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研究生:王嘉琪
研究生(外文):Chia-Chi Wang
論文名稱:探討不同含氯有機物污染場址之脫鹵微生物菌相與數量變化及共生微生物存在之意義
論文名稱(外文):Using Molecular Biotechnology to Explore the Meaning of Co-existed Microorganisms in Different Chlorinated Organics Contaminated Sites
指導教授:洪俊雄洪俊雄引用關係
指導教授(外文):Chun-Hsiung Hung
口試委員:張怡塘張育傑
口試委員(外文):Yi-Tang ChangYu-Jie Chang
口試日期:2015-07-29
學位類別:碩士
校院名稱:國立中興大學
系所名稱:環境工程學系所
學門:工程學門
學類:環境工程學類
論文種類:學術論文
論文出版年:2015
畢業學年度:103
語文別:中文
論文頁數:107
中文關鍵詞:脫鹵球菌還原脫鹵酶(RDase)甲烷菌四氯乙烯三氯乙烯
外文關鍵詞:Dehalococcoides sp.RDaseMethanogensco-existed microorganismstetrachloroethylenetrichloroethylene
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  本研究運用分子生物技術(PCR-DGGE、qPCR)探討台灣本島不同地區之含氯有機物污染場址之脫鹵微生物菌相與數量變化及與其共生微生物存在之意義。由PCR-DGGE分析結果可知,不同污染場址之脫鹵球菌菌相組成皆相當單純,經過定序比對後發現,各場址脫鹵球菌之16S rRNA gene序列相似度高,較無法清楚鑑定出在環境中進行脫鹵作用之脫鹵球菌差異。後續實驗輔以脫鹵球菌所具有之四種還原脫鹵酶(pceA、tceA、vcrA、bvcA,統稱RDase)作為分析對象,期望能以功能性基因分析並判斷存在環境中進行脫鹵作用之脫鹵球菌菌種。針對功能性基因進行DGGE分析的結果顯示,各樣本均僅有單一亮帶訊號,經由定序結果發現使用功能性基因雖然可縮小比對範圍,但仍無法確切地鑑定環境中之脫鹵球菌種類差異。
  另一方面,本研究場址中與脫鹵球菌共生之真細菌共有五種,分別為Rubrivivax sp.、Desulfobacter sp.、Rhodobacter sp.、Desulfuromonas sp.、Geobacter sp.。推測Rubrivivax sp.與Rhodobacter sp.在環境中扮演著分解現地有機物並提供脫鹵球菌電子供給者H2的角色;而Geobacter sp.與Desulfuromonas sp.則可能是負責將PCE還原至cis-DCE,雖然這兩株菌行不完全脫鹵作用,但環境中存在的脫鹵球菌隨後可依照其所能接受之電子接受者將cis-DCE降解至無毒的ETH。此外,現場址中與脫鹵球菌共生之甲烷菌有八種,分別為Methermicoccus sp.、Methanomassiliicoccus sp.、Methanobacterium sp.、Candidatus Methanoregula sp.、Methanosaeta sp.、Methanosarcina subterranean、Methanogenic archaeon、Methanosarcina sp.。這些菌株雖然以不同基質產生甲烷,但此結果與文獻指出PCE於甲烷化階段可接受電子進行還原脫氯作用相呼應,因此,由本研究於菌相結果顯示脫鹵球菌於脫氯作用中,環境存在真細菌群與甲烷菌群能夠以共代謝方式輔助脫鹵球菌執行完全還原脫氯作用,不易使受氯化有機物污染場址於整治過程因產生中間有毒產物而導致降解速率減緩,反而有利含氯有機物場址之生物整治。
  於數量方面,進行生物刺激確實有效使微生物數量大幅增加約102-104 folds可加速生物降解含氯有機物之速率,但過量的氯化有機物或電子接受者可能會導致微生物無法負荷而停止生長造成數量降低,故生物刺激方式需注意微生物的營養生理代謝反應。


  In this study, molecular biotechnology (PCR-DGGE and qPCR) was used to explore the variations of Dehalococcoides microbial structure as well as the meaning of co-existed microorganisms under different chlorinated organics contaminated sites in Taiwan. According to PCR-DGGE analysis results, the microorganism structure of Dehalococcoides sp. is relatively simple. Because 16S rRNA gene sequence of Dehalococcoides are highly similar to each other, it is difficult to identify which particular microorganism has direct contribution on dechlorination. Subsequently, the functional gene of Dehalococcoides sp.─ reductive dehalogenase gene (RDase) was used to analyze the microorganism structure of RDase, which results were as same as that of Dehalococcoides sp. 16S rRNA gene. Therefore, both Dehalococcoides sp. 16S rRNA gene and functional gene primers are not fully appropriate to identify the species of Dehalococcoides.
  On the other hand, the co-existed microorganisms with Dehalococcoides sp. were Rubrivivax sp., Desulfobacter sp., Rhodobacter sp., Desulfuromonas sp., and Geobacter sp., and they might have different function as Dehalococcoides sp. did in the contaminated sites. For example, the Rubrivivax sp. and Rhodobacter sp. could provid hydrogen for Dehalococcides sp. to reduce PCE, Geobacter sp. and Desulfuromonas sp. might be responsible for reducing PCE to cis-DCE. Furthermore, Methermicoccus sp. such as Methanomassiliicoccus sp.、Methanobacterium sp.、Candidatus Methanoregula sp.、Methanosaeta sp.、Methanosarcina subterranean、Methanogenic archaeon、Methanosarcina sp. were also detected in the contaminated sites. According to references, PCE could be reduced through methanogenesis, which means Methanogens and Dehalococcoides sp. could complexly perform dechlorination by co-metabolism.
  Dehalococcoides quantification analysis showed that the amount of Dehalococcoieds increased significantly about 102-104 folds by the help of biostimulation and chlorinated organic substances biodegradation rate was accelerated as well. In contrast, excessive chlorinated organics or electron acceptor may cause microbes not afford to grow and leads to biomass reduction. It should pay attention to maintain microorganism metabolism and activity if biostimulation was chose for in situ dechlorination treatment.

