Research

Marine viruses are the most numerous biological entities in the ocean, with an estimated abundance of 4 x 10³⁰.  They merit study not only because of their sheer abundance, but also because of the role they play in the Earth’s biogeochemical cycles.  Viral lysis of bacteria redirects the flow of nutrients among marine microbes, which ultimately affects the efficiency of the biological pump.  Viral diversity is important because most viruses are host-specific.  In preying on a certain type of bacteria, viruses affect the diversity and structure of the bacterial community, leading to changes in carbon and nutrient flows.  In turn, such variations can alter the amount of carbon dioxide in the Earth’s atmosphere.  However, studying viral diversity presents challenges.  Morphological similarities among many types of viruses make it preferable to use genetic methods of investigation, but the absence of a single gene common to all families of viruses hampers the identification of viruses in environmental samples.  Nonetheless, some genes are shared within phage families, and those signature genes can be used as markers to identify members of a family.  In addition, community profiling methods can fingerprint the diversity of a viral community.

Using a variety of techniques, my dissertation research aimed to expand our knowledge of viral diversity and dynamics by analyzing the viral community of the Sargasso Sea over a several-year period, through different seasons, and at different depths.  My first project developed phoH as a new signature gene for assessing marine viral diversity.  Diversity of the phoH gene was high, and most of the sequences recovered belonged to phylogenetic groups that did not contain any cultured representatives, indicating that cultured phage isolates do not adequately represent the diversity found in marine environments.  Composition of the phoH communities at each sampled location and depth was distinguishable according to phylogenetic clustering, although most phoH clusters were recovered from multiple sites.  Next, I built upon this project by analyzing the viral diversity of a depth profile at BATS through amplification and deep sequencing of the phoH gene.  This comprehensive study of the gene’s diversity over three different years, several seasons, and a range of depths from the surface to 1000 m revealed that the viruses at BATS contain a large pool of phoH sequences, but that most of those sequences are rare.  Overall, the phoH gene revealed depth-based, seasonal, and interannual differences in the diversity of the viral community at BATS.  Finally, I continued the extensive examination of viral diversity at BATS by using several signature genes and a fingerprinting technique to assess changes between winter and summer viral communities over two depths in three different years.  The results demonstrated that the viral communities at the surface and at 100 m depth were more similar to each other in winter, regardless of the year, than they were in summer, when the water column is stratified as opposed to well-mixed.  These findings may stem from physical factors such as UV irradiation of viral particles during stratification, as well as seasonal and depth-related differences in host communities associated with the depth of the mixed layer.