Here we describe the potential uptake and assimilation pathways for the essential nutrients C, N, P, and S in the acidophilic iron oxidiser Ferrovum strain JA12, a member of a novel genus among the Betaproteobacteria. Comparative genomics proved to be a powerful approach to give first insights into the biochemical potential of this novel genus and to understand the reasons for the dominating abundance of Ferrovum spp. in a pilot plant to remediate acid mine drainage.