以宏觀基因體分析新穎 Candidatus Dehalobacterium strain DLY  降解二氯甲烷機制

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丁律妤(Lu-Yu Ding) 查詢紙本館藏

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以宏觀基因體分析新穎 Candidatus Dehalobacterium strain DLY 降解二氯甲烷機制
(The mechanisms of novel Candidatus Dehalobacterium strain DLY for degrading dichloromethane with metagenomic analysis)

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摘要(中)

全球主要的污染物為含氯脂肪族碳氫化合物（Chlorinated aliphatic hydrocarbons, CAHs），因 CAHs 為重質非水溶相液體（Dense Non-aqueoes Phase Liquid, DNAPL），一旦進入地下水層則易形成污染團累積底層，造成難以根除的困境，二氯甲烷（Dichloromethane, DCM）污染議題在近年逐漸受到重視，而在國際上討論厭氧降解二氯甲烷菌株相對少。本實驗目的致力於培養及篩選台灣本土厭氧降解二氯甲烷菌群，以
二氯甲烷做為單一碳源進行增殖培養，發現菌屬 Dehalobacterium 成為主要優勢菌，在菌群 GW08 中佔比高達 81.2%。在 13 C 標記二氯甲烷進行培養實驗結果，以氣相層析質譜儀分析後確立代謝產物主要為二氧化碳（Carbon dioxide）及醋酸（Acetate），展現二氯甲烷降解透過 Wood-Ljungdahl pathway。以宏觀基因體進行分析（Metagenomic analysis），在平均核甘酸相似性及平均胺基酸相似性結果表明此株細菌為新穎菌株並命名為 Candidatus Dehalobacterium strain DLY。以反轉錄即時定量聚合酶連鎖反應（RT-qPCR）分析可能參與降解二氯甲烷 mec gene cassette 表現，結果中 10 個 mec 基因皆有顯著性增加，確立 mec gene cassette 參與將二氯甲烷與四氫葉酸（Tetrahydrofolate）形成5, 10-methylene-tetrahydrofolate，並透過 Wood-Ljungdahl pathway 產生二氧化碳及醋酸。本研究針對 Candidatus Dehalobacterium strain DLY 之降解途徑、產物、基因體及基因表現，建立降解二氯甲烷系統，提供以生物修復法整治二氯甲烷污染場址之策略。

摘要(英)

Chlorinated aliphatic hydrocarbons (CAHs) are the major pollutants globally. Due to CAHs are Dense Non-aqueous Phase Liquid (DNAPL), they can accumulate in the lower layers of contaminated groundwater, making their removal challenging. The issue of dichloromethane (DCM) pollution has gained attention in recent years, although there has been limited research on anaerobic DCM-degrading bacteria strains internationally. The bacteria consortia of DCM-contaminated groundwater were sampled. After the enrichment of this consortium using DCM as the sole carbon source in the defined medium, we found that the Dehalobacterium genus accounted for 81.2% of the community. To delineate the by-product of DCM by bacterial consortia, we proved that carbon dioxide and acetate were major by-product using gas chromatography-mass spectrometry (GC-MS) analysis. The stable carbon isotope experiments provided further evidence that the organism utilized carbon from DCM through the Wood-
Ljungdahl pathway. Metagenomic analysis was conducted. With the Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI) analysis, Candidatus Dehalobacterium strain DLY, one novel bacterium was confirmed. The discovery of the mec gene cassette in the
genome of Candidatus Dehalobacterium strain DLY suggests its potential involvement in the degradation of DCM. Using RT-qPCR analysis, it was found that all 10 mec genes showed a
significant increase. The involvement of the mec gene cassette in the degradation of DCM, leading to the formation of 5, 10-methylene-tetrahydrofolate and the subsequent production of carbon dioxide and acetate via the Wood-Ljungdahl pathway has been established. This study
focused on the degradation pathways, products, genome, and gene expression of Candidatus Dehalobacterium strain DLY in the context of DCM degradation. A comprehensive
understanding of these aspects was obtained, leading to the establishment of a DCM degradation system. This research provides a strategy for utilizing bioremediation methods to address dichloromethane-contaminated sites.

