Collaborative research: Evolutionary ecology of marine cyanophages

病毒-宿主相互作用的进化生态学是理解海洋生态系统中病毒诱导的死亡率的关键，因为病毒-宿主相互作用的模式和动态最终将决定病毒对营养循环的影响。最近的研究表明，海洋病毒的多样性和组成似乎随着时间和空间的变化而变化。这项研究的目标是超越简单地记录海洋病毒的生物地理模式，并开始探讨为什么海洋病毒的基因组成会随着时间和空间的变化而变化。这样做的部分挑战是，人们对海洋病毒的遗传多样性与其表型之间的关系知之甚少。为了应对这一挑战，私人投资者建议采取隔离方法，使用感染海洋聚球藻的裂解噬藻体作为模型系统。通过这种方式，他们可以比较每一种病毒分离株的基因和表型。该项目将测试压倒一切的假设，即海洋噬藻体的生物地理模式取决于所检查的特定基因，因为基因组的不同部分，最终，它们编码的表型面临不同的进化压力。为了做到这一点，调查人员将采取三管齐下的方法。首先，他们将识别“宿主范围基因”，即噬藻体宿主范围的遗传标记(噬菌体可以感染的特定宿主)。其次，他们将对北美太平洋和大西洋沿岸的噬藻体分离株进行时间序列研究，以比较三种类型噬藻体基因(保守的核心基因、寄主范围基因和寄主衍生基因)的时间和空间生物地理学。为了测试这些模式是否普遍适用于噬藻体，而不仅仅是可培养的分离物，研究人员将使用454测序技术直接从环境DNA中检查保守的核心基因的多样性。最后，使用来自时间序列的分离物，他们将表征噬藻体的表型。例如，他们将确定在不同温度下在宿主外的氰噬菌体的存活率。研究人员还将通过测试每个菌株感染不同范围的聚球藻菌株的能力来分析宿主范围。这项研究将利用马斯顿和马蒂尼实验室中大量的氰噬菌体收集。马斯顿已经从罗德岛水域分离氰噬菌体10年了，马蒂尼已经在南加州海岸收集了2年的分离物。它还将建立在之前NSF合作项目的一个已完成的长期恒化器实验的基础上，并建立在加州目前资助的一年时间序列的基础上(这是对马蒂尼的快速拨款，让她在厄尔尼诺年进行采样)。此外，该项目将利用九个氰噬菌体基因组的全基因组测序，这些基因组已经作为广泛的GBMF噬菌体、病毒和病毒组测序项目的一部分正在进行中。首先，这项研究将提供对海洋噬菌体进化生态学的一般见解，这些噬菌体是海洋营养循环的关键角色。此外，识别噬菌体寄主范围的遗传标记将对未来专注于噬菌体在海洋生物地球化学循环中的作用的研究非常有用。其次，该项目将为不同层次的学生提供出色的学习体验。该项目将支持每年培养8名本科生、1名博士生和1名博士后研究员。每年两名本科生(至少一名少数族裔学生)将参加水晶湾州立公园的科学教育实习，以开发展览、演讲和活动，在公园展示海洋科学；这些材料预计每年将使50,000多名游客受益。最后，这项研究的方方面面将被开发成RWU的探究性实验室练习，并被开发成K-12课程材料，供UCI新的教学科学学士学位使用。

The evolutionary ecology of virus-host interactions are key to understanding viral-induced mortality rates in marine ecosystems, as the pattern and dynamics of virus-host interactions will ultimately determine the influence of viruses on nutrient cycling. Recent studies suggest that the diversity and composition of marine viruses appears to vary over time and space. The goal of this research is to move beyond simply documenting biogeographic patterns in marine viruses and to begin to ask why the genetic composition of marine viruses varies over time and space. Part of the challenge in doing this is that little is known about how the genetic diversity of a marine virus relates to its phenotype. To address this challenge, the PIs propose to take an isolation approach, using lytic cyanophages that infect marine Synechococcus as a model system. In this way they can compare the genotype and phenotype of each virus isolate.Intellectual meritThis project will test the overarching hypothesis that the biogeographic patterns of marine cyanophages depend on the particular gene examined, as different parts of the genome, and ultimately, the phenotypes that they encode are under different evolutionary pressures. To do this, the investigators will use a three-pronged approach. First, they will identify "host range genes", or genetic markers of cyanophage host range (the particular hosts that a phage can infect). Second, they will conduct a time-series study of cyanophage isolates from the Pacific and Atlantic coasts of North America to compare the temporal and spatial biogeography of three types of cyanophage genes (conserved core genes, host range genes, and host-derived genes). To test that these patterns hold for cyanophage generally, and not just for culturable isolates, the investigators will examine the diversity of the conserved core gene directly from environmental DNA using 454 sequencing technology. Finally, using isolates from the time-series, they will characterize cyanophage phenotypes. For instance, they will determine the survival rates of cyanophage outside of the host under different temperatures. The investigators will also assay host range by testing the ability of each isolate to infect a diverse range of Synechococcus strains. This study will take advantage of the extensive cyanophage collections in Marston and Martiny's labs. Marston has been isolating cyanophage from Rhode Island waters for 10 years, and Martiny has been collecting isolates off the southern California coast for 2 years. It will also build on a completed long-term chemostat experiment from a prior NSF collaborative project and build on a currently funded 1-yr time-series in CA (a RAPID grant to Martiny to sample through the El Niño year). In addition, the project will leverage the whole genome sequencing of nine cyanophage genomes, which are already underway as part of the Broad-GBMF Phage, Virus, and Viriome Sequencing Project.Broader impactsThis project will have broad impacts on a number of levels. First, the research will provide general insights into the evolutionary ecology of marine bacteriophage, which are key players in marine nutrient cycling. In addition, identifying genetic markers of a phage's host range would be extremely useful for future studies that focus on the role of phage in marine biogeochemical cycles. Second, the project will provide an outstanding learning experience for students at a variety of levels. In total, this project will support the training of 8 undergraduates per year, 1 PhD students, and 1 postdoctoral researcher. Two undergraduates per year (at least one a minority student) will participate in a science-education internship with the Crystal Cove State Park to develop exhibits, talks, and activities to showcase marine science at the Park; these materials are expected to benefit more than 50,000 visitors per year. Finally, aspects of this research will be developed into inquiry-based laboratory exercises at RWU and into K-12 curriculum materials for use in UCI's new BS in Teaching Science.