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研究生： 林裕家
Lin, Yu-Jia
論文名稱： 利用變性梯度凝膠電泳與即時定量聚合酵素連鎖反應監測油污染場址在復育過程中微生物社會結構之變化
Monitoring the dynamic changes of microbial community during bioremediation of oil-polluted sites by denaturing gradient gel electrophoresis (DGGE) and real-time PCR
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 - 生命科學系
Department of Life Sciences
論文出版年： 2006
畢業學年度： 94
語文別： 中文
論文頁數： 75
中文關鍵詞： 即時定量PCR 、變性梯度凝膠電泳 、16S rRNA基因 、微生物社會結構 、石油碳氫化合物
外文關鍵詞： DGGE, phylogenetic analysis, Real-time PCR, bioremediation, Pseudomonas
相關次數： 點閱：120  下載：2 
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    • 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，能有效快速分解此類碳氫化合物的生物復育已被認為是一種必要的趨勢。本研究利用分子生物之方法，建立本土性油污染分解菌群之16S rRNA基因選殖資料庫，可提供引子與探針設計及實行生物復育之應用。本研究共對2油污染場址(LY與FD)進行分子選殖，建立16S rRNA基因選殖資料庫。與先前研究所建立之YK污染場址選殖資料庫共同分析，結果共獲得47個OTUs，其中已被報導過與油污分解相關之OTUs共有16個，分別屬於Pseudomonas、Burkholderia、Azoarcus、Xanthomonas、Bacillus、Comamonas、Nocardioides、Sphingomona與Alcaligenes菌屬，其中Pseudomonas所佔比例為21.6%，為此三場址中數量最多之油污分解菌群。
    此外，本研究自行修飾設計Pseudomonas菌屬16S rRNA基因專一性引子對PsF1與PsF3-PsR3。PsF1與真細菌16S rDNA廣泛性引子1392r配合使用可放大出一段約1100 bps之產物，可應用於以變性梯度凝膠電泳 (DGGE) 偵測Pseudomonas菌群結構。以semi-nested PCR-DGGE法偵測生物復育過程中Pseudomonas菌群結構之變化，結果顯示添加之營養鹽可能造成適應此環境且具有分解能力之Pseudomonas菌群大量生長，使指紋圖譜上出現特別顯著之條帶。然控制組與添加營養鹽之實驗組指紋圖譜有相同變化趨勢，皆於第24天之樣本中可發現最多量之條帶。PsF3-PsR3亦為Pseudomonas菌屬16S rRNA基因專一性引子對，可應用於即時定量PCR (Real-time PCR)之研究。本研究以Real-time PCR偵測復育場址於不同天數樣本中Pseudomonas 16S rRNA基因之數量，結果顯示各組別間Pseudomonas數量消長有相同之趨勢，皆於第14天到達最大數量之後遞減，至第24天到達最低。此外，針對控制組樣本所得數據加以分析，結果顯示各種生物復育方法對土壤中Pseudomonas族群含量皆造成一定影響，然油污降解能力在各組間則無明顯差異，顯示此場址原生菌群以有良好之油污分解能力。因此，在未來生物復育應用上，預先評估污染場址中原生菌群之油污分解能力為一不可或缺之指標，對於生物復育之時程與成本皆有很大之影響，具有相當之價值。

    Petroleum hydrocarbons are the most widespread contaminants in the environment. Several of petroleum hydrocarbons are known mutagens or carcinogens for human and other organisms. They are difficult to be degraded in the natural environment. Bioremediation is considered a useful method to degrade the petroleum hydrocarbons using the oil-degrading bacteria. In this study, cultivation-independent methods were used to study the microbial communities in petroleum contaminated sites. Phylogenetic analysis of bacterial 16S rRNA gene clone libraries from the LY、FD and YK petroleum contaminated soil showed that 16 of 47 OTUs (operational taxonomic units) were oil-degrading bacteria which belong to Pseudomonas、Burkholderia、Azoarcus、Xanthomonas、Bacillus、Comamonas、Nocardioides、Sphingomonas and Alcaligenes. Proteobacteria was the dominant group (66%) and Pseudomonas was the most abundant genus (21.6%) in these 3 clone libraries.
    In KH bioremediation site, there are 5 different treatments including bioaugmentation and biostimulation. Dynamic changes of bacterial communities in KH petroleum-contaminated site during bioremediation were monitored by PCR-DGGE, which used bacteria universal 16S rRNA gene primers. In the DGGE fingerprinting of KH site, the band at the same position with Pseudomonas markers was found in all samples. Our data indicate that Pseudomonas spp. may be important petroleum hydrocarbon-degradation bacteria in the KH site.
    The changes of population size of Pseudomonas in KH site during bioremediation were monitored by Real-time PCR. In all 5 different bioremediation-treatments, the population size of Pseudomonas reached maximum in the 14th day (6.80*104 – 2.04*105copy numbers/ng DNA) and decreased to minimum in the 24th day (7.20*103 – 1.52*104copy numbers/ng DNA). The TPH-d (total petroleum hydrocarbons-diesel) degrading profile of KH site showed that the TPH-d in soil was decreased to 50-60% in the 14th day and was almost degraded in 24th day. The results show that the Pseudomonas population size was affected by bioremediation treatment, but the TPH-d degrading rate of different bioremediation group were the same in KH site. The addition of bacteria or biosurfantant did not improve degradation of the TPH-d in KH site. Our findings indicate that the oil-degrading ability of original bacteria in contaminated site should be considered as an important factor for future bioremediation, and monitoring the variation of main oil-degrading bacteria can help us to understand the efficiency of bioremediation process, and enhance bioremediation.

