Ecology of diatom viruses: connecting physiology and field dynamics through host transcriptional responses

概述：病毒在水生生态系统中发挥着至关重要的作用。感染海洋细菌的噬菌体是浮游生物的丰富成员，有助于细胞死亡率、结构种群多样性并通过水平基因转移驱动基因组进化。感染真核浮游植物的病毒已被证明可诱导颗石藻的生命周期转换和程序性细胞死亡，并且是水生植物、触生植物和针藻类水华死亡的重要因素。然而，人们对感染最大、最多样化和生产力最高的藻类之一——硅藻的病毒知之甚少。目前仅报道了 13 种硅藻感染病毒，而对其感染机制、对宿主代谢的影响或该领域的多样性和动态知之甚少。考虑到硅藻的生态重要性，这是一个显着的知识差距。伪菱形藻多重系列上的克隆病毒感染可导致宿主在 12-16 小时内完全裂解。 P.多系列病毒 (PmDNAV) 是一种单链 DNA 病毒，具有 50 nm 的二十面体衣壳。 PmDNAV 感染所有海洋真核生物感染病毒中最广泛的宿主范围，裂解多系 P. 的其他菌株、拟菱形藻的其他物种以及包括许多中心硅藻在内的其他硅藻属。随着最近完成了宿主 P. multiseries 的基因组，我们现在有了一个模型系统来研究宿主对病毒感染的反应以及病毒对现场硅藻死亡率的潜在影响。该项目的目标是： 1．利用已建立的方法、使用各种宿主菌株和现场病毒浓缩物组合来分离和表征其他硅藻病毒2。使用 RNA-Seq 确定三种硅藻（P. multiseries、P. pungens 和 T. pseudonana）在病毒感染过程中的转录谱3。在西北太平洋硅藻为主的水域（P线）的沿海到开放海洋横断面的四个站点确定地表水宏病毒组，重点是单链DNA和单链RNA病毒的多样性和生物地理学。通过观察培养物中感染的基因组反应，可以鉴定其表达可诊断病毒感染的病毒和宿主基因。这些基因以及元病毒组中组装的病毒将与同一水域已有的真核元转录组相结合，以评估该领域的病毒活性。 智力价值：该项目旨在加强由伪菱形藻多系列 DNA 病毒的发现引发的模型系统。宿主病毒转录组学将为评估病毒对环境中硅藻群落的影响奠定基础。反过来，配对的元病毒组和元转录组将揭示有关硅藻病毒多样性和功能的新问题，然后可以通过受控的、基于培养的实验进一步探索这些问题。这项研究将是对硅藻病毒生态和功能的首次广泛探索，最终将有助于进一步将病毒和硅藻与全球生物地球化学循环联系起来，揭示复杂的有机相互作用，并为与海洋相关的公共卫生提供信息。 更广泛的影响：硅藻是生产性沿海海洋的主要初级生产者，对所有海洋体系的碳出口做出了重大贡献。病毒对物种分布和细胞丰度的影响对渔业健康和生态系统对气候变化的反应具有影响。更具体地说，伪菱形藻花会对公共健康和经济产生影响。该项目的另一个目标是通过为代表性不足的少数群体的学生提供早期研究经验、持续的财政支持、同行指导和国家层面的学科接触，扩大在环境科学领域攻读研究生的个人库。来自代表性不足群体的一名研究生和五名本科生将参与这项研究。

Overview: Viruses play critical roles in aquatic ecosystems. Phages infecting marine bacteria are abundant members of the plankton that contribute to cell mortality, structure population diversity and drive genome evolution though horizontal gene transfer. Viruses infecting eukaryotic phytoplankton have been demonstrated to induce both life cycle switching and programmed cell death in coccolithophorids and be significant agents of mortality in blooms of pelagophytes, haptophytes and raphidophytes. However, much less is known about viruses infecting one of the largest, most diverse and most productive groups of algae, the diatoms. Only thirteen diatom infecting viruses have been reported, and little is known about their mechanisms of infection, effects on host metabolism or diversity and dynamics in the field. This is a remarkable knowledge gap considering the ecological importance of the diatoms. Infection with a clonal virus on Pseudo-nitzschia multiseries can result in complete host lysis within 12-16 hours. The P. multiseries virus (PmDNAV) is a single stranded DNA virus with an icosahedral capsid of 50 nm. The PmDNAV infects the widest host range of any marine eukaryote-infecting virus, lysing other strains of P. multiseries, other species of Pseudo-nitzschia, and other genera of diatoms including many centric diatoms. With the recent completion of the genome of the host, P. multiseries, we now have a model system to investigate the response of the host to viral infection and the potential impacts of viruses on diatom mortality in the field. The objectives of this project are to:1. isolate and characterize additional diatom viruses utilizing established methods, using a variety of host strains and field viral concentrate combinations2. use RNA-Seq to determine the transcriptional profiles of three diatoms (P. multiseries, P. pungens and T. pseudonana) during the course of viral infection3. determine a surface water metavirome at four stations on a coastal to open ocean transect in diatom dominated waters in the Pacific Northwest (line P), with an emphasis on diversity and biogeography of ssDNA and ssRNA viruses. Viral and host genes whose expression is diagnostic of viral infection, will be identified by observing genomic responses to infection in culture. These genes, along with viruses assembled in the metaviromes, will be combined with eukaryotic metatranscriptomes already available from the same waters to assess virus activity in the field.Intellectual Merit: This project seeks to strengthen the model system initiated by the discovery of the Pseudo-nitzschia multiseries DNA virus. The host-virus transcriptomics will lay the groundwork for assessing the impact of viruses on diatom communities in the environment. In turn, the paired metaviromes and metatranscriptomes will reveal new questions about both diatom virus diversity and function that can then be further explored by controlled, culture-based experiments. This research will be the first extensive exploration of diatom virus ecology and function and will ultimately help further connect viruses and diatoms to global biogeochemical cycles, unravel complex organismal interactions, and inform ocean-related public health.Broader Impacts: Diatoms are the dominant primary producers in the productive coastal oceans and contribute significantly to carbon export across all oceanic regimes. Viral impacts on species distributions and cell abundances have implications for health of fisheries and ecosystem responses to climate change. More specifically, there are public health and economic impacts associated with Pseudo-nitzschia blooms. Another goal of this project is to broaden the pool of individuals who pursue graduate work in environmental sciences by providing students from underrepresented minority groups early research experience, sustained financial support, peer mentorship and exposure to the discipline at a national level. A graduate student and five undergraduates from underrepresented groups will be involved in the research.