The overall project has been supported by several funded proposals (subawards from C-DEBI):

Subaward# 41231607: Metagenomic and electron microscopic investigation of viruses and viral infections of prokaryotes in oceanic basement fluids
Project Summary:
Viruses profoundly influence the ecology and the evolution of all cellular life. Many viruses are lytic, infecting and lysing cells in the process of self-replication. Other viruses are temperate. Infection by a temperate virus most often leads to persistent (but reversible) merger of the viral genome and the host genome. This merger changes both the genotype and the phenotype of the host. In environments like the deep subsurface, where interactions between free virions and their hosts can be rate limiting, the majority of viruses are likely to be found in this mutualistic relationship with a host cell. Viruses are likely to have a major role in the microbial ecology of the ocean basement, but at present, the only data for this specific subsurface environment are some limited counts of virus-like particles. We propose to better constrain the estimates of viral abundance, determine the prevalence of lytic and temperate viral infections, and characterize the morphological and genetic diversity of viruses in ocean basement fluids using samples collected from boreholes on the Juan de Fuca Ridge. The data will shed light on the nature and extent of viral contributions to the ecology of this extensive, but understudied ecosystem.

Subaward# 59410979: Genomic and proteomic characterization of uncultivated viruses from large-volume samples of crustal fluids from the Juan de Fuca Ridge Flank
Project Summary:
Very little is known about the identities and consequences of viruses that interact with the distinctive microbial communities inhabiting oceanic crust. One of the challenges of studying the microorganisms and their viruses there is acquiring sufficient biomass for analysis. In a recent expedition to the Juan de Fuca Ridge Flank, we employed a novel passive filtration system that allowed us to sample the “microbial fraction” (bacteria, archaea) on one filter and the “viral fraction” on another from very large volume of water (10,000 L). This unique large-­‐volume sample allows us to perform analyses that were not possible with previous smaller samples. Specifically, we propose to fractionate the concentrated intact viruses into populations in a density gradient then analyze the fractions (morphology, genome and proteome). Fractionation improves our ability to assemble complete genomes and allows us to link the morphology of the viruses to their genomes and to identify which genes code for viral structural proteins. We will also prepare and analyze a metagenome from the “microbial fraction” to identify intracellular viruses and those integrated into host cell genomes. This will provide an unprecedented level of characterization for the uncultivated viruses and their relationship to their hosts in this remote habitat.

Subaward# 49059511
Project summary:
Viruses profoundly influence the ecology and the evolution of all cellular life. Many viruses are lytic, infecting and lysing cells in the process of self-replication. Other viruses are temperate and harbored within the cell. These viruses have the potential to change both the genotype and the phenotype of the host. Although the prevalence and importance of viruses in the oceanic water column is undisputable, the viral communities of the deep marine subsurface, which is likely the largest ecosystem on earth, remain largely undescribed. I propose to better constrain the estimates of viral abundance, determine the prevalence of lytic and temperate viral infections, and characterize the diversity of viruses in ocean basement fluids using samples collected from boreholes on the Juan de Fuca Ridge. The data will shed light on the nature and extent of viral contributions to the ecology of this extensive, but understudied ecosystem.