    中文摘要 ........................................................... I 英文摘要 ........................................................... II 致謝 .............................................................. III 目錄 .............................................................. IV 表目錄 ............................................................ VII 圖目錄 ............................................................ VIII 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 石油碳氫化合物的污染 ................................... 5 2-2 石油碳氫化合物在環境中的分解 ........................... 6 2-2-1 分解石油碳氫化合物的微生物 ................................ 6 2-3 分子生物技術應用於環境微生物生態之研究 ................. 7 2-3-1 聚合酵素鏈鎖反應 .......................................... 9 2-3-2 變性梯度凝膠電泳 .......................................... 10 2-3-3 限制酵素片段長度多型性分析法 .............................. 11 2-3-4 末端螢光標定限制酵素片段長度多型性分析法 .................. 12 2-3-5 螢光原位雜合法 ............................................ 13 2-3-6 單股構型多態性法 .......................................... 15 2-3-7 即時定量聚合酵素連鎖反應 .................................. 16 第三章 材料與方法 ................................................ 18 3-1 油污染土壤樣本來源 ........................................ 18 3-2 DNA 的萃取方法 ............................................ 18 3-2-1 Miller-modified method (MMB) .............................. 18 3-2-2 MoBio kit (Stults et al., 2001) ........................... 19 3-3 分析方法 .................................................. 20 3-3-1 聚合酵素鏈鎖反應(Polymerase chain reaction，PCR) .......... 20 3-3-2 瓊脂膠體電泳 .............................................. 22 3-3-3 16S rRNA基因分子選殖 (Cloning) ............................ 22 3-3-4 變性梯度凝膠電泳 .......................................... 23 3-3-5 變性梯度凝膠電泳上之DNA片段萃取 ........................... 23 3-3-6 限制酵素片段長度多型性分析法(Restriction Fragment Length Polymorphism(RFLP) ............................................................. 23 3-3-7 定序 ...................................................... 26 3-3-8 親緣關係分析 .............................................. 26 3-4 假單胞菌屬專一性引子之設計與PCR條件之建立 ................. 26 3-4-1 假單胞菌屬專一性引子PsF1之設計與PCR條件之建立 ............. 26 3-4-2 假單胞菌屬專一性Semi-nested PCR-DGGE偵測方法之建立 ........ 27 3-4-3 假單胞菌屬專一性引子對PsF3-PsR3之設計與PCR反應條件之最佳化 27 3-4-4 假單胞菌屬專一性引子對PsF3-PsR3之設計與PCR反應條件之最佳化 28 3-4-5 假單胞菌屬專一性即時定量PCR反應標準曲線之建立 ............. 28 3-5 主要儀器 .................................................. 29 第四章 結果與討論 ................................................ 30 4-1 利用分子生物技術分析油污土壤的菌群結構 .................... 30 4-1-1 LY油污土壤之選殖分析 ...................................... 30 4-1-2 FD油污土壤之選殖分析 ...................................... 32 4-1-3 油污染場址選殖資料庫之分析 ................................ 38 4-2 利用分子生物方法監測復育過程中油污土壤的菌群結構變化 ...... 44 4-2-1 以DGGE監測生物復育過程中土壤菌群結構之變化 ................ 44 4-3 以Semi-nested PCR-DGGE法快速檢測環境中油污染分解菌群-Pseudomonas菌屬 ................................................................. 47 4-3-1 Pseudomonas菌屬DGGE biomarker之建立 ....................... 47 4-3-2 以semi-nested PCR-DGGE法生物監測油污染土壤中假單胞菌屬菌群結構 ................................................................. 49 4-3-3 利用semi-nested PCR-DGGE法監測生物復育過程土壤中Pseudomonas菌屬菌群結構之變化 ........................................................... 52 4-4 土壤樣本中Pseudomonas菌群之定量分析 ....................... 55 4-4-1 Pseudomonas菌屬專一性引子之設計與Real-time PCR條件之建立 .. 55 4-4-2 以Real-time PCR偵測生物復育過程中Pseuomonas菌屬含量之變化 . 55 第五章 結論與建議 ................................................ 59 第六章 參考文獻 .................................................. 61 自述 ............................................................... 75 表目錄 Table 3-1 Primers used in this study ............................... 21 Table 3-2 Procedure of cloning .................................... 24 Table 3-3 Procedure of DGGE analysis ............................... 25 Table 4-1 Phylogenetic affiliations of the 16S rDNA clone library of the LY oil-contaminated soil sample ....................................... 35 Table 4-2 Phylogenetic affiliations of the 16S rDNA clone library of the FD oil-contaminated soil sample ....................................... 37 Table 4-3 Oil degrading bacterium in FD、LY、YK clone library ...... 43 Table 4-4 Phylogenetic affiliations of the DGGE cut band clone library50 圖目錄 Fig 1-1 Schematic representation the steps for studying of petroleum-contaminated soil bacterial community by culture-independent approaches ......................................................... 4 Fig 3-1. Semi-nested PCR-DGGE methods for monitoring Pseudomonas community structure .......................................................... 27 Fig 4-1. Phylogenetic dendrogram of 16S rDNA bacterial sequence from the LY oil-contaminated soil .............................................. 34 Fig 4-2. Phylogenetic dendrogram of 16S rDNA bacterial sequence from the FD oil-contaminated soil .............................................. 36 Fig 4-3. Phylogenetic dendrogram of 16S rDNA bacterial sequence from the LY、FD and YK oil-contaminated soil .................................... 42 Fig 4-4. DGGE fingerprinting and the illustration of the change of microbial community through week 0 to week 6 in KH bioremediation site. NE group46 Fig 4-5. Test of semi-nested PCR-DGGE method to detect Pseudomonas populations ......................................................... 48 Fig 4-6. DGGE fingerprinting and illustration of Pseudomonas populations in FD oil contaminated soil ............................................... 51 Fig 4-7. DGGE fingerprinting and the illustration of the dynamic change of Pseudomonas community through week 0 to week 6 in KH bioremediation site................................................................. 54 Fig 4-8. Variation of Pseudomonas 16S rRNA genes copy numbers during bioremediation ...................................................... 58

    美國毒性物質及疾病管制局網站。http://www.atsdr.cdc.gov/toxprofiles/tp123.html
    鄭竹逸。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。1997。
    張碧芬、袁紹英。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。1999。
    吳春生。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。2002。
    簡青紅。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。2003。
    邱憲明。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。國立成功大學生物學研究所碩士論文。2004。
    林徽鳴。利用變性梯度凝膠電泳與末端螢光標定限制酵素片段長度多型性分析法監測微生物社會之分子指紋變化。國立成功大學生物學研究所碩士論文。2005。
    潘柏岑。應用土耕法配合生物添加促進法整治柴油污染土壤之研究。2006。
    鄭幸雄。高場污染土壤離場生物復育技術驗證技服工作成果簡報。2006。
    Adriana F. P. Ururahy, Marcus D. M. Marins, Ronalt L. Vital, Irene Therezinha Gabardo. Effect of aeration on biodegradation of petroleum waste. Rev. Microbiol. 29: n4. 1998.