中文摘要 i
Abstract ii
目錄 iv
圖目錄 viii
表目錄 x
第一章 前言 1
第一節 研究緣起 1
第二節 研究目的 2
第二章 文獻回顧 3
第一節 氯化有機物介紹 3
第二節 氯化有機物污染整治方式 6
一、 物理處理技術 6
(一)抽取處理系統(Pump-and-treat system) 7
(二)土壤蒸氣萃取系統(Soli vapor extraction, SEV) 7
(三)現地玻璃化法(Vitrification and isolation) 8
二、 化學處理技術 8
(一)現地化學氧化法(In situ chemical oxidation, ISCO) 8
(二)透水性反應牆(Permeable Reactive Barrier,PRB) 9
三、 生物處理技術 9
(一)自然衰減(Bioattenuation) 9
(二)生物刺激(Biostimulation) 10
(三)生物添加(Bioaugmentation) 10
第三節 降解氯化有機污染物微生物介紹 11
一、 Dehalococcoides maccartyi strain 195 13
二、 Dehalococcoides sp. strain FL2、strain VS、strain BAV1 13
三、 Dehalococcoides maccartyi strain CBDB1 14
第四節 降解氯化有機污染物之代謝機制 15
一、 醱酵作用(Fermentation) 16
二、 氧化作用(Oxidation) 16
三、 還原脫鹵作用(Reductive Dehalogenation) 16
四、 共代謝作用(Cometabolism) 18
第五節 常見降解氯化有機物污染微生物之共生菌種 22
第六節 脫鹵球菌功能性基因介紹 24
第七節 分子生物學技術之應用 26
一、 16S rDNA與功能性基因 27
二、 聚合酶鏈鎖反應(PCR) 28
三、 變性梯度凝膠電泳(DGGE) 31
四、 基因選殖(Gene Cloning) 33
五、 即時定量聚合酶鏈鎖反應(Real-time PCR) 34
第八節 文獻閱讀心得及研究方向擬定 37
第三章 實驗材料與方法 38
第一節 實驗架構 38
第二節 實驗設備 39
第三節 實驗方法 40
一、樣本前處理 40
(一)樣本清洗 40
(二)DNA萃取 40
(三)DNA濃度量測 41
二、微生物菌群結構分析 41
(一)聚合酶鏈鎖反應(Polymerase chain reaction, PCR) 41
(二)瓊脂凝膠電泳(Agarose gel electrophoresis) 45
(三)變性梯度凝膠電泳 46
(四)Acrylamide/Bis 膠體之DNA純化 47
(五)菌種鑑定 47
三、微生物菌群數量分析 47
(一)基因選殖(Gene Cloning) 47
(二)即時定量聚合酶鏈鎖反應(Real-time PCR) 50
第四章 結果與討論 53
第一節 研究樣本來源說明 53
第二節 台灣現地不同污染場址之脫鹵球菌菌群結構分析 53
一、GW場址之脫鹵球菌菌群結構 53
二、C1場址之脫鹵球菌菌群結構 55
三、C2場址之脫鹵球菌菌群結構 55
第三節 脫鹵球菌菌種鑑定分析 57
第四節 運用功能性基因於脫鹵球菌菌群結構分析 61
一、 功能性基因應用於聚合酶鏈鎖反應器之條件分析 61
第五節 台灣現地不同污染場址之真細菌菌群結構分析 67
一、 GW場址之真細菌菌群結構 67
二、 C1場址之真細菌菌群結構 67
三、 C2場址之真細菌菌群結構 69
第六節 真細菌菌種鑑定分析 71
第七節 台灣現地不同污染場址之甲烷菌菌群結構分析 78
第八節 甲烷菌菌種鑑定分析 79
第九節 數量分析 87
第五章 結論與建議 89
第一節 結論 89
第二節 建議 91
參考文獻 92


中文文獻
王毅賢 (2002) 厭氧/好氧併同處理四氯乙烯之研究. 國立中興大學, 台中市.

呂政信 (2014) 現地透水性反應牆配置對含氯有機溶劑整治效率的影響. 國立交通大學, 新竹市.

洪詩怡 (2011) 飽和含水層中四氯乙烯厭氧分解之菌相分佈研究:管柱試驗. 中興大學, 台中市.

高靈韓 (2014) 應用固相微萃取技術預測實場底泥中四氯乙烯之生物有效性. 中興大學, 台中市.

張凱婷 (2013) 探討台灣含氯碳氫化合物污染場址之Dehalococcoides sp.族群數量及微生物菌相分析. 中興大學, 台中市.

