Please use this identifier to cite or link to this item: http://hdl.handle.net/11455/22385
標題: Gordonia terrae CC-NAPH129-6菌株對萘分解特性研究及定量偵測方法之建立
Characterization of naphthalene degradation and quantitative detection of Gordonia terrae strain CC-NAPH129-6
作者: 林俊良
Lin, Chun-Liang
關鍵字: Polycyclic aromatic hydrocarbons;多苯環芳香族化合物;PCR;bioremediation;聚合酶鏈鎖反應;生物復育
出版社: 生命科學系所
引用: 王琳麒, 李文智, 林素貞. 1995. 垃圾焚化爐底灰、旋風集塵器、濕式洗滌塔及煙道廢氣排放多環芳香烴化合物之研究. 第十廢棄物處理技術研討會論文集。第400-406頁。 陳瑞仁, 簡維政, 廖世瑚, 吳宗霖. 1996. 汽車排氣中PAHs及其排放微粒中碳成份之探討. 第十三屆空氣污染控制技術研討會論文專輯。第333-341頁。 Alan S. 2004. Environmental Biotechnology. Second Edition. Oxford university Press., New York. p187-188. Allen C. C. R., D. R. Boyd, M. J. Larkin, K. A. Reid, N. D. Sharma and K. Wilson. 1997. Metabolism of naphthalene, 1-napthol, indene, and indole by Rhodococcus sp. strain NCIMB 12038. Appl. Environ. Microbiol. 63: 151-155. Arenskötter, M., D. Bröker, and A. Steinbüchel. 2004. Biology of the metabolically diverse genus Gordonia. Appl. Environ. Microbiol. 70:3195-3204. Baldwin B. R., C. H. Nakatsu and L. Nies1. 2003. Detection and Enumeration of Aromatic Oxygenase Genes by Multiplex and Real-Time PCR. Appl. Environ. Microbiol. 69:3350-3358. Barnsley, E. A. 1976. Naphthalene metabolism by Pseudomonas: the oxidation of 1,2-dihydroxynaphthalene to 2-hydroxychromene- 2-carboxylic acid and the formation of 2-hydroxybenzalpyruvate. Biochem. Biophys Res. Commun. 72:1116-1121. Bassler, H. I., Flood, S. J. A. Livak, K. J. Marmaro, J. R. Knorr and C. A. Batt. 1995. Use of fluorogenic probe in a PCR-based assay for the detection of Listeria monocytogenes. Appl. Environ. Microbiol. 61: 3724-3728. Bjorseth, A. and T. Ramahl. 1983. Sources and Emission of PAH, Handbook of polycyclic Aromatic Hydrocarbons, Vol 1. Marcel Dekker, Inc. New York and Basel. Bonazountas M. 1991. Fate of hydrocarbons in soils: review of modeling practices. In: Kostecki PT, Calabrese EJ, Bell CE, eds. Hydrocarbon contaminated soils and groundwater; Vol. I: Analysis, fate, environmental and public health effect remediation. Chelsea, MI: Lewis Publishers, 167-185. Bosch, R., E. R. Moore, E. Garcia-Valdes and D. H. Pieper. 1999. NahW, a novel, inducible salicylate hydroxylase involved in mineralization of naphthalene by Pseudomonas stutzeri AN10. J Bacteriol. 181: 2315-2322. Braid, M.D., L.M. Daniels, and C.L. Kitts. 2003. Removal of PCR inhibitors from soil DNA by chemical flocculation. J. Microbiol. Method. 52: 389-393. Bürgmann, H., M. Pesaro, F. Widmer and J. Zeyer. 2001. A strategy for optimizing quality and quantity of DNA extracted from soil. J. Microbiol. Methods. 45: 7-20. Desjardin, L. E., Y. Chen, M. D Perkins, L. Teixeira, M. D. Cave and K. D. Eisennach. 1998. Comparison of the ABI 7700 system (TaqMan) and competitive PCR for quantification of IS6110 DNA in sputum during treatment of tuberculosis. J. Clin. Microbiol. 36: 1964– 1968. Duteau, N. M., J. D. Rogers, C. T. Bartholomay and K. F. Reardon. 1998. Species-Specific Oligonucleotides for Enumeration of Pseudomonas putida F1, Burkholderia sp. Strain JS150, and Bacillus subtilis ATCC 7003 in Biodegradation Experiments. Appl. Environ. Microbiol. 64: 4994-4999. Edward, J. B., 1977. Combustion and Formation and Emission of Trace Species. 