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

细菌、古生菌和原生生物主导着全球元素循环，它们在遗传、分类和功能上有着巨大的差异。然而，尽管海洋覆盖了地球表面的70%，但对海洋微生物多样性的范围、模式以及遗传、分类和功能多样性之间的关系却知之甚少。最不为人所知的变量之一是人类对原生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以及可能改变这种变化的程度、速率甚至途径的反馈机制是必要的。该项目将扩展现有的nsf资助的10多年月度海洋时间序列（微生物观测站），该序列集中在洛杉矶和圣卡塔利娜岛之间的一个地点，还包括受影响的洛杉矶港口地区附近的季度采样，以及几乎没有受影响的卡塔利娜海岸。南加州大学已经在洛杉矶港和卡塔利娜港开设了设施，每天都有船只往返（免费）。测量包括：(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基因的高通量标记序列、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)涉及碳、氮和硫循环核心过程的特定目标功能基因的分布和表达，(c)探索性亚转录组学以探索未预料到的功能。(4)整合这些：多元统计和网络方法，包括新开发的技术（如贝叶斯网络来检查因果关系）和高速计算方法来评估所观察到的生物多样性的遗传、分类和功能方面之间的关系。pi还将检查收集到的数据，以确定人类影响的港口与相对原始的港口之间的特征和特定影响（对生物身份和功能的影响）。整合：pi将使用网络和时间序列分析，以及其他统计工具来整合“经典”微生物和海洋学速率过程测量，流式细胞仪和微生物群落的微观特征，以及目标和非目标宏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（在有机体，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体（例如，在从可能被认为接近亚种到属水平的分辨率水平上）与特定测量功能、功能基因或特定其他分类群的关联如何不同——或者他们可能会看到特定的相关生物群在它们的关联中如何表现相似或不同。该项目提供了一个前所未有的、潜在的变革性机会，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，在一个得到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一个基本原始的海洋栖息地的梯度。远不止描述生物和功能的分布（这本身就是必要的第一步），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。更广泛的影响：该项目将包括对参与者的博士培训，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，pi的实验室通常包括来自代表性不足的少数民族的本科生，他们会参加。外展将包括一个互动网站，并在箭牌海洋科学中心与公众直接互动。

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.