Marine viral dynamics and incorporation into microbial association networks

海洋微生物数量极其丰富，是全球碳、氮、磷和铁生物地球化学循环的主要参与者和驱动力。在过去的二十年里，我们了解到，病毒是海洋系统中普遍存在的元素，对细胞海洋生物具有显着的生态、生物地球化学、遗传和进化影响，但我们对海洋病毒群落结构的动态及其与宿主（主要是细菌和浮游植物）群落结构的关系的了解却非常少。这些信息对于开发关于病毒作用以及病毒如何随时间和空间变化的正确概念和实用模型至关重要。该项目的目标是（1）主要是，描述自然病毒群落的一个重要子集及其动态以及细菌宿主群落，因为它们在南加州大学经过充分研究的海洋微生物观测站（洛杉矶和圣卡塔利娜岛中间）每天到每月的时间尺度上发生变化，测试有关重复模式、宿主范围效应和分类群时间关系的假设，以及（2）其次，通过统计连接特定类型的病毒，将这些病毒纳入微生物关联网络到特定的潜在主机。本研究的方法包括：（a）每天、每周和每月嵌套收集细菌和病毒的核酸样本，（b）从以前在海水中容易发现的一些中等特征的广泛病毒群（即T4样肌病毒、T7样足病毒）中扩增保守基因，作为代理系统发育标记，以及细菌rRNA基因（c）通过群落指纹识别筛选后，从混合扩增的细菌rRNA基因中进行广泛测序。产品，（d）将序列或指纹片段分箱到不同分辨率水平的操作分类单位（OTU）中，（e）使用统计方法评估结果，以检查时间模式，与其他病毒OTU，细菌，原生生物（仅每月）和环境参数的关系（包括时间滞后），（f）以数学方式将病毒OTU纳入微生物关联网络。现有的微生物观测站已经每月收集有关环境参数、细菌和原生生物的数据，因此病毒工作是对该项目的补充，提供了主要的增值部分。同样，该项目将向微生物观测站添加选定的每日和每周微生物数据。来自文献和 PI 初步结果的数据表明，他们拥有实现第一个目标的技术和能力，据我们所知，这将是其范围和类型的第一个此类数据集。研究人员在2006年就已经发表文章称，该地点5m深度的细菌群落在细菌群落组成方面表现出可预测的重复年度循环，因此对可预测的重复病毒群落的预期并非没有道理。他们还有一些初步数据显示一些病毒重复出现。第二个目标要求病毒和其他测量参数之间确实存在显着的统计关系，PI 预计会出现这种情况，但当然无法预测；如果无法证明，该结果本身将提供丰富的信息，并且会限制微生物/病毒相互作用的可能模式。 更广泛的影响：该项目将具有重要的培训部分，研究生将做大量的工作（现场、实验室、生物信息学和写作部分）作为其论文研究的一部分。研究人员还将将该项目与当地中学科学教师培训计划联系起来，将结果纳入培训模块，并与中学生经常参观的我们海洋实验室的社区外展联系起来。向更广泛的全球社区的推广将包括一个项目网站，其中包含协议、工作、结果和结论的非技术和技术描述。

Marine microbes are tremendously abundant and are major players and driving forces in global biogeochemical cycles of carbon, nitrogen, phosphorus, and iron. We learned over the past two decades that viruses are pervasive elements in marine systems, with significant ecological, biogeochemical, genetic, and evolutionary effects on cellular marine organisms, but we have remarkably little information about the dynamics of marine viral community structure and how it relates to the community structure of their hosts (largely bacteria and phytoplankton). Such information is critical for developing proper conceptual and practical models of the roles of viruses and how these change over time and space. The goals of this project are (1) primarily, to characterize a significant subset of the natural virus community and its dynamics, along with bacterial host communities, as they change over daily to monthly time scales at the USC well-studied marine Microbial Observatory site (midway between Los Angeles and Santa Catalina Island), testing hypotheses regarding repeating patterns, host range effects, and taxa-time relationships, and (2) secondarily, to incorporate these viruses into microbial association networks by statistically connecting particular types of viruses to specific potential hosts. Approaches for this study include: (a) nested daily, weekly, and monthly collection of bacteria and viruses for nucleic acid samples, (b) amplification of conserved genes, as proxy phylogenetic markers, from a few moderately-well-characterized broad viral groups previously readily found in seawater (i.e. the T4-like myoviruses, T7-like podoviruses), as well as bacterial rRNA genes (c) extensive sequencing, after screening by community fingerprinting, from the mixed amplified products, (d) binning of the sequences or fingerprint fragments into operational taxonomic units (OTUs) at different levels of resolution, (e) evaluation of the results with statistical approaches to examine temporal patterns, relationships (including time-lagged ones) with other viral OTUs, bacteria, protists (monthly only), and environmental parameters, (f) incorporating the viral OTUs mathematically into microbial association networks. Data on environmental parameters, bacteria, and protists are already being collected monthly for an existing Microbial Observatory, so the viral work is complementary to this project, providing a major value-added component. Similarly, this project will add selected daily and weekly microbial data to the Microbial Observatory. Data from the literature and from the PI's preliminary results show they have the technology and capability to meet the first goal, and to our knowledge this would be the first such data set of its scope and kind. The investigators have already published in 2006 that the bacterial communities at the 5m depth of this site show a predictable repeating annual cycle in bacterial community composition, so the expectation of a predictable repeating viral community is not unreasonable. They also have some preliminary data showing some repeated viral occurrences. The second goal requires that there are indeed significant statistical relationships between the viruses and other measured parameters, which the PI anticipates to be the case, but of course cannot predict; if they cannot be demonstrated, this result itself would be informative and would constrain the possible modes of microbial/viral interactions.BROADER IMPACTS: The project will have a significant training component, with a graduate student doing a considerable amount of the work (field, lab, bioinformatic, and writing components) as part of her dissertation research. The investigators also will link the project to a local secondary school science teacher training program, incorporating results into a training module, and also to community outreach at our marine lab, often visited by secondary school students. Outreach to the broader global community will include a project website with protocols, nontechnical and technical descriptions of the work, results, and conclusions.