The deep biosphere represents an ecosystem on Earth that may be under extreme limitations of energy (Hoehler and Jorgensen, 2013). Currently we have little understanding of how organisms evolve and/or adapt to this selection pressure. The activity of microorganisms in the subsurface may be at incredibly low rates, environmental data that suggests these organisms are surviving well below laboratory-determined maintenance energies (Hoehler and Jorgensen, 2013). How these organisms exist with such low energies is unknown, yet it is widely assumed that some sort of activity is maintained to allow cells to exist with hundreds to thousands of years as their potential turnover time (Lomstein et al. 2012). Microorganisms are expected to occupy deep marine sediments and underlying basalts, surviving on limited energy and potentially dividing on a thousand year time scale. For a microorganism to do this, and be only slightly active, is a difficult process to maintain, as many cells are programmed to be constantly active or face death. In order to maintain low levels of activity, cells may need additional control on which genes are activated in their genomes. In the surface world, particularly in eukaryotes, gene activity is controlled by factors including methylation of genes to silence activity. Methylation is now recognized as being present in many bacterial and archaeal genomes, and we hypothesized that this may be a prevalent lifestyle in subsurface organisms. We saw initial signals of methylation activity in a deep subsurface metatranscriptome and have shown which genes are methylated in a shallower sediment core. Methylation does appear to be a widespread phenomenon in microbial genomes of the subsurface, and additional tests will be needed to prove its overall control on the potential for microbial activity.