http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/73 2026-10-21T17:40:00Z 2026-10-21T17:40:00Z 黃競魰 Jing Wen Michelle Wong http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/92752 2026-07-22T13:49:23Z 2024-01-01T00:00:00Z

標題: 龜山島珊瑚群聚與淺海熱泉之好氧甲烷氧化活性; Aerobic methanotrophic activity in coral community and shallow-water hydrothermal vent in Kueishan Island 作者: 黃競魰; Jing Wen Michelle Wong 摘要: 甲烷是三大主要溫室氣體之一，其全球暖化潛勢為二氧化碳的28-34倍。甲烷遍佈全球，在自然環境中如海洋、濕地都可發現其存在。海洋中的甲烷可由甲烷氧化菌進行分解，其中好氧甲烷氧化菌可利用甲烷單氧化酶 (pMMO) 將甲烷分解成甲醇並進入下一步的分解作用。此外，在淺層海洋底泥的相關研究中也有發現好氧甲烷氧化菌的蹤跡。龜山島作為本次研究的主要地點，是個同時具有淺海熱泉及珊瑚群聚的一個特殊海域；在龜首的部分具有淺海熱液噴口聚集地，而在另一側龜尾的部分則有豐富生態的珊瑚群聚。龜山島的特殊地理環境能提供我們探討並比較兩種生態的甲烷氧化潛力及甲烷氧化菌相組成之間的差異。本研究利用甲烷培養實驗及次世代定序技術，分析龜山島淺海熱泉及珊瑚群聚底泥中甲烷氧化潛力及甲烷氧化菌相，同時也分析位於台灣南部的墾丁及綠島的珊瑚礁底泥，進一步探討珊瑚群聚的甲烷消耗能力。實驗結果顯示，龜山島珊瑚群聚的底泥相對於淺海熱泉的底泥具有較高的甲烷氧化潛力，且甲烷氧化菌所擁有的功能基因 (pmoA) 的豐度的結果及甲烷氧化菌的菌相組成，推測珊瑚群聚的甲烷氧化潛力可能比淺海熱泉高。另外，墾丁和綠島的珊瑚礁底泥結果也與龜山島珊瑚群聚呈現一樣的趨勢。本研究結果同時展示珊瑚群聚底泥與淺海熱泉底泥的甲烷氧化的能力，提供未來探討這兩種生態的甲烷氧化菌在甲烷循環過程中，所扮演的角色及甲烷減排可能貢獻。此外，通過在龜山島的近海熱泉的甲烷氧化能力及甲烷氧化菌組成，可以預測未來海洋酸化對海洋環境的甲烷氧化活動所造成的影響及菌相的變化。; Methane is a powerful greenhouse gas with 28-34 times greater global warming potential than carbon dioxide. However, methane has a shorter atmospheric lifetime, which means that reducing methane emissions could slow down the rate of global warming, faster than reducing carbon dioxide. Ocean is one of the natural methane budgets and in shallow layer marine sediment, aerobic methanotrophs which can consume methane to methanol through enzyme pMMO were found. Kueishan Island, our study site is a special geological area that has a shallow-water hydrothermal vent at the front of Kueishan Island (Head) and the coral community located behind Kueishan Island (Tail), which allowed us to compare both methanotrophic activity and aerobic methanotrophs composition in two ecosystem’s sediments. Here we show that sediments of two different ecosystems had different methane oxidation rate. At the Tail site (coral community), the methane-oxidation rate was higher than at the Head site (hydrothermal vent) and the pmoA gene copy number showed the same trend. The microbiome composition results showed that coral community had aerobic methanotrophs and the abundance changed after methane incubation. In sum, the coral community had a higher methane-consuming ability and the presence of aerobic methanotrophs, compared to the shallow hydrothermal vent in Kueishan Island; the outcome in other coral reef (Kenting and Lyudao) also supported the results shown in Kueishan Island. Our results provided insight into the ability of coral community sediments to methane consuming. The aerobic methanotrophs and their roles played in the ocean methane cycle need to be further explored in the future. In addition, we could predict the future of methanotrophic activity and change in microbiome composition under the ocean acidification and global change based on the results of shallow-water hydrothermal vent in Kueishan Island.