關鍵字(中)

★ 二氯甲烷
★ Dehalobacterium
★ mec gene cassette
★ Wood-Ljungdahl 途徑
★ 宏觀基因體

關鍵字(英)

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 xi
表目錄 xii
第壹章緒論（Introduction） 1
1.2 微生物生物整治 2
1.2.1 生物修復法應用於含氯有機物污染場址 2
1.2.2 厭氧菌群應用於含氯有機物污染場址 3
1.3 二氯甲烷(Dichloromethane, methylene chloride） 3
1.3.1 二氯甲烷對於環境及人體的危害與影響 3
1.3.2 二氯甲烷之型態、污染來源 4
1.3.3 二氯甲烷降解相關菌株 5
1.3.4 厭氧二氯甲烷降解細菌之代謝及降解路徑 6
第貳章實驗目的和實驗架構（Purpose and Architecture） 8
第參章實驗材料與方法（Materials and Methods） 10
3.1 實驗材料 10
3.1.1 常用藥品與試劑 10
3.2 實驗方法 12
3.2.1 厭氧降解二氯甲烷之菌群來源與繼代培養 12
3.2.2 菌株來源、保存與繼代培養(E.coli) 13
3.2.3 氣相層析火焰離子化偵檢器（Gas chromatography-flame ionization detector, GC-FID） 13
3.2.4 氣相層析質譜儀（Gas Chromatography-Mass Spectrometry, GC-MS） 14
3.2.5 細菌Genomic DNA萃取 14
3.2.6 細菌RNA萃取 15
3.2.7 反轉錄作用 16
3.2.8 DNA洋菜膠電泳 16
3.2.9 TSS法之大腸桿菌勝任細胞備製 17
3.2.10 TSS法之大腸桿菌勝任細胞轉型（Transformation） 17
3.2.11 DNA膠體純化 18
3.2.12 質體純化 18
3.2.13 聚合酶連鎖反應（Polymerase chain reaction, PCR） 19
3.2.14 即時聚合酶連鎖反應（Real-time polymerase chain reaction, qPCR） 19
3.2.15 反轉錄即時聚合酶連鎖反應（Reverse transcription-quantitative polymerase chain reaction, RT-qPCR） 20
3.2.16 Colony PCR 20
3.2.17 TA Clone基因選殖 21
3.2.18 醋酸濃度測定 21
3.2.19 次世代全基因定序（Next Generation Sequencing, NGS） 22
3.2.20 Full-length 16S rRNA gene amplicon analysis 23
3.2.21 宏觀基因體學分析(Metagenomic analysis) 24
3.2.22 平均核甘酸相似性Average Nucleotide Identity (ANI) 及平均胺基酸相似性 Average Amino acid Identity(AAI)分析 25
3.2.23 親緣關係樹狀圖分析（Phylogenomic analysis） 25
第肆章實驗結果（Results） 26
4.1 從台灣本土地下水中篩選降解二氯甲烷菌群其降解特性 26
4.2 厭氧降解二氯甲烷菌群GW08之菌相組成 26
4.3 以GC-MS分析13C標定二氯甲烷菌群降解之產物 27
4.4 台灣本土菌群菌種Dehalobacterium之宏觀基因體學分析 28
4.5 以RT-qPCR分析Ca. Dehalobacterium strain DLY降解二氯甲烷之代謝基因表現 29
第伍章討論（Discussion） 31
5.1 探討菌群GW08降解二氯甲烷之特性及代謝產物分析 31
5.1.1 探討菌群GW08培養條件及特性 31
5.1.2 以GC-MS分析菌群GW08降解二氯甲烷之代謝產物 32
5.2 探討菌群GW08菌相 33
5.2.1 菌群GW08中Dehalobacterium菌種佔比變化 33
5.2.2 菌群GW08菌相其他菌種組成及功能分析 33
5.2.3利用共現網絡（co-occurrence network）分析菌群中細菌間相互關係 34
5.3 Candidatus Dehalobacterium strain DLY菌種鑑定、命名 35
5.4 探討Candidatus Dehalobacterium strain DLY全基因特徵及代謝非氯化物之物質之可能性 36
5.5 探討Candidatus Dehalobacterium strain DLY降解二氯甲烷之mec gene cassette基因表現 40
第六章結論（Conclusion） 41
參考文獻（Reference） 42
圖表 49
附加資料（Supplementary File） 64

