can grow in the presence of toluene. Applied and Environmental Microbiology. 57: 1560-1562.
    Jame, E. B., and G. C. Douglas. 1985. Degradation and mineralization of the polycyclic aromatic hydrocarbons anthracene and naphthalene in intertidal marine sediments. Applied and Environmental Microbiology. 50: 81-90.
    Juan, L. Ramos, and Silvia Marqu´es. 1997. Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators. Annual Review of Microbiology. 51: 341–72.
    Kiyohara, H., and K. Nagao. 1978. The catabolism of phenanthrene and naphthalene by bacteria. Journal of General Microbiology. 105: 69-75.
    Koizumi, Y., Kelly, J. J., Nakagawa, T., Urakawa, H., El-Fantroussi, S., Al-Muzaini, S., Fukui, M., Urushigawa, Y., and Stahl, D. A. 2002. Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology. Applied and Environmental Microbiology. 68: 3215-3225.
    Kukor, J. J., Olsen, R. H., and Ballou, D. P. 1988. Cloning and expression of the catA and catBC gene clusters from Pseudomonas aeruginosa PAO. Journal of Bacteriology. 170: 4458-4465.
    Kukor, J. J., and Olsen, R. H. 1991. Genetic organization and regulation of a meta cleavage pathway for catechols produced from catabolism of toluene, benzene, phenol, and cresols by Pseudomonas pickettii PKO1. Journal of Bacteriology. 173: 4587-94.
    Kukor, J. J. and Olsen, R. H. 1996. Catechol 2,3-dioxygenases functional in oxygen-limited (hypoxic) environments. Applied and Environmental Microbiology. 62 : 1728-1740.
    Kulakov, L. A., Delcroix, V. A., Larkin, M. J., Ksenzenko, V. N., and Kulakova, A. N. 1998. Cloning of new Rhodococcus extradiol dioxygenase genes and study of their distribution in different Rhodococcus strains. Microbiology. 144: 955-63.
    Labuzek, S., Hupert-Kocurek, K. T., and Skurnik, M. 2003. Isolation and characterisation of new Planococcus sp. strain able for aromatic hydrocarbons degradation. Acta Microbiol. Pol. 52: 395-404.
    Laguerre, G., M. Allard, F. Revoy, and N. Amarger. 1994. Rapid identification of Rhixobia by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Applied and Environmental Microbiology. 60: 56-63.
    Laurie, A. D., and Lloyd-Jones, G. 1999. Conserved and hybrid meta-cleavage operons from PAH-degrading Burkholderia RP007. Biochem Biophys Res Commun. 262: 308-14.
    Leander, M., Vallaeys, T. and Fulthorpe, R. R. 1998. Primers for amplification and determination of the chloro- and dichloro-catechol 1,2-dioxygenases family. Canadian Journal of Microbiology. In press.
    Lee, J., J. Oh, K. R. Min, C.-K. Kim, K.-H. Min, K.-S. Lee, Y.-C. Kim, J.-Y. Lim, and Y. Kim. 1996. Structure of catechol 2,3-dioxygenase gene encoded in chromosomal DNA of Pseudomonas putida KF715. Biochemical and biophysical research communications. 224: 831-836.
    Liu, W. T., C. L. Huang, J. Y. Hu, L. Song, S. L. Ong, and W. J. Ng. 2002. Denaturing Gradient Gel Electrophoresis Polymorphism for Rapid 16S rDNA Clone Screening and Microbial Diversity Study. Journal of Bioscience and Bioengineering 93: 101-103.
    Ma, Y. and Herson, D. S. 1996. NCBI database direct submission. Biology, University of Delaware, Newark, DE, 19716, USA
    Margesin, R., D. Labbe, F. Schinner, C. W. Greer, and L. G. Whyte. 2003. Characterization of hydrocarbon-degrading microbial populations in contaminated and pristine alpine soils. Applied and Environmental Microbiology. 69: 3085-3092.
