轉錄體分析 Acetobacterium woodii 降解1,1,1-三氯乙烷機制並用以協助 Dehalococcoides進行還原脫氯

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林志豪(Chih-Hao Lin) 查詢紙本館藏

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轉錄體分析 Acetobacterium woodii 降解1,1,1-三氯乙烷機制並用以協助 Dehalococcoides進行還原脫氯
(The degradation mechanisms of Acetobacterium woodii toward 1,1,1-trichloroethane by transcriptome analysis and its role in assisting reductive dechlorination of Dehalococcoides)

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摘要(中)

1,1,1-三氯乙烷(1,1,1-Trichloroethane)是地下水污染的常見來源之一，不僅導致人類患癌，也抑制Dehalococcoides mccartyi(D. mccartyi) 進行三氯乙烯(Trichloroethene)的還原脫氯反應，而三氯乙烯也是主要地下水污染物之一。在研究中Acetobacterium woodii (A. woodii) 具有1,1,1-三氯乙烷的降解能力。然而，目前對於其降解機制仍不清楚。在本研究中欲探討在果糖生長下的A. woodii降解1,1,1-三氯乙烷時所參與的代謝途徑以及嘗試透過在1,1,1-三氯乙烷和三氯乙烯共汙染下共培養A. woodii和D. mccartyi以消除1,1,1-三氯乙烷抑制三氯乙烯脫氯作用。結果顯示，A. woodii能夠降解最高至2 mM的 1,1,1-三氯乙烷。為了進一步探討其潛在機制，我們使用轉錄組分析和RT-qPCR方法。結果表明，1,1,1-三氯乙烷誘導了22個與Wood-Ljungdahl途徑相關基因的上調表達，推測其可能與1,1,1-三氯乙烷的降解有相關性。為了減少1,1,1-三氯乙烷對D. mccartyi進行三氯乙烯脫氯的負面影響，接著我們建立了一個由D. mccartyi CWV2和A. woodii組成的共培養系統，該系統能夠協同降解1,1,1-三氯乙烷和三氯乙烯。本研究不僅為探討了A. woodii對1,1,1-三氯乙烷的降解機制提供了新的見解，也在1,1,1-三氯乙烷和三氯乙烯共污染的場地中利用A. woodii進行生物修復提供了多種策略。

摘要(英)

1,1,1-Trichloroethane (1,1,1-TCA), one of the common sources of groundwater contamination, not only causes cancer in humans but also inhibits the reductive dechlorination of trichloroethene (TCE) by Dehalococcoides mccartyi (D. mccartyi), which is the major groundwater contamination. Previous studies have reported that Acetobacterium woodii (A. woodii) exhibits 1,1,1-TCA degradation activity. However, the degradation mechanism remains unclear. This study aimed to identify for the key pathways involved in the degradation of 1,1,1-TCA by A. woodii when grown on fructose as a primary substrate, and to establish a co-culture consisting of D. mccartyi and A. woodii to alleviate the inhibitory effect of 1,1,1-TCA on the dechlorination of TCE. The results showed that A. woodii can degrade 2 mM of 1,1,1-TCA. To investigate the underlying mechanisms of 1,1,1-TCA degradation, we adopted transcriptomic analysis and RT-qPCR methods. The results indicated that 1,1,1-TCA induced the up-regulation of twenty-two genes related to Wood-Ljungdahl pathway, suggesting that this pathway was involved. To alleviate the negative impact of 1,1,1-TCA on TCE degradation by D. mccartyi, we established a co-culture consisting of D. mccartyi strain CWV2 and A. woodii to synergistically degrade both 1,1,1-TCA and TCE by providing fructose as the sole carbon source. This study not only provides new insight to reveal the degradation mechanism of 1,1,1-TCA by A. woodii, but also provide strategies for removing 1,1,1-TCA by A. woodii and then dechlorination of TCE in the both 1,1,1-TCA and TCE co-contaminated sites.