參考文獻

Abatenh, E., Gizaw, B., Tsegaye, Z., Wassie, M., 2017. The role of microorganisms in bioremediation-A review. Open Journal of Environmental Biology 2(1), 038-046.
Adams, G.O., Fufeyin, P.T., Okoro, S.E., Ehinomen, I., 2015. Bioremediation, biostimulation and bioaugmention: a review. International Journal of Environmental Bioremediation & Biodegradation 3(1), 28-39.
Adesodun, J., Mbagwu, J., 2008. Biodegradation of waste-lubricating petroleum oil in a tropical alfisol as mediated by animal droppings. Bioresource Technology 99(13), 5659-5665.
Adetutu, E.M., Gundry, T.D., Patil, S.S., Golneshin, A., Adigun, J., Bhaskarla, V., Aleer, S., Shahsavari, E., Ross, E., Ball, A.S., 2015. Exploiting the intrinsic microbial degradative potential for field-based in situ dechlorination of trichloroethene contaminated groundwater. Journal of Hazardous Materials 300, 48-57.
Ahmad, F., Zhu, D., Sun, J., 2020. Bacterial chemotaxis: a way forward to aromatic compounds biodegradation. Environmental Sciences Europe 32, 1-18.
Al-Sulaimani, H., Joshi, S., Al-Wahaibi, Y., Al-Bahry, S., Elshafie, A., Al-Bemani, A., 2011. Microbial biotechnology for enhancing oil recovery: current developments and future prospects. Biotechnol Bioinf Bioeng 1(2), 147-158.
Allocati, N., Federici, L., Masulli, M., Di Ilio, C., 2012. Distribution of glutathione transferases in Gram-positive bacteria and Archaea. Biochimie 94(3), 588-596.
An, M., Western, L.M., Say, D., Chen, L., Claxton, T., Ganesan, A.L., Hossaini, R., Krummel, P.B., Manning, A.J., Mühle, J., 2021. Rapid increase in dichloromethane emissions from China inferred through atmospheric observations. Nature Communications 12(1), 7279.
Andreesen, J.R., Fetzner, S., 2002. The molybdenum-containing hydroxylases of nicotinate, isonicotinate, and nicotine. Met Ions Biol Syst 39, 405-430.
Bell, A., Brunt, J., Crost, E., Vaux, L., Nepravishta, R., Owen, C.D., Latousakis, D., Xiao, A., Li, W., Chen, X., 2019. Elucidation of a sialic acid metabolism pathway in mucus-foraging Ruminococcus gnavus unravels mechanisms of bacterial adaptation to the gut. Nature Microbiology 4(12), 2393-2404.
Blazquez-Palli, N., Rosell, M., Varias, J., Bosch, M., Soler, A., Vicent, T., Marco-Urrea, E., 2019. Multi-method assessment of the intrinsic biodegradation potential of an aquifer contaminated with chlorinated ethenes at an industrial area in Barcelona (Spain). Environ. Pollut. 244, 165-173.
Burke, S.A., Lo, S.L., Krzycki, J.A., 1998. Clustered genes encoding the methyltransferases of methanogenesis from monomethylamine. J. Bacteriol. 180(13), 3432-3440.
Caccavo Jr, F., Coates, J.D., Rossello-Mora, R.A., Ludwig, W., Schleifer, K.H., Lovley, D.R., McInerney, M.J., 1996. Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe (III)-reducing bacterium. Archives of Microbiology 165, 370-376.
Carmona, M., Zamarro, M.T., Blázquez, B., Durante-Rodríguez, G., Juárez, J.F., Valderrama, J.A., Barragán, M.J., García, J.L., Díaz, E., 2009. Anaerobic catabolism of aromatic compounds: a genetic and genomic view. Microbiol. Mol. Biol. Rev. 73(1), 71-133.
Chan, C.C., Mundle, S.O., Eckert, T., Liang, X., Tang, S., Lacrampe-Couloume, G., Edwards, E.A., Sherwood Lollar, B., 2012. Large carbon isotope fractionation during biodegradation of chloroform by Dehalobacter cultures. Environmental Science & Technology 46(18), 10154-10160.
Chen, G., Fisch, A.R., Gibson, C.M., Erin Mack, E., Seger, E.S., Campagna, S.R., Löffler, F.E., 2020. Mineralization versus fermentation: evidence for two distinct anaerobic bacterial degradation pathways for dichloromethane. The ISME Journal 14(4), 959-970.
Chiu, P.C., Lee, M., 2001. 2-Bromoethanesulfonate affects bacteria in a trichloroethene- dechlorinating culture. Applied and Environmental Microbiology 67(5), 2371-2374.
Ciuffreda, L., Rodríguez-Pérez, H., Flores, C., 2021. Nanopore sequencing and its application to the study of microbial communities. Computational and Structural Biotechnology Journal 19, 1497-1511.
