油汙棲地功能性總基因體的研究: 微生物多樣性及機能性基因分析

• Main Author: 蔣鎮宇
• Other Authors: 生命科學系
• Language: Chinese
• Published: 2020
• Subjects: 油汙； 功能性總體基因體學；油汙降解基因；微生物多樣性；正向天擇; Petroleum pollution； Functional metagenomics； Oil degradation genes； Microbial diversity； Positive selection; Antarc*; Antarctica
• Online Access: http://ir.lib.ncku.edu.tw/handle/987654321/206735; http://ir.lib.ncku.edu.tw/bitstream/987654321/206735/1/index.html

計畫編號︰MOST109-2621-B006-003-MY2 執行機構: 國立成功大學生命科學系 研究期間: 2020-08~2021-07 地球上的原始生命誕生於與現今環境迥異的條件中，經過長時間的演化，大多數的生命形式適應於一般的氣候與地理條件之下，而原始的微生物依然保有環境適應的特性，加上基因水平移入或趨同演化，更加添了遺傳的多樣性，生存在極端環境中的微生物因此代表了寶貴的生物資源。本研究利用總體基因體學解析油汙逆境下，土壤微生物的群聚組成，透過油汙耐性測試鑑定出可能的指標物種，分離出的優勢微生物候選物種，將以次世代定序技術以及生物資訊分析，組裝其基因體序列並預測關鍵基因，此外，針對候選物種，進行功能性總體基因體分析，將基因體破碎的DNA片段，透過轉殖，在高油汙處理下篩選出存活的轉殖細菌，以此鑑定出降解油汙的關聯基因，並透過演化基因體分析，檢測其天擇模式。欲回答的問題有四: 1.油汙環境下的微生物種多樣性是否顯著低於一般的棲地？2.油汙下的微生物是屬於特定微生物種類，而有所謂的分類群的熱點分布或是廣泛分布於所有微生物？3. 在分解油汙的微生物群中，一如Psedomonas 及Bacillus，降解油汙的功能性基因是否為一次演化? 4. 候選物種的油汙分解基因是否受到正向天擇的調控？ Life on Earth began under a unique condition from the present. Through long evolutionary processes, most life forms live in common climatic conditions, while many microorganisms are able to thrive even in extreme habitats, such as hydrothermal vents in deep sea and the frozen lands of Antarctica. Evolutionary mechanisms, such as horizontal transfer and convergent evolution, also created genetic and physiological diversities of bacteria. Accordingly, exploring the microbial diversity in the extreme environments would enable us to understand the adaptations and application of those invaluable biodiversity resources. With the advancement of next-generation sequencing and metagenomics, microbiologists are able to decipher the unseen world without microbial culture. In this study, we aim to analyze the microbial diversity in soil contaminated by petroleum and to identify the candidate bacterial species for digesting oil pollutants based on metagenomics approaches and tolerance experiments. Genomes of these candidate species will be sequenced and assembled using next generation sequencing; candidate genes will be thereby predicted based on bioinformatics analysis. Functional metagenomics will be conducted via gene transformation and expression to identify DNA fragments carried in the transformed bacteria that survive in the high-concentration petroleum. Modes of natural selection will be examined at the candidate genes. In this study, four questions will be addressed: 1. Is the species diversity of polluted habitats lower than that of unpolluted habitats? 2. Are the bacteria growing in polluted habitats restricted to some taxa as a taxonomic hotspot? 3. How many times of evolution of the trait of oil degradation in genera like Bacillus and Pseudomonas? 4. Are the degradation genes that are associated with bacterial adaptation shaped by positive selection?