關鍵字(中)

★ Acetobacterium woodii
★ 1,1,1-三氯乙烷
★ 共培養
★ Dehalococcoides
★ 共汙染

關鍵字(英)

★ Acetobacterium woodii
★ 1,1,1-TCA
★ co-culture
★ Dehalococcoides
★ co-contamination

論文目次

國立中央大學圖書館學位論文授權書 i
國家圖書館學位論文延後公開申請書 ii
國立中央大學碩士班研究生論文指導教授推薦書 iii
國立中央大學碩士班研究生論文口試委員審定書 iv
致謝 v
摘要 vi
Abstract vii
目錄 viii
圖目錄 x
表目錄 xii
第壹章緒論 (Introduction) 1
1.1 研究動機 1
1.2 1,1,1-三氯乙烷抑制多氯乙烯還原脫氯 2
1.3 1,1,1-三氯乙烷之厭氧生物降解 2
1.4 Acetobacterium 降解有機鹵化物 3
第貳章實驗目的及架構 6
第参章實驗材料與方法 (Materials and Methods) 8
3.1 實驗材料 8
3.1.1 常用藥品與試劑 8
3.2 實驗方法 11
3.2.1 DCB-1 厭氧菌培養基配置 11
3.2.2 Acetobacterium spp.菌株的保存與來源 11
3.2.3 Dehalococcoides mccartyi菌株的保存與來源 13
3.2.4 細菌Genomic DNA 萃取 14
3.2.5 氣相層析儀分析 15
3.2.6 定量聚合酶連鎖反應 (qPCR) 16
3.2.7 細菌RNA萃取 16
3.2.8 RNA反轉錄 17
3.2.9 醋酸濃度測定 18
3.2.10 轉錄組分析 19
第肆章實驗結果 (Result) 21
4.1 Acetobacterium woodii共代謝降解1,1,1-三氯乙烷 21
4.2 轉錄體分析Acetobacterium降解時1,1,1-三氯乙烷下基因表現 22
4.3 Dehalococcoides mccartyi與Acetobacterium woodii共培養協同降解1,1,1-三氯乙烷及三氯乙烯 23
第伍章討論(Discussion) 26
5.1 Acetobacterium woodii降解1,1,1-三氯乙烷時之生理特性 26
5.2 分析Acetobacterium woodii潛在參與降解1,1,1-三氯乙烷之代謝路徑 27
5.3 Dehalococcoides 藉由與Acetobacterium woodii 共培養消除1,1,1-三氯乙烷抑制三氯乙烯脫氯反應之效果 30
第陸章結論 (Conclusion) 32
參考文獻 (Reference) 33
圖表 39
附加資料 (Supplementary Data) 54

