One of the major challenges in the study of deep subsurface microbiology is determining the geochemical processes performed by uncultured microorganisms. These microorganisms are often abundant and diverse, but have been identified only by taxonomic marker genes. We addressed this issue by sequencing whole genomes from individual cells of key groups of uncultured archaea and bacteria. This allowed us to link metabolic functions and phylogenetic identities to each other as well as to key environmental factors such as the source of organic matter. By accessing samples from IODP Leg 347: Baltic Sea Paleoenvironment, we compared whole genomes from individual cells across glacial and interglacial periods. We found that the most abundant bacteria and archaea in sediments up to 85 meters below the seafloor were able to be sorted with flow cytometry and sequenced, yielding new single cell genomes from deeply-branching clades. Different clades had different sets of genes, that were conserved between single cell genomes of the same clade. Quantitative PCR showed that bacteria were dominant over archaea in these sediments. We continue to explore the links between microbial phylogeny and function in these deep subsurface prokaryotic communities.