COLLABORATIVE RESEARCH: The role of marine Crenarchaeota in nitrification and links among biogeochemical processes in the eastern tropical North Pacific and Gulf of California

硝化作用是氨通过亚硝酸盐两步氧化为硝酸盐的过程，它通过改变氮的存在形式在全球氮循环中发挥关键作用，从而影响不同生物群和生物地球化学过程对氮的可获得性和有效性，实际上，负责固定和从海洋中去除氮的过程最终可能通过硝化作用联系在一起。长期以来，人们一直认为，硝化的第一步，也是限速步骤，氨氧化，被限制在领域细菌中的几个组中。然而，最近发现的氨氧化古生菌(AOA)严重挑战了我们对海洋硝化作用的微生物生态和生物地球化学的理解。在这个项目中，斯坦福大学和夏威夷大学马诺阿分校的研究人员将试图定量限制海洋克伦考古塔对海洋硝化作用的贡献，并调查与加利福尼亚州海湾(GOC)和热带北太平洋东部(ETNP)其他形式的氮代谢的联系。具体目标是：(1)量化GOC和ETNP上层水柱(0-100米)中七个站点的15N-氨氧化速率以及细菌和古生菌的amoA基因和转录本；(2)通过将13C标记的重碳酸盐吸收到古生膜脂类中，确定Crenaceota是否正在积极固定无机碳(即自养)；(3)量化相同深度和站点的亚硝酸盐氧化速率和亚硝酸盐氧化剂丰度；(4)将这些测量扩展到最小氧气带(OMZ)内的多个深度；(5)研究GOC和ETNP OMZ中氨氧化古菌和氮损失过程之间的潜在耦合，以及(6)通过与NSF资助的工作相结合，将我们的结果放在更广泛的海洋学角度，检查最终在OMZ产生的缺氮水域的固氮。研究人员预测，在上层水柱和OMZ中，海洋裸体考古动物将在氨氧化过程中发挥主导作用--基于AMOA的丰度、基因表达、对同位素标记的无机碳的活性固定以及与测量速率的相关性。他们还预计，AOA与氧化(亚硝酸盐氧化)和还原N代谢(如Anammox)之间的代谢耦合将是明显的。就更广泛的影响而言，硝化作用在将有机物矿化与厌氧脱氮联系起来方面发挥着关键作用，该项目将提供关于硝化作用和基础微生物群落如何受到关键环境梯度的影响以及它们与其他N循环过程的联系的关键信息。最终，这项多学科研究应该为所有海洋系统中这一生物地球化学重要过程的生态和调控提供洞察力。拟议的研究有很好的教育机会，私人投资机构有成功指导和毕业硕士和/或博士学生的历史，并促进了学生出版物和在全国会议上的演讲。本科生、研究生和博士后教育将通过积极参与巡航和巡航后分析来进一步发展，在这些分析中，学生将与分子微生物生态学和稳定同位素生物地球化学方面的专家合作，并学习一系列最先进的实验和分析方法。

Nitrification, the two-step oxidation of ammonia to nitrate via nitrite, plays a critical role in the global nitrogen (N) cycle by changing the form in which N occurs, and consequently influencing the accessibility and availability of N to different groups of organisms and biogeochemical processes, indeed, the processes responsible for the fixation and removal of N from the ocean may ultimately be connected by nitrification. It has long been assumed that the first and rate-limiting step of nitrification, ammonia oxidation, is restricted to a few groups within the domain Bacteria. However, the recent discovery of ammonia-oxidizing Archaea (AOA) has seriously challenged our understanding of the microbial ecology and biogeochemistry of nitrification in the ocean. In this project, researchers at Stanford University and the University of Hawaii at Manoa will attempt to constrain quantitatively the contribution of marine Crenarchaeota to oceanic nitrification and investigate connections to other forms of nitrogen metabolism in the Gulf of California (GOC) and the eastern tropical North Pacific (ETNP). The specific objectives are to: (1) quantify 15N-ammonium oxidation rates, and bacterial and archaeal amoA genes and transcripts, at seven stations in the upper water column (0-100m) of the GOC and ETNP; (2) determine if Crenarchaeota are actively fixing inorganic carbon (i.e., autotrophic) based on uptake of 13C--labeled bicarbonate into archaeal membrane lipids; (3) quantify nitrite oxidation rates and nitrite-oxidizer abundances at the same depths and stations; (4) extend these measurements to multiple depths within the oxygen minimum zone (OMZ); (5) examine potential coupling between ammonia-oxidizing archaea and nitrogen loss processes in the OMZ of the GOC and ETNP, and (6) place our results in a broader oceanographic perspective by tying into NSF-funded work examining nitrogen fixation in N-deficient waters ultimately generated in OMZs. The researchers predict that marine Crenarchaeota will play a dominant role in ammonia oxidation-based on amoA abundance, gene expression, active fixation of isotopically-labeled inorganic carbon, and correlation to measured rates?in both the upper water column and OMZ. They also expect that metabolic coupling between AOA and both oxidative (nitrite oxidation) and reductive N metabolisms (e.g., anammox) will be apparent.With regard to broader impacts, nitrification plays a pivotal role in linking organic matter mineralization to anaerobic nitrogen removal, and this project will provide critical information regarding how nitrification and the underlying microbial communities are influenced by key environmental gradients, as well as their connections to other N-cycling processes. Ultimately, this multi-disciplinary study should provide insights into the ecology and regulation of this biogeochemically-important process in all marine systems. The proposed research has excellent educational opportunities, and the PIs have a history of successfully mentoring and graduating Masters and/or Ph.D. students and fostering student publications and presentations at national meetings. Undergraduate, graduate, and postdoctoral education will be furthered through active participation in the cruise and post-cruise analyses, where students will work collaboratively with experts in molecular microbial ecology and stable isotope biogeochemistry, and learn a spectrum of state-of-the-art experimental and analytical methods.