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

维度：合作研究：硝化作用对塑造海洋浮游生物多样性的重要性

• 批准号: 1046098
• 负责人: James Moffett
• 金额: $ 59.93万
• 依托单位: University of Southern California
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-10-01 至 2015-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1046098&HistoricalAwards=false
• 关键词: Dimensions; Collaborative; Research; Significance; nitrification

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.

智力优点。微生物维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。在这个周期中的一个关键步骤，是通过自养微生物将氨对亚硝酸盐氧化的是一个世纪的思想，该世纪由一些受限的细菌属介导。明显的氨氧化，也许大多数，现在归因于先前神秘的古细菌（AOA）在海洋和陆地环境中都具有很高的丰度。研究人员的事先生理和环境分析（该提案的基础）表明，AOA在海洋光学区域内活跃，并且它们在海洋环境中的竞争性适应性至少部分归因于对氨的高亲和力？在氨浓度下以接近最大的生长速率生长，氨无法维持已知的细菌氨氧化剂？以及一种基于铜的不寻常的呼吸系统，可以使它们在有限的环境中更具竞争力。这些先前分析的引人注目的推断是，AOA改变并可能控制光学区域其他微生物组合的固定氮形式，通过将氨（一种几乎普遍可用的氮形式）转化为亚硝酸盐，仅适用于亚硝酸盐，这种形式仅适用于硝酸盐氧化细菌和某些苯二颗粒的形式。如果正确，这会对生物多样性产生重大影响。 PI将使用蛋白质和高吞吐量测序的最新技术进步来评估硝化在塑造生物多样性（基因组和元基因组学），活性（转录组，蛋白质组和稳定的同位素探测）以及控制重要微量元件（铜）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，他们将提高对分类法的一般理解。更直接地，对AOA对再生硝酸盐的贡献的功能知识将改善基于硝酸盐同化的新海洋生产（？生物泵？）的估计，过去，哪些人主要忽略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​​改变对海洋氮周期的理解，对新产量的估计，并最终将更好地理解人类活动对这种关键营养周期的影响。氮循环已被反应性氮的人为输入深远影响到陆生，海洋和大气系统中吗？对海洋生物生产产生重大影响，增加了N20的排放，氮污染和富营养化。同样，人们对氮循环与生产力侵蚀性生态系统之间的关系也很糟糕。海洋系统越来越受海洋酸化和反应性氮的大气输入的影响。由于这两种变化都大大改变了可用于微生物的氮，因此这些与环境相关的AOA反应的表征与理解酸化和人为氮对主要海洋过程的影响有关。这项工作还将为高中教师和学生提供出色的跨学科研究机会。推广将增强学生和教师对微生物在N周期等全球元素周期中的作用的理解。这项研究还将增强NSF.Integration资助的硝化研究协调网络成员之间的合作。提议的项目包括生物多样性的三个维度（功能遗传和分类学）。首先，该项目由功能构成：对地球上最重要的营养周期之一，即氮循环的微生物控制。其次，这是由于最近的遗传分析的动机，该分析将新颖的古细菌（临时分配给古细菌的新王国，thaumarchaeota）与控制海洋中的氨氧化的控制相关联。第三，它建立在导致其中心假设的生理和环境数据的引人入胜的综合之上？通过改变并可能控制氮的形式，AOA还可以在地球上最有效的环境之一中改变生物多样性和生态功能。它确定了特定的分类学命令。全球丰富的AOA之间的巨大遗传多样性？几乎完全由基因测序调查分类，因此缺乏形式描述？使将成员资格分为生态相关的群体或进化枝至关重要，以作为发展正式分类法的前奏。研究人员已经组建了一群具有特定专业知识的研究人员，并具有独特的资格，可以以整合的方式解决研究目标。