陳秋楊 (2013) 生物處理廢水、資源回收及污染整治. 明志科技大學.

劉瑋晨 (2009) 以基因分析法評估三氯乙烯污染地下水之微生物整治成效. 國立中山大學, 高雄市.

李季眉, and 盧至人 (1997) 含溶解性甲烷單氧氧化酵素之甲烷氧化菌對三氯乙烯之分解 (II).


網路資料
環保署土壤及下水污染整治網
http://sgw.epa.gov.tw/public/ContaminatedSitesMap/Default.aspx?SituationType=Rem_Bulletin

曾怡禎, and 張權英 (2001) 利用分子生物方法分析微生物群落結構.
URL http://www.epa.gov.tw/b/b0100.asp?Ct_Code=06X0001330X0004607

透水性反應牆圖片來源
http://tupian.baike.com/a1_13_34_01300000291746133182342818674_jpg.html
英文文獻
Achenbach Laurie A, Carey Jennifer, and Madigan Michael T (2001) Photosynthetic and phylogenetic primers for detection of anoxygenic phototrophs in natural environments. Applied and Environmental Microbiology 67: 2922-2926.

Aktaş Özgür, Schmidt Kathrin R., Mungenast Sarah, Stoll Claudia, and Tiehm Andreas (2012) Effect of chloroethene concentrations and granular activated carbon on reductive dechlorination rates and growth of Dehalococcoides spp. Bioresource Technology 103: 286-292.

Amann Rudolf I, Krumholz Lee, and Stahl David A (1990) Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. Journal of bacteriology 172: 762-770.

Backlund A. S., Bohlin J., Gustavsson N., and Nilsson T. (2009) Periplasmic c cytochromes and chlorate reduction in Ideonella dechloratans. Appl Environ Microbiol 75: 2439-2445.

Baker Paul W, Futamata Hiroyuki, Harayama Shigeaki, and Watanabe Kazuya (2001) Molecular diversity of pMMO and sMMO in a TCE-contaminated aquifer during bioremediation. FEMS microbiology ecology 38: 161-167.

Behrens S., Azizian M. F., McMurdie P. J., Sabalowsky A., Dolan M. E., Semprini L., and Spormann A. M. (2008) Monitoring abundance and expression of "Dehalococcoides" species chloroethene-reductive dehalogenases in a tetrachloroethene-dechlorinating flow column. Appl Environ Microbiol 74: 5695-5703.

Beja Oded, Suzuki Marcelino T., Heidelberg John F., Nelson William C., Preston Christina M., Hamada Tohru, Eisen Jonathan A., Fraser Claire M., and DeLong Edward F. (2002) Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415: 630-633.

Benigni Romualdo, Bossa Cecilia, Battistelli Chiara Laura, and Tcheremenskaia Olga (2013) IARC Classes 1 and 2 carcinogens are successfully identified by an alternative strategy that detects DNA-reactivity and cell transformation ability of chemicals. Mutation Research/Genetic Toxicology and Environmental Mutagenesis 758: 56-61.

Bond Philip L, Hugenholtz Philip, Keller Jurg, and Blackall Linda L (1995) Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Applied and Environmental Microbiology 61: 1910-1916.

Bouvet Philippe JM, and Grimont Patrick AD (1986) Taxonomy of the genus Acinetobacter with the recognition of Acinetobacter baumannii sp. nov., Acinetobacter haemolyticus sp. nov., Acinetobacter johnsonii sp. nov., and Acinetobacter junii sp. nov. and emended descriptions of Acinetobacter calcoaceticus and Acinetobacter lwoffii. International journal of systematic bacteriology 36: 228-240.

Bräuer Suzanna L, Cadillo-Quiroz Hinsby, Ward Rebekah J, Yavitt Joseph B, and Zinder Stephen H (2011) Methanoregula boonei gen. nov., sp. nov., an acidiphilic methanogen isolated from an acidic peat bog. Int J Syst Evol Microbiol 61: 45-52.

Braker Gesche, Zhou Jizhong, Wu Liyou, Devol Allan H., and Tiedje James M. (2000) Nitrite Reductase Genes (nirK and nirS) as Functional Markers To Investigate Diversity of Denitrifying Bacteria in Pacific Northwest Marine Sediment Communities. Appl. Environ. Microbiol. 66: 2096-2104.

Brandis-Heep Astrid, Gebhardt Norbert A, Thauer Rudolf K, Widdel Friedrich, and Pfennig Norbert (1983) Anaerobic acetate oxidation to CO2 by Desulfobacter postgatei. Archives of microbiology 136: 222-229.

Breitenstein Antje, Saano Aimo, Salkinoja-Salonen Mirja, Andreesen Jan R., and Lechner Ute (2001) Analysis of a 2,4,6-trichlorophenol-dehalogenating enrichment culture and isolation of the dehalogenating member Desulfitobacterium frappieri strain TCP-A. Archives of microbiology 175: 133-142.

Brown T. A. (2004) Gene Cloning and DNA analysis - An introduction.


Bunge Michael, Adrian Lorenz, Kraus Angelika, Opel Matthias, Lorenz Wilhelm G, Andreesen Jan R, Görisch Helmut, and Lechner Ute (2003) Reductive dehalogenation of chlorinated dioxins by an anaerobic bacterium. Nature 421: 357-360.

Bustin Stephen A (2000) Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. Journal of molecular endocrinology 25: 169-193.