    Amann, R. I., W. Ludwig, and K. H. Schliefer. Phylogenetic identication and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 143-169. 1995.
    Andrew J. Daugulis, Brian G. Amsden, Justina Bochanysz & Ahmed Kayssi. Delivery of benzene to Alcaligenes xylosoxidans by solid polymers in atwo-phase partitioning bioreactor. Biotechnol Lett 25: 1203–1207. 2003.
    Ashok, B. T., S. Saxena, and J. Musarrat. Isoation and characterization of four polycyclic aromatic hydrocarbon degrading bacteria from soil near an oil refinery. Lett Appl Microbiol 21: 246-248. 1995.
    Avrahami, S., and R. Conrad. Patterns of community change among ammonia oxidizers in meadow soils upon long-term incubation at different temperatures. Appl Environ Microbiol 69:6152-64. 2003.
    Ayala-Del-Rio, H. L., S. J. Callister, C. S. Criddle, and J. M. Tiedje. Correspondence between community structure and function during succession in phenol- and phenol-plus-trichloroethene-fed sequencing batch reactors. Appl Environ Microbiol 70:4950-60. 2004.
    Banat, I. M. Biosurfactant production and possible uses in microbial enhanced oil recovery and oil pollution remediation. Biores Technol 51: 1–12. 1995.
    Banat, I. M., R. S. Makkar, and S. S. Cameotra. Potential commercial applications of microbial surfactants. Appl Microbiol Biotechnol 53:495–508. 2000.
    Bongkeun Song, Norberto J. Palleroni, and Max M. Hggblom. Isolation and characterization of diverse halobenzoate-degrading denitrifying bacteria from soils and sediments. Appl Environ Microbiol 66: 3446-3453.2000.
    Bano, N., and J. T. Hollibaugh. Phylogenetic composition of bacterioplankton assemblages from the Arctic Ocean. Appl Environ Microbiol 68:505-18. 2002.
    Beaulieu, M., V. Becaert, L. Deschenes, and R. Villemur. Evolution of Bacterial Diversity during Enrichment of PCP-Degrading Activated Soils. Microb Ecol 40:345-356. 2000.
    Bragg, J. R., R. C. Prince, E. J. Harner, and R. M. Atlas. Effectiveness of bioremediation for the Exxon Valdez oil spill. Nature 368:413–418. 1994.
    Brakstad, O. G., and K. Bonaunet. Biodegradation of Petroleum Hydrocarbons in Seawater at Low Temperatures (0-5 degrees C) and Bacterial Communities Associated with Degradation. Biodegradation 17:71-82. 2006.
    Brakstad, O. G., K. Bonaunet, T. Nordtug, and O. Johansen. Biotransformation and dissolution of petroleum hydrocarbons in natural flowing seawater at low temperature. Biodegradation 15:337-46. 2004.
    Brito, E. M., R. Guyoneaud, M. Goni-Urriza, A. Ranchou-Peyruse, A. Verbaere, M. A. Crapez, J. C. Wasserman, and R. Duran. Characterization of hydrocarbonoclastic bacterial communities from mangrove sediments in Guanabara Bay, Brazil. Res Microbiol 2006.
    Cameotra, S. S., and R. S. Makkar. Synthesis of biosurfactants in extreme conditions. Appl Microbiol Biotechnol 50:520–529. 1998.
    Cerniglia, C. E. Aromatic hydrocarbons: metabolism by bacteria, fungi, and algae. Review of Biochemical Toxicology. 3: 321-361. 1982.
    Cavalca, L., E. Dell'Amico, and V. Andreoni. Intrinsic bioremediability of an aromatic hydrocarbon-polluted groundwater: diversity of bacterial population and toluene monoxygenase genes. Appl Microbiol Biotechnol 64:576-87. 2004.
    Chaillan, F., A. Le Fleche, E. Bury, Y. H. Phantavong, P. Grimont, A. Saliot, and J. Oudot. Identification and biodegradation potential of tropical aerobic hydrocarbon-degrading microorganisms. Res Microbiol 155:587-95. 2004.
