Collaborative Research: Inferring Cellular Lysis and Regeneration of Organic Matter by Marine Viruses

合作研究：推断海洋病毒对有机物的细胞裂解和再生

• 批准号: 1829640
• 负责人: Matthew Sullivan
• 金额: $ 83.82万
• 依托单位: Ohio State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-10-01 至 2023-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1829640&HistoricalAwards=false
• 关键词: Collaborative; Research; Inferring; Cellular; Lysis

Viral infections of marine microbes can transform the fate of microbial populations that fuel global ocean biogeochemical cycles. For example, viral infections of microbes lead to the release of carbon and nutrients back into the environment. This regeneration of carbon and nutrients stimulates the activity of other microbes and diverts carbon and nutrients from larger organisms in marine food webs. Because virus-microbe infections are relatively specific, it is critical to identify those pairs of viruses and microbes that may disproportionally contribute to the turnover of carbon and nutrients in the ocean. This project will develop quantitative approaches and tools to quantify which viruses infect which microbes and to use these data to quantify how viral infections of microbes collectively shape nutrient and carbon cycles in the North Atlantic Ocean. The project will analyze virus-microbe interactions in mesocosms at the Bigelow Laboratory for Ocean Sciences in mid-coast Maine and during open ocean expeditions to the Bermuda Atlantic Time-Series Study (BATS) site. An interdisciplinary team will leverage recent advances in molecular biology, computational biology, and mathematical modeling to identify virus-host partners and their impact on the movement of elements through marine systems. This project will support three graduate students, six undergraduate students and one postdoctoral researcher in an interdisciplinary context. Research advances will be translated into reproducible software methods to be disseminated via the community cyberinfrastructure platform iVirus, with additional training materials presented as part of a viral methods and informatics workshop held at The Ohio State University. The translation of discoveries to the public will be furthered by the involvement of journalism undergraduate students at the University of Tennessee-Knoxville. This project builds upon advances in the molecular toolkit of viromics to develop an integrated approach to characterize lineage-specific rates of infection, lysis, and nutrient release induced by marine viruses in open ocean ecosystems. It will combine theory, in vitro experiments, and in situ sampling to (i) extend a robust inference method for estimating virus-microbe cross-infection networks from time-series data; (ii) establish and characterize in-vitro protocols for inferring cross-infectivity in complex communities using culture-independent methods; (iii) estimate lineage-specific rates of lysis and regeneration of nutrients in marine systems, including applications to coastal and open ocean ecosystems. Project aims focus on quantifying the extent to which virus-induced lysis and regeneration of carbon and nutrients is heterogeneously distributed across microbial populations. To do so, the project will incorporate time series measurements of abundance information (via metagenomes) and activity information (via metatranscriptomes). In so doing, it will advance efforts to understand community-scale interactions rather than those amongst a single virus-host pair. Theoretical methods and in vitro protocols will directly infer lineage-specific infection, lysis, and nutrient release rates in coastal- and open-ocean ecosystems in the North Atlantic Ocean. Results will be used to identify key links that disproportionately influence bulk nutrient release. A novel PCR-based approach will augment and validate the core inference approach. Overall, the project aims to enhance our understanding of how viruses contribute to marine ecosystem function.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.

海洋微生物的病毒感染可以改变微生物种群的命运，为全球海洋生物地球化学循环提供动力。例如，微生物的病毒感染导致碳和营养物质释放回环境中。碳和营养物质的再生刺激了其他微生物的活动，并从海洋食物网中较大的生物体中转移了碳和营养物质。由于病毒-微生物感染相对特异性，因此识别那些​​可能对海洋中碳和营养物质周转做出不成比例贡献的病毒和微生物对至关重要。该项目将开发定量方法和工具来量化哪些病毒感染哪些微生物，并使用这些数据来量化微生物的病毒感染如何共同塑造北大西洋的营养和碳循环。 该项目将在缅因州中部海岸的毕格罗海洋科学实验室以及百慕大大西洋时间序列研究（BATS）站点的公海探险期间分析中宇宙中病毒与微生物的相互作用。一个跨学科团队将利用分子生物学、计算生物学和数学模型的最新进展来识别病毒宿主伙伴及其对海洋系统中元素运动的影响。该项目将在跨学科背景下支持三名研究生、六名本科生和一名博士后研究员。 研究进展将转化为可复制的软件方法，通过社区网络基础设施平台 iVirus 进行传播，并在俄亥俄州立大学举办的病毒方法和信息学研讨会上提供额外的培训材料。 田纳西大学诺克斯维尔分校新闻系本科生的参与将进一步推动将发现成果向公众转化。该项目以病毒组学分子工具包的进展为基础，开发一种综合方法来表征开放海洋生态系统中海洋病毒诱导的谱系特异性感染、裂解和营养物释放率。它将理论、体外实验和原位采样相结合，以（i）扩展一种稳健的推理方法，用于根据时间序列数据估计病毒-微生物交叉感染网络； (ii) 使用独立于培养的方法建立和表征用于推断复杂群落中交叉感染性的体外协议； (iii) 估计海洋系统中营养物质的特定谱系裂解和再生速率，包括在沿海和公海生态系统中的应用。该项目的目标是量化病毒诱导的碳和营养物裂解和再生在微生物种群中的异质分布程度。为此，该项目将纳入丰度信息（通过宏基因组）和活动信息（通过元转录组）的时间序列测量。这样做，它将推动了解社区规模的相互作用，而不是单个病毒-宿主对之间的相互作用。理论方法和体外实验方案将直接推断北大西洋沿海和公海生态系统中谱系特异性感染、裂解和营养物释放率。 结果将用于确定对大量养分释放产生不成比例影响的关键环节。 一种新颖的基于 PCR 的方法将增强和验证核心推理方法。总体而言，该项目旨在增强我们对病毒如何促进海洋生态系统功能的理解。该奖项反映了 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。

项目成果

Accurate viral genome reconstruction and host assignment with proximity-ligation sequencing

通过邻近连接测序进行准确的病毒基因组重建和宿主分配

• DOI: 10.1101/2021.06.14.448389
• 发表时间: 2021
• 期刊: bioRxiv
• 作者: Uritskiy, G.