    Mesarch, M. B., C. H. Nakatsu and L. Nies. 2000. Development of catechol 2,3-dioxygenase-specific primers for monitoring bioremediation by competitive quantitative PCR. Applied and Environmental Microbiology. 66: 678-683.
    Mesarch, M. B., C. H. Nakatsu and L. Nies. 2004. Bench-scale and field-scale evaluation of catechol 2,3-dioxygenase specific primers for monitoring BTX bioremediation. Water Research. 38: 1281-1288.
    Miller, D. N., J. E. Bryant, E. L. Madsen, and W. C. Ghiorse. 1999. Evaluation and optimatization of DNA extraction and purification procedures for soil and sediment samples. Applied and Environmental Microbiology. 65: 4715-5724.
    Moyer, C. L., J. M. Tiedjue, F. C. Dobbs, and D. M. Karl. 1996. A computer-stimulated restriction fragment length polymorphism analysis of bacterial small-subunit rRNA genes: efficacy of selected tetrameric restriction enzymes for studies of microbial diversity in nature. Applied and Environmental Microbiology. 62: 2501-2507.
    Muller, R. 1986. Bacterial degradation of xenobiotics. Journal of General Microbiology. 105: 69-75.
    Murakami, S., Kohsaka, C., Okuno, T., Takenaka, S., and Aoki, K. 2004. Purification, characterization, and gene cloning of cis,cis-muconate cycloisomerase from benzamide-assimilating Arthrobacter sp. BA-5-17. FEMS Microbiology Letters. 231: 119-24.
    Muyzer, G., E. C. de Waal, and A. G. Uitterlinden. 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.
    Muyzer, G., A. Teske, C. O. Wirsen, and H. W. Jannasch. 1995. Phylogenetic relationship of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Archives of Microbiology. 164:165-172.
    Muyzer, G., and K. Smalla. 1998. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Leeuwenhoek 73:127-141.
    Neidle, E. L., C. Hartnett, S. Bonitz, and L. N. Ornston. 1988. DNA sequence of the Acinetobacter calcoaceticus catechol 1,2-dioxygenase I structural gene catA: evidence for evolutionary divergence of intradiol dioxygenase by acquisition of DNA repetitions. Journal of Bacteriology. 170: 4874–4880.
    Ogunseitan, O. A., I. L. Delgado, Y. L. Tsai, and B. H. Olson. 1991. Effect of 2-Hydroxybenzoate on the Maintenance of naphthalene-degrading Pseudomonads in seeded and unseeded soil. Applied and Environmental Microbiology. 57: 2873-2879.
    Okuta, A., K. Ohnishi, and S. Harayama. 1998. PCR isolation of catechol 2,3-dioxygenase gene fragments from environmental samples and their assembly into functional genes. Gene. 212: 221-228.
    Olsen, G. J., D. J. Lane, S. J. Giovannoni, N. R. Pace, and D. A. Stahl. 1987. Microbial and evolution: a ribosomal RNA approach. Annual. Review Microbiology. 40: 337.
    Palchaudhuri, S., and A. ChakraBarty. 1976. Isolation of plasmid deoxyribonucleic acid from Pseudomonas putida. Journal of Bacteriology. 126: 410-416.
    Palleroni, N.J. (1984) Genus I. Pseudomonas. In Bergey’s Manual of Systematic Bacteriology Vol. 1, ed. Krieg, N.R. pp. 141–199. Baltimore: Williams & Wilkins.
    Perez-Luz, S., Adela, Y. M., and Catalan, V. 2004. Identification of waterborne bacteria by the analysis of 16S-23S rRNA intergenic spacer region. Journal of Applied Microbiology. 97. 191-204.
    Rosvita, E. Milo, Fiona, M. Duffner, and R. Miiller. 1999. Catechol 2,3-dioxygenase from the thermophilic, phenol-degrading Bacillus thermoleovorans strain A2 has unexpected low thermal stability. Extremophiles. 3: 185-190.