Chelius Marisa K, Henn Jennifer A, and Triplett Eric W (2002) Runella zeae sp. nov., a novel gram-negative bacterium from the stems of surface-sterilized Zea mays. Int J Syst Evol Microbiol 52: 2061-2063.

Cheng Lei, Qiu Tian-Lei, Yin Xiao-Bo, Wu Xiao-Lei, Hu Guo-Quan, Deng Yu, and Zhang Hui (2007) Methermicoccus shengliensis gen. nov., sp. nov., a thermophilic, methylotrophic methanogen isolated from oil-production water, and proposal of Methermicoccaceae fam. nov. Int J Syst Evol Microbiol 57: 2964-2969.

Chistoserdova Ludmila, Gomelsky Larissa, Vorholt Julia A, Gomelsky Mark, Tsygankov Yuri D, and Lidstrom Mary E (2000) Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph. Microbiology 146: 233-238.

Chistoserdova Ludmila, Lapidus Alla, Han Cliff, Goodwin Lynne, Saunders Liz, Brettin Tom, Tapia Roxanne, Gilna Paul, Lucas Susan, and Richardson Paul M (2007) Genome of Methylobacillus flagellatus, molecular basis for obligate methylotrophy, and polyphyletic origin of methylotrophy. Journal of bacteriology 189: 4020-4027.

Christ John A, Ramsburg C Andrew, Abriola Linda M, Pennell Kurt D, and Löffler Frank E (2005) Coupling aggressive mass removal with microbial reductive dechlorination for remediation of DNAPL source zones: a review and assessment. Environmental Health Perspectives: 465-477.

Chung Jinwook, Krajmalnik-Brown Rosa, and Rittmann Bruce, E (2007) Bioreduction of trichloroethene using a hydrogen-based membrane biofilm reactor. Environmental Science & Technology 42: 477-483.
Collins MD, Lund BM, Farrow JAE, and Schleifer KH (1983) Chemotaxonomic Study of an Alkalophilic Bacterium, Exiguobacterium aurantiacum gen. nov., sp. nov. Journal of general microbiology 129: 2037-2042.

De Wildeman S., Diekert G., Van Langenhove H., and Verstraete W. (2003) Stereoselective Microbial Dehalorespiration with Vicinal Dichlorinated Alkanes. Applied and Environmental Microbiology 69: 5643-5647.

Dijk JA, Stams AJM, Schraa G, Ballerstedt H, De Bont JAM, and Gerritse J (2003) Anaerobic oxidation of 2-chloroethanol under denitrifying conditions by Pseudomonas stutzeri strain JJ. Applied microbiology and biotechnology 63: 68-74.

Dolfing Jan (1990) Reductive dechlorination of 3-chlorobenzoate is coupled to ATP production and growth in an anaerobic bacterium, strain DCB-1. Archives of microbiology 153: 264-266.

Dridi Bédis, Fardeau Marie-Laure, Ollivier Bernard, Raoult Didier, and Drancourt Michel (2012) Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces. Int J Syst Evol Microbiol 62: 1902-1907.

Egli Christine, Scholtz Rudolf, Cook Alasdair M, and Leisinger Thomas (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: 257-261.

El Fantroussi Saïd, Naveau Henry, and Agathos Spiros N (1998) Anaerobic dechlorinating bacteria. Biotechnology progress 14: 167-188.

Fathepure Babu Z, and Boyd Stephen A (1988) Dependence of tetrachloroethylene dechlorination on methanogenic substrate consumption by Methanosarcina sp. strain DCM. Applied and Environmental Microbiology 54: 2976-2980.

Futagami Taiki, Goto Masatoshi, and Furukawa Kensuke (2008) Biochemical and genetic bases of dehalorespiration. The chemical record 8: 1-12.

Gälli Rene, and McCARTY PERRY L (1989) Biotransformation of 1, 1, 1-trichloroethane, trichloromethane, and tetrachloromethane by a Clostridium sp. Applied and Environmental Microbiology 55: 837-844.

Gantzer Charles J, and Wackett Lawrence P (1991) Reductive dechlorination catalyzed by bacterial transition-metal coenzymes. Environmental Science & Technology 25: 715-722.

Gribble Gordon W (1998) Naturally occurring organohalogen compounds. Accounts of Chemical Research 31: 141-152.

Häggblom Max M, and Bossert Ingeborg D (2003) Halogenated organic compounds-a global perspective. In Dehalogenation: Springer, pp. 3-29.

Hallbeck Lotta, and Pedersen Karsten (2014) The Family Gallionellaceae. In The Prokaryotes: Springer, pp. 853-858.

Hallin Sara, and Lindgren Per-Eric (1999) PCR Detection of Genes Encoding Nitrite Reductase in Denitrifying Bacteria. Appl. Environ. Microbiol. 65: 1652-1657.

Harmsen Hermie JM, Van Kuijk Bernardina LM, Plugge Caroline M, Akkermans Antoon DL, De Vos Willem M, and Stams Alfons JM (1998) Syntrophobacter fumaroxidans sp. nov., a syntrophic propionate-degrading sulfate-reducing bacterium. International journal of systematic bacteriology 48: 1383-1387.

He Jianzhong, Ritalahti Kirsti M., Aiello Michael R., and Löffler Frank 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: 996-1003.

