臺灣博碩士論文加值系統

四方圈合海脊為一個背斜海脊，是一個收集甲烷的良好地形。應用高解析的測深儀(bathymetry)、深拖側掃聲納圖像(deep-towed sidescan sonar imagery)、高解析震波剖面探測(high-resolution seismic profiling)以及海底拖式攝影機(towed video observations)分析均確認四方圈合海脊是天然氣水合物累積的潛力區。四方圈合海脊亦具有強甲烷滲漏點，造就了以甲烷碳源為基礎的典型冷泉(cold seep)化學自養菌群落(chemosynthetic community)和高密度具甲烷氧化菌共生的貽貝與蝦蟹。2015年海洋研究船三號OR3-1900航次自台灣四方圈合海脊C5-6測站使用V-Corer (Video-guided multicorer)獲得的岩心底泥樣品，經增殖培養後純化出甲烷古菌FWC-SCC2。菌株FWC-SCC2與Methanofollis tationis Chile 9T的16S rDNA序列達98.2%相似性，與其它甲烷泡菌屬已發表菌株的16S rDNA相似性達96-98%。但菌株FWC-SCC2與甲烷泡菌屬的物種分析平均核苷酸一致性(Average nucleotide identity, ANI) 與基因組對基因組距離分析(Genome to genome distance analysis, GGDA)，結果分別為78.2-79.8%以及17.8-23.8%，支持菌株FWC-SCC2為甲烷泡菌屬的新種。菌株FWC-SCC2細胞為直徑0.8-1.2 μm的不規則球菌，其表層蛋白分子量為116.4 kDa；可以利用甲酸和H2/CO2作為碳源進行甲烷化作用。菌株FWC-SCC2最適生長條件範圍為37C、0.17 M氯化鈉及pH 6.7-7.0。在基因體的分析上發現菌株FWC-SCC2與其他甲烷泡菌屬菌株相比具38個獨特的蛋白質直系同源群(Clusters of Orthologous Groups of proteins, COGs)，在38個COGs中包含有鐵離子的ABC運輸蛋白(ABC-type iron transport system FetAB)、對苯二酚單氧化酶YgiN (Quinol monooxygenase YgiN)兩種和耐氧性相關的COGs以及維持細胞膜完整性的噬菌體休克蛋白A (Phage shock protein A)。

Four Way Closure Ridge is an anticlinal ridge that represents an ideal trap for methane hydrate accumulations through the analyses of high-resolution bathymetry, deep-towed sidescan sonar imagery, high-resolution seismic profiling and towed video observations of the seafloor. Four Way Closure Ridge is one of the sites with intensive methane seepages to bring up a typical cold seep used methane as substrate chemosynthetic community and with highly dense mussel bed with shrimps, crabs and clams was found at this site. A mesophilic, hydrogenotrophic methanogen, strain FWC-SCC2, was isolated from deep-sea sediment obtained at the C5-6 station at Four Way Closure Ridge region by the R/V Ocean Researcher III during ORIII-1900 cruise in 2015. Phylogenetic analysis revealed that strain FWC-SCC2 was most closely related to Methanofollis tationis Chile 9T (98.2% 16S rRNA gene sequence similarity) and share 96-98 % 16S rRNA gene sequence similarity with other valid Methanofollis species. Genome relatedness between strain FWC-SCC2 and Methanofollis genus was computed using both average nucleotide identity (ANI) and genome-to-genome distance analysis (GGDA) with values of 78.2-79.8% and 17.8-23.8%, respectively. Based on the morphological, phenotypic and phylogenetic characteristics presented here, it is suggested that strain FWC-SCC2 represents a new species of genus Methanofollis. The cells were irregular cocci, non-motile with 0.8-1.2 μm in diameter. The Mr of surface-layer protein was 116.4 kDa. Strain FWC-SCC2 used H2/CO2 or formate as catabolic substrates. The growth conditions were at 20-40C, 0-0.85 M NaCl and pH 5.9-8.2. Comparative genomic analysis between strain FWC-SCC2 and other Methanofollis reveals strain FWC-SCC2 have 38 unique COGs, included ABC-type iron transport system FetAB, quinol monooxygenase YgiN, two type aerotolerant COGs and phage shock protein A that can maintain cell membrane integrity.