2nd Edition. Ann Arbor Science Publishers. Edward, U., T. Rogall, H. Blocker, M. Emde and E. C. Bottger. 1989. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res. 17: 7843-7853. Fukushima, M., K. Kakinuma and R. Kawaguchi. 2002. Phylogenetic analysis of Salmonella, Shigella, and Escherichia coil strain of the basis of the gyrB gene sequence. J. Chin. Microbiol. 40: 2779-2785. Garcia-Martinez, J., S. G. Acinas, A. I. Anton, and F. Rodriquez-Valera. 1999. Use of the 16S-23S ribosomal genes spacer region in studies of prokaryotic diversity. J. Microbiol. Methods. 36:55-64. Gibson, D. T. And V. Subramanian. 1984. Microbial degradation of aromatic hydrocarbons, p181-252.In D. T. Gibson(ed.), Microbial degradation of organic compounds. Dekker. New York, N. Y. Gonzalez, F. J. and H. V. Gelboin. 1994. Role of human cytochrome P450 in the metabolic activation of chemical carcinogens and toxins. Drug Metab. Rev. 26: 165-183. Goyal, A. K and G. J. Zylstra. 1996. Molecular cloning of novel genes for polycyclic aromatic hydrocarbon degradation from Comamonas testosteroni GZ39. Appl Environ Microbiol. 62: 230-236. Grimmer, G., 1983. Enviromental carcinogeus : Polycyclic Aromatic Hydrocarbons. CRC Press, Boca Raton. Ground E., B. Denecke and R. Eichenlaub. 1992. Naphthalene degradation via salicylate and gentisate by Rhodococcus sp. strain B4. Appl. Environ. Microbiol. 58: 1874-1877. Grüntzig, V., S. C. Nold, J. Zhou and J. M. Tiedje. 2001. Pseudomonas stutzeri nitrite reductase gene abundance in environmental samples measured by real-time PCR. Appl. Environ. Microbiol. 67: 760–768. Guengerich, F. P. 1991. Oxidation of toxic and carcinogenic chemicals by human cytochrome P450 enzymes. Chem. Res. Toxicol. 4: 391-407. Harvey, R. G. 1991. Polycyclic Aromatic Hydrocarbons: Chemistry and Carcinogenicity. Cambridge University Press, Cambridge. Herrick, J. B., K. G. Stuart-kell, W. C. Ghiorse and E. L. Madsen. 1997. Natural Horizontal Transfer of a Naphthalene Dioxygenase Gene between Bacteria Native of a Coal Tar-Contaminated Field Site. Appl. Environ. Microbiol. 63: 2330-2337. Higgins, J. A., J. Ezzell, B. J. Hinnebusch, M. Shipley, E. A. Henchal and M. S. Ibrahim. 1998. Nuclease PCR assay to detect Yersinia pestis. J.Clin. Microbiol. 36: 2284– 2288. Holben, W. E., 1994. Isolation and purification of bacterial DNA from soil. In: Mickelson, S.H. (Ed.), Methods of Soil Analysis, Part 2, Soil Science Society of America, Madison, WI, pp. 727-751. Holliger, C. and A. J. B. Zehnder. 1996. Anaerobic biodegradation of hydrocarbons. Curr. Opin. Biotech. 7: 326-330. Hristova, K. R. C. H. Lutenegger and K. M. Scow. 2001. Detection and Quantification of Methyl tert-Butyl Ether-Degrading strain PM1 by Real-Time TaqMan PCR. Appl. Environ. Microbiol. 67: 5154-5160. Hugenholtz, P., B. M. Goebel and N. R. Pace. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180: 4765-4774. Iwamoto, T and M. Nasu. 2001. Current Bioremediation Practice and Perspective. J. Biosci. Bioeng. 92: 1-8. Jorge, L. M. R., R. A. Michael, W. U. John, V. T. Tamara and M. U. James. 2002. Use of both 16S rRNA and engineered functional genes with real-time PCR to quantify an engineered, PCB-degrading Rhodococcus in soil. J. Microbiol. Methods. 