The evolutionary ecology of virus-host interactions are key to understanding viral-induced mortality rates in marine ecosystems, as the pattern and dynamics of virus-host interactions will ultimately determine the influence of viruses on nutrient cycling. Recent studies suggest that the diversity and composition of marine viruses appears to vary over time and space. The goal of this research is to move beyond simply documenting biogeographic patterns in marine viruses and to begin to ask why the genetic composition of marine viruses varies over time and space. Part of the challenge in doing this is that little is known about how the genetic diversity of a marine virus relates to its phenotype. To address this challenge, the PIs propose to take an isolation approach, using lytic cyanophages that infect marine Synechococcus as a model system. In this way they can compare the genotype and phenotype of each virus isolate.
Intellectual merit This project will test the overarching hypothesis that the biogeographic patterns of marine cyanophages depend on the particular gene examined, as different parts of the genome, and ultimately, the phenotypes that they encode are under different evolutionary pressures. To do this, the investigators will use a three-pronged approach. First, they will identify "host range genes", or genetic markers of cyanophage host range (the particular hosts that a phage can infect). Second, they will conduct a time-series study of cyanophage isolates from the Pacific and Atlantic coasts of North America to compare the temporal and spatial biogeography of three types of cyanophage genes (conserved core genes, host range genes, and host-derived genes). To test that these patterns hold for cyanophage generally, and not just for culturable isolates, the investigators will examine the diversity of the conserved core gene directly from environmental DNA using 454 sequencing technology. Finally, using isolates from the time-series, they will characterize cyanophage phenotypes. For instance, they will determine the survival rates of cyanophage outside of the host under different temperatures. The investigators will also assay host range by testing the ability of each isolate to infect a diverse range of Synechococcus strains. This study will take advantage of the extensive cyanophage collections in Marston and Martiny's labs. Marston has been isolating cyanophage from Rhode Island waters for 10 years, and Martiny has been collecting isolates off the southern California coast for 2 years. It will also build on a completed long-term chemostat experiment from a prior NSF collaborative project and build on a currently funded 1-yr time-series in CA (a RAPID grant to Martiny to sample through the El Niño year). In addition, the project will leverage the whole genome sequencing of nine cyanophage genomes, which are already underway as part of the Broad-GBMF Phage, Virus, and Viriome Sequencing Project.
Broader impacts This project will have broad impacts on a number of levels. First, the research will provide general insights into the evolutionary ecology of marine bacteriophage, which are key players in marine nutrient cycling. In addition, identifying genetic markers of a phage's host range would be extremely useful for future studies that focus on the role of phage in marine biogeochemical cycles. Second, the project will provide an outstanding learning experience for students at a variety of levels. In total, this project will support the training of 8 undergraduates per year, 1 PhD students, and 1 postdoctoral researcher. Two undergraduates per year (at least one a minority student) will participate in a science-education internship with the Crystal Cove State Park to develop exhibits, talks, and activities to showcase marine science at the Park; these materials are expected to benefit more than 50,000 visitors per year. Finally, aspects of this research will be developed into inquiry-based laboratory exercises at RWU and into K-12 curriculum materials for use in UCI's new BS in Teaching Science.
Microbial communities are an abundant and essential component of the world’s oceans. These communities consist of many different types of bacteria, archaea and small eukaryotes that are responsible for creating food for larger marine organisms, decomposing organic matter, and converting nutrients into usable forms. In other words, these single-celled organisms help drive the global cycling of carbon and nutrients in the oceans. One important microbial group is the marine cyanobacteria. Cyanobacteria are photosynthetic and, like land plants, use light to convert carbon dioxide from the atmosphere into carbohydrates that can be used by other organisms. Cyanobacteria thus are at the base of the marine food web and are responsible for up to 30% of the oceans’ primary productivity. Viruses that can infect cyanobacteria (called cyanophages) are also extremely abundant in the oceans. These viruses influence the marine food web by infecting and killing cyanobacteria, making these cells unavailable to organisms higher up on the food chain. The interactions between cyanobacteria and viruses are dynamic and complex and while the outcomes of these interactions directly affect marine biogeochemical cycles, it has been difficult to predict exactly how viruses at any particular time or place will influence cyanobacteria mortality. This is in part due to the fact that cyanobacteria can develop resistance to co-occurring viruses. Viruses, in response, can evolve to overcome resistance and also frequently carry in their genomes cyanobacteria-derived genes that may help them better infect specific hosts in particular environments. Despite their importance, we know very little about the diversity of cyanophages except that their diversity is very high. We do not know much about what that genetic diversity means; for instance, what genes control whether a virus can infect a particular type of cyanobacterium or how fast the virus kills its host. However, this detailed information is essential to predict how viruses affect other marine organisms and ocean nutrient cycling. This project used cyanobacteria and cyanophages to ask how and why the diversity of marine viruses varies over time and space. During the project, we completed a five-year time-series where we sampled cyanophages from both the Pacific and Atlantic coasts of North America. We sampled in such a way to facilitate comparisons between the locations and ask how other environmental and biological measurements correlated with cyanophage diversity in a sample. We then sequenced the genomes of a variety of the viral isolates to investigate which particular genes varied over space and time. We also used the viral genomes to search for particular genes that might act as "markers" of which bacterial hosts a virus could infect. Finally, we compared the genetic information with measured "traits" of the cyanophages – like which bacteria they infect and how fast they infect them. We found that like other organisms, cyanophages are highly seasonal. Some cyanophage types dominate in the summer months and others dominate in the winter months. We also found that there was very little overlap in the diversity of viruses in southern California and Rhode Island. We investigated these trends further and saw that the strength of UV at the time was highly correlated with changes in the virus community over time and space. This suggests that some viruses may be more or less susceptible to UV damage, but this hypothesis needs to be tested further. Finally, we saw that the genetic variation within a cyanophage "type" is highly restricted to particular genes and regions of the genome. The identification of these genes and regions can now be compared to measured traits of the cyanophages and will help us understand the effect these viruses have on their host populations. This project has had broad impacts on a number of levels. First, the research has provided general insights into the distribution of marine cyanophage, which are key players in marine nutrient cycling. The over 110 full genome sequences of cyanophage isolates obtained in this study have enabled us to examine the evolutionary mechanisms that may be responsible for local adaptations to hosts and/or environments. The virus collection, sequenced genomes, and other collected data is (or shortly will be) available to other researchers to aid in further investigations. Second, the project provided an outstanding learning experience for students. At Roger Williams University, this project supported the training and research of 13 undergraduate students and one high school student. These students learned how to design experiments, analyze experimental data, write papers and use a variety of laboratory equipment. RWU undergraduate students contributed to and appear as co-authors on published papers. Upon graduation from RWU, students involved in this project went on to pursue graduate degrees in the sciences or obtained jobs in the biotech industry.
