部分亞硝化-厭氧銨氧化(Partial Nitritation-Anammox, PN-A)被認為是廢水處理場域追求永續發展的低碳排生物除氮技術，然而以PN-A程序處理低濃度銨氮廢水，如都市污水，仍相當困難。PN-A透過好氧的氨氧化菌將氨氧化至亞硝(部分硝化)，接著厭氧銨氧化菌將剩餘的銨與亞硝轉化成氮氣，達成去除廢污水中的氮污染。為使好氧菌與厭氧菌在單一反應槽中共存與合作，PN-A常透過間歇曝氣來控制系統的供氧量與槽中溶氧濃度，使得槽內溶氧環境在微好氧與缺氧間變動。然而低溶氧及低銨氮濃度造成氨氧化反應活性低落，使部分硝化成為PN-A系統用於處理低濃度銨氮廢水的主要瓶頸。近年來新發現的完全氨氧化菌能夠獨自進行氨以及亞硝氧化，是都市污水廠活性污泥槽中優勢的硝化菌，但對其在PN-A系統中的角色仍不清楚。完全氨氧化菌是否在PN-A系統中只進行部分硝化並與厭氧銨氧化菌合作，及如何控制此合作關係來處理低濃度銨氮廢水仍有待探討。在此博士論文中，我提出「完全氨氧化菌其氨氧化及亞硝氧化兩路徑可分開調控」之假說，並認為可透過反應槽操作使完全氨氧化菌進行部分硝化，達成與厭氧銨氧化菌合作處裡低濃度銨氮廢水之目標，並在此目標之下，進一步以多源體學(meta-omics)探討系統中的微生物族群如何適應間歇曝氣條件下變動的溶氧環境。
本博士論文包含了四個研究，皆於一實驗室規模的PN-A反應槽進行。章節3.1探討進流銨氮濃度對PN-A的影響。此章研究成功的共同培養與放大完全氨氧化菌與厭氧銨氧化菌成為反應槽中優勢菌群，並達到>70%的總氮去除效率。多變量分析結果支持完全氨氧化菌對反應槽中銨氧化反應有重要貢獻。進一步的批次實驗顯示高濃度的游離氨會抑制完全氨氧化菌的活性與生長，但低濃度的游離氨可促進完全氨氧化菌進行部分硝化。章節3.2探討PN-A是否可在高水量負荷的條件下有效處理低濃度銨氮廢水。在此章研究中，反應槽進流低濃度銨氮廢水(60 mg-N/L)，並階段性將水力停留時間縮短至4小時。在最高進流銨氮負荷(0.36 kg-N/m3/day)的條件下，PN-A反應槽可穩定去除~80%的氮污染。接著，我透過抑制劑將系統中氨氧化菌的活性抑制，確認完全氨氧化菌為主要的氨氧化反應貢獻者，並提供亞硝予厭氧銨氧化菌。此外，基因表現分析顯示生物膜有利於此合作關係。我以實驗證實完全氨氧化菌與厭氧銨氧化菌的於PN-A系統中的合作關係，並進一步展示此合作關係可有效處理高水量負荷的低濃度銨氮廢水。
在間歇曝氣操作下，PN-A 系統中的微生物體循環經歷微好氧和缺氧的溶氧環境。本論文的第四章以多源體學探討微生物族群如何適應微好氧-缺氧循環。章節4.1中，多源基因體學分析結果顯示系統中關鍵菌群普遍具有高氧氣親和力的terminal oxidase與去毒化活性氧物質相關基因，使關鍵菌群能成功適應操作於間歇曝氣條件下的PN-A反應槽。在此基礎上，章節4.2進一步以多源轉錄體學研究間歇曝氣對關鍵族群基因表現之影響。結果顯示，在間歇曝氣條件下，大多數核心菌種同時表現好氧與無氧呼吸相關的基因。有趣的是，PN-A 相關菌群對溶氧變化有著不同的反應。氨氧化菌Nitrosomonas對溶氧變化最敏感，其過半數基因其表現受到間歇曝氣的曝氣與停止曝氣影響，且在間歇曝氣下比在持續曝氣條件下有更高的轉錄活性。相比之下，厭氧銨氧化菌和完全氨氧菌在週期性微氧-缺氧條件下維持穩定的轉錄活性。
整體而言，本博士論文成功發展完全氨氧化菌主導的PN-A膜生物反應槽，在高銨氮負荷條件下，可有效穩定地處理低濃度銨氮廢水。本論文的成果支持此系統在廢水處理廠永續轉型中可扮演重要角色，有助於未來污水處理廠達成能量中和、淨零碳排之目標。此外，本論文中多體學的研究對 PN-A 系統中微生物群落在間歇曝氣下的複雜交互作用和代謝機制提供了深入地的見解，有助於開發精準控制微生物體的PN-A操作策略。

The partial nitritation–anammox (PN-A) process represents a significant advancement in sustainable nitrogen removal biotechnology. PN-A relies on the close cooperation of aerobic nitrifiers and anaerobic anammox bacteria within a single reactor. To ensure the proper functioning of PN-A populations, the reactor is typically operated under oxygen-limited conditions with intermittent aeration, creating cyclically microaerobic (aerated) and anoxic (nonaerated) periods. However, its application to low-strength ammonium wastewater remains challenging because low oxygen levels and low ammonia conditions compromise ammonia oxidation, making partial nitritation the rate-limiting step in PN-A systems treating low-strength ammonium wastewater. Comammox Nitrospira, capable of complete ammonia oxidation to nitrate, have shown remarkable adaptability to oligotrophic and low-oxygen environments, potentially aiding ammonia oxidation in PN-A. However, the key challenge lies in managing their ammonia- and nitrite-oxidizing activities and their interaction with anammox bacteria to foster a stable and mutually beneficial symbiotic partnership, an area where knowledge remains limited.