    Saikei, R. K., D. H. Gelfand, S. Scharf, S. J. Scharf, R. Higuchi, G. T. Horn, K. B. Mullis, and H. A. Erlich. 1988. Primer-directed enzymatic amplification of DNA with thermostable DNA polymerase. Science 239: 487-491.
    Saint, C. P., N. C. McClure, and W. A. Venables. 1990. Physical map of the aromatic amine and m-toluate catabolic plasmid pTDN1 in Pseudomonas putida：isolation of a unique meta-cleavage pathway. Journal of General Microbiology. 136: 615-625.
    Saitou, N. and N. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular and Biological Evolution. 4: 406-425.
    Sanakis, Y., Mamma, D., Christakopoulos, P., and Stamatis, H. 2003. International Journal of Biological Macromolecules. 33: 101-106.
    Sekiguchi, Y., Y. Kamagata, K. Syutsubo, A. Ohashi, H. Harada, and K. Nakamura. 1998. Phylogenetic diversity of mesophilic and thermophilic granular sludges determined by 16S rRNA gene analysis. Microbiology 144: 2655-2665.
    Shen, X. H., Liu, Z. P., and Liu, S. J. 2004. Functional identification of the gene locus (ncg12319 and characterization of catechol 1,2-dioxygenase in Corynebacterium glutamicum. Biotechnology Letters. 26: 575-580.
    Shimp, R. J., and F. K. Pfaender. 1985. Influence of easily degradable naturally occurring carbon substrates on biodegradation of monosubstituted phenols by aquatic bacteria. Applied and Environmental Microbiology. 49: 394-401.
    Shuttleworth, K. L., and C. E. Cerriglia. 1996. Bacterial degradation of low concentration of phenanthrene and inhibition by naphthalene. Microbial Ecology. 31: 305-317.
    Sinclair, M. I., P. C. Maxwell, B. R. Lyon, and B. W. Holloway. 1986. Chromosomal location of TOL plasmid DNA in Pseudomonas putida. Journal of Bacteriology. 168: 1302-1308.
    Smith, M. R. 1990. The biodegradation of aromatic hydrocarbons by bacteria. Biodegradation. 1: 191-206.
    Stillwell, L. C., S. J. Thurston, R. P. Schneider, M. F. Romine, and J. K. Fredrickson. 1995. Physical mapping and characterization of a catabolic plasmid from the deep-subsurface bacterium Sphingomonas sp. strain F199. Journal of Bacteriology. 177: 4537-4539.
    Stringfellow, W. T., and M. D. Aitken. 1995. Competitive metabolism of naphthalene, methylnaphthalenes, and fluorine by phenanthrene-degrading Pseudomonads. Applied and Environmental Microbiology. 61: 357-362.
    Stults, J. R., Snoeyenbos-West, O., Methe, B., Lovley, D. R., Chandler, D.P. 2001. Application of the 5' fluorogenic exonuclease assay (TaqMan) for quantitative ribosomal DNA and rRNA analysis in sediments. Applied and Environmental Microbiology. 67: 2781-2789.
    Suzuki, K., Ichimura, A., Ogawa, N., and Hasebe, A. 2002. Differential expression of two catechol 1,2-dioxygenases in Burkholderia sp. strain TH2. Journal of bacteriology. 184: 5714-5722.
    Takeda, Y., Takase, K., Yamato, I., and Abe, K. 1998. Sequencing and characterization of the xyl operon of a gram-positive bacterium, Tetragenococcus halophila. Applied and Environmental Microbiology. 64: 2513-2519.
    Tran, K., C. C. Yu and E. Y. Zeng. 1997. Organic pollutants in the coastal environment off San Diego, California. 2.petrogenic and biogenic sources of aliphatic hydrocarbons. Environmental Toxicology and Chemistry. 16 : 189-195.