Csonka, L.N., 1989. Physiological and genetic responses of bacteria to osmotic stress. Microbiological Reviews 53(1), 121-147.
Dekant, W., Jean, P., Arts, J., 2021. Evaluation of the carcinogenicity of dichloromethane in rats, mice, hamsters and humans. Regul. Toxicol. Pharmacol. 120, 104858.
Ding, C., Zhao, S., He, J., 2014. AD Desulfitobacterium sp. strain PR reductively dechlorinates both 1, 1, 1‐trichloroethane and chloroform. Environ. Microbiol. 16(11), 3387-3397.
Duranti, S., Ruiz, L., Lugli, G.A., Tames, H., Milani, C., Mancabelli, L., Mancino, W., Longhi, G., Carnevali, L., Sgoifo, A., 2020. Bifidobacterium adolescentis as a key member of the human gut microbiota in the production of GABA. Scientific Reports 10(1), 1-13.
Egli, C., Tschan, T., Scholtz, R., Cook, A.M., Leisinger, T., 1988. Transformation of tetrachloromethane to dichloromethane and carbon dioxide by Acetobacterium woodii. Applied and Environmental Microbiology 54(11), 2819-2824.
Fagervold, S.K., Watts, J.E., May, H.D., Sowers, K.R., 2005. Sequential reductive dechlorination of meta-chlorinated polychlorinated biphenyl congeners in sediment microcosms by two different Chloroflexi phylotypes. Applied and Environmental Microbiology 71(12), 8085-8090.
Fagin, J., Bradley, J., Williams, D., 1980. Carbon monoxide poisoning secondary to inhaling methylene chloride. Br. Med. J. 281(6253), 1461.
Fennell, D.E., Nijenhuis, I., Wilson, S.F., Zinder, S.H., Häggblom, M.M., 2004. Dehalococcoides ethenogenes strain 195 reductively dechlorinates diverse chlorinated aromatic pollutants. Environmental Science & Technology 38(7), 2075-2081.
Franke, T., Deppenmeier, U., 2018. Physiology and central carbon metabolism of the gut bacterium Prevotella copri. Mol. Microbiol. 109(4), 528-540.
Furukawa, K., Miyazaki, T., 1986. Cloning of a gene cluster encoding biphenyl and chlorobiphenyl degradation in Pseudomonas pseudoalcaligenes. J. Bacteriol. 166(2), 392- 398.
Galinski, E., Trüper, H., 1982. Betaine, a compatible solute in the extremely halophilic phototrophic bacterium Ectothiorhodospira halochloris. FEMS Microbiol. Lett. 13(4), 357-360.
Galperin, M.Y., Wolf, Y.I., Makarova, K.S., Vera Alvarez, R., Landsman, D., Koonin, E.V., 2021. COG database update: focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Res. 49(D1), D274-D281.
Geesink, P., Taubert, M., Jehmlich, N., von Bergen, M., Küsel, K., 2022. Bacterial necromass is rapidly metabolized by heterotrophic bacteria and supports multiple trophic levels of the groundwater microbiome. Microbiology Spectrum 10(4), e00437-00422.
Gordillo, F., Chávez, F.P., Jerez, C.A., 2007. Motility and chemotaxis of Pseudomonas sp. B4 towards polychlorobiphenyls and chlorobenzoates. FEMS Microbiol. Ecol. 60(2), 322-328.
Grabowski, A., Tindall, B.J., Bardin, V., Blanchet, D., Jeanthon, C., 2005. Petrimonas sulfuriphila gen. nov., sp. nov., a mesophilic fermentative bacterium isolated from a biodegraded oil reservoir. International Journal of Systematic and Evolutionary Microbiology 55(3), 1113-1121.
Grant, J.R., Enns, E., Marinier, E., Mandal, A., Herman, E.K., Chen, C.-y., Graham, M., Van Domselaar, G., Stothard, P., 2023. Proksee: in-depth characterization and visualization of bacterial genomes. Nucleic Acids Res., gkad326.
Gribble, G.W., 2009. Naturally occurring organohalogen compounds-a comprehensive update. Springer Science & Business Media.
Han, G., Shin, S.G., Lee, J., Shin, J., Hwang, S., 2017. A comparative study on the process efficiencies and microbial community structures of six full-scale wet and semi-dry anaerobic digesters treating food wastes. Bioresource Technology 245, 869-875.
Harwood, C.S., Parales, R.E., Dispensa, M., 1990. Chemotaxis of Pseudomonas putida toward chlorinated benzoates. Applied and Environmental Microbiology 56(5), 1501-1503.
