Dimensions: Pattern and Process in Marine Bacterial, Archaeal, and Protistan Biodiversity, and Effects of Human Impacts

维度：海洋细菌、古菌和原生生物多样性的模式和过程，以及人类影响的影响

• 批准号: 1136818
• 负责人: Jed Fuhrman
• 金额: $ 199.96万
• 依托单位: University of Southern California
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-10-01 至 2017-03-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1136818&HistoricalAwards=false
• 关键词: Dimensions; Pattern; Process; Marine; Bacterial

Bacteria, Archaea, and Protists dominate global elemental cycling and are immensely diverse genetically, taxonomically, and functionally. Yet the extent of marine microbial diversity, its patterns, and relationships among genetic, taxonomic, and functional diversity are very poorly characterized, even though the ocean covers 70% of the planet's surface. Among the least well known variables is the effect of human impacts on native marine microbial systems, although it is recognized that impacted systems are more prone to events like harmful algal blooms. Knowledge of these relationships and impacts are necessary to anticipate the responses of biota to global changes and feedback mechanisms that may alter the extents, rates, and even pathways of such changes. This project will expand upon an existing NSF-funded 10+-year monthly ocean time series (Microbial Observatory) that has focused on a single site midway between Los Angeles and Santa Catalina Island, to also include quarterly sampling adjacent to the impacted LA Harbor region to the barely-impacted Catalina coast. USC already runs facilities in LA Harbor and Catalina, with daily boats between (no cost). Measurements include (1) Genetic diversity: high throughput DNA sequences of "housekeeping" and functional genes. (2) Taxonomic diversity: high throughput tag sequences of small subunit ribosomal RNA genes, flow cytometry, automated image analysis (3) Functional Diversity: (a) Functional measurements (carbon fixation and respiration rates, microbial growth and grazing rates, cell size, morphology, and biomass variations), (b) distribution and expression of particular target functional genes involved with processes central to the cycles of carbon, nitrogen, and sulfur, (c) exploratory metatranscriptomics to explore functionalities that were not anticipated. (4) Integrating these: Multivariate statistical and network approaches including newly developed techniques (e.g. Bayesian networks to examine cause-effect relationships), and high speed computational approaches to assess the relationships among the genetic, taxonomic, and functional aspects of biodiversity observed. The PIs will also examine the collected data for signatures and specific effects (on organism identity and functions) associated with human impacted harbor site vs. the relatively pristine one. Integration: The PIs will use network and time series analysis, along with other statistical tools to integrate "classical" microbial and oceanographic rate process measurements, flow cytometric and microscopic characterizations of communities, along with targeted as well as untargeted metagenomics and metatranscriptomics to relate genetic and taxonomic diversity with specific functions (at organismal, food web, and system levels). For example, they should be able to determine how different variants of particular taxa (e.g. at resolution levels ranging from what might be considered near the subspecies to genus levels) would differ in their association with particular measured functions, functional genes, or particular other taxa - or they might see how particular clusters of related organisms behave similarly or differently in their associations. This project offers an unprecedented and potentially transformative opportunity to combine and integrate measurements of genetic, taxonomic, and functional diversity along with direct measurements of system function in a well studied marine system that includes a gradient from one of the world's busiest harbors to a largely pristine ocean habitat. Far beyond just describing the distributions of organisms and functions (itself a necessary first step), they will specifically link spatial and temporal variations in a variety of functions with variations in genetic and taxonomic community composition.Broader Impacts: The project will involve PhD training of participants as well as a direct connection to K-12 education via the COSEE teacher-training program at USC. Additionally, the PIs' labs routinely include undergraduate students from underrepresented minorities, who would participate. Outreach will include an interactive website and direct interaction with the public at the Wrigley Marine Science Center.

细菌、古生菌和原生生物在全球元素循环中占据主导地位，在遗传、分类和功能上都有极大的差异。然而，尽管海洋覆盖了地球表面的70%，但海洋微生物多样性的程度、模式以及遗传、分类和功能多样性之间的关系的描述非常糟糕。最不为人所知的变量之一是人类影响对本地海洋微生物系统的影响，尽管人们认识到，受影响的系统更容易发生有害藻华等事件。了解这些关系和影响对于预测生物群对全球变化的反应和反馈机制是必要的，这些反馈机制可能会改变这种变化的程度、速度甚至路径。该项目将扩展现有的由NSF资助的每月10年以上的海洋时间序列(微生物观测站)，该序列专注于洛杉矶和圣卡塔利纳岛之间的一个单一地点，还包括受影响的洛杉矶港口地区到几乎未受影响的卡塔琳娜海岸附近的季度采样。南加州大学已经在洛杉矶港和卡塔利纳运营设施，每天都有船只(免费)。衡量标准包括：(1)遗传多样性：“管家”和功能基因的高通量DNA序列。(2)分类多样性：小亚基核糖体RNA基因的高通量标签序列、流式细胞术、自动图像分析(3)功能多样性：(A)功能测量(碳固定和呼吸速率、微生物生长和放牧速率、细胞大小、形态和生物量变化)，(B)参与碳、氮和硫循环的关键过程的特定靶功能基因的分布和表达，(C)探索未预料到的功能的元转录操作。(4)整合这些方法：多元统计和网络方法，包括新开发的技术(例如，检验因果关系的贝叶斯网络)，以及评估所观察到的生物多样性的遗传、分类和功能方面之间关系的高速计算方法。PIS还将检查收集的数据，以寻找与人类受影响的港口和相对原始的港口相关的签名和特定影响(对生物体身份和功能)。整合：PIS将使用网络和时间序列分析，以及其他统计工具，整合“经典”微生物和海洋学速率过程测量、流式细胞术和群落的微观特征，以及定向和非定向的元基因组学和元转录组学，以将遗传和分类多样性与特定功能(在生物体、食物网和系统层面)联系起来。例如，他们应该能够确定特定分类群的不同变种(例如，在分辨率水平上，从可能被认为接近亚种的东西到属的水平)与特定的测量功能、功能基因或特定的其他分类群之间的联系将如何不同--或者他们可能会看到相关生物的特定集群在它们的联系中如何表现相似或不同。该项目提供了一个前所未有的、可能具有变革性的机会，将遗传、分类和功能多样性的测量与系统功能的直接测量结合起来，在一个经过充分研究的海洋系统中，包括从世界上最繁忙的港口之一到基本上原始的海洋栖息地的坡度。除了描述生物体和功能的分布(本身是必要的第一步)，它们还将具体地将各种功能的时空变化与遗传和分类群落组成的变化联系起来。广泛的影响：该项目将涉及参与者的博士培训，以及通过南加州大学COSEE教师培训计划与K-12教育的直接联系。此外，私人投资机构的实验室通常包括来自代表性不足的少数族裔的本科生，他们将参加。外展将包括一个互动网站和箭牌海洋科学中心与公众的直接互动。