Exploring nitrification within engineered aquatic environments

城市污水的处理涉及利用废物成分作为能源的微生物（细菌和古细菌），并在此过程中，减少污水对接收这些处理过的水的河流和湖泊中的鱼类和其他野生动物的毒性。了解硝化过程中涉及的微生物种群和过程（在呼吸氧气的同时使用氨和亚硝酸盐作为能源）对于优化水处理过程和基础设施设计至关重要。尽管一个多世纪以来，氨氧化细菌和亚硝酸盐氧化细菌被认为是硝化作用的唯一贡献者，但氨氧化古细菌和硝化螺旋菌能够完全氨氧化（comammox）的发现极大地扩展了水生、陆地和工程环境中硝化作用的知识。我的研究小组将使用工程水处理系统，如水族馆过滤器和安大略省圭尔夫的旋转生物接触器，比较硝化菌的种群，多样性，功能和相互作用，特别强调新发现的古细菌和comammox细菌参与氨氧化。我们还将描述我们最近培养的古菌的生理和代谢特征，重点是确定它们对氨的亲和力和吸收有机碳源的能力。我们还将验证这样一个假设，即这些氨氧化古菌可以胜过更传统的氨氧化剂，因为它们可以利用细菌无法利用的有机碳基质。我们还将应用尖端的显微方法来可视化这些生物膜内部硝化贡献者的空间分布，这将有助于我们更好地理解这些表面上看起来对相同过程负责的独特群体的相互作用。由于在废水生物膜中发现的古细菌也存在于人类皮肤上，我们将探索从多个物种和身体部位采集的哺乳动物皮肤样本上的微生物，以帮助确定这些古细菌的自然栖息地，并研究它们与宿主健康的潜在相互作用。总之，我的基础研究项目将揭示与氮循环相关的基因、细胞和分子与工程水处理系统，作为这些过程的强大的微观世界，因为它们发生在无数的水生、陆地和宿主相关的环境在全球范围内。

Treatment of municipal wastewater involves microorganisms (bacteria and archaea) using the components of waste as energy sources and, in the process, reducing the toxicity of effluent for fish and other wildlife in the rivers and lakes that receive this treated water. Understanding the microbial populations and processes involved in the process of nitrification (use of ammonia and nitrite as energy sources while breathing oxygen) is essential for optimizing water treatment processes and infrastructure design. Although ammonia-oxidizing bacteria and nitrite-oxidizing bacteria were regarded as sole contributors to nitrification for over a century, the discovery of both ammonia-oxidizing archaea and Nitrospira bacteria capable of complete ammonia oxidation (comammox) greatly expands knowledge of nitrification within aquatic, terrestrial, and engineered environments. My research team will use engineered water treatment systems, such as aquarium filters and rotating biological contactors in Guelph, Ontario, to compare populations, diversity, functions, and interactions of nitrifiers, with a particular emphasis on the newly discovered archaea and comammox bacteria involved in ammonia oxidation. We will also characterize the physiology and metabolism of the archaea we cultivated recently, with a focus on identifying their affinity for ammonia and ability to assimilate organic carbon sources. We will also test the hypothesis that these ammonia-oxidizing archaea can outcompete more traditional ammonia oxidizers because they can take advantage of organic carbon substrates that their bacterial counterparts cannot use. We will also apply cutting-edge microscopic approaches to visualize the spatial distributions of these contributors to nitrification within biofilm itself, which will help us better understand interactions of these unique groups that superficially appear to be responsible for the same processes. Because the archaea found in the wastewater biofilms are also found on human skin, we will explore the microorganisms on mammalian skin samples taken from multiple species and body sites to help identify the natural habitat of these archaea and investigate their potential interactions with host health. Together, my basic research program will shed new light on the genes, cells, and molecules that are relevant to nitrogen cycling with engineered water treatment systems, which serve as powerful microcosms of these same processes as they occur in myriad aquatic, terrestrial, and host-associated environments on a global scale.