Hayoun, K., Geersens, E., Laczny, C.C., Halder, R., Lázaro Sánchez, C., Manna, A., Bringel, F., Ryckelynck, M., Wilmes, P., Muller, E.E., 2020. Dichloromethane degradation pathway from unsequenced Hyphomicrobium sp. MC8b rapidly explored by pan- proteomics. Microorganisms 8(12), 1876.
Hoang, A., Fagan, K., Cannon, D.L., Rayasam, S.D., Harrison, R., Shusterman, D., Singla, V., 2021. Assessment of methylene chloride–related fatalities in the United States, 1980-2018. JAMA Internal Medicine 181(6), 797-805.
Holland, S.I., Edwards, R.J., Ertan, H., Wong, Y.K., Russell, T.L., Deshpande, N.P., Manefield, M.J., Lee, M., 2019. Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture. PeerJ 7, e7775.
Holland, S.I., Ertan, H., Montgomery, K., Manefield, M.J., Lee, M., 2021. Novel dichloromethane-fermenting bacteria in the Peptococcaceae family. The ISME Journal 15(6), 1709-1721.
Holland, S.I., Vázquez-Campos, X., Ertan, H., Edwards, R.J., Manefield, M.J., Lee, M., 2022. Metaproteomics reveals methyltransferases implicated in dichloromethane and glycine betaine fermentation by ‘Candidatus Formimonas warabiya’strain DCMF. Frontiers in Microbiology 13.
Honda, T., Fujita, T., Tonouchi, A., 2013. Aminivibrio pyruvatiphilus gen. nov., sp. nov., an anaerobic, amino-acid-degrading bacterium from soil of a Japanese rice field. International Journal of Systematic and Evolutionary Microbiology 63(Pt_10), 3679- 3686.
Hossaini, R., Chipperfield, M., Montzka, S., Leeson, A., Dhomse, S., Pyle, J., 2017. The increasing threat to stratospheric ozone from dichloromethane, Nat. Commun., 8, 15962.
Humans, I.W.G.o.t.E.o.C.R.t., Cancer, I.A.f.R.o., Organization, W.H., 1999. Re-evaluation of Some Organic Chemicals, Hydrazine and Hydrogen Peroxide: Other compounds reviewed in plenary sessions. IARC.
Imhoff, J.F., 1986. Osmoregulation and compatible solutes in eubacteria. FEMS Microbiol. Rev. 2(1-2), 57-66.
Joint, F., Additives, W.E.C.o.F., Organization, W.H., 1992. Evaluation of certain food additives and naturally occurring toxicants: thirty-ninth report of the Joint FAO. World Health Organization.
Kaiser, J.-P., Feng, Y., Bollag, J.-M., 1996. Microbial metabolism of pyridine, quinoline, acridine, and their derivatives under aerobic and anaerobic conditions. Microbiological Reviews 60(3), 483-498.
Karp, P.D., Billington, R., Caspi, R., Fulcher, C.A., Latendresse, M., Kothari, A., Keseler, I.M., Krummenacker, M., Midford, P.E., Ong, Q., 2019. The BioCyc collection of microbial genomes and metabolic pathways. Briefings in Bioinformatics 20(4), 1085-1093.
Kleindienst, S., Chourey, K., Chen, G., Murdoch, R.W., Higgins, S.A., Iyer, R., Campagna, S.R., Mack, E.E., Seger, E.S., Hettich, R.L., 2019. Proteogenomics reveals novel reductive dehalogenases and methyltransferases expressed during anaerobic dichloromethane metabolism. Applied and Environmental Microbiology 85(6), e02768-02718.
Kleindienst, S., Higgins, S.A., Tsementzi, D., Chen, G., Konstantinidis, K.T., Mack, E.E., Löffler, F.E., 2017. ‘Candidatus Dichloromethanomonas elyunquensis’ gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family. Syst. Appl. Microbiol. 40(3), 150-159.
Konstantinidis, K.T., Rosselló-Móra, R., Amann, R., 2017. Uncultivated microbes in need of their own taxonomy. The ISME Journal 11(11), 2399-2406.
Kueper, B.H., Stroo, H.F., Vogel, C.M., Ward, C.H., 2014. Chlorinated solvent source zone remediation. Springer.
Lacal, J., Alfonso, C., Liu, X., Parales, R.E., Morel, B., Conejero-Lara, F., Rivas, G., Duque, E., Ramos, J.L., Krell, T., 2010. Identification of a chemoreceptor for tricarboxylic acid cycle intermediates: differential chemotactic response towards receptor ligands. J. Biol. Chem. 285(30), 23126-23136.
Lalucat, J., Bennasar, A., Bosch, R., García-Valdés, E., Palleroni, N.J., 2006. Biology of Pseudomonas stutzeri. Microbiol. Mol. Biol. Rev. 70(2), 510-547.
Leedham Elvidge, E., Oram, D., Laube, J., Baker, A., Montzka, S., Humphrey, S., O′Sullivan, D., Brenninkmeijer, C., 2015. Increasing concentrations of dichloromethane, CH 2 Cl 2, inferred from CARIBIC air samples collected 1998–2012. Atmospheric Chemistry and Physics 15(4), 1939-1958.
