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

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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.