臺灣博碩士論文加值系統

甲烷(Methane)俗稱天然氣(Natural gas)是人類經常使用的重要能源之一。大量甲烷在低溫高壓的含水環境下，會形成固態籠晶狀(Clathrate)的天然氣水合物(Gas hydrate)。天然氣水合物擁有分布廣、潔淨、儲量大等優勢，是近年來最具潛力的替代能源。研究團隊於台灣西南外海探勘，發現有明顯的海底仿擬反射(BSR)訊號、海洋底水高甲烷濃度與溶解硫化物濃度以及異常淺的硫酸鹽-甲烷界面(SMI)深度之現象，顯示此區域普遍有豐富的甲烷水合物賦存。根據碳同位素研究顯示這些甲烷多為生物性來源，是由甲烷古菌(Methanoarchaea; Methanogen)產生。為探討台灣西南海域深海底泥或天然氣水合物潛力區的甲烷古菌微生物相。2008-2011年間，以海洋研究船(Ocean Reasearch I and III, ORI and ORIII)於台灣西南海域泥火山群、變形前緣區、好景海脊、被動大陸邊坡等區域採集岩心樣本。透過增殖培養、連續稀釋法等策略，陳玟潔在被動大陸邊坡KP-9鑽井區篩選出菌株CWC-04。經由親緣關係比對，甲烷古菌CWC-04與Methanocella屬的物種相似度則為91.28-93.67%，顯示菌株CWC-04可能是Methanocellaceae科的新屬新種。菌株CWC-04為短桿具有鞭毛之氫利用型甲烷古菌，且較已知甲烷細胞屬標準菌株可生長於較低溫(20°C)、偏酸(pH 5.4)、高鹽度(0.68 M NaCl)之環境。以Illumina MiSeq™進行全基因體定序組裝後，獲得全長3.19 Mb的基因片段，是目前甲烷細胞屬內基因體最大、富含AT鹼基對之菌株。菌株CWC-04的1175個COGs中，有53個獨特的COGs，其中又以[COG(R)]佔最多數，而有947個COGs是與甲烷細胞屬菌株之間所共有的。另於增殖培養過程中，發現菌液由混濁轉變為澄清。透過電子顯微鏡觀察、菌液吸光值及甲烷累積圖之生長曲線測定等結果顯示菌株CWC-04確實被大小為170 nm球形且外套膜看似黑莓外觀之病毒VMce (Virus of Methanocella)感染。在深海環境天然氣水合物潛力區以甲烷為主的生態系統中，包括以甲烷生成作用獲得能量之甲烷古菌、共生的細菌群落(如硫酸還原菌)及以厭氧甲烷氧化作用獲取生理代謝能量的厭氧甲烷氧化古菌(ANME)等微生物在系統內的關係以及感染甲烷古菌病毒的出現，顯示快速的碳循環可能在基於甲烷之生態系統中發揮作用。

Methane, also known as natural gas, is one of the most important sources of energy that humans often use. Gas hydrates usually forms when methane and water freeze at high pressures and relatively low temperatures. They are widely distributed, clearest and the largest source of hydrocarbons on Earth. Enormous volumes of gas hydrate (methane hydrate) are considered as one of the new alternative energy in the 21st century. To explore the diversity of methanoarchaea at deep sea gas hydrate habitats, we tried to isolate methanogen from sediment samples of the gravity core collected at station 22 at KP-9 area southwestern Taiwan from ORIII-1368 cruise in 2009. The methanogen enrichment cultures were incubated in minimal and rich methanogen basal media with formate, acetate or methanol as substrate for methanogenesis. After the enrichment strategies combined the serial sub-transfer and vancomycin addition to inhibit the growth of bacteria, a pure and novel hydrogenotrophic methanogen, strain CWC-04, was obtained. Cells of strain CWC-04 were rod-shape (1.4-2.9 μm long by 0.5-0.6 μm wide) with flagellum.The phylogenetic analyses of the 16S rRNA gene confirmed its affiliation with Methanocellales, and Methanocella arvoryzae MRE50T was the most closely related species. The sequence identities of 16S rRNA gene between strain CWC-04 and MRE50T were 93.67%. Strain CWC-04 utilized H2+CO2, formate, formate+acetate, 2-propanol or 2-butanol as catabolic substrates and growth occurs at 20-45°C (optimally at 42°C), at pH 5.35-7.31 (optimum pH 5.35) and with less than 0.68 M of NaCl (optimum 0.17 M). Rifampicin was inhibit the growth of strain CWC-04 but tetracycline was not. The genome size of strain CWC-04 was 3.19 Mb and the DNA G+C content as determined by genome sequencing, was 46.19 mol%. Of the 1175 COGs identified within the strain CWC-04, all but 53 were identified within other Methanocella species, and 947 (80.60%) orthologue groups were shared by all COGs. Based on the morphological, phylogenetic and genomics characteristics presented here, it is evident that strain CWC-04 represents a novel genus and new species of family Methanocellaceae. The optical density of CWC-04 culture dropped abruptly upon entering the late-log growth phase and the virus-like particles (170 nm in diameter) were observed on and around the cells. This observation demonstrated strain CWC-04 harbors a lytic virus. The spherical shape with a diameter of 170 nm and a blackberry-like envelope of the virion was named as VMce (Virus of Methanocella). The investigation of the methane based ecosystem under sea have been focused mainly in the relation within methane producer, bacterial syntroph and AOM. The occurrence of methanoarchaeal viruses suggested the rapid carbon cycling may play a role in this methane based ecosystem.