Lemke, L.D., Abriola, L.M., Goovaerts, P., 2004. Dense nonaqueous phase liquid (DNAPL) source zone characterization: Influence of hydraulic property correlation on predictions of DNAPL infiltration and entrapment. Water Resources Research 40(1).
Liu, H., Wang, J., Wang, A., Chen, J., 2011. Chemical inhibitors of methanogenesis and putative applications. Appl. Microbiol. Biotechnol. 89, 1333-1340.
Liu, S., Ren, F., Zhao, L., Jiang, L., Hao, Y., Jin, J., Zhang, M., Guo, H., Lei, X., Sun, E., 2015. Starch and starch hydrolysates are favorable carbon sources for Bifidobacteria in the human gut. BMC Microbiol. 15(1), 1-9.
Livak, K.J., Schmittgen, T.D., 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2− ΔΔCT method. Methods 25(4), 402-408.
Loffler, F.E., Ritalahti, K.M., Tiedje, J.M., 1997. Dechlorination of chloroethenes is inhibited by 2-bromoethanesulfonate in the absence of methanogens. Applied and Environmental Microbiology 63(12), 4982-4985.
Lomans, B.P., Maas, R., Luderer, R., Op den Camp, H.J., Pol, A., van der Drift, C., Vogels, G.D., 1999. Isolation and characterization of Methanomethylovorans hollandica gen. nov., sp. nov., isolated from freshwater sediment, a methylotrophic methanogen able to grow on dimethyl sulfide and methanethiol. Applied and Environmental Microbiology 65(8), 3641- 3650.
London, J., Knight, M., 1966. Concentrations of nicotinamide nucleotide coenzymes in micro- organisms. Microbiology 44(2), 241-254.
Lopez-Siles, M., Duncan, S.H., Garcia-Gil, L.J., Martinez-Medina, M., 2017. Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics. The ISME Journal 11(4), 841-852.
Loubinoux, J., Valente, F.M., Pereira, I.A., Costa, A., Grimont, P.A., Le Faou, A.E., 2002. Reclassification of the only species of the genus Desulfomonas, Desulfomonas pigra, as Desulfovibrio piger comb. nov. International Journal of Systematic and Evolutionary Microbiology 52(4), 1305-1308.
Lu, S., Wang, J., Chitsaz, F., Derbyshire, M.K., Geer, R.C., Gonzales, N.R., Gwadz, M., Hurwitz, D.I., Marchler, G.H., Song, J.S., 2020. CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res. 48(D1), D265-D268.
Mägli, A., Messmer, M., Leisinger, T., 1998. Metabolism of dichloromethane by the strict anaerobe Dehalobacterium formicoaceticum. Applied and Environmental Microbiology 64(2), 646-650.
Major, D.W., McMaster, M.L., Cox, E.E., Edwards, E.A., Dworatzek, S.M., Hendrickson, E.R., Starr, M.G., Payne, J.A., Buonamici, L.W., 2002. Field demonstration of successful bioaugmentation to achieve dechlorination of tetrachloroethene to ethene. Environmental Science & Technology 36(23), 5106-5116.
Meier-Kolthoff, J.P., Göker, M., 2019. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nature Communications 10(1), 2182.
Mägli, A., Wendt, M., Leisinger, T., 1996. Isolation and characterization of Dehalobacterium formicoaceticum gen. nov. sp. nov., a strictly anaerobic bacterium utilizing dichloromethane as source of carbon and energy. Archives of Microbiology 166(2), 101- 108.
Muller, E.E., Bringel, F., Vuilleumier, S., 2011. Dichloromethane-degrading bacteria in the genomic age. Research in Microbiology 162(9), 869-876.
Murdoch, R.W., Chen, G., Kara Murdoch, F., Mack, E.E., Villalobos Solis, M.I., Hettich, R.L., Loffler, F.E., 2021. Identification and widespread environmental distribution of a gene cassette implicated in anaerobic dichloromethane degradation. Glob Chang Biol.
Murray, R., Schleifer, K., 1994. Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes. International Journal of Systematic and Evolutionary Microbiology 44(1), 174-176.
Němec, M., Zachariáš, J., 2018. The Krásná Hora, Milešov, and Příčovy Sb-Au ore deposits, Bohemian Massif: mineralogy, fluid inclusions, and stable isotope constraints on the deposit formation. Mineralium Deposita 53(2), 225-244.