He Shaomei, Gall Daniel L, and McMahon Katherine D (2007) “Candidatus Accumulibacter” population structure in enhanced biological phosphorus removal sludges as revealed by polyphosphate kinase genes. Applied and Environmental Microbiology 73: 5865-5874.


Heid C. A., Stevens J., Livak K. J., and Williams P. M. (1996) Real time quantitative PCR. Genome Res. 6: 986-994.

Hendrickson Edwin R, Payne Jo Ann, Young Roslyn M, Starr Mark G, Perry Michael P, Fahnestock Stephen, Ellis David E, and Ebersole Richard C (2002) Molecular analysis of Dehalococcoides 16S ribosomal DNA from chloroethene-contaminated sites throughout North America and Europe. Applied and Environmental Microbiology 68: 485-495.

Higuchi Russell, Fockler Carita, Dollinger Gavin, and Watson Robert (1993) Kinetic PCR Analysis: Real-time Monitoring of DNA Amplification Reactions. Nat Biotech 11: 1026-1030.

Holliger Christof, Regeard Christophe, and Diekert Gabriele (2003) Dehalogenation by anaerobic bacteria. In Dehalogenation: Springer, pp. 115-157.

Holmes V. F., He J., Lee P. K., and Alvarez-Cohen L. (2006) Discrimination of multiple Dehalococcoides strains in a trichloroethene enrichment by quantification of their reductive dehalogenase genes. Appl Environ Microbiol 72: 5877-5883.

Holscher T., Gorisch H., and Adrian L. (2003) Reductive Dehalogenation of Chlorobenzene Congeners in Cell Extracts of Dehalococcoides sp. Strain CBDB1. Applied and Environmental Microbiology 69: 2999-3001.

Hu Liang Bin, Yang Jing Dong, Zhou Wei, Yin Yu Fen, Chen Jian, and Shi Zhi Qi (2009) Isolation of a Methylobacillus sp. that degrades microcystin toxins associated with cyanobacteria. N Biotechnol 26: 205-211.

Hu Pingsha, Lang Juan, Wawrousek Karen, Yu Jianping, Maness Pin-Ching, and Chen Jin (2012) Draft genome sequence of Rubrivivax gelatinosus CBS. Journal of bacteriology 194: 3262-3262.

Hunkeler D, Aravena R, and Butler BJ (1999) Monitoring microbial dechlorination of tetrachloroethene (PCE) in groundwater using compound-specific stable carbon isotope ratios: microcosm and field studies. Environmental Science & Technology 33: 2733-2738.
Imachi Hiroyuki, Sakai Sanae, Sekiguchi Yuji, Hanada Satoshi, Kamagata Yoichi, Ohashi Akiyoshi, and Harada Hideki (2008) Methanolinea tarda gen. nov., sp. nov., a methane-producing archaeon isolated from a methanogenic digester sludge. Int J Syst Evol Microbiol 58: 294-301.

Iwamoto tomotada, and Masao NASu (2001) Current bioremediation practice and perspective a review. B IOSCIENCAEN DB IOENGINEERING 92: 1-8.

Jayachandran Gopalakrishnan, Görisch Helmut, and Adrian Lorenz (2003) Dehalorespiration with hexachlorobenzene and pentachlorobenzene by Dehalococcoides sp. strain CBDB1. Archives of microbiology 180: 411-416.

Jenkins Owen, Byrom David, and Jones Dorothy (1987) Methylophilus: a new genus of methanol-utilizing bacteria. International journal of systematic bacteriology 37: 446-448.

Johnson David R, Lee Patrick KH, Holmes Victor F, and Alvarez-Cohen Lisa (2005a) An internal reference technique for accurately quantifying specific mRNAs by real-time PCR with application to the tceA reductive dehalogenase gene. Applied and Environmental Microbiology 71: 3866-3871.

Johnson David R, Lee Patrick KH, Holmes Victor F, Fortin Alexander C, and Alvarez-Cohen Lisa (2005b) Transcriptional expression of the tceA gene in a Dehalococcoides-containing microbial enrichment. Applied and Environmental Microbiology 71: 7145-7151.

Jordan Jeanne A (2000) Real-time detection of PCR products and microbiology. A Trends Guide 12: 61-66.

Kalmbach Sibylle, Manz Werner, Wecke Jörg, and Szewzyk Ulrich (1999) Aquabacterium gen. nov., with description of Aquabacterium citratiphilum sp. nov., Aquabacterium parvum sp. nov. and Aquabacterium commune sp. nov., three in situ dominant bacterial species from the Berlin drinking water system. International journal of systematic bacteriology 49: 769-777.

KAMAGATA YOICHI, and MIKAMI EIICHI (1991) Isolation and characterization of a novel thermophilic Methanosaeta strain. International journal of systematic bacteriology 41: 191-196.
Karataş Serdar, Hasar Halil, Taşkan Ergin, Özkaya Bestamin, and Şahinkaya Erkan (2014) Bio-reduction of tetrachloroethen using a H2-based membrane biofilm reactor and community fingerprinting. Water Res 58: 21-28.

Katayama Taiki, Yoshioka Hideyoshi, Mochimaru Hanako, Meng Xian-Ying, Muramoto Yoshiyuki, Usami Jun, Ikeda Hidefumi, Kamagata Yoichi, and Sakata Susumu (2014) Methanohalophilus levihalophilus sp. nov., a slightly halophilic, methylotrophic methanogen isolated from natural gas-bearing deep aquifers, and emended description of the genus Methanohalophilus. Int J Syst Evol Microbiol 64: 2089-2093.

