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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 湯森林(Sen-Lin Tang) | |
dc.contributor.author | Yu-Jing Chiou | en |
dc.contributor.author | 邱育敬 | zh_TW |
dc.date.accessioned | 2021-05-20T00:53:16Z | - |
dc.date.available | 2025-08-10 | |
dc.date.available | 2021-05-20T00:53:16Z | - |
dc.date.copyright | 2020-09-22 | |
dc.date.issued | 2020 | |
dc.date.submitted | 2020-08-17 | |
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dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/8383 | - |
dc.description.abstract | 珊瑚擁有不同的微生物夥伴,比如真菌、藻類及細菌等,且彼此有著複雜的交互作用。珊瑚的不同部位居住著不同的微生物,其中有一屬的細菌被稱為內生桿菌,常被發現在珊瑚的黏液及組織中。內生桿菌群集的豐度會隨著珊瑚的健康程度而有所不同,相比於生病的或受環境壓迫的珊瑚,健康的珊瑚體具有較高豐度的內生桿菌,因此內生桿菌被認為與珊瑚健康有關係,並且被認為是一群珊瑚健康的益生菌。近年來,環境快速變遷導致珊瑚大量死亡,益生菌成為其中一個拯救或復育珊瑚的手段。內生桿菌為珊瑚益生菌的重要候選菌種之一,但目前由石珊瑚分離的可培養內生桿菌只有兩株,其中Endozoicomonas montiporae CL-33T為第一株具有基因體序列的內生桿菌,並且在基因體分析中發現E. montiporae CL-33T具有與宿主互動的基因而且可能在珊瑚遇到逆境時保護宿主的粒線體,來防止其失去功能,並且當珊瑚沒有足夠的葡萄糖時可以促使宿主轉而利用脂質,促進糖質新生。今年另一個研究從基因體方面證實了內生桿菌藉由代謝二甲基巯基丙酸(dimethylsulfoniopropionate, DMSP ),產生氣候調節化合物,二甲基醚(dimethyl suldife, DMS)參與珊瑚的硫循環。 鑑於目前只有兩株由珊瑚分離的內生桿菌,分離更多可培養的內生桿菌可以幫助我們更暸解其與珊瑚可能的互動關係。在這個研究中,我們分別由澎湖及墾丁分離兩株新的內生桿菌,E. penghunesis 4G與E. ruthgatesii 8E ,兩株菌與最近的內生桿菌E. euniceicola 16S rRNA的親緣關係相似性分別為96.68%及96.99%。兩株菌在最適生長溫度、鹽度及酸鹼值上展現了不同的特性,E. ruthgatesii 8E的最適生長溫度為25°C、pH值7、鹽度1-2%,而E. penghunesis 4G則最適合生長於20至25°C,pH值8、鹽度1-2%。除此之外,我們也將兩株新菌進行基因體定序,並且獲得低污染(污染<1%),接近完整(>97%)的基因體。在基因體大小上,E. penghunesis 4G為5.73 Mb,E. ruthgatesii 8E則具有目前內生桿菌中最大的基因體,7.1Mb,也具有假定可以將DMSP當成碳源並代謝成DMS的基因操縱組。進一步我們量化從珊瑚分離出的這四株內生桿菌消耗DMSP與產生DMS的濃度,並發現E. ruthgatesii 8E 相比於E. acroporae Acr-14T可以消耗更多的DMSP。最後本論文提出兩株內生桿菌屬新種,並首度量化珊瑚優勢共棲菌的DMSP消耗量及DMS產生量。 | zh_TW |
dc.description.abstract | Corals harbor diverse microbial partners (e.g., fungi, algae, and bacteria), leading to complex yet intriguing mesh of interactions among and within coral holobiont. Different organs of coral harbor diverse microbial communities, such as members of genus Endozoicomonas are abundant in coral mucus and epidermal tissues. Interestingly, Endozoicomonas are often abundant in healthy corals and their abundance declines in diseased or stressed corals, consequently, members of this genus are hypothesized to be potential probiotics of coral health. Recently, the identification of beneficial microorganisms for coral has been at the center of developing probiotics for coral reefs to mitigate stress from heat-induced coral bleaching. Endozoicomonas species which are potential candidates for coral probiotics lack cultured isolates with only two species