Collaborative Research:RUI:Characterization of Synechococcus-cyanophage interactions across phylogenetic and temporal scales

病毒感染影响海洋中营养物质的流动以及生态上重要的微生物群落的多样性和结构。了解哪些病毒感染哪些宿主对于了解病毒的确切影响至关重要，但在病毒感染特定细菌类型的广泛程度以及这种情况如何随时间变化的知识方面仍然存在重大空白。该项目包括对来自罗德岛纳拉甘西特湾的数百种共生光合细菌（来自聚球菌属的蓝藻细菌）和感染它们的病毒（噬藻病毒）进行分离和表征，以评估它们相互感染的程度，并确定控制交叉感染的特定基因。从纳拉甘西特湾收集了10多年的DNA，用于跟踪聚球菌和噬藻菌群落，以确定病毒-宿主相互作用如何在季节性周期和年复一年的时间里塑造天然聚球菌和噬藻菌群落的多样性。这项工作提供了自然群落中单个病毒-宿主相互作用如何导致沿海生态系统中特定种类的病毒和细菌随着时间的推移稳定共存的知识。本项目支持15名本科生、1名研究生和1名博士后进行科学教学的有效实践培训。将研究结果整合到本科课程和推广活动中，为学生提供了真正的机会，为当地初中和高中学生的研究和参与做出贡献。科学家和学生组成的团队正在对纳拉甘西特湾（Narragansett Bay）的一种模型可处理系统——共生藻球菌和噬藻体的自然群落进行系统发育方面的研究，以表征噬菌体-宿主在不同多样性和时间尺度上的相互作用。该团队的目标是从纳拉甘西特湾分离出约100种聚球菌和约200种噬藻体，并对这些分离物进行感染检测和比较基因组学。他们对聚藻球菌和噬藻体的高度可变位点进行扩增子测序，以表征从广泛到精细的遗传尺度（生态型到种内变异）的群落动态，对10年来每月存档的样本进行测序，并对两年多的时间序列进行新的每周测序。这些研究解决了以下三个关键问题：1)是否存在遗传亲缘性的固有边界（即生态型、物种或更精细的水平），在这个边界上，感染网络的模式从基本上是嵌套的转变为基本上是模块化的？(2)决定感染边界（即宿主范围和噬菌体易感性）的潜在机制和遗传位点是什么？(3)不同系统发育水平上的宿主-噬菌体相互作用如何在短期（几周到几个月）和长期（一年到一年）的时间尺度上影响群落结构？这个项目的结果有助于更好地理解浮游植物和浮游细菌群落是如何被病毒捕食塑造的，以及宿主和噬菌体多样性是如何在海洋中产生、维持和构建的。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Viral infection influences the flow of nutrients in the oceans and the diversity and structure of ecologically important microbial communities. Understanding which viruses infect which hosts is critical to understanding the exact impact of viruses, but there are still critical gaps in knowledge about how widely viruses can infect specific bacteria types and how this can change over time. This project includes the isolation and characterization of hundreds of co-occurring photosynthetic bacteria (cyanobacteria from the genus Synechococcus) and viruses that infect them (cyanophage) from Narragansett Bay, Rhode Island to assess the degree to which they can infect each other and identify specific genes that control cross-infection. DNA collected for over 10 years from Narragansett Bay is used to track Synechococcus and cyanophage communities to determine how virus-host interactions play out in shaping the diversity of natural Synechococcus and cyanophage communities over seasonal cycles and from year to year. This work provides knowledge of how individual viral-host interactions in a natural community can lead to the stable co-existence of particular species of viruses and bacteria in a coastal ecosystem over time. This project supports 15 undergraduate student researchers, a graduate student and a postdoctoral fellow who also receives training in effective practices in science teaching. Integration of the study’s results into undergraduate courses and outreach activities facilitates authentic opportunities for students to contribute to research and engagement of local junior and senior high school students.The team of scientists and students are conducting a phylogenetically-informed study of natural communities of co-occurring Synechococcus and cyanophage, a model tractable system in Narragansett Bay, to characterize phage-host interactions across different scales of diversity and time. The team’s goal is to isolate a large collection of ~100 Synechococcus and ~200 cyanophage from Narragansett Bay and to conduct infection assays and comparative genomics on these isolates. They employ amplicon sequencing of highly variable loci for both Synechococcus and cyanophage to characterize community dynamics across broad to fine genetic scales—ecotypes to within-species variants—for 10 years of archived monthly samples and a new weekly time-series over two years. These studies address the following three key questions: 1) Are there inherent boundaries of genetic relatedness (i.e. ecotype, species, or finer levels) at which the patterns of infection networks fundamentally shift from being mostly nested to mostly modular? (2) What are the underlying mechanisms and genetic loci that determine the boundaries of infection, i.e., host range and phage susceptibility? and, (3) How do host-phage interactions at different phylogenetic levels influence community structure over short (weeks to months) and long (year-to-year) time scales? Results from this project help to better understand how phytoplankton and bacterioplankton communities are shaped by viral predation and how host and phage diversity is created, maintained, and structured in the oceans.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.