Dimensions: Collaborative Research: Significance of nitrification in shaping planktonic biodiversity in the ocean

智力优势。微生物维持氮的生态地球化学循环，这是地球上最重要的营养循环之一。这个循环的关键步骤是由自养微生物将氨氧化成亚硝酸盐，世纪以来，人们一直认为这是由少数几种限制性细菌属介导的。重要的氨氧化，也许是大多数，现在归因于一个以前神秘的古菌群-氨氧化古菌（AOA）-在海洋和陆地环境中的高丰度。调查人员先前的生理和环境分析，为这项建议的基础，已经表明，AOA是活跃的海洋透光带内，他们在海洋环境中的竞争力健身至少部分归因于一个非常高的亲和力氨？在不能维持已知细菌氨氧化剂的氨浓度下以接近最大生长速率生长？以及一种不寻常的铜基呼吸系统，这可能使它们在铁有限的环境中更具竞争力。从这些先前的分析中得出的令人信服的推论是，AOA通过将氨（一种几乎普遍存在的氮形式）转化为亚硝酸盐（一种仅可用于亚硝酸盐氧化细菌和一些浮游植物的形式），改变并可能控制透光层内其他微生物组合的固定氮形式。如果是正确的，这对生物多样性有重大影响。PI将使用蛋白质和高通量测序的最新技术进步来评估硝化作用在塑造生物多样性（基因组和宏基因组学），活性（转录组，蛋白质组和稳定同位素探测）以及控制重要微量元素（铜）可用性方面的重要性。反过来，通过解决影响AOA多样性，分布和活动的环境和生物变量，他们将推进对其分类的一般理解。更直接地说，AOA对再生硝酸盐的贡献的功能知识将改善新的海洋生产的估计（？生物泵？）基于硝酸盐同化，在过去大多忽略了硝化作用作为硝酸盐主要来源的重要性。这些研究将共同改变对海洋氮循环的理解，对新产量的估计，并最终更好地了解人类活动对这一关键营养循环的影响。更广泛的影响。氮循环已经深刻地影响到陆地，海洋和大气系统的活性氮的人为输入？对海洋生物生产、增加N20排放、氮污染和富营养化具有或预计具有重大影响。同样，人们对海洋生态系统中氮循环和生产力之间的关系也缺乏了解。海洋系统日益受到海洋酸化和大气中活性氮输入的影响。由于这两种变化极大地改变了微生物可利用的氮，这些环境相关AOA的响应的表征对于理解酸化和人为氮输入对主要海洋过程的影响具有巨大的相关性。这项工作也将为高中教师和学生提供一个极好的跨学科研究机会。外联活动将加强学生和教师对微生物在全球元素循环（如氮循环）中的作用的理解。该研究还将加强由NSF资助的硝化研究协调网络成员之间的合作。拟议的项目包括并整合了生物多样性的三个方面（功能、遗传和分类）。首先，该项目是由功能框架：微生物控制地球上最重要的营养循环之一，氮循环。第二，它是由最近的遗传分析，关联活动的一个新的分支的海洋（暂时分配到一个新的王国内的海洋，Thaumarchaeota）与控制氨氧化在海洋中。第三，它是建立在一个令人信服的综合生理和环境数据，导致其中心假设？通过改变和可能控制氮的形式，AOA也改变了地球上最具生产力的环境之一的生物多样性和生态功能。它确定了一个特定的分类必要性。全球丰富的AOA中巨大的遗传多样性？几乎完全由基因测序调查编目，因此缺乏正式的描述？使得将成员分解为生态相关的组或分支作为开发正式分类学的前奏至关重要。研究人员已经召集了一组研究人员，他们在每个维度上都具有特定的专业知识，并且具有独特的资格来解决以综合方式概述的研究目标。

Intellectual Merit. Microorganisms sustain the biogeochemical cycling of nitrogen, one of the most important nutrient cycles on earth. A key step in this cycle, the oxidation of ammonia to nitrite by autotrophic microorganisms, was for a century thought mediated by a few restricted bacterial genera. Significant ammonia oxidation, perhaps most, is now attributed to a previously enigmatic group of Archaea - the ammonia-oxidizing archaea (AOA) - of high abundance in both marine and terrestrial environments. The investigators prior physiological and environmental analyses, the foundation for this proposal, have shown that AOA are active within the marine photic zone and that their competitive fitness in the marine environment is at least in part attributable to an extremely high affinity for ammonia ? growing at near maximum growth rates at concentrations of ammonia that would not sustain known bacterial ammonia oxidizers ? and an unusual copper-based respiratory system that may render them more competitive in iron limited environments. The compelling inference from these prior analyses is that AOA alter and possibly control the forms of fixed nitrogen available to other microbial assemblages within the photic zone by converting ammonia, a nearly universally available form of nitrogen, into nitrite, a form only available to nitrite oxidizing bacteria and some phytoplankton. If correct, this has a significant impact on biodiversity. The PIs will use the most recent technological advances in protein and high throughput sequencing to evaluate the significance of nitrification in shaping biodiversity (genomic and metagenomics), activity (transcriptome, proteome and stable isotope probing), and in controlling availability of an important trace element (copper). In turn, by resolving the environmental and biotic variables that influence the diversity, distribution and activity of AOA, they will advance general understanding of their taxonomy. More directly, functional knowledge of the contribution of AOA to regenerated nitrate will improve estimates of new ocean production (?biological pump?) based on nitrate assimilation, which in the past has mostly neglected the importance of nitrification as a major source of nitrate. Together these studies will transform understanding of the marine nitrogen cycle, estimates of new production, and will ultimately provide a better understanding of the impact of human activity on this critical nutrient cycle.Broader impacts. The nitrogen cycle has been profoundly affected by anthropogenic inputs of reactive nitrogen into terrestrial, marine, and atmospheric systems ? having, or predicted to have, major impacts on marine biological production, increased N20 emissions, nitrogen pollution, and eutrophication. Likewise, there is a poor understanding of the relationship between nitrogen cycling and productivity inmarine ecosystems. Marine systems are increasingly affected by ocean acidification and by atmospheric inputs of reactive nitrogen. Since both changes greatly alter nitrogen available to microorganisms, the characterization of the response of these environmentally relevant AOA is of tremendous relevance to understanding the affect of acidification and anthropogenic nitrogen inputs on major ocean processes. The work will also provide an excellent interdisciplinary research opportunity for high school teachers and students. Outreach will enhance understanding among students and teachers of the role of microorganisms in global elemental cycles such as the N cycle. The research will also enhance collaboration among members of the Nitrification Research Coordination Network funded by NSF.Integration. The proposed project encompasses and integrates the three dimensions (functional genetic, and taxonomic) of biodiversity. First, the project is framed by function: microbial control of one of the most important nutrient cycles on earth, the nitrogen-cycle. Second, it is motivated by recent genetic analyses that associate activities of a novel clade of Archaea (provisionally assigned to a new kingdom within the Archaea, the Thaumarchaeota) with control of ammonia oxidation in the ocean. Third, it is built upon a compelling synthesis of physiological and environmental data that lead to its central hypothesis ? that by altering and possibly controlling the form of nitrogen, the AOA also alter biodiversity and ecological function in one of the most productive environments on earth. It identifies a specific taxonomic imperative. The tremendous genetic diversity among the globally abundant AOA ? catalogued almost exclusively by gene sequencing surveys and therefore lacking formal description ? makes it essential to resolve membership into ecologically relevant groups or clades as a prelude to developing a formal taxonomy. The investigators have assembled a group of researchers with specific expertise in each of dimension and uniquely qualified to address the research objectives outlined in an integrative way.