Kotik M., Davidova A., Voriskova J., and Baldrian P. (2013) Bacterial communities in tetrachloroethene-polluted groundwaters: a case study. Sci Total Environ 454-455: 517-527.

Krajmalnik-Brown Rosa, Hölscher Tina, Thomson Ivy N, Saunders F Michael, Ritalahti Kirsti M, and Löffler Frank E (2004) Genetic identification of a putative vinyl chloride reductase in Dehalococcoides sp. strain BAV1. Applied and Environmental Microbiology 70: 6347-6351.

Löffler Frank E, Sun Qing, Li Jieran, and Tiedje James M (2000) 16S rRNA Gene-Based Detection of Tetrachloroethene-Dechlorinating Desulfuromonas andDehalococcoides Species. Applied and Environmental Microbiology 66: 1369-1374.

López-Cortés Alejandro, Schumann Peter, Pukall Rüdiger, and Stackebrandt Erko (2006) Exiguobacterium mexicanum sp. nov. and Exiguobacterium artemiae sp. nov., isolated from the brine shrimp Artemia franciscana. Systematic and Applied Microbiology 29: 183-190.

Labrenz Matthias, Brettar Ingrid, Christen Richard, Flavier Sebastien, Botel Julia, and Hofle Manfred G. (2004) Development and Application of a Real-Time PCR Approach for Quantification of Uncultured Bacteria in the Central Baltic Sea. Appl. Environ. Microbiol. 70: 4971-4979.

LARKIN JOHN M, and WILLIAMS PATRICIA M (1978) Runella slithyformis gen. nov., sp. nov., a curved, nonflexible, pink bacterium. International journal of systematic bacteriology 28: 32-36.
Lee P. K., Johnson D. R., Holmes V. F., He J., and Alvarez-Cohen L. (2006) Reductive dehalogenase gene expression as a biomarker for physiological activity of Dehalococcoides spp. Appl Environ Microbiol 72: 6161-6168.

Lei Shih-En (2000) Cleanup TCE and PCE-contaminated Site Using Bioremediation Technology.

Linde Hans-Jörg, Hahn Joachim, Holler Ernst, Reischl Udo, and Lehn Norbert (2002) Septicemia due to Acinetobacter junii. Journal of clinical microbiology 40: 2696-2697.

Lindqvist M. H., Johansson N., Nilsson T., and Rova M. (2012) Expression of chlorite dismutase and chlorate reductase in the presence of oxygen and/or chlorate as the terminal electron acceptor in Ideonella dechloratans. Appl Environ Microbiol 78: 4380-4385.

Liu Wen-Tso, Marsh Terence L, Cheng Hans, and Forney Larry J (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Applied and Environmental Microbiology 63: 4516-4522.

Liu Wen-Tso, Mino Takashi, Nakamura Kazunori, and Matsuo Tomonori (1996) Glycogen accumulating population and its anaerobic substrate uptake in anaerobic-aerobic activated sludge without biological phosphorus removal. Water Res 30: 75-82.

Loffler F. E., Yan J., Ritalahti K. M., Adrian L., Edwards E. A., Konstantinidis K. T., Muller 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. Int J Syst Evol Microbiol 63: 625-635.

Love John L., Scholes Paula, Gilpin Brent, Savill Marion, Lin Susan, and Samuel Laly (2006) Evaluation of uncertainty in quantitative real-time PCR. Journal of Microbiological Methods 67: 349-356.

Lovley Derek R, WMte David ?, and Pye Kenneth (1993) Reduction of Fe (in) in sediments by sulphate-reducing bacteria. Nature 361.

Lu Huabing, Oehmen Adrian, Virdis Bernardino, Keller Jürg, and Yuan Zhiguo (2006) Obtaining highly enriched cultures of Candidatus Accumulibacter phosphates through alternating carbon sources. Water Res 40: 3838-3848.

Maness Pin-Ching, Smolinski Sharon, Dillon Anne C, Heben Michael J, and Weaver Paul F (2002) Characterization of the oxygen tolerance of a hydrogenase linked to a carbon monoxide oxidation pathway in Rubrivivax gelatinosus. Applied and Environmental Microbiology 68: 2633-2636.

Maness Pin-Ching, and Weaver Paul F. (2002) Hydrogen production from a carbon-monoxide oxidation pathway in Rubrivivax gelatinosus. International Journal of Hydrogen Energy 27: 1407-1411.

Matturro B., Tandoi V., and Rossetti S. (2013) Different activity levels of Dehalococcoides mccartyi revealed by FISH and CARD-FISH under non-steady and pseudo-steady state conditions. N Biotechnol 30: 756-762.

Maymo-Gatell Xavier, Chien Yueh-tyng, Gossett James M, and Zinder Stephen H (1997) Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 276: 1568-1571.

Maymo´-Gatell Xavier, Anguish Timothy, and Zinder Stephen H. (1999) Reductive Dechlorination of Chlorinated Ethenes and 1,2-Dichloroethane by “Dehalococcoides ethenogenes” 195. Applied and Environmental Microbiology 65: 3108–3113.