中文摘要 i
Abstract ii
目錄 iii
表目錄 vi
圖目錄 vii
壹、前言 1
貳、前人研究 3
一、台灣西南外海四方圈合海脊的地質特色及天然氣水合物蘊藏區 3
二、四方圈合海脊冷泉區生物 3
三、四方圈合海脊冷泉區微生物多樣性 5
四、深海底泥中以甲烷為主的生態系 6
五、甲烷古菌(Methanogen, Methanoarchaea) 8
(一)甲烷古菌分類 9
1.甲烷囊菌屬(Methanoculleus) 10
2.甲烷泡菌屬(Methanofollis) 12
六、研究目的與重要結果 14
參、材料與方法 15
一、採樣時間與地點 15
二、除氧操作系統、藥劑與培養基 15
(一)除氧操作系統(Hungate station) 15
(二)MB/W及MM/W medium配製 15
(三)還原劑與碳源製備 17
(四)抗生素制備 17
(五)TGC (thioglycollate)培養基配製 18
三、甲烷古菌增殖培養與厭氧轉殖接種 18
(一)接菌 18
(二)氣象層析儀偵測樣品甲烷氣體產量 19
(三)抗生素添加 20
(四)連續稀釋法 20
(五)厭氧操作箱(Coy chamber) 20
(六)Roll-tube方法 20
四、微生物形態觀察 21
(一)位相差顯微鏡觀察細胞形態 21
(二)穿透式電子顯微鏡經負染方式觀察細胞形態 21
(三)場發射掃描電子顯微鏡觀察細胞 22
五、生長與生理生化特性分析 23
(一)甲烷古菌使用碳源的配製與測試 23
(二)抗生素抗性測試 23
(三)生長曲線的測定 24
(四)溫度生長範圍測試 24
(五)鹽濃度生長範圍測試 24
(六)酸鹼度生長範圍測試 25
(七)SDS感受性測試 25
(八)表面蛋白(Surface layer)之製備 26
(九)蛋白質電泳分析(SDS-PAGE) 26
六、核酸萃取與分析 27
(一)甲烷古菌增殖樣品DNA萃取 27
(二)甲烷古菌染色體DNA萃取 28
(三)核酸純度與定量分析 29
(四)聚合酶連鎖反應 29
(五)核酸膠體電泳 29
(六)PCR增幅樣品回收 30
(七)DNA黏合反應 31
(八)勝任細胞製備 31
(九)質體轉形作用 32
(十)質體DNA萃取與純化 32
七、核酸定序與親緣關係分析 33
(一)16S rRNA基因定序與序列分析 33
(二)染色體DNA定序與序列比較 34
肆、結果與討論 36
一、四方圈合海脊底泥甲烷古菌之增殖培養與純化 36
二、自四方圈合海脊底泥純化之甲烷古菌菌株FWC-SCC2 36
(一)細胞形態 37
(二)16S rRNA基因序列與系統演化分析 38
(三)生理特性分析 38
(四)基因體分析 41
1.菌株FWC-SCC2與甲烷泡菌屬菌株基因體資訊 41
2.菌株FWC-SCC2與甲烷泡菌屬菌株間蛋白質直系同源群比較 42
3.菌株FWC-SCC2鞭毛基因 43
4.甲烷代謝途徑 44
三、部分純化甲烷古菌 45
(一)PR1-G0-0-10_C2_A 45
(二)PR1-G2-0-10_C2_M 45
伍、結論 46
陸、表與圖 47
柒、參考文獻 67
捌、附錄 78

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