參考文獻

Adamson, D.T. and Parkin, G.F. 2000. Impact of mixtures of chlorinated aliphatic hydrocarbons on a high-rate, tetrachloroethene-dechlorinating enrichment culture. Environmental Science & Technology 34(10), 1959-1965.
Alonso, F., Beletskaya, I.P. and Yus, M. 2002. Metal-mediated reductive hydrodehalogenation of organic halides. Chemical Reviews 102(11), 4009-4092.
Bache, R. and Pfennig, N. 1981. Selective isolation of Acetobacterium woodii on methoxylated aromatic acids and determination of growth yields. Archives of Microbiology 130, 255-261.
Balch, W.E., Schoberth, S., Tanner, R.S. and Wolfe, R. 1977. Acetobacterium, a new genus of hydrogen-oxidizing, carbon dioxide-reducing, anaerobic bacteria. International Journal of Systematic and Evolutionary Microbiology 27(4), 355-361.
Bertsch, J. and Müller, V. 2015. CO metabolism in the acetogen Acetobacterium woodii. Applied and Environmental Microbiology 81(17), 5949-5956.
Bertsch, J., Siemund, A.L., Kremp, F. and Müller, V. 2016. A novel route for ethanol oxidation in the acetogenic bacterium Acetobacterium woodii: the acetaldehyde/ethanol dehydrogenase pathway. Environmental Microbiology 18(9), 2913-2922.
Chan, W.W., Grostern, A., Löffler, F.E. and Edwards, E.A. 2011. Quantifying the effects of 1, 1, 1-trichloroethane and 1, 1-dichloroethane on chlorinated ethene reductive dehalogenases. Environmental Science & Technology 45(22), 9693-9702.
Dönig, J. and Müller, V. 2018. Alanine, a novel growth substrate for the acetogenic bacterium Acetobacterium woodii. Applied and Environmental Microbiology 84(23), e02023-02018.
Davidova, M., Tarasova, N., Mukhitova, F. and Karpilova, I. 1994. Carbon monoxide in metabolism of anaerobic bacteria. Canadian Journal of Microbiology 40(6), 417-425.
De Wildeman, S., Neumann, A., Diekert, G. and Verstraete, W. 2003. Growth-substrate dependent dechlorination of 1, 2-dichloroethane by a homoacetogenic bacterium. Biodegradation 14, 241-247.
Ding, C., Alvarez-Cohen, L. and He, J. 2018. Growth of Dehalococcoides mccartyi species in an autotrophic consortium producing limited acetate. Biodegradation 29, 487-498.
Ding, C., Chow, W.L. and He, J. 2013. Isolation of Acetobacterium sp. strain AG, which reductively debrominates octa-and pentabrominated diphenyl ether technical mixtures. Applied and Environmental Microbiology 79(4), 1110-1117.
Ding, C., Zhao, S. and He, J. 2014. A Desulfitobacterium sp. strain PR reductively dechlorinates both 1, 1, 1‐trichloroethane and chloroform. Environmental Microbiology 16(11), 3387-3397.
Doherty, R.E. 2000. A history of the production and use of carbon tetrachloride, tetrachloroethylene, trichloroethylene and 1, 1, 1-trichloroethane in the United States: part 1—historical background; carbon tetrachloride and tetrachloroethylene. Environmental Forensics 1(2), 69-81.
Duhamel, M., Wehr, S.D., Yu, L., Rizvi, H., Seepersad, D., Dworatzek, S., Cox, E.E. and Edwards, E.A. 2002. Comparison of anaerobic dechlorinating enrichment cultures maintained on tetrachloroethene, trichloroethene, cis-dichloroethene and vinyl chloride. Water Research 36(17), 4193-4202.
Egli, C., Scholtz, R., Cook, A.M. and Leisinger, T. 1987. Anaerobic dechlorination of tetrachloromethane and 1, 2-dichloroethane to degradable products by pure cultures of Desulfobacterium sp. and Methanobacterium sp. FEMS Microbiology Letters 43(3), 257-261.
Egli, C., Tschan, T., Scholtz, R., Cook, A.M. and Leisinger, T. 1988. Transformation of tetrachloromethane to dichloromethane and carbon dioxide by Acetobacterium woodii. Applied and Environmental Microbiology 54(11), 2819-2824.
Gantzer, C.J. and Wackett, L.P. 1991. Reductive dechlorination catalyzed by bacterial transition-metal coenzymes. Environmental Science & Technology 25(4), 715-722.
Gälli, R. and McCARTY, P.L. 1989. Biotransformation of 1, 1, 1-trichloroethane, trichloromethane, and tetrachloromethane by a Clostridium sp. Applied and Environmental Microbiology 55(4), 837-844.
Grostern, A. and Edwards, E.A. 2006. A 1, 1, 1-trichloroethane-degrading anaerobic mixed microbial culture enhances biotransformation of mixtures of chlorinated ethenes and ethanes. Applied and Environmental Microbiology 72(12), 7849-7856.
Haiko, J. and Westerlund-Wikström, B. 2013. The role of the bacterial flagellum in adhesion and virulence. Biology 2(4), 1242-1267.
Hashsham, S.A. and Freedman, D.L. 1999. Enhanced biotransformation of carbon tetrachloride by Acetobacterium woodii upon addition of hydroxocobalamin and fructose. Applied and Environmental Microbiology 65(10), 4537-4542.
