In this talk, Bhattacharya will present work in his lab using a potentially transformational approach to marine genomics and ecology referred to as single cell genomics (SCG). Although relatively well established with prokaryotes, SCG has only recently been applied to the more complex genomes of eukaryotes. Working with collaborators at the Bigelow Laboratory for Ocean Science, SCG methods were used to generate draft genome assemblies from individual picobiliphyte (bacterial-sized planktonic protists) cells captured in the ocean. In contrast with the recent description of this phylum as photosynthetic, no evidence was found of plastid DNA nor of nuclear-encoded plastid-targeted proteins, which suggests that these picobiliphytes are heterotrophs. Genome data from one cell were dominated by sequences from a widespread single-stranded DNA virus, which was absent from the other two cells. These latter two cells however contained non-eukaryote DNA derived from marine Bacteroidetes and large DNA viruses that presumably are prey items. Therefore, our shotgun sequencing approach to uncultured marine protists revealed distinct interactions of individual cells. Generally, SCG offers the possibilityto gain access not only to the native DNA of cells but also to the DNAs of prey, symbionts, and pathogens associated with each cell. This seminar will also discuss SCG work with the Paulinella model that has begun to uncover the connections between phagotrophy, horizontal gene transfer (HGT), and primary plastid endosymbiosis. Ultimately, it may be possible to reconstruct HGT events at the level of individual cells and populations in nature.