Nijenhuis, I., Schmidt, M., Pellegatti, E., Paramatti, E., Richnow, H.H., Gargini, A., 2013. A stable isotope approach for source apportionment of chlorinated ethene plumes at a complex multi-contamination events urban site. Journal of Contaminant Hydrology 153, 92-105.
Nzila, A., Razzak, S.A., Zhu, J., 2016. Bioaugmentation: an emerging strategy of industrial wastewater treatment for reuse and discharge. International Journal of Environmental Research and Public Health 13(9), 846.
Oren, A., 2021. Nomenclature of prokaryotic ‘Candidatus’ taxa: establishing order in the current chaos. New Microbes and New Infections 44, 100932.
Österberg, S., Skärfstad, E., Shingler, V., 2010. The σ‐factor FliA, ppGpp and DksA coordinate transcriptional control of the aer2 gene of Pseudomonas putida. Environ. Microbiol. 12(6), 1439-1451.
Pérez-de-Mora, A., Lacourt, A., McMaster, M.L., Liang, X., Dworatzek, S.M., Edwards, E.A., 2018. Chlorinated electron acceptor abundance drives selection of Dehalococcoides mccartyi (D. mccartyi) strains in dechlorinating enrichment cultures and groundwater environments. Frontiers in Microbiology 9, 812.
Pal, A.K., Singh, J., Soni, R., Tripathi, P., Kamle, M., Tripathi, V., Kumar, P., 2020. The role of microorganism in bioremediation for sustainable environment management, Bioremediation of pollutants. Elsevier, pp. 227-249.
Pallen, M.J., 2021. The status Candidatus for uncultured taxa of Bacteria and Archaea: SWOT analysis. International Journal of Systematic and Evolutionary Microbiology 71(9).
Paul, L., Ferguson Jr, D.J., Krzycki, J.A., 2000. The trimethylamine methyltransferase gene and multiple dimethylamine methyltransferase genes of Methanosarcina barkeri contain in-frame and read-through amber codons. J. Bacteriol. 182(9), 2520-2529.
Payne, R.B., Fagervold, S.K., May, H.D., Sowers, K.R., 2013. Remediation of polychlorinated biphenyl impacted sediment by concurrent bioaugmentation with anaerobic halorespiring and aerobic degrading bacteria. Environmental Science & Technology 47(8), 3807-3815.
Ragsdale, S.W., Pierce, E., 2008. Acetogenesis and the Wood–Ljungdahl pathway of CO2 fixation. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1784(12), 1873- 1898.
Richter, M., Rosselló-Móra, R., Oliver Glöckner, F., Peplies, J., 2016. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32(6), 929-931.
Rodriguez-R, L.M., Konstantinidis, K.T., 2014. Bypassing cultivation to identify bacterial species. Microbe 9(3), 111-118.
Schwille, F., Pankow, J.F., 1988. Dense chlorinated solvents in porous and fractured media- model experiments.
Seyedabbasi, M.A., Newell, C.J., Adamson, D.T., Sale, T.C., 2012. Relative contribution of DNAPL dissolution and matrix diffusion to the long-term persistence of chlorinated solvent source zones. Journal of Contaminant Hydrology 134, 69-81.
Shestakova, M., Sillanpää, M., 2013. Removal of dichloromethane from ground and wastewater: A review. Chemosphere 93(7), 1258-1267.
Slunge, D., Andersson, I., Sterner, T., 2022. REACH authorisation and the substitution of hazardous chemicals: The case of trichloroethylene. Journal of Cleaner Production 364, 132637.
Sourjik, V., Wingreen, N.S., 2012. Responding to chemical gradients: bacterial chemotaxis. Curr. Opin. Cell Biol. 24(2), 262-268.
Stams, A., Hansen, T., 1984. Fermentation of glutamate and other compounds by Acidaminobacter hydrogenoformans gen. nov. sp. nov., an obligate anaerobe isolated from black mud. Studies with pure cultures and mixed cultures with sulfate-reducing and methanogenic bacteria. Archives of Microbiology 137, 329-337.
Starkey, R., 2014. REACH authorisation or substitution of trichloroethylene–future options? Taylor & Francis.
Stroo, H.F., Major, D.W., Gossett, J.M., 2010. Bioaugmentation for anaerobic bioremediation of chlorinated solvents. In Situ Remediation of Chlorinated Solvent Plumes, 425-454.
Substances, A.f.T., Registry, D., 2015. Priority list of hazardous substances. ATSDR Atlanta.