He, J., Holmes, V.F., Lee, P.K. and Alvarez-Cohen, L. 2007. Influence of vitamin B12 and cocultures on the growth of Dehalococcoides isolates in defined medium. Applied and Environmental Microbiology 73(9), 2847-2853.
He, J., Ritalahti, K.M., Aiello, M.R. and Loffler, F.E. 2003. Complete detoxification of vinyl chloride by an anaerobic enrichment culture and identification of the reductively dechlorinating population as a Dehalococcoides species. Applied and Environmental Microbiology 69(2), 996-1003.
Heise, R., Müller, V. and Gottschalk, G. 1989. Sodium dependence of acetate formation by the acetogenic bacterium Acetobacterium woodii. Journal of Bacteriology 171(10), 5473-5478.
Hermon, L., Hellal, J., Denonfoux, J., Vuilleumier, S., Imfeld, G., Urien, C., Ferreira, S. and Joulian, C. 2019. Functional genes and bacterial communities during organohalide respiration of chloroethenes in microcosms of multi-contaminated groundwater. Frontiers in Microbiology 10, 89.
Hess, V., Oyrik, O., Trifunović, D. and Müller, V. 2015. 2, 3-Butanediol metabolism in the acetogen Acetobacterium woodii. Applied and Environmental Microbiology 81(14), 4711-4719.
Hess, V., Schuchmann, K. and Müller, V. 2013. The ferredoxin: NAD+ oxidoreductase (Rnf) from the acetogen Acetobacterium woodii requires Na+ and is reversibly coupled to the membrane potential. Journal of Biological Chemistry 288(44), 31496-31502.
Humans, I.W.G.o.t.E.o.C.R.t. 2014. Trichloroethylene, Tetrachloroethylene, and Some Other Chlorinated Agents. IARC Monographs on the Evaluation of Carcinogenic Risks to Humans 106, 1.
Jordan, A., Stoy, P. and Sneddon, H.F. 2020. Chlorinated solvents: their advantages, disadvantages, and alternatives in organic and medicinal chemistry. Chemical Reviews 121(3), 1582-1622.
Jugder, B.-E., Ertan, H., Bohl, S., Lee, M., Marquis, C.P. and Manefield, M. 2016. Organohalide respiring bacteria and reductive dehalogenases: key tools in organohalide bioremediation. Frontiers in Microbiology 7, 249.
Kamariah, N., Huber, R.G., Bond, P.J., Müller, V. and Grüber, G. 2020. 3D reconstruction and flexibility of the hybrid engine Acetobacterium woodii F-ATP synthase. Biochemical and Biophysical Research Communications 527(2), 518-524.
Karekar, S.C., Srinivas, K. and Ahring, B.K. 2019. Kinetic study on heterotrophic growth of Acetobacterium woodii on lignocellulosic substrates for acetic acid production. Fermentation 5(1), 17.
Kremp, F., Poehlein, A., Daniel, R. and Müller, V. 2018. Methanol metabolism in the acetogenic bacterium Acetobacterium woodii. Environmental Microbiology 20(12), 4369-4384.
Löffler, F.E., Yan, J., Ritalahti, K.M., Adrian, L., Edwards, E.A., Konstantinidis, K.T., Müller, J.A., Fullerton, H., Zinder, S.H. and Spormann, A.M. 2013. Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi. International Journal of Systematic and Evolutionary Microbiology 63(Pt_2), 625-635.
Lechtenfeld, M., Heine, J., Sameith, J., Kremp, F. and Müller, V. 2018. Glycine betaine metabolism in the acetogenic bacterium Acetobacterium woodii. Environmental Microbiology 20(12), 4512-4525.
Leo, F., Schwarz, F.M., Schuchmann, K. and Müller, V. 2021. Capture of carbon dioxide and hydrogen by engineered Escherichia coli: hydrogen-dependent CO2 reduction to formate. Applied Microbiology and Biotechnology 105(14-15), 5861-5872.
Love, M.I., Huber, W. and Anders, S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15(12), 1-21.
Middleton, D. 2021. Carcinogenicity of 1, 1, 1-trichloroethane and four other industrial chemicals. Lancet Oncology.
Moon, J., Dönig, J., Kramer, S., Poehlein, A., Daniel, R. and Müller, V. 2021. Formate metabolism in the acetogenic bacterium Acetobacterium woodii. Environmental Microbiology 23(8), 4214-4227.
Payne, K.A., Quezada, C.P., Fisher, K., Dunstan, M.S., Collins, F.A., Sjuts, H., Levy, C., Hay, S., Rigby, S.E. and Leys, D. 2015. Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation. Nature 517(7535), 513-516.
Peters, V., Janssen, P. and Conrad, R. 1998. Efficiency of hydrogen utilization during unitrophic and mixotrophic growth of Acetobacterium woodii on hydrogen and lactate in the chemostat. FEMS Microbiology Ecology 26(4), 317-324.
Puentes Jácome, L.A., Wang, P.-H., Molenda, O., Li, Y.X., Islam, M.A. and Edwards, E.A. 2019. Sustained dechlorination of vinyl chloride to ethene in Dehalococcoides-enriched cultures grown without addition of exogenous vitamins and at low pH. Environmental Science & Technology 53(19), 11364-11374.
