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

智力上的功绩。微生物支持氮的生物地球化学循环，这是地球上最重要的营养循环之一。在这个循环中的一个关键步骤，即自养微生物将氨氧化为亚硝酸盐，一个世纪以来一直被认为是由几个受限的细菌属介导的。重要的氨氧化，也许最重要的是，现在归因于一个以前神秘的古生代--氨氧化古生菌(AOA)--在海洋和陆地环境中都很丰富。研究人员先前的生理和环境分析--这一提议的基础--已经表明，AOA在海洋光区内活跃，它们在海洋环境中的竞争适应性至少部分归因于对氨的极高亲和力？在氨浓度不足以维持已知细菌氨氧化菌的情况下，以接近最大的生长速度生长？以及一种不同寻常的以铜为基础的呼吸系统，这可能会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--转化为亚硝酸盐，从而改变并可能控制光区内其他微生物可利用的固定氮的形式，亚硝酸盐是一种只对亚硝酸氧化细菌和一些浮游植物可用的形式。如果这是正确的，这将对生物多样性产生重大影响。PIS将利用蛋白质和高通量测序方面的最新技术进步，评估硝化作用在塑造生物多样性(基因组和元基因组学)、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、分布和活性的环境和生物变量，他们将促进对其分类的总体理解。更直接的是，对AOA对再生硝酸盐的贡献的功能性知识将改善对新海洋产量(生物泵)的估计。基于硝酸盐同化作用，过去大多忽视了硝化作用作为硝酸盐的主要来源的重要性。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，并最终将更好地理解人类活动对这一关键营养循环的影响。陆地、海洋和大气系统中人为输入的活性氮对氮循环产生了深远的影响吗？对海洋生物生产、N20排放增加、氮污染和富营养化产生重大影响。同样，人们对海洋生态系统中氮素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输入活性氮的影响。由于这两个变化都极大地改变了微生物可利用的氮，因此这些与环境相关的AOA的响应特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极大的意义。这项工作也将为高中教师和学生提供一个绝佳的跨学科研究机会。推广活动将加强学生和教师对微生物在全球元素循环中的作用的了解，例如氮循环。这项研究还将加强由国家科学基金会一体化资助的硝化研究协调网络成员之间的合作。拟议的项目涵盖并综合了生物多样性的三个方面(功能、遗传和分类)。首先，该项目以功能为框架：对地球上最重要的营养循环之一--氮循环--进行微生物控制。其次，最近的基因分析表明，一个新的古生界分支(暂时归属于古生界内的一个新王国--塔乌姆考古群)的活动与控制海洋中的氨氧化有关。第三，它是建立在令人信服的生理和环境数据综合的基础上的，这些数据导致了它的中心假设？通过改变并可能控制氮的形式，AOA还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。它标识了特定的分类命令性。全球丰富的农产品中存在着巨大的遗传多样性？几乎完全由基因测序调查编目，因此缺乏正式描述？这使得必须将成员分解为生态相关的组或支系，作为发展正式分类学的前奏。研究人员已经组建了一组研究人员，他们在每个方面都具有特定的专业知识，并具有以综合方式处理概述的研究目标的独特资格。

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.