    Treccani, V., N. Walker, and G. H. Wiltshier. 1954. The metabolis of naphthalene by soil bacteria. Journal of Bacteriology. 11: 341-348.
    Tsai, Y.-L., and B. H. Olson. 1992. Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Applied and Environmental Microbiology. 58: 2292-2295.
    Tsien, H. C. and R. S. Hanson. 1992. Soluble methane monooxygenase component B gene probe for identification of methanotrophs that rapidly degrade trichloroethylene. Applied and Environmental Microbiology. 58: 953-960.
    Tsuda, M., and T. Iino. 1987. Genetic analysis of a transposon carrying toluene degrading genes on a TOL plasmid pWWO. Molecular General Genetic. 210: 270-276.
    Tsuda, M., and T. Iino. 1990. Naphthalene degrading genes on plasmid NAH7 are on a defective transposon. Molecular General Genetic. 223. 33-39.
    Van Dyke, M. I., and A. J. McCarthy. 2002. Molecular biological detection and characterization of Clostridium population in municipal landfill sites. Applied and Environmental Microbiology. 68: 2049-2053.
    Volkering, F., A. M. Breure, and J. G. van Andel. 1993. Effect of micro-organisms on the bioavilabiliy and biodegradation of crystalline naphthalene. Applied and Environmental Microbiology. 40: 535-540.
    Wang, C. L., Takenaka, S., Murakami, S. and Aoki, K. 2001. Production of catechol from benzoate by the wild strain Ralstonia species Ba-0323 and characterization of its catechol 1,2-dioxygenase. Bioscience, Biotechnology, and Biochemistry. 65: 1957-1964.
    Wheatcroft R., and P. A. Williams. 1981. Rapid method for the study of both stable and unstable plasmids in Pseudomonas. Journal of General Microbiology. 124: 433-437.
    Widada, J., Nojiri, H., Kasuga, K. and Yoshida, T. 2002. Molecular detection and diversity of polycyclic aromatic hydrocarbon-degrading bacteria isolated from geographically diverse sites. Applied and Environmental Microbiology. 58: 202-209.
    Widjojoatmodjo, M. N., A. C. Fluit, R. Torensma, G. P. H. T. Verdonk, and J. Verhoef. 1992. The magnetic immuno polymerase chain reaction assay for direct detection of salmonellae in fecal samples. Journal of Clinical Microbiology. 30. 3195-3199.
    Williams, P. A., and K. Murray. 1974. Metabolism of Benzoate and the Methylbenzoates by Pseudomonas putida (arvilla) mt-2：evidence for the existence of a TOL plasmid. Journal of Bacteriology. 120: 416-423.
    William, P. A., F. A. Catteral, and K. Murray. 1975. Metabolism of naphthalene, 2-methylnaphthalene, salicylate, and benzoate by Pseudomonas putida PG： regulation of tangential pathways. Journal of Bacteriology. 124: 679-685.
    Witt, G. 1995. Polycyclic aromatic hydrocarbons in water and sediment of the Baltic Sea. Marine Pollution Bulletin. 31: 237-248.
    Woese, C. R. 1987. Bacterial evolution. Microbiological Reviews. 51: 221-271.
    Yen, K. M. and Gunsalus, I. C. 1985. Regulation of naphthalene catabolic genes of plasmid NAH7. Journal of Bacteriology. 162:1008-1013.
    Yrjala, K., Paulin, L., and Romantschuk, M.. 1997. Novel organization of catechol meta-pathway genes in Sphingomonas sp. HV3 pSKY4 plasmid. FEMS Microbiology Letters. 154: 403-8.
    Zhuang, W.-Q., Tay, J. -H., Maszenan, A. M. and Tay, S. T. –L. 2002. Bacillus naphthovoranssp. nov. from oil-contaminated tropical marine sediments and its role in naphthalene biodegradation. Applied Microbiology and Biotechnology 58: 547–553.

    下載圖示 校內：2009-08-09公開
    校外：2009-08-09公開
    QR CODE