The nitrogen (N) cycle represents one of the most well studied systems yet the taxonomic diversity of the organisms that contribute to it is mostly unknown, or linked to poorly characterized microbial groups. While progress has allowed functional groups to be refined, they still rely on a priori knowledge of enzymes involved, and the assumption of functional conservation, with little connection to the role the transformation plays for specific organisms. Here, we use soil microcosms to test the impact of N deposition on prokaryotic communities. By combining chemical, genomic and transcriptomic analysis we are able to identify and link changes in community structure to specific organisms catalyzing given chemical reactions. Urea deposition led to a decrease in prokaryotic richness, and a shift in community composition. This was driven by replacement of stable native populations, which utilize energy from N-linked redox reactions for maintenance, with fast responding populations that use this energy for growth. This model can be used to predict response to N disturbances and allows us to identify putative life strategies of different functional, and taxonomic, groups thus providing insights into how they persist in ecosystems by niche differentiation.