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具有重要生态意义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，但对于病毒感染特定细菌类型的范围以及这种情况如何随时间变化的了解仍然存在重大差距。该项目包括从罗德岛州纳拉甘西特湾分离和鉴定数百种共生光合细菌（来自聚球藻属的蓝藻）和感染它们的病毒（噬蓝菌体），以评估它们相互感染的程度，并识别控制交叉感染的特定基因。十多年来从纳拉甘西特湾收集的 DNA 用于追踪聚球藻和噬藻体群落，以确定病毒与宿主的相互作用如何在季节周期和年复一年中塑造天然聚球藻和噬藻体群落的多样性。这项工作提供了关于自然群落中个体病毒与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。该项目支持 15 名本科生研究人员、一名研究生和一名博士后研究员，他们还接受了科学教学有效实践的培训。将研究结果纳入本科课程和外展活动，为学生提供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。科学家和学生团队正在对共存的聚球藻和噬藻体（纳拉甘西特湾的一个模型易处理系统）的自然群落进行系统发育研究，以表征不同多样性和时间尺度上的噬菌体与宿主的相互作用。该团队的目标是从纳拉甘西特湾分离出大量约 100 种聚球藻和约 200 种噬藻体，并对这些分离株进行感染测定和比较基因组学。他们对聚球藻和噬藻体的高度可变位点进行扩增子测序，以从广泛到精细的遗传尺度（从生态型到种内变异）表征群落动态，包括 10 年存档的每月样本和两年多的新每周时间序列。这些研究解决了以下三个关键问题：1）是否存在遗传相关性的固有边界（即生态型、物种或更精细的水平），感染网络的模式从根本上从大多数嵌套转变为大多数模块化？ （2）决定感染边界（即宿主范围和噬菌体易感性）的潜在机制和基因位点是什么？ (3)不同系统发育水平上的宿主-噬菌体相互作用如何影响短期（几周到几个月）和长期（每年）时间尺度的群落结构？该项目的结果有助于更好地了解病毒捕食如何塑造浮游植物和浮游细菌群落，以及海洋中宿主和噬菌体多样性如何创建、维持和构建。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力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.