51: 181-189. Jones, R. M., B. Britt-Compton and P. A. Williams. 2003. The naphthalene catabolic (nag) genes of Ralstonia sp. strain U2 are an operon that is regulated by NagR, a LysR-type transcriptional regulator. J Bacteriol. 185: 5847-53. Jeffrey, A. M., H. J. C. Yeh, D. M. Jerina, T. R. Patel, J. F. Davey and D. T. Gibson. 1975. Initial reactions in the oxidation of naphthalene Pseudomonas putida. Biochem. 14:575-584. Kauppi, B., K. Lee, E. Carrendano, R. E. Parales, D. T. Gibson, H. Eklund and S. Ramaswamy. 1998. Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase. Structure. 6:571-586. Kikuchi, T., K. Iwasaki, H. Nishihara, Y. Takamura and O. Yagi. 2002. Quantitative and rapid detection of the trichloroethylene-degrading bacterium Methylocystis sp. M in groundwater by real-time PCR. Appl Microbiol Biotechnol. 59:731-736 Kiyohara, H., K. Nagao, K. Kouno and K. Yano. 1982. Phenanthrene-degrading phenotype of Alcaligenes faecalis AFK2. Appl Environ Microbiol. 43(2): 458-461. Kulakov, L. A., S. Chen, C. R. A. Christopher and J. L. Michael. 2005. Web-Type evolution of Rhodococcus gene cluster associated with utilization of naphthalene. Appl Environ Microbiol. 71: 1754-1764. Labarca, C. and K. Paigen. 1980. A simple, rapid, and sensitive DNA assay procedure Anal. Biochem. 102: 344-352. Larkin, M. J. and M. J. Day. 1986. The metabolism of carbaryl by three bacterial isolates, Pseudomonas spp. (NCIB12042 and 12043) and Rhodococcus sp. (NCIB12038) from garden soil. J. Appl. Bacteriol. 60: 233-242. Larkin, M. J., C. C. R. Allen, L. A. Kulakov and D. A. Lipscomb. 1999. Purification and characterization of a novel naphthalene dioxygenase from Rhodococcus sp. strain NCIMB12038. J. Bacteriol. 181: 6200-6204. Marston, C. P., C. Pereira, J. Ferguson, K. Fischer, O. Hedstrom, W-M. Dashwood and W. Barid. 2001. Effect of a complex environmental mixture form coal tar containing polycyclic aromatic hydrocarbons (PAH) on the tumor initiation, PAH-DNA binding and metabolic activation of carcinogenic PAH in mouse epidermis. Menzie, C. A., B. B. Potocki and J. Stantodonato. 1992. Exposure to Carcinogenic PAHs in the environment. Environ. Sci. and Techonol. 26:1278-1284. Marx, R. B. and M. D. Aitken. 1999. Quantification of chemotaxis to naphthalene by Pseudomonas putida G7. Appl Environ Microbiol. 65: 2847-2852. Miller, D.N., J.E. Bryant, E.L. Madsen, and W.C. Ghiorse. 1999. Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl. Environ. Microbiol. 65: 4715-4724. Moreira D. 1998. Efficient removal of PCR inhititors using agarose- embedded DNA preparations. Nucleic Acids Research. 26: 3309-3310. National Reseach Council (NRC). 1993. In situ Bioremediation: When Does It Work? B. E. Rittmann, Chairman, National Academy Press, Washington D. C. Pahl, A., U. Kuhlbrandt, K. Brune, M. Rollinghoff and A. Gressner. 1999. Quantitative detection of Borrelia burgdorferi by realtime PCR. J. Clin. Microbiol. 37: 1958-1963. Van Raemdonck, H., A. Maes , W. Ossieur, K. Verthé, T. Vercauteren, W. Verstraete and N. Boon. 2006. Real time PCR quantification in groundwater of the dehalorespiring Desulfitobacterium dichloroelimi- nans strain DCA1. J. Microbiol. Methods. In Press. Rollins, D. M. and R. R. Colwell. 