    Chang, B. V., C. M. Yang, C. H. Cheng, and S. Y. Yuan. Biodegradation of phthalate esters by two bacteria strains. Chemosphere 55:533-8. 2004.
    Chang, J. H., S. K. Rhee, Y. K. Chank, and N. H. Chang. Desulfurization of diesel oils by a newly isolated dibenzothiophene-degrading Nocardia sp. strain CYKS2. Biotechnol. Prog 14:851–855. 1998.
    Chen, C. C., Teng, L. J., and Chang, T. C. Identification of Clinically Relevant Viridans Group Streptococci by Sequence Analysis of the 16S-23S Ribosomal DNA Spacer Region. J Clin Microbiol 42:2651-2657. 2004.
    Chen, X., J. Shi, Y. Chen, X. Xu, S. Xu, and Y. Wang. Tolerance and biosorption of copper and zinc by Pseudomonas putida CZ1 isolated from metal-polluted soil. Can J Microbiol 52:308-316. 2006.
    Constanti, M., J. Giralt, and A. Bourdon. Desulfurization of dibenzothiophene by bacteria. World J Microbiol Biotechnol. 10:510–516.1994.
    Constanti, M., J. Giralt, and A. Bordons. Degradation and desulfurization of dibenzothiophene sulfone and other sulfur compounds by Agrobacterium MC501 and a mixed culture. Enzyme Microb. Technol. 19: 214–219. 1996.
    Coppock, R. W., and M. S. Monstrom. Toxicology of oil-field pollutants in cattle: a review. Vet. Hum. Toxicol. 37:569–576. 1995.
    Corbella, M. E., and A. Puyet. Real-time reverse transcription-PCR analysis of expression of halobenzoate and salicylate catabolism-associated operons in two strains of Pseudomonas aeruginosa. Appl Environ Microbiol 69:2269-75. 2003.
    Denaro, R., G. D'Auria, G. Di Marco, M. Genovese, M. Troussellier, M. M. Yakimov, and L. Giuliano. Assessing terminal restriction fragment length polymorphism suitability for the description of bacterial community structure and dynamics in hydrocarbon-polluted marine environments. Environ Microbiol 7:78-87. 2005.
    Desai, J. D., and I. M. Banat. Microbial production of surfactants and their commercial potential. Microbiol. Mol Biol Rev 61:47–64. 1997.
    Devers, M., G. Soulas, and F. Martin-Laurent. Real-time reverse transcription PCR analysis of expression of atrazine catabolism genes in two bacterial strains isolated from soil. J Microbiol Methods 56:3-15. 2004.
    Dudley, M. W., and J. W. Frost. Biocatalytic desulfurization of arylsulfonates. Bioorg. Med Chem. 2:681–690. 1994.
    Duarte, G. F., A. S. Rosado, L. Seldin, W. de Araujo, and J. D. van Elsas. Analysis of bacterial community structure in sulfurous-oil-containing soils and detection of species carrying dibenzothiophene desulfurization (dsz) genes. Appl Environ Microbiol 67:1052-62. 2001.
    Dunbar, J., L. O. Ticknor, and C. R. Kuske. Assessment of the microbial diversity in four southwest US soils by 16S rRNA gene T-RFLP. Appl Environ Microbiol 66:2943–2950. 2000.
    Evans, F. F., L. Seldin, G. V. Sebastian, S. Kjelleberg, C. Holmstrom, and A. S. Rosado. 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. Lett Appl Microbiol 38:93-8. 2004.
    Fazi, S., S. Amalfitano, J. Pernthaler, and A. Puddu. Bacterial communities associated with benthic organic matter in headwater stream microhabitats. Environ Microbiol 7:1633-40. 2005.
    Fedi, S., V. Tremaroli, D. Scala, J. R. P. Jimenez, F. Fava, L. Young and, D. Zannoni. T-RFLP analysis of bacterial communities in cyclodextrin-amended bioreactors developed for biodegradation of polychlorinated biphenyls. Res Microbiol 156:201–210. 2005.
    Freeborn, R. A., K. A. West, V. K. Bhupathiraju, S. Chauhan, B. G. Rahm, R. E. Richardson, and L. Alvarez-Cohen. Phylogenetic analysis of TCE-dechlorinating consortia enriched on a variety of electron donors. Environ Sci Technol 39:8358-68. 2005.
    Gareth Lloyd-Jonesa, Andrew D. Lauriea, Aynsley C. Tizzard. Quantification of the Pseudomonas population in New Zealand soils by fluorogenic PCR assay and culturing techniques. J Microbiol Methods 60: 217– 224. 2005.
    Gerdes, B., R. Brinkmeyer, G. Dieckmann, and E. Helmke. Influence of crude oil on changes of bacterial communities in Arctic sea-ice. FEMS Microbiol Ecol 53:129-39. 2005.
    Gilbert, S. C., J. Morton, S. Buchanan, S. Oldfield, and A. Roberts. Isolation of a unique benzothiophene-desulfurizing bacterium, Gordona sp. strain 213E (NCIMB 40816) and characterization of the desulfurization pathway. Microbiol 144:2545–2553.1998.
    Goyal, A. K., and G. J. Zylstra. Molecular cloning of novel genes for polycyclic aromatic hydrocarbon degradation from Comamonas testosteroni GZ39. Appl Environ Microbiol 62:230-6. 1996.
    Goyal, A. K., and G. J. Zylstra. Genetics of naphthalene and phenanthrene degradation by Comamonas testosteroni. J. Ind. Microbiol Biotechnol 19:401–407. 1997.
