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Award Detail

Awardee:ROGER WILLIAMS UNIVERSITY
Doing Business As Name:Roger Williams University
PD/PI:
  • Marcia F Marston
  • (401) 254-3311
  • mmarston@rwu.edu
Award Date:06/27/2013
Estimated Total Award Amount: $ 376,616
Funds Obligated to Date: $ 376,616
  • FY 2013=$376,616
Start Date:09/01/2013
End Date:08/31/2017
Transaction Type:Grant
Agency:NSF
Awarding Agency Code:4900
Funding Agency Code:4900
CFDA Number:47.050
Primary Program Source:040100 NSF RESEARCH & RELATED ACTIVIT
Award Title or Description:Collaborative proposal: Cyanophage-Synechococcus interactions in complex communities
Federal Award ID Number:1332782
DUNS ID:063926380
Parent DUNS ID:063926380
Program:BIOLOGICAL OCEANOGRAPHY

Awardee Location

Street:Office of Sponsored Programs
City:Bristol
State:RI
ZIP:02809-2921
County:Bristol
Country:US
Awardee Cong. District:01

Primary Place of Performance

Organization Name:Roger Williams University
Street:One Old Ferry Road
City:Bristol
State:RI
ZIP:02809-2921
County:Bristol
Country:US
Cong. District:01

Abstract at Time of Award

Viral-induced mortality of marine microorganisms alters the quantity and quality of pools of dissolved organic matter in the oceans, shuttling organic matter back into the microbial loop and away from the larger marine food web. A major hindrance to understanding the role of viruses in biogeochemical cycling is that we know surprisingly little about which viruses infect which bacteria in the marine environment. In this project, a network-based framework will be used to investigate marine phage-bacteria interactions in complex, multispecies communities. The research focuses on cyanophages, viruses that infect Synechococcus, an ecologically important cyanobacterium in the oceans. There are three parts of the project. The first part will identify genetic signatures of cyanophage-Synechococcus interactions by using laboratory evolution experiments and genomic sequencing. The second part will examine the temporal and spatial diversity of these candidate interaction genes in natural cyanophage populations, by comparing the full genome sequences of hundreds of isolates previously collected over many years. The third part will adapt the new method of viral-tagging to natural host populations to characterize cyanophage-Synechococcus interaction networks in the environment. Intellectual Merit: The role of viruses in global marine biogeochemical cycles depends on viral-induced mortality rates, which have been estimated to vary widely. The pattern and dynamics of who infects whom are central to our understanding of these rates as well as the role viruses play in marine nutrient cycling. This project will also contribute generally to our knowledge about viral diversity. The vast majority of marine viral sequences are not similar to any known diversity, and it is reasonable to conclude that many of these genes have to do with host recognition and infection. Finally, this project will develop a method of characterizing phage-bacteria interactions in natural, diverse microbial communities, thereby opening avenues for similar studies of viruses in other environments. Broader Impacts: The project will provide training for 15 undergraduate students (including students from the California Alliance for Minority Participation in Science, Engineering, and Mathematics), 2 graduate students and a postdoc. The project will also build on a science-education internship program that was developed with Crystal Cove State Park in California. The Park is host to more than 1.2 million visitors and 10,000 K-12 students each year. The outcome of this program will be topical science teaching kits that reside in the Marine Research Facility of the Park to be used by middle and high school teachers and students. These kits will connect marine microbiological research to the standards-based curricula of California and National Science Standards, educate the public on this NSF research and assist in the training of Science, Technology, Engineering, and Math (STEM) K-12 teachers. The results will be disseminated at national conferences, including American Educational Researchers Association (AERA) and National Association of Research on Science Teaching (NARST), while the curriculum and video productions will be hosted on the website of the UCI Center for Learning in the Arts Sciences and Sustainability.

Publications Produced as a Result of this Research

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Hanson CA, Marston MF and Martiny JBH "Biogeographic Variation in Host Range Phenotypes and Taxonomic Composition of Marine Cyanophage Isolates" Frontiers in Microbiology, v.7, 2016, p.doi: 10.3. doi:10.3389/fmicb.2 

Crummett LT, Puxty RJ, Weihe C, Marston MF and Martiny JBH "The genomic content and context of auxiliary metabolic genes in marine cyanomyoviruses" Virology, v.499, 2016, p.219. doi:0042-6822 

Marston MF and Martiny JBH "Genomic diversification of marine cyanophages into stable ecotypes" Environmental Microbiology, v.18, 2016, p.4240. doi:1462-2920 


Project Outcomes Report

Disclaimer

This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.

Viruses are one of the most abundant entities in the ocean. Most of the viruses in the ocean infect bacteria, cyanobacteria, and eukaryotic phytoplankton. These cells form the base of the marine food web, providing energy for the animals that eat them. A significant proportion of bacterial and algal communities can be killed by viruses on a daily basis, thus viruses regulate the abundance and diversity of their hosts, and also play a key role in nutrient cycling in the oceans. Most marine viruses have a specific host range, that is they can only infect certain types of cells, yet the long-term dynamics that allow both viruses and their host cells to persist in the ocean are not well understood. In this study, we focused on viruses that infect marine cyanobacteria, abundant small photosynthetic cells. The goal of this project was to examine the genetics of virus-host interactions in order to gain a better understanding of which viruses infect which cyanobacteria in the oceans and the evolutionary consequences of these interactions.

First, we used whole genome sequencing of natural cyanophage isolates collected from the coastal waters of Southern New England to examine the ecology, genomic structure, and diversification of viral communities. We found that cyanophages formed distinct clusters that remained genetically stable for a decade or longer. In other words, we were able to isolate viruses that were almost genetically identical up to 10 years apart. Nevertheless, among isolates belonging to the same cluster, highly variable regions within the genome were identified. We hypothesized that these regions contained genes that are important in helping the virus to recognize and infect particular cell types. To test this hypothesis, we then used long-term laboratory coevolution experiments to help identify the cyanophage genes that changed during interactions with their cyanobacterial hosts. In particular, we were interested in which host genes enabled a cell to become resistant to viruses and conversely which viral genes evolved to allow the virus to overcome that resistance. At the end of the 6-month co-evolution experiments, we sequenced the full genomes of over 20 Synechococcus isolates and 30 cyanophage isolates. In the Synechococcus cells, viral resistance was typically conferred by only a few single point mutations and we did not observe a correlation between the number of mutations in a Synechococcus cell and its level of resistance. In contrast, as viruses evolved to overcome the cells’ resistance, we observed an accumulation of mutations over time that was directly correlated with the virus’s ability to overcome host resistance. Understanding how coevolution shapes cyanophage genomes will provide insight into the dynamics that allow both host and viral populations to coexist and persist in the marine environment.

At Roger Williams University, nine undergraduates directly participated in this project during the summer and academic year. These students learned a variety of laboratory techniques as well as how to design experiments and analyze experimental data as they completed individual projects. They also gained experience in bioinformatics and scientific communication. Most students who participated in this research continued on to graduate school or obtained jobs as research assistants in academic or industry labs. In addition, inquiry-based laboratory exercises related to this research were incorporated into RWU’s BIO370L Virology lab and BIO200L Genetics lab courses. This project resulted in three research publications and several more are in preparation. All genomic data that was generated has been deposited in GenBank and is publicly available. In addition, an overview of the datasets generated in this project can be found at http://www.bco-dmo.org/project/529066.


Last Modified: 11/26/2017
Modified by: Marcia F Marston

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