Heterotrophy supports much of the energy-starved life in the deep biosphere, yet we know almost nothing about the pathways by which organic matter (OM) is remineralized in the deep subseafloor. The microbes responsible for OM breakdown in the subsurface are taxonomically diverse, but their lack of resemblance to well-characterized lab cultures makes it impossible to use taxonomy alone to predict the nature of their interactions with OM. Even when metagenomes or metatranscriptomes are available to provide functional information, common analysis tools only categorize annotated genes into general classes that do not distinguish between degradative, synthetic, or housekeeping processes. We approached this problem by expressing, purifying, characterizing, and analyzing proteins from the uncultured phylum, Bathyarchaeota. We explored the possibilities for long term starvation in marine organisms in a review paper, and developed software for data processing of OM degradation. We monitored marine sediments in lab to look for growth dynamics in natural populations of microbes, and quantified the abundance and evolutionary distance of uncultured microbes in the public database. In total, we were able to identify new potential roles for uncultured archaea in OM degradation.