In oligotrophic environments like groundwater, microorganisms can adapt to the nutrient limited conditions through the development of cooperative or antagonistic interactions, or through the general adaptation and regulation of their metabolism. Microbial communities in groundwater are highly complex and often dominated by microorganisms that lack cultivated representatives, including members of the Candidate Phyla Radiation (CPR). These ultra-small sized bacteria have streamlined genomes that lack metabolic functions thought to be essential for life, suggesting that they depend on other microorganisms for these cellular components. This lifestyle hampers the cultivation of CPR, which traditionally relies upon the isolation of single microorganisms. Thus, understanding the repertoire of interaction mechanisms and the metabolic potential of groundwater bacteria is limited to laboratory investigations of a few isolates or based exclusively on genome-derived information. Collectively, the findings presented within this dissertation demonstrate how groundwater microbial communities are structured and influenced by species interactions as well as by the metabolic potential of individual members. While the predicted role of key players like Cand. Roizmanbacterium ADI133 has significantly contributed to the understanding of groundwater ecology, this dissertation further highlights the importance of trophic interactions in the terrestrial subsurface. However, novel cultivation strategies are needed to learn more about the role of yet uncultivated microorganisms, including the CPR.