McDonald I. R., and Murrell J. C. (1997) The methanol dehydrogenase structural gene mxaF and its use as a functional gene probe for methanotrophs and methylotrophs. Appl. Environ. Microbiol. 63: 3218-3224.

Nakatsu Cindy H, Hristova Krassimira, Hanada Satoshi, Meng Xian-Ying, Hanson Jessica R, Scow Kate M, and Kamagata Yoichi (2006) Methylibium petroleiphilum gen. nov., sp. nov., a novel methyl tert-butyl ether-degrading methylotroph of the Betaproteobacteria. Int J Syst Evol Microbiol 56: 983-989.
Nielsen Alex T., Liu Wen-Tso, Filipe Carlos, Leslie Grady JR., Molin Soren, and Stahl David A. (1999) Identification of a Novel Group of Bacteria in Sludge from a Deteriorated Biological Phosphorus Removal Reactor. Applied and Environmental Microbiology 65: 1251-1258.

Nishino Shirley F, and Spain Jim C (1995) Oxidative Pathway for the Biodegradation of Nitrobenzene by Comamonas sp. Strain JS765. Applied and Environmental Microbiology 61: 2308-2313.

Öberg Gunilla (2002) The natural chlorine cycle–fitting the scattered pieces. Applied microbiology and biotechnology 58: 565-581.

Ohta H, and Hattori T (1985) In Validation of the publication of new names and new combinations previously effectively published outside the IJSB. List No. 17. Int. J. Syst. Bacteriol 35: 223-225.

Ouellette Anthony JA, and Wilhelm Steven W (2003) Toxic cyanobacteria: the evolving molecular toolbox. Frontiers in Ecology and the Environment 1: 359-366.

PATEL GIRISHCHANDRA B, and SPROTT G DENNIS (1990) Methanosaeta concilii gen. nov., sp. nov.(“Methanothrix concilii”) and Methanosaeta thermoacetophila nom. rev., comb. nov. International journal of systematic bacteriology 40: 79-82.

Purkhold Ulrike, Pommerening-Roser Andreas, Juretschko Stefan, Schmid Markus C., Koops Hans-Peter, and Wagner Michael (2000) Phylogeny of All Recognized Species of Ammonia Oxidizers Based on Comparative 16S rRNA and amoA Sequence Analysis: Implications for Molecular Diversity Surveys. Appl. Environ. Microbiol. 66: 5368-5382.

Röling Wilfred FM (2014) The Family Geobacteraceae. The Prokaryotes: Deltaproteobacteria and Epsilonproteobacteria: 157-172.

Ranchou-Peyruse Anthony, Herbert Rodney, Caumette Pierre, and Guyoneaud R矇my (2006) Comparison of cultivation-dependent and molecular methods for studying the diversity of anoxygenic purple phototrophs in sediments of an eutrophic brackish lagoon. Environmental microbiology 8: 1590-1599.
Rivett Michael O., Dearden Rachel A., and Wealthall Gary P. (2014) Architecture, persistence and dissolution of a 20 to 45 year old trichloroethene DNAPL source zone. Journal of Contaminant Hydrology 170: 95-115.

Rivett Michael O., Turner Ryan J., Glibbery Penny, and Cuthbert Mark O. (2012) The legacy of chlorinated solvents in the Birmingham aquifer, UK: Observations spanning three decades and the challenge of future urban groundwater development. Journal of Contaminant Hydrology 140–141: 107-123.

Rotthauwe JH , Witzel KP , and Liesack W (1997) The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammoniaoxidizing populations Appl, Environ. Microbiol. 63: 4704-4712.

Samain E., Dubourguier H. C., and Albagnac G. (1984) Isolation and characterization of Desuljobulbus elongatus sp. nov. from a mesophilic industrial digester. Systematic and Applied Microbiology 5: 391-401.

Sambrook J., Fritsch E.F., and Maniatis T. (1989) Strategies for Cloning in Plasmid Vectors. In Molecular Cloning. A laboratory manual
USA: Cold Spring Harbor Laboratory Press, p. 1.53.

Schmidt Marie, Lege Sascha, and Nijenhuis Ivonne (2014) Comparison of 1,2-dichloroethane, dichloroethene and vinyl chloride carbon stable isotope fractionation during dechlorination by two Dehalococcoides strains. Water Res 52: 146-154.

Shelton Daniel R, and Tiedje James M (1984) Isolation and partial characterization of bacteria in an anaerobic consortium that mineralizes 3-chlorobenzoic acid. Applied and Environmental Microbiology 48: 840-848.

Shimizu Satoru, Ueno Akio, Naganuma Takeshi, and Kaneko Katsuhiko (2015) Methanosarcina subterranea sp. nov., a methanogenic archaeon isolated from a deep subsurface diatomaceous shale formation. Int J Syst Evol Microbiol 65: 1167-1171.


Slater Gregory F, Sherwood Lollar Barbara, Sleep Brent E, and Edwards Elizabeth A (2001) Variability in carbon isotopic fractionation during biodegradation of chlorinated ethenes: Implications for field applications. Environmental Science & Technology 35: 901-907.

Smidt H., and de Vos W. M. (2004) Anaerobic microbial dehalogenation. Annu Rev Microbiol 58: 43-73.

Song Donald L, Conrad Mark E, Sorenson Kent S, and Alvarez-Cohen Lisa (2002) Stable carbon isotope fractionation during enhanced in situ bioremediation of trichloroethene. Environmental Science & Technology 36: 2262-2268.

