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。了解哪些病毒会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范围有多大以及这种情况如何随着时间的推移而发生变化的知识方面仍然存在关键差距。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的光合细菌(聚球藻属的蓝藻)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。从纳拉甘西特湾收集了10多年的DNA被用来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性循环和年复一年地塑造自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单个病毒与宿主的相互作用如何导致特定种类的病毒和细菌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方面的培训。将这项研究的结果整合到本科课程和推广活动中，有助于为学生提供真正的机会，为当地初中生和高中生的研究和参与做出贡献。科学家和学生团队正在对共生聚球藻和噬藻体的自然群落进行系统发育方面的研究，这是纳拉甘西特湾一个易于处理的模型系统，以表征不同尺度和时间的噬菌体与宿主之间的相互作用。该团队的目标是从纳拉甘西特湾分离出大量的~100个聚球藻和~200个噬氰体，并对这些分离物进行感染分析和比较基因组学。他们使用聚球藻和噬藻体的高度可变基因的扩增子测序来表征从广泛到精细的遗传尺度上的群落动态-从生态型到种内变异-为期10年的每月存档样本和超过两年的新的每周时间序列。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)，在该边界上，感染网络的模式从主要是嵌套的转变为主要是模块化的？(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的易感性？以及，(3)不同系统发育水平上的宿主-噬菌体相互作用如何在短(周到月)和长(年到年)的时间尺度上影响群落结构？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塑造的，以及宿主和噬菌体多样性是如何在海洋中创建、维持和构建的。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势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.