1986. Viable but nonculturable stage of Campylobacter jejuni and its role in survival in the natural aquatic environment. Appl. Environ. Microbiol. 52: 531-538. Rozsak, D. B. and R. R. Colwell. 1987. Survival strategies of bactera in the natural environment. Microbiol Rev. 51: 365-379. Röling, W. F. M., M. G. Milner, D. M. Jones, K. Lee, F. Daniel, R. J. P. Swannell and I. M. Head1. 2002. Robust Hydrocarbon Degradation and Dynamics of Bacterial Communities during Nutrient-Enhanced Oil Spill Bioremediation. Appl. Environ. Microbiol. 68: 5537-5548. Richert, K., E. Brambilla and E. Stackebrandt. 2005. Development of PCR primers specific for the amplification and direct sequencing of gyrB genes from microbacteria, order Actinomycetales. J. Microbiol. Methods. 60: 115– 123. Sharp, P. A., B. Sugden. 1973. Detection of two restriction endonuclease activities in Haemophilus parainfluenzae using analytical agarose-ethidium bromide electrophoresis." Biochemistry 12: 3055-3063. Selenska, S. and W. Klingmüller. 1991. DNA recovery and direct detection of Tn5 sequences form soil. Lett. Appl. Microb. 13: 21-24. Shen, F. T., H. L. Lu, J. L. Lin, W. S. Huang, A. B. Arun and C. C. Young. 2006. Phylogenetic analysis of members of the metabolically diverse genus Gordonia based on proteins encoding the gyrB gene. Res Microbiol. 157: 367-375. Simon M. J., T. D. Osslund, R. Saunders, B. D. Ensley, S. Suggs, A. Harcourt, W. C. Suen, D. L. Gibson and G. J. Zylstra. 1993. Sequences of genes encoding naphthalene dioxygenase in Pseudomonas putida strains G7 and NCIB 9816-4. Gene. 127: 31-37. Southern, E. M. 1975. Detection of specific sequences among DNA fragments separate by gel electrophoresis. J. Mol. Biol. 98: 503-517. Suzuki, M.T., L. T. Taylor and E. F. DeLong. 2000. Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5’-nuclease assays. Appl. Environ. Microbiol. 66: 4605– 4614. Tasi, Y. L. and B. H. Olsan. 1991. Rapid method for direct extraction of DNA from soil and sediments. Appl. Environ. Microbiol. 57:1070-1074. Usha, V. 1989. Metabolism of Polycyclic Aromatic Hydrocarbons in the Aquatic Environment. CRC press. Bocaraton, Florida. Watt, P. M. and D. Higgins. 1994. Structure and function of type Ⅱ DNA topoisomerases. Biochem. J. 303:681-695. Watanabe, K., Nelson, J. S., Harayama, S., Kasai, H. 2001. ICB database: the gyr B database: the gyrB database for identification and classification of bacteria. Nucleic Acids Res. 29: 344-345. Yamamoto, S and S. Harayama. 1996. Phylogenetic analysis of Acinetobacter strains based on the nucleotide sequences of gyrB genes and on the amino acid sequences of their products. Int J Syst Bacteriol. 46: 506-511. Yanez, M. A., V. Catalan, D. Apraiz, M. J. Figueras and A. J. Martinezmurcia. 2003. Phylogenetic analysis of members of the genus Aeromonas based of gyrB gene sequences. Int. J. Syst. Evol. Microbiol. 53: 875-883 Young, C. C., R. L. Burghoff, L. G. Keim, V. Minakbernero, J. R. Lute and S. M. Hinton. 1993. Polyvinylpyrrolidone-agarose gel- electrophoresis purification of polymerase chain reaction amplifiable DNA from soil. Appl. Environ. Microbiol. 59: 1972-1974.