Spring Stefan, Schumann Peter, and Spröer Cathrin (2005) Methanogenium frittonii Harris et al. 1996 is a later synonym of Methanoculleus thermophilus (Rivard and Smith 1982) Maestrojuan et al. 1990. Int J Syst Evol Microbiol 55: 1097-1099.

Stapleton Raymond D., Ripp Steven, Jimenez Luis, Cheol-Koh Sung, Fleming James T., Gregory Igrid R., and Sayler Gary S. (1998) Nucleic acid analytical approaches in bioremediation: site assessment and characterization. J Microbiol Methods 32: 165-178.

Steinberg Lisa M, and Regan John M (2008) Phylogenetic comparison of the methanogenic communities from an acidic, oligotrophic fen and an anaerobic digester treating municipal wastewater sludge. Applied and Environmental Microbiology 74: 6663-6671.

Sung Youlboong, Ritalahti Kirsti M, Sanford Robert A, Urbance John W, Flynn Shannon J, Tiedje James M, and Löffler Frank E (2003) Characterization of two tetrachloroethene-reducing, acetate-oxidizing anaerobic bacteria and their description as Desulfuromonas michiganensis sp. nov. Applied and Environmental Microbiology 69: 2964-2974.

Suyama Akiko, Yamashita Masaki, Yoshino Sadazo, and Furukawa Kensuke (2002) Molecular characterization of the PceA reductive dehalogenase of Desulfitobacterium sp. strain Y51. Journal of bacteriology 184: 3419-3425.

Thiruvenkatachari R., Vigneswaran S., and Naidu R. (2008) Permeable reactive barrier for groundwater remediation. Journal of Industrial and Engineering Chemistry 14: 145-156.

Thrash J Cameron, Pollock Jarrod, Torok Tamas, and Coates John D (2010) Description of the novel perchlorate-reducing bacteria Dechlorobacter hydrogenophilus gen. nov., sp. nov. and Propionivibrio militaris, sp. nov. Applied microbiology and biotechnology 86: 335-343.

Throback Ingela Noredal, Enwall Karin, Jarvis Asa, and Hallin Sara (2004) Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiology Ecology 49: 401-417.

Tiehm Andreas, and Schmidt Kathrin R. (2011) Sequential anaerobic/aerobic biodegradation of chloroethenes—aspects of field application. Current Opinion in Biotechnology 22: 415-421.

Utkin Ilya, Woese Carl, and Wiegel Juergen (1994) Isolation and characterization of Desulfitobacterium dehalogenans gen. nov., sp. nov., an anaerobic bacterium which reductively dechlorinates chlorophenolic compounds. International journal of systematic bacteriology 44: 612-619.

van Pée Karl-Heinz, and Unversucht Susanne (2003) Biological dehalogenation and halogenation reactions. Chemosphere 52: 299-312.

Vogel Timothy M, and McCARTY PERRY L (1985) Biotransformation of tetrachloroethylene to trichloroethylene, dichloroethylene, vinyl chloride, and carbon dioxide under methanogenic conditions. Applied and Environmental Microbiology 49: 1080-1083.

Wagner Michael, Rath Gabriele, Amann Rudolf, Koops Hans-Peter, and Schleifer Karl-Heinz (1995) In situ Identification of Ammonia-oxidizing Bacteria. Systematic and Applied Microbiology 18: 251-264.

Widdel Friedrich, and Pfennig Norbert (1981) Studies on dissimilatory sulfate-reducing bacteria that decompose fatty acids. Archives of microbiology 129: 395-400.
WORAKIT SUCHADA, BOONE DAVID R, MAH ROBERT A, ABDEL-SAMIE MOHIY-ELDIN, and El-Halwagi MM (1986) Methanobacterium alcaliphilum sp. nov., an H2-utilizing methanogen that grows at high pH values. International journal of systematic bacteriology 36: 380-382.

XUN LUYING, BOONE DAVID R, and MAH ROBERT A (1989) Deoxyribonucleic acid hybridization study of Methanogenium and Methanocorpusculum species, emendation of the genus Methanocorpusculum, and transfer of Methanogenium aggregans to the genus Methanocorpusculum as Methanocorpusculum aggregans comb. nov. International journal of systematic bacteriology 39: 109-111.

Zellner G, Alten C, Stackebrandt E, De Macario E Conway, and Winter J (1987) Isolation and characterization of Methanocorpusculum parvum, gen. nov., spec. nov., a new tungsten requiring, coccoid methanogen. Archives of microbiology 147: 13-20.

Zellner Gerhard, Boone David R, Keswani Jyoti, Whitman William B, Woese Carl R, Hagelstein Anja, Tindall BJ, and Stackebrandt Erko (1999) Reclassification of Methanogenium tationis and Methanogenium liminatans as Methanofollis tationis gen. nov., comb. nov. and Methanofollis liminatans comb. nov. and description of a new strain of Methanofollis liminatans. International journal of systematic bacteriology 49: 247-255.

Zhou Jizhong, Fries Marcos R, Chee-Sanford Joanne C, and Tiedje James M (1995) Phylogenetic analyses of a new group of denitrifiers capable of anaerobic growth on toluene and description of Azoarcus tolulyticus sp. nov. International journal of systematic bacteriology 45: 500-506.



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