2024-01-01T00:00:00Z 姚巽鈞 Syun-Jyun Yao http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/105960 2026-10-14T17:37:59Z 2026-01-01T00:00:00Z

標題: 龜山島熱泉地區與珊瑚群落底泥之微生物群落結構與甲烷氧化潛力分析; Microbial community and methane oxidation potential in sediments from shallow hydrothermal vent and coral community at Kueishan island 作者: 姚巽鈞; Syun-Jyun Yao 摘要: 龜山島位於台灣東北海域，在相近的地理尺度下存在淺海熱泉與珊瑚群落兩種截然不同的生態系。甲烷為僅次於二氧化碳的第二大溫室氣體，近年全球排放量持續攀升，而淺海沿岸沉積物因有機質豐富且距離大氣較近，被認為是海洋甲烷排放的重要來源區域。然而淺海熱泉與珊瑚群落環境研究有關於微生物參與之甲烷生成及甲烷氧化較為缺乏。本研究採集龜山島淺海熱泉底泥與珊瑚群落底泥進行添加甲烷培養實驗，萃取DNA後，以shotgun metagenomics為核心工具了解兩環境底泥於添加甲烷培養與否下的微生物群落、甲烷生成及氧化潛力、生物地球化學循環。結果顯示，珊瑚群落底泥的甲烷消耗量顯著高於熱泉底泥。而底泥微生物群落組成主要受地點影響，甲烷培養對整體組成影響有限。熱泉底泥以嗜酸性硫氧化菌Acidihalobacter屬為優勢菌群，整體微生物多樣性較低；珊瑚群落底泥則維持較高的微生物多樣性。產甲烷菌在兩種底泥中的相對豐度均極低，以熱泉底泥尤為稀少。且所有樣本均未檢測到甲烷生成關鍵基因mcr。添加甲烷培養使兩地區底泥均呈現type I甲烷氧化菌的相對豐度增加，以Methylomonas屬增幅最大，其次為Methylococcus屬及Methylomarinum屬，甲烷氧化的pmo基因豐度亦於甲烷培養組中明顯上升。本研究在添加甲烷培養的組別共組裝出五個 Methylococcaceae科甲烷氧化菌MAG（metagenome-assembled genomes），來自熱泉底泥的三個MAG被分類於未正式命名屬PGZD01（最近緣為Methylotuvimicrobium屬），來自珊瑚群落底泥的兩個MAG則屬於未正式命名屬WTBX01（最近緣為Methylomarinum及Methylomonas）。五個MAG與各自最近緣代表基因體低於95%物種界定閾值，顯示其極可能各自代表尚未被正式描述的潛在新種，可為後續純培養分離提供基因組層次的參考依據。; Kueishan Island, located in the northeastern offshore waters of Taiwan, hosts two ecologically distinct ecosystems within a similar geographic scale: shallow-water hydrothermal vents and coral reef communities. Methane is the second largest greenhouse gas after carbon dioxide, and global emissions have been continuously increasing in recent years. Shallow coastal sediments, due to their rich organic matter content and proximity to the atmosphere, are considered an important source region of marine methane emissions. However, studies on methane production and methane oxidation mediated by microorganisms in shallow-water hydrothermal vents and coral reef environments remain relatively limited. In this study, sediments from shallow-water hydrothermal vents and coral reef communities of Kueishan Island were collected and subjected to methane-enriched incubation experiments. After DNA extraction, shotgun metagenomics was used as the approach to investigate microbial community composition, methane production and oxidation potential, and biogeochemical cycling in sediments from both environments under methane-amended and non-amended conditions. The results showed that methane consumption in coral community sediments was significantly higher than in hydrothermal vent sediments. The microbial community composition of the sediments was mainly influenced by location, and methane incubation had limited effects on the overall community composition. Hydrothermal vent sediments were dominated by the acidophilic sulfur-oxidizing genus Acidihalobacter, and exhibited relatively low microbial diversity. In contrast, coral reef sediments maintained higher microbial diversity. Methanogenic archaea were present at very low relative abundance in both sediments, particularly in hydrothermal vent. In addition, no key methanogenesis gene mcr was detected in any of the samples. Methane incubation increased the relative abundance of Type I methanotrophs in sediments from both regions, with Methylomonas showing the greatest increase, followed by Methylococcus and Methylomarinum. The abundance of the methane oxidation gene pmo also increased in methane-enriched samples. In this study, five methanotrophic metagenome-assembled genomes (MAGs) belonging to the family Methylococcaceae were recovered from methane-amended treatments. Three MAGs from hydrothermal vent sediments were classified into the uncharacterized genus PGZD01, with the closest relative being the genus Methylotuvimicrobium. The two MAGs from coral reef sediments were classified into the uncharacterized genus WTBX01, with the closest relatives being Methylomarinum and Methylomonas. All five MAGs shared less than 95% similarity to their closest reference genomes based on ANI, indicating that they likely represent previously undescribed potential novel species, and may provide genome-level references for future cultivation and isolation studies.

