Collaborative Research: Do Diverse Members of the Epsilonproteobacteria Employ a Novel Nitrate Reduction Pathway?

智力优势：氮是所有生物生长所需的关键营养物质。氮在地球上主要以气体形式存在，绝大多数生物无法吸收。因此，无论是作为铵、亚硝酸盐还是硝酸盐的固定氮，都是激烈竞争的对象。地球表面氮的大多数转化是由微生物催化的，包括不同固定氮种之间的相互转化。生长的首选氮种是铵，在生态系统中通常是一种限制性营养物质。该项目将详细介绍一种新的方法，通过这种方法某些微生物“呼吸”或呼吸硝酸盐并产生铵。它们这样做的原因和人类呼吸氧气的原因一样，是为了保存能量。硝酸盐呼吸本身并不新鲜，但这项研究的主要模式细菌——深海鹦鹉螺（Nautilia proundicola）所使用的机制是新颖的，可能对它在深海热液喷口谋生很重要。还将研究深孔菌的近亲，它们携带编码相同途径的基因，并且最常在动物身上发现，例如在人类的口腔和鸡的肠道中。这种途径对这些生物体的益处目前尚不清楚。通过了解这些细菌的氮代谢，我们将更多地了解氮是如何在环境中移动的，也许还能了解与动物相关的细菌是如何在远离宿主的环境中生存的。该项目旨在利用基因组科学的最新技术进步，即高通量转录组学，并将其与更传统的生理方法相结合，以表征这种新的硝酸盐还原途径。该项目将最终确定该途径的关键酶和中间体，以及它是如何被调节的。更广泛的影响：pi将在基因组微生物生理学方面培训几名本科生和两名研究生，通过跨机构和跨学科的研究加强学习。除了传统的微生物生理学和基本的氮化学外，所有的学生都将接触到最先进的高通量基因组学方法。他们将通过讲习班接受负责任的研究行为方面的正式培训，并通过在国家会议和出版物上发言以口头和书面形式介绍他们的研究，从而加强他们的专业发展。这些活动将被纳入美国国家科学基金会资助的硝化网络RCN的战略计划。最后，这些结果将通过教师培训研讨会传播给K-12学生，并通过特拉华大学海岸日等活动传播给公众，平均每年出席人数超过8000人，并在其他机会出现时由pi进行不太正式的演讲。

Intellectual Merit:Nitrogen is a key nutrient that all living beings need to grow. Nitrogen exists on planet Earth predominantly in gaseous form, inaccessible for assimilation to the vast majority of organisms. Hence fixed nitrogen, either as ammonium, nitrite or nitrate, is competed for vigorously. Most transformations of nitrogen in the Earth's surface are catalyzed by microbes including the interconversion between different fixed nitrogen species. The preferred nitrogen species for growth is ammonium, often a limiting nutrient in ecosystems. This project will detail a new means by which certain microbes "breathe" or respire nitrate and produce ammonium. They do this for the same reason humans breathe oxygen, to conserve energy. Nitrate respiration is not new per se, but the mechanism used by the primary model bacterium for this study, Nautilia profundicola, is novel and may be important for it to making a living at deep-sea hydrothermal vents. Relatives of N. profundicola will also be studied that carry the genes encoding the same pathway and are most often found in association with animals, for example in the oral cavity of humans and in the guts of chickens. The benefit of this pathway to these organisms is currently unclear. By understanding the nitrogen metabolism of these bacteria, we will learn more about how nitrogen moves in the environment and perhaps also how animal-associated bacteria survive in the environment away from their hosts. This project is designed to take advantage of the most recent technological advances in genome sciences, namely high-throughput transcriptomics, and combine it with more traditional physiological approaches to characterize this novel nitrate reduction pathway. This project will ultimately define the key enzymes and intermediates of this pathway and how it is regulated. Broader Impacts:The PIs will train several undergraduate students and two graduate students in genome-enabled microbial physiology, enhancing learning through cross-institutional and cross-disciplinary research. All students will be exposed to state of the art high-throughput genomics approaches in addition to traditional microbial physiology and basic nitrogen chemistry. They will be formally trained in the responsible conduct of research through workshops and their professional development will be enhanced by presenting their research in both oral and written form via presentations at national meetings and publications. These activities will be integrated into the strategic plan of the NSF-funded Nitrification Network RCN. Finally, these results will be disseminated to K-12 students via teacher-training workshops and to the public via events like the University of Delaware's Coast Day, with an average annual attendance of over 8,000, and others as opportunities arise for less formal presentations by the PIs.