地球上存在著非常多樣的生物，其中微生物佔最大的比例。儘管目前仍有約99%的微生物無法在實驗室的環境中培養，但它們控制著地球上每個生態系統中的生地化循環 (biogeochemical cycles) 。因此，了解微生物的多樣性，分佈，功能以及描述它們與生態系統的關係就變得很重要。在過去的三十年中，非傳統培養方法，諸如高通量測序方法（16S核糖核酸基因擴增子定序，全基因組，單細胞定序）等，徹底改變了我們對微生物多樣性以及微生物生態學的了解。
本論文共分六章，主要是結合多組學方法 (multi-omics approaches)來做生物資訊分析，進而描述海洋（珊瑚礁）和淡水（湖泊）生態系統中細菌群落的分佈，功能以及它們的相互作用關係。第一章為介紹當前多體學研究背景知識以及對水生微生物生態學中的應用，特別著重於不同生態系統中的細菌群落功能關係 (community functional relationships)。第二章描述從海洋珊瑚(Aropora sp.)中分離到的一種新的內生桿菌物種 (Endozoicomonas) 的全基因體，揭示了這種廣泛分佈在不同的海洋無脊椎動物中的細菌屬 (genus) 的多樣性。再者，第三章是描述開創性地發現內生桿菌在珊瑚硫循環中的作用以及如何幫助珊瑚減輕環境壓力。從全基因體與功能性分析的證據中顯示內生桿菌 (Endozoicomonas acroporae) 具有能夠降解氣候冷化氣體先驅物二甲基巰基丙酸 (dimethylsulfoniopropionate) 產生氣候冷化氣體二甲基硫 (dimethylsulfide)。第四章比較台灣兩個亞高山湖泊鴛鴦湖和翠峰湖的表水與空氣中的細菌群落組成，結果顯示兩個不同營養程度(trophic state)的湖泊具有各自獨立的細菌群落，隨時間的改變細菌群落不具有顯著的變化。但空氣中的細菌群落是多樣性高並且具有時空變化。第五章則藉由超過八週的移地實驗 (reciprocal-transplant experiment) 研究「功能性冗餘假說」(functional redundancy)。利用多體學的分析方法發現水生微生物群系的部分功能冗餘 (partial functional redundancy)中解析程度是影響描繪群落功能關係的主要因素之一 (resolution dependency)。最後，第六章則將每個章節做的簡短總結並闡述水生微生物生態學領域中未來的研究方向與展望。

Tremendous diversity exists on our planet, with microbes contributing to the largest proportion of total biomass. Although about 99% of the microbes cannot be cultured under laboratory-controlled environment, they govern biogeochemical cycles in every ecosystem on Earth. Thus, it becomes important to understand their diversity, distribution, function, and delineate their relationship with the ecosystem through alternative approaches to culture-dependent methods. In the past three decades, culture-independent methods such as high-throughput sequencing approaches (amplicon, whole-metagenomes, single-cell) have revolutionized our understanding of microbial diversity and microbial ecology.
This dissertation embodies five chapters and comprises mainly of bioinformatics analyses using multi-omics approaches to delineate the distribution, function, and role of the bacterial community in marine (coral as a model system) and fresh-water (lakes as model systems) ecosystems. The first chapter is a general introduction to multi-omics approaches, their current knowledge, and application in aquatic microbial ecology with a special focus on community functional relationships in different ecosystems. The second chapter describes the genomes of a novel bacterial species from genus Endozoicomonas isolated from sea coral Acropora sp., enriching the diversity of this important bacterial genus which is widespread in different marine invertebrates. Further, the third chapter reports seminal findings on the role of Endozoicomonas in coral sulfur-cycle and stress mitigation, providing the first genomic and functional evidence on the ability of Endozoicomonas acroporae species to metabolize dimethylsulfoniopropionate (DMSP) to dimethylsulfide (DMS), a climate active gas. The fourth chapter describes and compares the bacterial community in surface water and the air above, the two sub-alpine Lakes, Yuan-Yang and Tsuei-Feng, of Taiwan, which revealed different bacterial communities in these lakes, attributed to their different trophic states that remained stable over time. However, the bacterial communities in the air were diverse and had spatial and temporal variance. The fifth chapter investigates the hypothesis of functional redundancy empirically through a first of its kind reciprocal-transplant experiment conducted over six weeks in Yuan-Yang and Tsuei-Feng lakes, utilizing a multitude of omics approaches and reporting partial functional redundancy in aquatic microbiomes. Lastly, the sixth chapter concludes this dissertation with short summaries of each project and prospects of this dissertation giving a glimpse of future directions in the field of aquatic microbial ecology.

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