生物廢水系統是處理石化廢水中一個具有經濟性的方法，石化廢水中通常含有人工合成的含氯有機化合物，此有機物一旦沒有經過妥善處理就排放至環境水體中會造成環境及人體健康相當大的危害。含氯有機化合物的存在亦會使廢水系統中的微生物無法完全降解有機物，而使出流的有機物濃度偏高。
本研究將針對某石化廠的生物反應系統來探討其廢水中有機物無法降解完全的原因。透過現有的實廠數據以及實驗室內的COD降解實驗測試，研究微生物在好氧、缺氧及其他不同條件之下的降解效率，尋找關鍵因子幫助實場優化其生物反應槽。除此之外，本研究亦會利用定量型聚合酶鏈鎖反應，針對總菌群及hyphomicrobium，分析其基因含量與RNA表現量，探討水質與微生物變化的關係，評估分子生物技術作為實廠操作依據的可行性，以降低系統異常的頻率。
藉由COD降解實驗中，可發現汙泥在好氧的條件下COD降解效率較高，其COD比降解效率比缺氧提高約239%，另外減少汙泥胞外聚合物的產生、提供充足的氧氣與營養鹽的添加分別至少可提升55%、18%及7%的COD比降解效率。而將原本的營養鹽，尿素，改為硝酸則可至少提升11%的COD比降解效率。在硝酸好氧批次實驗中，計算每次COD消耗所利用的硝酸，發現COD與硝酸降解比皆為20~30的情況之下，判斷微生物在此廢水中會利用有機物為碳源、硝酸為氮源，利用氧氣作為電子接受者進行氧化還原反應以降解有機物。
在分子生物技術方面，發現hyphomicrobium 會在好氧的狀況下降解硝酸，且其基因含量會受到進流硝酸濃度的調控。另外其RNA表現量也隨著COD比降解效率的增加跟著增加，顯示此菌在系統中會進行作用，幫助系統中有機物的降解。

Biological treatment is an economic strategy commonly used for wastewater treatment. Petrochemical industrial wastewater usually containing some chlorinated organic compounds may cause environmental issues when being discharged to water bodies without sufficient treatment. However, the chlorinated organic compounds are usually difficult for microorganisms to degrade, resulting high COD in effluents of Petrochemical Wastewater treatment plant (PC WWTP).
A full scale PC WWTP was investigated in this study with water quality analyses and molecular biotechnologies to explore the incompletely degradation of COD in biological process. In order to find the key factors of COD degradation in the process, batch experiments were conducted under different conditions like dissolved oxygen concentration, nutrients addition, aerobic, anoxic, different nitrogen sources and the presence of soluble extracellular polymeric substances.
According to the batch experiments, the specific COD degradation rates were higher under aerobic condition, which increased 239% when being compared to anoxic condition. Specific COD degradation rates could increase by 55%, 18% and 7%, respectively, in the batches with lower EPS content, sufficient DO and additional nutrients. Moreover, changing nitrogen sources from urea to nitrate could also increase 11% of specific COD degradation rate. It should be noted that the consumption ration of COD to nitrate in the batch experiments were between 20 to 30, implying that microorganisms in the sludge may use COD as carbon sources, nitrate as nitrogen sources and oxygen as electron acceptors.
From the results of NGS analysis and quantitative PCR, hyphomicrobium was found in the sludge and accounted for 16% of the total bacteria. Hyphomicrobium was been prove that could degrade nitrate under aerobic condition, explaining the nitrate decrease in the system. Gene concentration of hyphomicrobium in PC WWTP was strongly affected by influent nitrate concentration. The expression of hyphomicrobium also increased with the increase of specific COD degradation rate, indicating hyphomicrobium could be benefit to COD degradation.

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