Ragsdale, S.W. and Pierce, E. 2008. Acetogenesis and the Wood–Ljungdahl pathway of CO2 fixation. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1784(12), 1873-1898.
Ritalahti, K.M., Amos, B.K., Sung, Y., Wu, Q., Koenigsberg, S.S. and Löffler, F.E. 2006. Quantitative PCR targeting 16S rRNA and reductive dehalogenase genes simultaneously monitors multiple Dehalococcoides strains. Applied and Environmental Microbiology 72(4), 2765-2774.
Ross, D.E., Marshall, C.W., Gulliver, D., May, H.D. and Norman, R.S. 2020. Defining genomic and predicted metabolic features of the Acetobacterium genus. Msystems 5(5), e00277-00220.
Scheutz, C., Durant, N.D., Hansen, M.H. and Bjerg, P.L. 2011. Natural and enhanced anaerobic degradation of 1, 1, 1-trichloroethane and its degradation products in the subsurface–a critical review. Water Research 45(9), 2701-2723.
Schoelmerich, M.C., Katsyv, A., Sung, W., Mijic, V., Wiechmann, A., Kottenhahn, P., Baker, J., Minton, N.P. and Müller, V. 2018. Regulation of lactate metabolism in the acetogenic bacterium Acetobacterium woodii. Environmental Microbiology 20(12), 4587-4595.
Schuchmann, K., Chowdhury, N.P. and Müller, V. 2018. Complex multimeric [FeFe] hydrogenases: biochemistry, physiology and new opportunities for the hydrogen economy. Frontiers in Microbiology 9, 2911.
Schuchmann, K. and Müller, V. 2013. Direct and reversible hydrogenation of CO2 to formate by a bacterial carbon dioxide reductase. Science 342(6164), 1382-1385.
STUPPERICH, E., EISINGER, H.J. and KRÄUTLER, B. 1988. Diversity of corrinoids in acetogenic bacteria: P‐Cresolylcobamide from Sporomusa ovata, 5‐methoxy‐6‐methylbenzimidazolylcobamide from Clostridium formicoaceticum and vitamin B12 from Acetobacterium woodii. European Journal of Biochemistry 172(2), 459-464.
Sun, B., Griffin, B.M., Ayala-del-Rı́o, H.L., Hashsham, S.A. and Tiedje, J.M. 2002. Microbial dehalorespiration with 1, 1, 1-trichloroethane. Science 298(5595), 1023-1025.
Tang, S. and Edwards, E.A. 2013. Identification of Dehalobacter reductive dehalogenases that catalyse dechlorination of chloroform, 1, 1, 1-trichloroethane and 1, 1-dichloroethane. Philosophical Transactions of the Royal Society B: Biological Sciences 368(1616), 20120318.
Trifunović, D., Schuchmann, K. and Müller, V. 2016. Ethylene glycol metabolism in the acetogen Acetobacterium woodii. Journal of Bacteriology 198(7), 1058-1065.
Vargas, C., Ahlert, R.C., Abbott, E.E. and Gayton, M.G. 2018 Anaerobic degradation of chlorinated solvents, pp. 339-346, CRC Press.
Wang, S., Qiu, L., Liu, X., Xu, G., Siegert, M., Lu, Q., Juneau, P., Yu, L., Liang, D. and He, Z. 2018. Electron transport chains in organohalide-respiring bacteria and bioremediation implications. Biotechnology Advances 36(4), 1194-1206.
Wen, L.-L., Chen, J.-X., Fang, J.-Y., Li, A. and Zhao, H.-P. 2017. Effects of 1, 1, 1-trichloroethane and triclocarban on reductive dechlorination of trichloroethene in a TCE-reducing culture. Frontiers in Microbiology 8, 1439.
Westphal, L., Wiechmann, A., Baker, J., Minton, N.P. and Müller, V. 2018. The Rnf complex is an energy-coupled transhydrogenase essential to reversibly link cellular NADH and ferredoxin pools in the acetogen Acetobacterium woodii. Journal of Bacteriology 200(21), e00357-00318.
Wiechmann, A., Ciurus, S., Oswald, F., Seiler, V.N. and Müller, V. 2020. It does not always take two to tango:“Syntrophy” via hydrogen cycling in one bacterial cell. ISME J 14(6), 1561-1570.
Wong, Y.K., Holland, S.I., Ertan, H., Manefield, M. and Lee, M. 2016. Isolation and characterization of Dehalobacter sp. strain UNSWDHB capable of chloroform and chlorinated ethane respiration. Environmental Microbiology 18(9), 3092-3105.
Yan, J., Ritalahti, K.M., Wagner, D.D. and Löffler, F.E. 2012. Unexpected specificity of interspecies cobamide transfer from Geobacter spp. to organohalide-respiring Dehalococcoides mccartyi strains. Applied and Environmental Microbiology 78(18), 6630-6636.
Yang, M.I., Previdsa, M., Edwards, E.A. and Sleep, B.E. 2020. Two distinct Dehalobacter strains sequentially dechlorinate 1, 1, 1-trichloroethane and 1, 1-dichloroethane at a field site treated with granular zero valent iron and guar gum. Water Research 186, 116310.
Yang, Y., Cápiro, N.L., Yan, J., Marcet, T.F., Pennell, K.D. and Löffler, F.E. 2017. Resilience and recovery of Dehalococcoides mccartyi following low pH exposure. FEMS Microbiology Ecology 93(12), fix130.

指導教授

陳師慶

審核日期

2023-7-20

推文