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

RII Track-2 FEC：VOM 中的 G2P：微生物病毒基因组与表型组连接的实验和分析框架

基本信息

批准号：
1736030
负责人：
K. Wommack
金额：
$ 599.91万
依托单位：
University of Delaware
依托单位国家：
美国
项目类别：
Cooperative Agreement
财政年份：
2017
资助国家：
美国
起止时间：
2017-08-01 至 2024-07-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1736030&HistoricalAwards=false
关键词：
RII Track FEC G2P VOM

项目摘要

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.

非技术描述土壤、沉积物和水环境中的病毒会感染微生物并影响生态系统。虽然人们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仍是未知的。仅根据 DNA 序列来预测任何特定病毒-微生物系统的生物学和生态特征或表型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 合作 (RII Track-2 FEC) 奖项旨在提高从基因组数据预测微生物病毒 (VoM) 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研究人员合作小组将研究感染海洋和淡水浮游植物的病毒，以及感染与重要豆科作物（尤其是大豆）共生的细菌群的病毒。总的来说，全球浮游植物种群负责创造大量的生物量，支持较大水生生物的营养需求。在这个过程中，浮游植物维持了大气中一半的氧气。增强对浮游植物病毒内基因组与表型组联系的了解将有助于改进预测过量碳和营养物质对生态系统影响的模型。在食品供应链中，豆类，特别是大豆，是植物蛋白的极其重要的来源，可满足数十亿人的营养需求。更好地了解感染豆科植物细菌共生体的病毒的基因组与表型组的联系，最终可能会带来提高大豆等关键农作物生产力的新技术。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。四名早期职业教师将接受其他六名知名教师调查员的指导。整个项目团队将为中小学生准备教育材料并提供夏令营机会。技术说明RII Track-2 FEC 奖项是特拉华大学、内布拉斯加大学林肯分校、夏威夷大学和 Roger 共同努力的成果威廉姆斯大学。计划中的研究旨在将微生物病毒 (VoM) 的基因组特征与表型生活史特征联系起来，并利用这些联系促进对 VoM 在生态系统中作用的科学理解。该项目团队将测试 VoM 中的几种基因组到音素假设，重点关注宿主范围、爆发大小、潜伏期和传染性等表型特征。包括乳液微流控技术、下一代测序和生物信息学在内的集成高通量方法将用于研究以微型浮游植物、真核浮游植物和固氮细菌为代表的病毒宿主系统。该项目团队将从大豆田、热带海洋和湖泊的不同环境梯度中收集样本，并假设选择不同的 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，称为基因组组织病毒信息学规则手册？ VIRGO 并将其纳入现有的病毒宏基因组生物信息学注释社区资源，称为宏基因组探索病毒信息学资源 (VIROME)。参与该项目的四名早期职业教员将得到成功的中后期职业教员的指导。该团队将共同培训博士后、研究生和本科生，并向包括 K-12 学生和公众在内的不同受众宣传环境病毒学的重要性。

项目成果

期刊论文数量（37）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Ingestion kinetics of mixotrophic and heterotrophic flagellates

混合营养和异养鞭毛虫的摄入动力学

DOI：
10.1002/lno.12320
发表时间：
2023-02
期刊：
Limnology and Oceanography
影响因子：
4.5
作者：
Edwards, Kyle F.;Li, Qian;Steward, Grieg F.
通讯作者：
Steward, Grieg F.

Whole-Genome Sequence of the Cyanobacterium Synechococcus sp. Strain WH 8101

蓝藻聚球藻的全基因组序列。

DOI：
10.1128/mra.01593-19
发表时间：
2020-02-01
期刊：
Microbiology Resource Announcements
影响因子：
0.8
作者：
M. Marston;Shawn W. Polson
通讯作者：
Shawn W. Polson

Chloroviruses

氯病毒

DOI：
10.3390/v12010020
发表时间：
2019-12-23
期刊：
Viruses
影响因子：
0
作者：
J. V. Van Etten;I. Agarkova;D. Dunigan
通讯作者：
D. Dunigan

Iroki: automatic customization and visualization of phylogenetic trees

Iroki：系统发育树的自动定制和可视化

DOI：
10.7717/peerj.8584
发表时间：
2020-02-26
期刊：
PeerJ
影响因子：
2.7
作者：
Ryan M. Moore;Amelia O. Harrison;S. McAllister;Shawn W. Polson;K. E. Wommack
通讯作者：
K. E. Wommack

Chloroviruses Lure Hosts through Long-Distance Chemical Signaling

氯病毒通过长距离化学信号引诱宿主

DOI：
10.1128/jvi.01688-18
发表时间：
2019-04
期刊：
Journal of Virology
影响因子：
5.4
作者：
Dunigan, David D.;Al;Al;Agarkova, Irina V.;DeLong, John P.;Van Etten, James L.;Shisler, Joanna L.
通讯作者：
Shisler, Joanna L.