Sun, L., Toyonaga, M., Ohashi, A., Tourlousse, D.M., Matsuura, N., Meng, X.-Y., Tamaki, H., Hanada, S., Cruz, R., Yamaguchi, T., 2016. Lentimicrobium saccharophilum gen. nov., sp. nov., a strictly anaerobic bacterium representing a new family in the phylum Bacteroidetes, and proposal of Lentimicrobiaceae fam. nov. International Journal of Systematic and Evolutionary Microbiology 66(7), 2635-2642.
Tamura, K., Stecher, G., Kumar, S., 2021. MEGA11: molecular evolutionary genetics analysis version 11. Mol. Biol. Evol. 38(7), 3022-3027.
Tang, S., 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.
Tatusova, T., DiCuccio, M., Badretdin, A., Chetvernin, V., Nawrocki, E.P., Zaslavsky, L., Lomsadze, A., Pruitt, K.D., Borodovsky, M., Ostell, J., 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44(14), 6614-6624.
Thangaraj, M., Amutha, S., 2018. Mgephi: Modified gephi for effective social network analysis. International Journal of Scientific Research in Computer Science, Engineering and Information Technology 1(1), 39-50.
Trudinger, C., Etheridge, D., Sturrock, G., Fraser, P., Krummel, P., McCulloch, A., 2004. Atmospheric histories of halocarbons from analysis of Antarctic firn air: Methyl bromide, methyl chloride, chloroform, and dichloromethane. Journal of Geophysical Research: Atmospheres 109(D22).
Trueba-Santiso, A., Parladé, E., Rosell, M., Lliros, M., Mortan, S.H., Martínez-Alonso, M., Gaju, N., Martín-González, L., Vicent, T., Marco-Urrea, E., 2017. Molecular and carbon isotopic characterization of an anaerobic stable enrichment culture containing Dehalobacterium sp. during dichloromethane fermentation. Sci. Total Environ. 581, 640- 648.
Ueki, A., Goto, K., Ohtaki, Y., Kaku, N., Ueki, K., 2017. Description of Anaerotignum aminivorans gen. nov., sp. nov., a strictly anaerobic, amino-acid-decomposing bacterium isolated from a methanogenic reactor, and reclassification of Clostridium propionicum, Clostridium neopropionicum and Clostridium lactatifermentans as species of the genus Anaerotignum. International Journal of Systematic and Evolutionary Microbiology 67(10), 4146-4153.
USEPA, 2020. Superfund Remedy Report 16th Edition.
Wang, X., Xin, J., Yuan, M., Zhao, F., 2020. Electron competition and electron selectivity in abiotic, biotic, and coupled systems for dechlorinating chlorinated aliphatic hydrocarbons in groundwater: A review. Water Research 183, 116060.
Wanner, P., Parker, B.L., Chapman, S.W., Lima, G., Gilmore, A., Mack, E.E., Aravena, R., 2018. Identification of degradation pathways of chlorohydrocarbons in saturated low- permeability sediments using compound-specific isotope analysis. Environmental Science & Technology 52(13), 7296-7306.
Wargo, M.J., 2013. Homeostasis and catabolism of choline and glycine betaine: lessons from Pseudomonas aeruginosa. Applied and Environmental Microbiology 79(7), 2112-2120.
Wei, X., Ouyang, K., Long, T., Liu, Z., Li, Y., Qiu, Q., 2022. Dynamic variations in rumen fermentation characteristics and bacterial community composition during in vitro fermentation. Fermentation 8(6), 276.
Wilson, J.D., 2000. Toxicological profile for methylene chloride.
Wong, Y.K., Holland, S.I., Ertan, H., Manefield, M., Lee, M., 2016. Isolation and characterization of Dehalobacter sp. strain UNSWDHB capable of chloroform and chlorinated ethane respiration. Environ. Microbiol. 18(9), 3092-3105.
Xiao, Z., Jiang, W., Chen, D., Xu, Y., 2020. Bioremediation of typical chlorinated hydrocarbons by microbial reductive dechlorination and its key players: A review. Ecotoxicology and Environmental Safety 202, 110925.
Ye, D., Quensen III, J.F., Tiedje, J.M., Boyd, S.A., 1999. 2-Bromoethanesulfonate, sulfate, molybdate, and ethanesulfonate inhibit anaerobic dechlorination of polychlorobiphenyls by pasteurized microorganisms. Applied and Environmental Microbiology 65(1), 327-329.
林財富, 2023. 重質非水相液體(DNAPL)汙染場址調查及整治.

指導教授

陳師慶

審核日期

2023-7-20

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