RII Track-2 FEC: G2P in VOM: An Experimental and Analytical Framework for Genome to Phenome Connections in Viruses of Microbes

非技术描述土壤、沉积物和水环境中的病毒感染微生物并影响生态系统。虽然已经对病毒对生态系统的影响有了很高的了解，但病毒与微生物相互作用的细节在很大程度上是未知的。仅基于DNA序列来预测任何特定病毒-微生物系统的生物和生态特征或现象组的能力是非常有限的。这项以研究基础设施改进Track-2为重点的EPSCoR协作奖(RII Track-2 FEC)旨在提高从基因组数据预测微生物病毒(VOMS)表型特征的能力。来自特拉华州、罗德岛州、内布拉斯加州和夏威夷的一个合作研究小组将研究感染海洋和淡水浮游植物的病毒，以及感染与重要豆类作物形成共生关系的细菌群的病毒，最著名的是大豆。总体而言，全球浮游植物种群负责创造大量的生物量，以支持较大的水生生物的营养需求。在这个过程中，浮游植物维持着大气中一半的氧气。加强对浮游植物病毒内基因组到物候组联系的理解，将有助于改进预测过量碳和营养物质对生态系统的影响的模型。在食品供应链中，豆类，特别是大豆，是支持数十亿人营养需求的极其重要的植物蛋白来源。更好地了解感染豆类细菌共生体的病毒的基因组与表型组之间的联系，最终可能会带来提高大豆等关键农艺作物生产率的新技术。该项目团队包括教师、博士后和学生，他们将参与协作研究，并通过研讨会和会议分享方法、最佳实践和结果。四名职业生涯早期的教职员工将接受其他六名资深教职调查人员的指导。整个项目团队将为中小学生准备教材并提供夏令营机会。技术说明这个RII Track-2 FEC奖是为了表彰特拉华大学、内布拉斯加-林肯大学、夏威夷大学和罗杰·威廉姆斯大学的合作努力。这项计划中的研究试图将微生物病毒(VOMS)的基因组特征与表型生活史特征联系起来，并利用这些联系来促进对VOMS在生态系统中作用的科学理解。该项目团队将在VOMS中测试几种基因组到音素的假说，重点放在寄主范围、爆发大小、潜伏期和传染性等表观特征上。将使用包括乳滴微流控技术、下一代测序和生物信息学在内的综合高通量方法来研究以微藻、真核浮游植物和重氮营养细菌为代表的病毒宿主系统。该项目团队将在大豆田、热带海洋和湖泊的环境梯度上收集样本，假设是为了选择不同的vom表型特征。研究人员将建立一种新的生物信息学分析工具，称为基因组组织的病毒信息学规则手册？Virgo并将其合并到现有的用于对病毒元基因组进行生物信息注释的社区资源中，该资源被称为用于元基因组探索的病毒信息学资源(病毒)。四名从事这一项目的早期教师将由成功的职业中期和后期教师指导。该团队将共同努力，培训博士后、研究生和本科生，并向包括K-12学生和普通公众在内的不同受众宣传环境病毒学的重要性。

Non-technical descriptionThe viruses in soils, sediments, and water environments infect microbes and impact the ecosystems. While there is a high-level understanding of viral impacts on ecosystems, the details of the viral-microbe interactions are largely unknown. The ability to predict the biological and ecological features, or phenome, of any particular virus-microbe system based on DNA sequence alone is highly limited. This Research Infrastructure Improvement Track-2 Focused EPSCoR Collaborations (RII Track-2 FEC) award seeks to advance the ability to predict the phenomic features of the viruses of microbes (VoMs) from genomic data. A collaborative team of researchers from Delaware, Rhode Island, Nebraska, and Hawaii will study viruses that infect marine and freshwater phytoplankton, and viruses that infect a bacterial group that forms a symbiosis with important legume crops, most notably, soybean. Collectively, global phytoplankton populations are responsible for creating vast stores of biomass that support the nutritional needs of larger aquatic organisms. In this process phytoplankton sustain half of the oxygen within the atmosphere. Enhanced understanding of genome to phenome links within phytoplankton viruses will aid in improving models that predict the impacts of excess carbon and nutrients on ecosystems. Within the food supply chain, legumes, soybeans in particular, are an extraordinarily important source of plant protein supporting the nutritional needs of billions of people. Better understanding of genome to phenome connections for viruses infecting bacterial symbionts of legumes could eventually lead to new technologies for improving the productivity of critical agronomic crops such as soybean. The project team includes faculty, postdocs and students who will engage in collaborative research and share methodologies, best practices, and results through workshops and meetings. Four early career faculty will be mentored by six other well-established faculty investigators. The entire project team will prepare educational materials and provide summer camp opportunities for middle and elementary schools students.Technical descriptionThis RII Track-2 FEC award is for a collaborative effort among University of Delaware, University of Nebraska-Lincoln, University of Hawaii, and Roger Williams University. The planned research seeks to connect genomic features of viruses of microbes (VoMs) with phenotypic life-history traits and use these connections to advance scientific understanding of the role of VoMs in ecosystems. The project team will test several genome to phoneme hypotheses in VoMs, focusing on phenomic features such as host range, burst size, latent period and infectivity. An integrated high-throughput approach including emulsion-droplet microfluidic technologies, next generation sequencing, and bioinformatics, will be used to study viral-host systems representative of picophytoplankton, eukaryotic phytoplankton, and diazotrophic bacteria. The project team will collect samples across environmental gradients from soybean fields, tropical oceans, and lakes, hypothesized to select for different VoM phenomic traits. The researchers will build a new bioinformatics analysis tool known as the Viral Informatics Rulebook for Genome Organization ? VIRGO and incorporated it into an existing community resource for bioinformatic annotation of viral metagenomes known as the Viral Informatics Resource fOr Metagenome Exploration (VIROME). Four early-career faculty members engaged in this project will be mentored by successful mid and later career faculty. The team will work together in training postdocs, graduate students and undergraduate students as well as in communicating the importance of environmental virology to diverse audiences including K-12 students and the general public.