isolated from scleractinian corals. Endozoicomonas montiporae CL-33T the first cultured and genome sequenced isolate has been shown to have the potential to internalize and interact with host cells and harbor genes to protect mitochondrial dysfunction and promote gluconeogenesis in the host. A recent study provided first genomic and functional evidence of the role of Endozoicomonas in the coral sulfur cycle by metabolizing dimethylsulfoniopropionate (DMSP) to climate active gas dimethylsulfide (DMS). With only two cultured isolates to date, it becomes important to identify and culture new species from this diverse genus in order to ascertain its role in coral reefs. In this study, we isolated and cultured two novel bacteria species, E. penghuensis 4G and E. ruthgatesii 8E from dominant coral Acroporae sp. of the coast of Penghu Archipelago and Kenting, Taiwan, respectively. The nearest neighbor of these new species is E. eunicicola (16S rRNA gene identity: 96.68%, 96.99% respectively). The two isolates exhibit different physiological and biochemical characteristics (optimal pH, temperature and salinity). E. ruthgatesii 8E grows in on optimal temperature of 25 °C, with an optimal pH of 7 and salinity 1-2 %, whereas E. penghuensis 4G grows at a temperature of 20-25 °C, a pH, and salinity of 8 and 1-2%, respectively. Furthermore, we sequenced and assembled high-quality (contamination <1%) near-complete (>97%) draft genomes of the two species. E. ruthgatesii 8E has the largest genome (7.1 Mb) in cultured species of Endozoicomonas to date, but E. penghuensis 4G has a genome size (5.73 Mb) comparable other species. E. ruthgatesii 8E harbors a putative operon to metabolize DMSP to DMS and use it as a carbon source. Quantification of DMSP usage by E. ruthgatesii 8E shows that it can metabolize more DMSP than previously characterized E. acroporae. Further, genomic analysis is being conducted to answer the intriguing question, why does E. ruthgatesii 8E have a disproportionate genome size. Overall, in this study we discovered two novel Endozoicomonas species and is the first study to quantify DMSP consumption and DMS production by a coral-associated dominant bacterium. | en |
dc.description.provenance | Made available in DSpace on 2021-05-20T00:53:16Z (GMT). No. of bitstreams: 1 U0001-2707202016002700.pdf: 30966099 bytes, checksum: 7282f83570a83d5d87bb7e86914afaa5 (MD5) Previous issue date: 2020 | en |