2026-01-01T00:00:00Z 林軒彤 Hsuan-Tung Lin http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/90473 2026-07-22T13:38:49Z 2023-01-01T00:00:00Z

標題: 龜山島周遭海域底泥線蟲之群落; The study of nematode communities in the sediment surrounding Turtle Island 作者: 林軒彤; Hsuan-Tung Lin 摘要: 海洋線蟲是海底沉積物當中數量最為豐富的小型底棲動物，他們會參與棲地的養分循環與食物網，作為微生物與大型底棲生物間的能量橋梁。因為海洋線蟲對於環境的變動相當敏感，所以可作為評估生態系統的生物指標。龜山島是一座火山島，龜山島的東南方具有多座淺海熱泉，相對地，龜山島的西方則是具有珊瑚礁生態系。從熱泉區到非熱泉區，龜山島大型底棲生物群落變動已有多份研究探討，然而小型底棲動物則未有調查。因此，本研究在環繞龜山島的6個地點進行不同時間點底泥的採集以探討其海洋線蟲群落。採樣地點包括3個熱泉生態系 (近泉、遠泉與CO2泉)、1個珊瑚礁生態系 (龜尾)、2個過渡地點位於熱泉與珊瑚礁之間 (龜北、龜南)。底泥除了用於線蟲的分離外，還會進行粒徑大小的分析與底泥化學組成的分析。結果顯示，珊瑚礁環境的線蟲豐度會隨著時間變化，於春季與夏季豐度會呈現上升的趨勢。近泉與遠泉的線蟲數量無論時間點都非常少，但CO2泉的春季數量大增，並於夏季稍下降。地點不僅影響線蟲在不同時間點的變動情形，還會影響線蟲的群落組成。底泥的物化性質中底泥粒徑與SO42-、Mg2+、Cl-是顯著造成線蟲群落組成差異的重要環境因子。CO2泉以熱泉相關物種及耐受性強的周遭物種為主要組成；龜北獨有物種比例高，以適應粗顆粒的物種為主；龜尾則以適應細顆粒的物種為主。此外，龜尾、龜南到近遠泉則呈現豐度與組成上的連續性變化。; Free-living marine nematodes are the most abundant meiobenthos in marine sediment. They participate in the nutrient cycle and the food web of the habitat, and serve as an energy bridge between macrobenthos and microorganisms. Because free-living marine nematodes are sensitive to environmental variations, they can be served as bioindicators to assess ecosystems. Turtle Island is a volcanic island, the southeastern of the island locates clusters of hydrothermal vents. By contrast, the western has no vent and contains a coral reef ecosystem. Several studies have investigated the composition of macrobenthos around hydrothermal vents of Turtle Island, but there is no survey about meiobenthos. Therefore, we collected sediment samples from 6 sampling sites surrounding Turtle Island each season for a year to investigate the free-living marine nematode communities. The sampling sites included 3 vent sites (Near vent, Far vent, and CO2 vent), 1 coral reef ecosystem (Tail), and 2 buffer sites, between the vent sites and the coral reef (North and South). In addition to the extraction of nematodes, the sediment samples were also analyzed for grain size distribution and chemical ion composition. The results showed that the abundance of nematodes in the coral reef changed over time, with an increasing trend in spring and summer. The number of nematodes in Near vent and Far vent was quite low no matter the time point, but the number of nematodes in CO2 vent increased greatly in spring and decreased slightly in summer. Sampling sites affected not only the temporal variation of the nematode abundance, but also had an impact on the nematode composition. Among the physical and chemical properties of sediment, grain size, SO42-, Mg2+, and Cl- were crucial environmental factors that significantly caused differences in the composition of nematode communities. CO2 vent were mainly composed of vent-related species and surrounding species with strong tolerance. North had own special community, mainly species adapted to very coarse sand. Tail was dominated by species adapted to medium sand. Furthermore, Tail, South, Far vent, and Near vent showed a continuum of changes in the nematode abundance and composition.