摘要 i
Abstract ii
目錄 iv
表目錄 vii
圖目錄 viii
壹、前言 1
貳、前人研究 3
一、海域甲烷水合物(Marine methane hydrate) 3
二、古菌(Archaea) 3
(一) 泉古菌門(Crenarchaeota) 4
(二) 廣域古菌門(Euryarchaeota) 4
(三) 驚奇古菌門(Thaumarchaeota) 5
(四) 奈古菌門(Nanoarchaeota) 5
三、甲烷古菌及其對人類的影響與應用 5
(一) 甲烷古菌(Methanoarchaea)分類 6
(1) 甲烷桿菌目(Methanobacteriales) 6
(2) 甲烷球菌目(Methanococcales) 7
(3) 甲烷細胞目(Methanocellales) 8
(4) 甲烷微菌目(Methanomicrobiales) 8
(5) 甲烷八疊球菌目(Methanosarcinales) 10
(6) 甲烷火菌目(Methanopyrales) 12
(7) 甲烷熱原體菌目(Methanomassiliicoccales) 12
(二) 甲烷古菌對人類的影響與應用 12
四、甲烷生態系 13
(一) 海底泥火山 15
(二) 冷泉及天然氣水合物潛力區 16
五、台灣西南海域天然氣水合物潛力區相關研究 17
(一)KP-9鑽井區(KP-9 area) 18
(二) 泥火山群 18
(三) 變形前緣區(Deformation Front) 19
(四) 好景海脊(Good Weather Ridge) 20
(五) 台灣西南海域已純化甲烷古菌純菌株 20
六、微生物分類與鑑定 21
七、研究目的與重要結果 22
參、材料與方法 24
一、採樣時間與地點 24
二、除氧操作系統、藥劑與培養液 24
(一) 除氧操作系統(Hungate station) 24
(二) MB/W及MM/W 厭氧培養液配製 24
(三) 還原劑與碳源製備 25
(四) 抗生素溶液製備 26
(五) TGC (Thioglycollate)培養液配製 26
三、甲烷古菌増殖培養(Enrichment)與厭氧轉殖接種 26
(一) 接菌 27
(二) 氣相層析儀偵測樣本甲烷氣體 27
(三) 抗生素添加 27
(四) 連續稀釋法 28
(五) 滾管技術(Roll tube) 28
四、Roll tube菌株篩選 28
(一) 厭氧操作箱(Coy chamber) 29
(二) 挑取roll tube內單一菌落 29
五、微生物形態觀察 29
(一) 位相差顯微鏡(Phase-contrast microscope)觀察細胞形態 29
(二) 穿透式電顯(Transmission Electron Micrograph)觀察菌體與病毒 29
(三) 場發射掃描式電顯(Scanning Electron Microscope)觀察細胞 30
六、生長與生理生化特性分析 30
(一) 生長曲線測定 30
(二) 碳源利用測試 31
(三) 生長需求測試 31
(四) 溫度及生長範圍測試 32
(五) 氯化鈉濃度生長範圍測試 32
(六) 酸鹼值生長範圍測試 32
(七) SDS感受性測試 33
(八) 抗生素耐受性測試 33
七、核酸萃取與定量、膠體電泳分析 33
(一) 甲烷古菌染色體DNA萃取 33
(二) 核酸純度與定量分析 34
(三) 聚合酶連鎖反應(PCR) 34
(四) 核酸膠體電泳分析 35
(五) PCR增幅樣品純化回收 35
(六) DNA接黏反應(Ligation) 36
八、勝任細胞的製備與質體轉形作用 36
(一) 勝任細胞(Competent cell)之培養基製備 36
(二) 製備勝任細胞 37
(三) 質體轉形作用(Transformation) 37
(四) 質體抽取與純化 37
九、核酸定序與序列親緣關係分析 38
(一) 16S rRNA基因定序與序列分析 38
(二) 染色體DNA定序 39
十、基因體功能比較分析 39
(一) 編碼鞭毛與RCC-1蛋白之基因搜尋 39
(二) 蛋白質直系同源群(COGs)分析與范恩圖(Venn Diagram)繪製 40
十一、病毒收集與液相層析(FPLC)膠體管柱分離純化 40
(一) 病毒收集 40
(二) 液相層析膠體管柱分離純化 41
肆、結果與討論 43
一、KP-9鑽井區測站22的甲烷細胞科新屬新種–甲烷古菌CWC-04 43
(一) 甲烷古菌CWC-04增殖純化過程 43
(二) 菌株CWC-04在甲烷古菌的系統演化分類位階探討 43
(三) 甲烷古菌CWC-04細胞形態 44
(四) 生理特性分析 45
(五) 甲烷古菌CWC-04基因體功能比較分析 47
二、感染甲烷古菌CWC-04之病毒VMce (Virus of Methanocella) 49
(一) 病毒與宿主CWC-04之關係 49
(二) 病毒收集與純化 50
(三) VMce病毒結構觀察 51
三、台灣西南外海天然氣水合物潛力區岩心底泥甲烷古菌增殖培養與純化 51
伍、結論與展望 53
陸、表與圖 55
柒、參考文獻 78
捌、附錄 93
Appendix 1. fla operon related genes in genus Methanocella. 94
Appendix 2. 53 unique COGs in strain CWC-04 96
Appendix 3. The viruses of methanogens. 99

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