    Harayama, S., and K. N. Timmis. Catabolism of aromatic hydrocarbons by Pseudomonas. In K. F. Chater (ed.), Genetics of bacterial diversity, Academic Press, London, United Kingdom. 151–174. 1989.
    Harayama, S., Y. Kasai, and A. Hara. Microbial communities in oil-contaminated seawater. Curr Opin Biotechnol 15:205-14. 2004.
    Heinrich, K., Susanne, K., Roger, W. Pickup, and Peter, A. Williams. Evolutionary conservation of genes coding for meta pathway enzymes within TOL plasmids pWWO and pWW53. Journal of Bacteriology. 164: 887-895. 1985.
    Hogan, J., O. Sherlock, D. Ryan, C. Whelan, S. Francesconi, R. Rivilla, and D. N. Dowling. Fluorescence resonance energy transfer (FRET) based molecular detection of a genetically modified PCB degrader in soil. FEMS Microbiol Lett 236:349-57. 2004.
    Hristova, K. R., C. M. Lutenegger, and K. M. Scow. Detection and quantification of methyl tert-butyl ether-degrading strain PM1 by real-time TaqMan PCR. Appl Environ Microbiol 67:5154-60. 2001.
    Hudak, A. J., and D. P. Cassidy. Stimulating in-soil rhamnolipid production in a bioslurry reactor by limiting nitrogen. Biotechnol Bioeng 88:861-8. 2004.
    Innis, M. A., and D. H. Gelfand. 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. 1990.
    Jae-Chang Cho1,2 and James M. Tiedje1,3. Quantitative Detection of Microbial Genes by Using DNA Microarrays. Appl Environ Microbiol 68: 1425-1430. 2002.
    Jeong, H. S., D. J. Lim, S. H. Hwang, S. D. Ha, and J. Y. Kong. Rha of phenanthrene-degrading fluorescent Pseudomonas biovars. Appl Environ Microbiol 62:3818–3825. 1996.
    Junca, H.,and D.H. Pieper. 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: 95–110. 2004.
    Kahng, H. Y., and K. H. Oh. Molecular detection of catabolic genes for polycyclic aromatic hydrocarbons in the reed rhizosphere of Sunchon Bay. J Microbiol 43:572-6. 2005.
    Katia Regina Arajo da Silvaa, Joana Falco Sallesb, Lucy Seldina and Jan Dirk van Elsasb. Application of a novel Paenibacillus-specific PCR-DGGE method and sequence analysis to assess the diversity of Paenibacillus spp. in the maize rhizosphere. J Microbiol Methods 54: 213-231. 2003.
    Katsivela, E., E. R. Moore, D. Maroukli, C. Strompl, D. Pieper, and N. Kalogerakis. Bacterial community dynamics during in-situ bioremediation of petroleum waste sludge in landfarming sites. Biodegradation 16:169-80. 2005.
    Khan, I. U., and J. S. Yadav. Real-time PCR assays for genus-specific detection and quantification of culturable and non-culturable mycobacteria and pseudomonads in metalworking fluids. Mol Cell Probes 18:67-73. 2004.
    Kim, S. J., D. H. Choi, D. S. Sim, and Y. S. Oh. Evaluation of bioremediation effectiveness on crude oil-contaminated sand. Chemosphere 59:845-52. 2005.
    King, S., B. R. McCord, and R. G. Rieflerb. Capillary electrophoresis single-strand conformation polymorphism analysis for monitoring soil bacteria. Journal of Microbiological Methods 60: 83– 92. 2005.
    Kitaguchi, A., N. Yamaguchi, and M. Nasu. Enumeration of respiring Pseudomonas spp. in milk within 6 hours by fluorescence in situ hybridization following formazan reduction. Appl Environ Microbiol 71:2748-52. 2005.
    Kostantinidis, K. T., N. Isaacs, J. Fett, S. Simpson, D. T. Long, and T. L. Marsh. Microbial diversity and resistance to copper in metal-contaminated lake sediment. Microb Ecol 45 :191–202. 2003.
    Kourkine, I. V., C. N. Hestekin, and A. E. Barron. Technical challenges in applying capillary electrophoresis-single strand conformation polymorphism for routine genetic analysis. Electrophoresis 23: 1375–1385. 2002.
    Kukor, J. J. and Olsen, R. H. Catechol 2,3-dioxygenases functional in oxygen-limited (hypoxic) environments. Appl Environ Microbiol 62: 1728-1740. 1996.
    Labana, S., G. Pandey, and R. K. Jain. Desulphurization of dibenzothiophene and diesel oils by bacteria. Lett Appl Microbiol 40:159-63. 2005.
    L'Abbee, J. B., D. Barriault, and M. Sylvestre. Metabolism of dibenzofuran and dibenzo-p-dioxin by the biphenyl dioxygenase of Burkholderia xenovorans LB400 and Comamonas testosteroni B-356. Appl Microbiol Biotechnol 67:506-14. 2005.
    Laguerre, G., M. Allard, F. Revoy, and N. Amarger. Rapid identification of Rhixobia by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Appl Environ Microbiol 60: 56-63. 1994.
    Leander, M., Vallaeys, T. and Fulthorpe, R. R. Primers for amplification and determination of the chloro- and dichloro-catechol 1,2-dioxygenases family. Canadian Journal of Microbiology. 1998.
    Lee, D., Y. Zo, and S. Kim. Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-singlestrand- conformation polymorphism. Appl Environ Microbiol 62: 3112– 3120. 1996.
