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

硝化作用是通过亚硝酸盐将氨氧化为硝酸盐的两步反应，通过改变氮的存在形式，从而影响氮对不同生物群体和生物地球化学过程的可获得性和有效性，在全球氮循环中起着至关重要的作用。长期以来，人们一直认为硝化的第一步和限速步骤，氨氧化，仅限于细菌范围内的少数群体。然而，最近氨氧化菌（AOA）的发现严重挑战了我们对海洋微生物生态学和硝化作用的生物地球化学的认识。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Crenarchaeota对海洋硝化作用的贡献，并调查加州湾（GOC）和热带北太平洋东部（ETNP）与其他形式的氮代谢的联系。 具体目标是：（1）在GOC和ETNP的上层水柱（0- 100 m）的七个站点定量15 N-铵氧化速率，以及细菌和古细菌amoA基因和转录本;（2）确定Crenarchaeota是否积极固定无机碳（即，（3）在相同的深度和站位对亚硝酸盐氧化速率和亚硝酸盐氧化剂丰度进行量化;（4）将这些测量扩展到最小氧区（OMZ）内的多个深度;（5）研究GOC和ETNP的OMZ中氨氧化古菌与氮损失过程之间的潜在耦合，（6）通过与NSF资助的研究最终在OMZ产生的缺氮沃茨中的固氮作用的工作相结合，将我们的结果置于更广泛的海洋学视角中。 研究人员预测，海洋Crenarchaeota将在氨氧化中发挥主导作用-基于amoA丰度，基因表达，同位素标记的无机碳的主动固定，以及与测量速率的相关性。在上层水体和外姆带都有 他们还预计AOA与氧化（亚硝酸盐氧化）和还原氮代谢（例如，关于更广泛的影响，硝化作用在有机物矿化与厌氧脱氮之间起着关键作用，该项目将提供有关硝化作用和底层微生物群落如何受到关键环境梯度影响的关键信息，以及它们与其他N循环过程的联系。最终，这项多学科的研究应该为所有海洋系统中这一重要的地球化学过程的生态学和调控提供见解。拟议的研究有很好的教育机会，PI有成功指导和毕业硕士和/或博士的历史。学生和促进学生出版物和在国家会议上的介绍。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得到进一步发展，学生将与分子微生物生态学和稳定同位素地球化学专家合作，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.