摘要: 
多苯環芳香族化合物 (polycyclic aromatic hydrocarbons, PAHs) 廣泛存於環境中,由於其具有致癌性與致突變性對人體的健康造成重大的威脅,因此針對污染的環境進行整治復育已成為現階段最重要的工作。本研究從柴油污染的土壤分離出具分解萘 (naphthalene) 能力的菌株Gordonia terrae CC-NAPH129-6。將Gordonia terrae CC-NAPH129-6菌株接種 7.8×107 CFU/ml 及 6.7×105 CFU/ml 的初始菌數於含 30 mg/l 萘之最小無機鹽液態培養基,分別經過 18 及 24 小時,能將其降解至偵測極限 (0.1mg/l) 以下。利用針對革蘭性陽性菌所設計之引子 RnarAa124 /RnarAa1275 進行聚合酶鏈鎖反應,能成功增殖到 1054 bp 核苷酸片段,經序列比對與 Rhodococcus sp. P400之naphthalene dioxygenase large subunit (narAa) 有具有最高的相似度 99.6%。從Pseudomonas屬與Rhodococcus屬之相似於naphthalene dioxygenase large subunit 基因種系樹狀圖顯示, G. terrae CC-NAPH129-6 菌株的 naphthalene dioxygenase α subunit 的基因與 Rhodococcus 屬的 naphthalene 群叢最為接近。此結果顯示naphthalene dioxygenase α subunit 的基因可能由 Rhodococcus 屬經水平傳播至 G. terrae CC-NAPH129-6 菌株。以 gyrB 基因設計G. terrae CC-NAPH129-6 菌種特異性引子 GTSF/GTSR,利用 G. terrae CC-NAPH129-6 親緣關係接近的 Gordonia 屬的11株菌株確定引子特異性。在土壤及地下水中 G. terrae CC-NAPH129-6 菌株之 DNA濃度或菌數量與CT值具有良好的線性關係,其偵測極限分別為 32 ρg及24 ρg 的 DNA 濃度與 5 × 104 CFU/ml 及 7.6 × 104 CFU/g soil 的菌數量。本研究成果將可提供快速及準確的監測方法以利於應用
G. terrae CC-NAPH129-6 菌株於污染場址中,進行生物復育時菌數的變動的監測。

Polycyclic aromatic hydrocarbons (PAHs), widely distributed environmental toxics, are potential carcinogenic and mutagenic chemicals to human health. Since PAHs tend to accumulate at soil, bioremediation through soil microorganisms is of choice. The Gordonia terrae strain CC-NAPH129-6 was isolated form diesel oil-contaminated soil for the capability to degrade naphthalene. While 7.8×107 CFU/ml or 6.7×105 CFU/ml culture in naphthalene-containing medium (30 mg/l) with strain CC-NAPH129-6 could degrade naphthalene completely with detection limit at 0.1 mg/l in 18 hours or 24 hours, respectively. Using the PCR primer RnarAa124 /RnarAa1275, designed from Rhodococcus naphthalene dioxygenase large subunit gene (narAa) region, the DNA fragment with 1054 bp was amplified with chromosomal DNA of CC-NAPH129-6 as template. The narAa of stain CC-NAPH129-6 shares 99.6% similarity with narAa of Rhodococcus sp. P400. And the phylogenetic tree of the naphthalene dioxygenase α subunit-like genes indicated that the narAa of strain CC-NAPH129-6 was clustered with Rhodococcus sp. It indicated the possibility of horizontal gene transfer of naphthalene dioxygenase from Rhodococcus to Gordonia terrae strain CC-NAPH129-6 which encountered the insult of naphthalene. Specific primers were designed for the gyrB gene region, and the specificity was confirmed with 11 related Gordonia genus. The linear relationship between the threshold fluorescence (CT) value and the quantity of G. terrae strain CC-NAPH129-6 genomic DNA or cell density was measured. The detection limit for CC-NAPH129-6 real-time PCR assay was 32 ρg DNA and 5 × 104 CFU/ml for groundwater samples or 24 ρg of DNA and 7.6 × 104 CFU/g for soil samples. Investigation shown here could be applied to monitor the in situ bioremediation of G. terrae CC-NAPH129-6.
URI: http://hdl.handle.net/11455/22385
其他識別: U0005-2308200616130600
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