    Liu, W. T., C. L. Huang, J. Y. Hu, L. Song, S. L. Ong, and W. J. Ng. Denaturing Gradient Gel Electrophoresis Polymorphism for Rapid 16S rDNA Clone Screening and Microbial Diversity Study. J. Biosci Bioeng. 93:101-103. 2002.
    Liu, W. T., T. L. Marsh, H. Cheng, and L. J. Forney. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63:4516-22. 1997.
    Lloyd-Jones, G., A. D. Laurie, and A. C. Tizzard. Quantification of the Pseudomonas population in New Zealand soils by fluorogenic PCR assay and culturing techniques. J Microbiol Methods 60:217-24. 2005.
    Locatelli, L., S. Tarnawski, J. Hamelin, P. Rossi, M. Aragno, and N. Fromin. Specific PCR amplification for the genus Pseudomonas targeting the 3' half of 16S rDNA and the whole 16S-23S rDNA spacer. Syst Appl Microbiol 25:220-7. 2002.
    Ma, Y. and Herson, D. S. NCBI database direct submission. Biology, University of Delaware, Newark, DE, 19716, USA. 1996.
    Ma, Y., L. Wang, and Z. Shao. Pseudomonas, the dominant polycyclic aromatic hydrocarbon-degrading bacteria isolated from Antarctic soils and the role of large plasmids in horizontal gene transfer. Environ Microbiol 8:455-65. 2006.
    Makkar, R. S., and S. S. Cameotra. An update on the use of unconventional substrates for biosurfactant production and their new applications. Appl. Microbiol. Biotechnol. 58:428–434. 2002.
    Makkar, R. S., and S. S. Cameotra. Production of biosurfactant at mesophilic and thermophilic conditions by a strain of Bacillus subtilis. J Ind Microbiol Biotechnol 20:48–52. 1998.
    McLellan, S. L., D. Warshawsky, and J. R. Shann. The effect of polycyclic aromatic hydrocarbons on the degradation of benzo[a]pyrene by Mycobacterium sp. strain RJGII-135. Environ Toxicol Chem 21:253-9. 2002.
    Meyer, A. F., D. A. Lipson, A. P. Martin, C. W. Schadt, and S. K. Schmidt. Molecular and metabolic characterization of cold-tolerant alpine soil Pseudomonas sensu stricto. Appl Environ Microbiol 70:483-9. 2004.
    Mezey, P. G. , Z. Zimpel, P. Warburton, P. D. Walker, D. G. Irvine, X.D. Huang, D. G. Dixon and B. M. Greenberg. Use of quantitative shape-activity relationships to model the photoinduced toxicity of polycyclic aromatic hydrocarbons：Electron density shape features accurately predict toxicity. Environ Toxicol Chem 17:1207－1215. 1998.
    Mills, D. K., K. Fitzgerald, C. D. Litchfield, and P. M. Gillevet. A comparison of DNA profiling techniques for monitoring nutrient impact on microbial community composition during bioremediation of petroleum-contaminated soils. J Microbiol Methods 54:57-74. 2003.
    Miller, D. N., J. E. Bryant, E. L. Madsen, and W. C. Ghiorse. Evaluation and optimatization of DNA extraction and purification procedures for soil and sediment samples. Appl Environ Microbiol 65: 4715-5724. 1999.
    Moeseneder, M. M., C. Winter, J. M. Arrieta, and G. J. Herndl. Terminal-restriction fragment length polymorphism (T-RFLP) screening of a marine archaeal clone library to determine the different phylotypes. J Microbiol Methods 44:159-72. 2001.
    Moyer, C. L., J. M. Tiedjue, F. C. Dobbs, and D. M. Karl. 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. Appl Environ Microbiol 62: 2501-2507. 1996.
    Muller, R. Bacterial degradation of xenobiotics. Journal of General Microbiology 105: 69-75. 1986.
    Mussmann, M., K. Ishii, R. Rabus, and R. Amann. Diversity and vertical distribution of cultured and uncultured Deltaproteobacteria in an intertidal mud flat of the Wadden Sea. Environ Microbiol 7:405-18. 2005.
    Mutnuri, S., N. Vasudevan, and M. Kaestner. Degradation of anthracene and pyrene supplied by microcrystals and non-aqueous-phase liquids. Appl Microbiol Biotechnol 67:569-76. 2005.
    Muyzer, G., A. Teske, C. O. Wirsen, and H. W. Jannasch. Phylogenetic relationship of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch Microbiol 164:165-172. 1995.
    Muyzer, G., E. C. de Waal, and A. G. Uitterlinden. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 659-700. 1993.
    Muyzer, G., and K. Smalla. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73:127-141. 1998.
    Nam, I. H., H. B. Hong, Y. M. Kim, B. H. Kim, K. Murugesan, and Y. S. Chang. Biological removal of polychlorinated dibenzo-p-dioxins from incinerator fly ash by Sphingomonas wittichii RW1. Water Res 39:4651-60. 2005.
    Nekodzuka, S., N. Toshiaki, T. Nakajima-Kambe, N. Nobura, J. Lu, and Y. Nakahara. Specific desulfurization of debenzothiophene by Mycobacterium strain G3. Biocatal. Biotransform. 15:21–27. 1997.
    Nicol, G. W., L. A. Glover, and J. I. Prosser. The impact of grassland management on archaeal community structure in upland pasture rhizosphere soil. Environ Microbiol 5:152-62. 2003.
    Nielsen, J. L., C. Klausen, P. H. Nielsen, M. Burford, and N. O. Jorgensen. Detection of activity among uncultured Actinobacteria in a drinking water reservoir. FEMS Microbiol Ecol 55:432-8. 2006.
