While the complexity of prokaryote communities in soil is well understood, there remains a paucity of studies characterizing the impact of viruses on hosts, biogeochemistry and rates of ecosystem processes. Microbially-mediated nitrification, central to the global nitrogen cycle and responsible for fertilizer losses in soil, is performed by taxonomically and functionally restricted autotrophic bacteria and archaea and has led them to become established model groups for linking diversity, evolution, ecophysiology and function in soil. Here we describe the subsequent use of their viruses for studying viral ecology. To identify active interactions between nitrifying prokaryotes and viruses, the transfer of assimilated carbon from autotrophic prokaryotes to viruses was examined using DNA stable isotope probing coupled with metagenomic analysis. Combining with a novel hybrid analysis using GC mol% fractionation enabled identification of novel virus families infecting ammonia oxidizing archaea (AOA). However, to characterize those also infecting ammonia- and nitrite oxidizing bacteria, a second approach used filtration of virus like particles from nitrifying soil microcosms after differential inhibition to alleviate competition and increase abundance of viruses infecting non-inhibited groups. This dramatically increased the recovery of high-quality virus genomes, all representing novel virus families. Soil AOA viruses did not contain auxiliary genes associated with ammonia oxidation but were enriched in multicopper oxidase and oxidoreductase genes, indicating a role in other aspects of host energy metabolism during infection. Infection of nitrifiers is a dynamic process suggesting that understanding virus interactions during nitrification may inform approaches for augmenting activity and associated nitrogen losses.