dc.description.tableofcontents | 誌謝 i 摘要 ii Abstract iv 目錄 vi 圖目錄 ix 表目錄 xi 中英文對照表 xii 一、前人研究 1 1.1 珊瑚簡介 1 1.1.1 珊瑚礁生態系 1 1.1.2 造礁珊瑚 1 1.2 珊瑚與其微生物 2 1.2.1 珊瑚共生體 2 1.2.2 珊瑚不同部位的共棲菌 3 1.3 內生桿菌 5 1.3.1 內生桿菌與其宿主的關係 6 1.3.2 內生桿菌之區域性 7 1.3.3 內生桿菌基因體特性 7 1.4 內生桿菌屬與珊瑚之間的互動 8 1.5 研究動機與目的 10 二、材料與方法 11 2.1 採樣時間、地點及物種 11 2.2.1 富營養培養基配方 11 2.2.2 基本培養基配方 11 2.2 內生桿菌分離培養 11 2.2.1 菌種純化 11 2.2.2 菌株保存 12 2.2.3 富營養培養基配方 12 2.2.4 聚合酶連鎖反應 13 2.2.5 基本培養基配方 13 2.3 微生物形態觀察 14 2.3.1 穿透式電子顯微鏡菌體觀察 14 2.3.2 穿透式電子顯微鏡菌體切片觀察 14 2.3.3 場發射掃描式電子顯微鏡菌落觀察 15 2.3.4 解剖式顯微鏡菌落形態觀察 16 2.3.5 革蘭氏染色 16 2.4 生長與生理生化特性分析 16 2.4.1 生長曲線 16 2.4.2 最佳溫度生長測試 17 2.4.3 最佳鹽度生長測試 17 2.4.4 最佳酸鹼值生長測試 17 2.4.5 氧氣需求測試 18 2.4.6 氧化酶測試 18 2.4.7 觸酶測試 18 2.4.8 運動性觀察-軟洋菜運動性觀察 19 2.4.9 API ZYM 套組試驗 19 2.4 基因體分析 19 2.5.1 全基因體次世代定序 19 2.5.2 基因體序列組裝 20 2.5.3 基因體組裝品質鑑定 20 2.5.4 基因體註解 20 2.5.5 原噬菌體分析 21 2.5.6 第三型分泌蛋白 (Type III Secretion System proteins, T3SS) 21 2.5.7 16S rRNA 親緣關係樹 22 2.5.8 DddD親緣關係樹 22 2.6 DMSP代謝成DMS的能力 22 2.6.1 DMSP共培養 22 2.6.2 鹼調控裂解DMSP減量線製備 23 2.6.3 DMS減量線製備 23 2.6.4 鹼調控裂解DMSP及DMS定量 24 三、結果 26 3.1 菌種分離及初步鑑定 26 3.1.1 PCR初步鑑定結果 26 3.2 形態學分析 26 3.2.1 菌落形態 26 3.2.2 革蘭氏染色 27 3.2.3 穿透式電子顯微鏡菌體形態 27 3.2.4 超薄切片穿透式電子顯微鏡鏡檢 27 3.2.5 場發式發射掃描式電子顯微鏡菌落觀察 28 3.3 生理生化特性分析 28 3.3.1 最適生長鹽度 28 3.3.2 最適生長pH 28 3.3.3 最適生長溫度 29 3.3.4 生長曲線 29 3.3.5 氧氣耐受性 29 3.3.6 氧化酶與催化酶測定 30 3.3.7 軟培養基運動性觀察 30 3.3.8 API ZYM 酵素活性反應套組反應結果 30 3.4 基因體分析 31 3.4.1 全基因體次世代定序 31 3.4.2 基因體組裝結果 31 3.4.3 基因體品質鑑定 31 3.4.4 基因體註解及基因預測 32 3.4.5 原噬菌體分析 32 3.4.6 第三型分泌系統分析 (T3SS) 分析 33 3.4.7 16S rRNA 親緣關係樹 33 3.4.8 DddD親緣關係樹 34 3-5 DMSP分解成DMS的活性 34 3.5.1 DMSP不同濃度試驗 34 3.5.2 鹼調控裂解DMSP減量線 35 3.5.3 鹼調控裂解DMSP定量 35 3.5.4 DMS減量線 36 3.5.5 DMS定量 36 四、討論 38 4.1 電子顯微鏡觀察的菌體形態學 38 4.2 生理生化特徵 39 4.3 基因體功能 41 4.3.1 原噬菌體 41 4.3.2 移動能力及化學趨性 42 4.3.3 滲透壓調節物質 43 4.4 DMSP與DMS定量 43 4.4.1 DMSP消耗量 44 結論與展望 46 圖與表 47 參考文獻 98 | |
dc.language.iso | zh-TW | |
dc.title | 兩株台灣軸孔珊瑚內生桿菌新種之特性與基因體分析 | zh_TW |
dc.title | Characterization and Genomic Analysis of Two Novel Endozoicomonas Species from coral Acropora in Taiwan | en |
dc.type | Thesis | |
dc.date.schoolyear | 108-2 | |
dc.description.degree | 碩士 | |
dc.contributor.coadvisor | 謝志豪(Chih-hao Hsieh) | |
dc.contributor.oralexamcommittee | 陳俊堯(Chun-Yao Chen),楊姍樺(Shan-Hua Yang),吳羽婷(Yu-Ting Wu) | |
dc.subject.keyword | 內生桿菌,軸孔珊瑚,基因體分析,生理特性分析, | zh_TW |
dc.subject.keyword | Endozoiocmonas,Acropora sp.,genomic analysis,physiological analysis, | en |
dc.relation.page | 103 | |
dc.identifier.doi | 10.6342/NTU202001918 | |
dc.rights.note | 同意授權(全球公開) | |
dc.date.accepted | 2020-08-17 | |
dc.contributor.author-college | 理學院 | zh_TW |
dc.contributor.author-dept | 海洋研究所 | zh_TW |
dc.date.embargo-lift | 2025-08-10 | - |
顯示於系所單位: | 海洋研究所 |
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