    Noah, K. S., D. F. Bruhn, and G. A. Bala. Surfactin production from potato process effluent by Bacillus subtilis in a chemostat. Appl Biochem Biotechnol 121-124:465-73. 2005.
    Norris, T. B., J. M., Wraith, R. W. Castenholz,and T. R. McDermott. Soil microbial community structure across a thermal gradient following a geothermal heating event. Appl Environ Microbiol 68:6300–6309. 2002.
    Odd G. Brakstad, Kristin Bonaunet, Trond Nordtug & istein Johansen. 2004. Biotransformation and dissolution of petroleum hydrocarbons in natural flowing seawater at low temperature. Biodegradation 15:337–346, 2004.
    Ogino, A., H. Koshikawa, T. Nakahara, and H. Uchiyama. Succession of microbial communities during a biostimulation process as evaluated by DGGE and clone library analyses. J Appl Microbiol 91:625-35. 2001.
    Olsen, G. J., D. J. Lane, S. J. Giovannoni, N. R. Pace, and D. A. Stahl. Microbial and evolution: a ribosomal RNA approach. Annual. Review Microbiology. 40:337. 1987.
    Palleroni, N. J. Pseudomonas classification. A new case history in the taxonomy of gram-negative bacteria. Antonie Van Leeuwenhoek 64:231-51. 1993.
    Paul, D., G. Pandey, J. Pandey, and R. K. Jain. Accessing microbial diversity for bioremediation and environmental restoration. Trends Biotechnol 23:135-42. 2005.
    Payne, W. J. Denitrification, John Wiley and Sons, N. Y. 1981.
    Pernthaler, A., J. Pernthaler, and R. Amann. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl Environ Microbiol 68:3094-101. 2002.
    Perez-Luz, S., Adela, Y. M., and Catalan, V. Identification of waterborne bacteria by the analysis of 16S-23S rRNA intergenic spacer region. J Appl Microbio. l97:191-204. 2004.
    Piskonen, R., M. Nyyssonen, T. Rajamaki, and M. Itavaara. Monitoring of accelerated naphthalene-biodegradation in a bioaugmented soil slurry. Biodegradation 16:127-34. 2005.
    Rabus, R., M. Kube, J. Heider, A. Beck, K. Heitmann, F. Widdel, and R. Reinhardt. The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1. Arch Microbiol 183:27-36. 2005.
    Rahman, K. S., T. J. Rahman, S. McClean, R. Marchant, and I. M. Banat. Rhamnolipid biosurfactant production by strains of Pseudomonas aeruginosa using low-cost raw materials. Biotechnol Prog 18:1277-81. 2002.
    Ramos-Gonzalez, M. I., P. Godoy, M. Alaminos, A. Ben-Bassat, and J. L. Ramos. Physiological characterization of Pseudomonas putida DOT-T1E tolerance to p-hydroxybenzoate. Appl Environ Microbiol 67:4338-41. 2001.
    Ribas, F., J. Perramon, A. Terradillos, J. Frias and F. Lucena. The Pseudomonas group as an indicator of potential regrowth in water distribution systems. J Appl Microbiol 88: 704-710. 2000.
    Rosvita, E. Milo, Fiona, M. Duffner, and R. Miiller. Catechol 2,3-dioxygenase from the thermophilic, phenol-degrading Bacillus thermoleovorans strain A2 has unexpected low thermal stability. Extremophiles 3:185-190. 1999.
    Roy, S., J. Gendron, M. C. Delhomenie, L. Bibeau, M. Heitz, and R. Brzezinski. Pseudomonas putida as the dominant toluene-degrading bacterial species during air decontamination by biofiltration. Appl Microbiol Biotechnol 61:366-73. 2003.
    Saikei, R. K., D. H. Gelfand, S. Scharf, S. J. Scharf, R. Higuchi, G. T. Horn,K. B. Mullis, and H. A. Erlich. Primer-directed enzymatic amplification of DNA with thermostable DNA polymerase. Science 239:487-491. 1988.
    Sandrin, C., F. Peypoux, and G. Michel. Coproduction of surfactin and iturin A, lipopeptides with surfactant and antifungal properties, by Bacillus subtilis. Biotechnol Appl Biochem 12:370-5. 1990.
    Saul, D. J., J. M. Aislabie, C. E. Brown, L. Harris, and J. M. Foght. Hydrocarbon contamination changes the bacterial diversity of soil from around Scott Base, Antarctica. FEMS Microbiol Ecol 53:141-55. 2005.
    Scarpellini, M., L. Franzetti, and A. Galli. Development of PCR assay to identify Pseudomonas fluorescens and its biotype. FEMS Microbiol Lett 236:257-60. 2004.
    Schmalenberger, A., and C.C. Tebbe. Bacterial diversity in maizer hizospheres: conclusions on the use of genetic profiles based on PCR-amplified partial small subunit rRNA genes in ecological studies. Molecular Ecology. 12: 251– 262. 2003.
    Schmalenberger, A., F. Schweiger, and C.C. Tebbe. Effect of primers hybridizing to different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling. Appl Environ Microbiol 67:3557– 3563. 2001.
    Sedgley, C., B. Applegate, A. Nagel, and D. Hall. Real-time imaging and quantification of bioluminescent bacteria in root canals in vitro. J Endod 30:893-8. 2004.
    Sekiguchi, Y., Y. Kamagata, K. Syutsubo, A. Ohashi, H. Harada, and K. Nakamura. Phylogenetic diversity of mesophilic and thermophilic granular sludges determined by 16S rRNA gene analysis. Microbiol 144:2655-2665. 1998.