A lab-scale reactor was operated for the PN-A process. In the first study on the effects of ammonium concentrations, efficient nitrogen removal was achieved only when comammox and anammox bacteria dominated the reactor, suggesting the substantial contribution of comammox Nitrospira to ammonia oxidation. Moreover, low concentrations of free ammonia inhibit nitrite oxidation of comammox Nitrospira more than their ammonia oxidation, serving as a control strategy to achieve partial nitritation. In the following study, we investigated the effects of hydraulic loadings. A stable and symbiotic relationship between comammox Nitrospira and anammox bacteria was established and experimentally validated in the reactor, achieving high nitrogen removal efficiency under a high loading of 0.36 kg-N/m³/day. Gene expression results indicated that the biofilm environment fosters cooperation between comammox and anammox bacteria. These findings offer novel insights into the cooperative interplay between comammox Nitrospira and anammox bacteria, potentially reshaping nitrogen cycling management in engineered environments and facilitating the use of PN-A systems for low-strength ammonium wastewater treatment.
Microbial populations in the PN-A systems experience microaerobic and anoxic cycling, yet our understanding of their responses to these conditions is limited. This dissertation uses meta-omics techniques to explore how intermittent aeration manipulates the microbiome in the PN-A reactor. Firstly, metagenomics was employed to decipher the genomic content of core species and their adaptations to cyclically microaerobic-anoxic environments. The results showed that utilizing trace amounts of oxygen and alleviating oxidative stress is essential for the core members that exhibited ecological success in this system. Building on this, this dissertation further investigated how intermittent aeration regulates the microbiome using metatranscriptomics in combination with metagenomics. The results showed that most core species simultaneously expressed genes encoding enzymes for both aerobic and anaerobic energy production under intermittent aeration. In particular, Nitrosomonas species were susceptible to changes in redox conditions and were more active under intermittent aeration than continuous aerobic conditions. Interestingly, anabolism of PN-A populations was differentially regulated by intermittent aeration, with significant alterations in the transcription of genes regarding anabolism observed in Nitrosomonas species. In contrast, anammox bacteria and comammox Nitrospira remained relatively persist in transcription under cyclic microaerobic-anoxic conditions. These findings shed light on the adaptation and regulation of core microbes in response to distinctive redox environments in the PN-A reactor, aiding the development of microbial ecology-driven wastewater treatment technologies.
In summary, this dissertation provides critical insights into microbial communities' complex interactions and metabolic adaptations in the PN-A system under intermittent aeration. By integrating metagenomic and metatranscriptomic approaches, it advances our understanding of the fundamental mechanisms governing microbial responses to dynamic redox conditions. These findings contribute to developing more efficient and stable PN-A technology for sustainable wastewater treatment and expand the scientific knowledge of microbial ecology and metabolic regulation in engineered environments under microaerobic-anoxic conditions. Thus, this work represents a significant contribution to both technological innovation and scientific discovery in the field of environmental engineering.

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