2023-01-01T00:00:00Z Kuan-Ying Chen 陳冠螢 http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/56142 2026-07-22T11:13:31Z 2014-01-01T00:00:00Z

標題: 龍膽石斑之全基因體定序組裝與功能註解分析; Whole Genome Assembly and Annotation of the Giant Grouper, Epinephelus lanceolatus in Next Generation Sequencing 作者: Kuan-Ying Chen; 陳冠螢 摘要: 本研究以現今台灣重要具高經濟價值的養殖魚種龍膽石斑（Epinephelus lanceolatus）為研究對象，利用次世代定序技術，取得短序列散彈槍式基因體定序資料，以全新組裝（de novo Assembly）的方式，得到龍膽石斑的基因體支架 (scaffold)，並由其中預測其可轉譯蛋白質序列，以作為基因體表現概況、調節機制，與免疫相關反應之功能性研究的重要基礎。 本研究比較數種不同組裝策略，其中以ALLPATHS-LG組裝軟體，加上SOAPdenovo組裝軟體裡的GapCloser程式所組裝的結果，其質與量均為最佳，可作為基因體組裝後續的分析基礎。組裝序列共有13,897條scaffolds，序列總和為1.09 Gbp。為了找出石斑魚基因體中所存在的基因，我們以AUGUSTUS演算模型，選用八目鰻 (Petromyzon marinus, 俗名：sea lamprey) 的基因模型做為參考進行預測，共可轉譯出42,433條蛋白質序列，其中92.6%的序列，能在nr蛋白質資料庫中找到對應序列（blastp, E-value：1E-5）。分析所對應序列的物種組成，有2/3以上皆屬脊索動物門輻鰭綱之物種，其餘1/3則為微生物序列，可能與樣本採集過程污染有關。將含有細菌的序列濾除後，保留9,473條scaffolds，序列長度總和為1.06 Gbp，與一般對石斑魚所估計的基因體大小 (1.1G bp) 接近；由此 9,473 條龍膽石斑的基因體支架得到的蛋白質序列為29,184條，有26,056條蛋白質(89.3 %)序列可在nr找到對應序列（blastp, E-value：1E-5），這些對應序列中有 93% 歸屬於輻鰭魚綱。與KEGG資料庫的比對後，有26,328筆對應結果，與 Pfam資料庫共有24,193條序列有蛋白質模組構造的註解，SignalP預測顯示有1,283條蛋白具有訊息胜肽，tmHMM分析顯示有5,302條預測具有穿膜蛋白構造。在比較基因體學的部分，本研究選用河魨(Fugu rubripes)、斑馬魚(Danio rerio)及吳郭魚(Oreochromis niloticus)，將所預測出的轉譯蛋白序列進行互相比對，可發現任兩物種之間的可對應序列都接近 80% 或更高。 最後我們將組裝序列與註解結果資料整合，建構成線上資料庫，呈現石斑魚最完整的基因序列目錄與相關的調控代謝網路，將在日後整合轉錄體的相關資料，可於線上即時分析差異表現基因所涉及的代謝網路與找出相關參與基因群，以深入更廣泛地方式來瞭解複雜的調控機制。本研究期望能對龍膽石斑相關研究有所助益，並能對龍膽石斑基因體更深入的瞭解，進而對龍膽石斑成長、育種與病理等基礎研究有所助益。; Giant grouper (Epinephelus lanceolatus) is one of the most economically valuable aquaculture species in Taiwan. Its genome is estimated in 1.1G and has not been fully sequenced. In this study, we apply next-generation sequencing (NGS) technology to obtain whole genome shotgun sequences, then to do de novo assembly for recover the genome of E. lanceolatus from short reads. Then we annotate the genome of E. lanceolatus. Four different assembly strategies are evaluated for the best one to conclude genome scaffold. We chose ALLPATHS-LG as the assembler and used GapCloser to further fill the intra-scaffold gaps. Total 13,897 scaffolds, in total length sum of 1.09 G bp, were derived, from which 42,433 putative protein coding genes were predicted by AUGUSTUS using gene model of sea lamprey (Petromyzon marinus). Overall 92.6% of the protein products were annotated by nr (blastp, E-value: 1E-5). Among these best matched nr sequences, more than two-thirds protein coding sequences are from Phylum Actinopterygii, and the other one-third match to bacterial proteins. It indicate a possible source of sample contamination. We further remove scaffolds of bacterial origin and the final set is 9,473 scaffolds, sum up to 1.06 G bp; 29,184 protein sequences were derived and 89.3% of the best matched sequences were from Phylum Actinopterygii. There are 26,328 protein sequences mapped on KEGG database. We further annotated these protein sequences using Pfam, SignalP and tmHMM to reveal protein structure information. We use the whole set of protein coding genes derived from E. lanceolatus, Fugu rubripes, Danio rerio and Oreochromis niloticus and find the best hits for each proteins mutually by blast. About 80% of the protein sequences can find match between any two species. Finally, we integrated the protein coding sequences with their annotations into a web database. This database will be open and become a helpful grouper genome resource for research community. It will benefit the grouper researchers for studying physiology and pathology, as well as for defining genetic traits such as fast growing rate and disease resistance for breeding.

2014-01-01T00:00:00Z