Collaborative research: 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，但关于病毒感染特定细菌类型的范围以及如何随时间变化的知识仍然存在重大差距。该项目包括从罗得岛的纳拉甘塞特湾分离和鉴定数百种共存的光合细菌（聚球藻属的蓝细菌）和感染它们的病毒（噬藻体），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。从纳拉甘塞特湾收集了10多年的DNA用于跟踪聚球藻和噬藻体群落，以确定病毒-宿主相互作用如何在季节周期和年复一年的时间内塑造天然聚球藻和噬藻体群落的多样性。这项工作提供了自然群落中个体病毒-宿主相互作用如何导致特定病毒和细菌物种随着时间的推移在沿海生态系统中稳定共存的知识。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，他们也接受了科学教学有效实践的培训。将研究结果整合到本科课程和外展活动中，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。科学家和学生团队正在进行一项遗传学研究，研究共同发生的聚球藻和噬藻体的自然群落，这是纳拉甘塞特湾的一个模型易处理系统，以表征不同多样性和时间尺度上的噬菌体-宿主相互作用。该团队的目标是从纳拉甘塞特湾分离出大量的约100个聚球藻和约200个噬藻体，并对这些分离株进行感染测定和比较基因组学。他们采用聚合球菌和噬藻体的高度可变位点的扩增子测序，以表征广泛到精细的遗传尺度-生态型到种内变异-的群落动态，为期10年的存档月度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（即生态类型，物种或更精细的水平），感染网络的模式从根本上从主要嵌套转变为主要模块化？(2)决定感染边界的潜在机制和遗传位点是什么，即，宿主范围和噬菌体易感性？不同系统发育水平的宿主-噬菌体相互作用如何影响短（数周至数月）和长（一年到一年）时间尺度上的群落结构？该项目的结果有助于更好地了解浮游植物和浮游细菌群落是如何被病毒捕食形成的，以及海洋中宿主和噬菌体的多样性是如何产生、维持和结构化的。该奖项反映了NSF的法定使命，并被认为值得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来支持。

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.