    Shi, Y., M. D. Zwolinski, M. E. Schreiber, J. M. Bahr, G. W. Sewell, and W. J. Hickey. Molecular analysis of microbial community structures in pristine and contaminated aquifers: field and laboratory microcosm experiments. Appl Environ Microbiol 65:2143-50. 1999.
    Smith, M. R. The biodegradation of aromatic hydrocarbons by 95 bacteria. Biodegradation. 1: 191-206. 1990.
    Song, Z., S. R. Edwards, and R. G. Burns. Biodegradation of naphthalene-2-sulfonic acid present in tannery wastewater by bacterial isolates Arthrobacter sp. 2AC and Comamonas sp. 4BC. Biodegradation 16:237-52. 2005.
    Story, S. P., S. H. Parker, J. D. Kline, T. R. Tzeng, J. G. Mueller, and E. L. Kline. Identification of four structural genes and two putative promoters necessary for utilization of naphthalene, phenanthrene, fluoranthene by Sphingomonas paucimobilis var. EPA505. Gene 260:155-69. 2000.
    Supaphol, S., S. Panichsakpatana, S. Trakulnaleamsai, N. Tungkananuruk, P. Roughjanajirapa, and A. G. O'Donnell. The selection of mixed microbial inocula in environmental biotechnology: example using petroleum contaminated tropical soils. J Microbiol Methods 65:432-41.. 2006.
    Tani, K., M. Muneta, K. Nakamura, K. Shibuya, and M. Nasu. Monitoring of Ralstonia eutropha KT1 in groundwater in an experimental bioaugmentation field by in situ PCR. Appl Environ Microbiol 68:412-6. 2002.
    Teira, E., T. Reinthaler, A. Pernthaler, J. Pernthaler, and G. J. Herndl. Combining catalyzed reporter deposition-fluorescence in situ hybridization and microautoradiography to detect substrate utilization by bacteria and Archaea in the deep ocean. Appl Environ Microbiol 70:4411-4. 2004.
    Thompson, I. P., C. J. van der Gast, L. Ciric, and A. C. Singer. Bioaugmentation for bioremediation: the challenge of strain selection. Environ Microbiol 7:909-15. 2005.
    Tsai, Y.-L., and B. H. Olson. Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Appl Environ Microbiol. 58: 2292-2295. 1992.
    Tsien, H. C. and R. S. Hanson. Soluble methane monooxygenase component B gene probe for identification of methanotrophs that rapidly degrade trichloroethylene. Appl Environ Microbiol 58: 953-960. 1992.
    Van Dyke, M. I., and A. J. McCarthy. Molecular biological detection and characterization of Clostridium population in municipal landfill sites. Appl Environ Microbiol 68:2049-2053. 2002.
    Van Hamme, J. D., A. Singh, and O. P. Ward. 2003. Recent advances in petroleum microbiology. Microbiol Mol Biol Rev 67:503-49.
    Vinas, M., J. Sabate, C. Guasp, J. Lalucat, and A. M. Solanas. Culture-dependent and -independent approaches establish the complexity of a PAH-degrading microbial consortium. Can J Microbiol 51:897-909. 2005.
    Vinas, M., J. Sabate, M. J. Espuny, and A. M. Solanas. Bacterial community dynamics and polycyclic aromatic hydrocarbon degradation during bioremediation of heavily creosote-contaminated soil. Appl Environ Microbiol 71:7008-18. 2005.
    Watanabe, K., H. Futamata, and S. Harayama. Understanding the diversity in catabolic potential of microorganisms for the development of bioremediation strategies. Antonie Van Leeuwenhoek 81:655-63. 2002.
    Wenderoth, D. F., P. Rosenbrock, W. R. Abraham, D. H. Pieper, and M. G. Hofle.. Bacterial community dynamics during biostimulation and bioaugmentation experiments aiming at chlorobenzene degradation in groundwater. Microb Ecol 46:161-76. 2003
    Widada, J., H. Nojiri, K. Kasuga, T. Yoshida, H. Habe, and T. Omori. Molecular detection and diversity of polycyclic aromatic hydrocarbon-degrading bacteria isolated from geographically diverse sites. Appl Microbiol Biotechnol 58:202-9. 2002.
    Widmer, F., R. J. Seidler, P. M. Gillevet, L. S. Watrud, and G. D. Di Giovanni. A highly selective PCR protocol for detecting 16S rRNA genes of the genus Pseudomonas (sensu stricto) in environmental samples. Appl Environ Microbiol 64:2545-53. 1998.
    Witzig, R., H. Junca, H. J. Hecht, and D. H. Pieper. Assessment of toluene/biphenyl dioxygenase gene diversity in benzene-polluted soils: links between benzene biodegradation and genes similar to those encoding isopropylbenzene dioxygenases. Appl Environ Microbiol 72:3504-14. 2006.
    Woese, C. R. Bacterial evolution. Microbiol. Rev. 51:221-271. 1987.
    Wu, M., L. Song, J. Ren, J. Kan, and P. Y. Qian. Assessment of microbial dynamics in the Pearl River Estuary by 16S rRNA terminal restriction fragment analysis. Continental Shelf Research. 24:1925–1934. 2004.
    Yakimov, M. M., M. M. Amor, M. Bock, K. Bodekaer, and H. L. Fredrickson, and K. N. Timmis. The potential of Bacillus licheniformis for in situ enhanced oil recovery. J. Petrol Sci Eng 18:147–160. 1997.
    Yu, C. P., R. Ahuja, G. Sayler, and K. H. Chu. Quantitative molecular assay for fingerprinting microbial communities of wastewater and estrogen-degrading consortia. Appl Environ Microbiol 71:1433-44. 2005.

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