The microbial communities of the deep subsurface are as complex and diverse as the variety of ecosystems present. By using culture-independent techniques, several branches of the tree of life have been phylogenetically extended and therefore shedding light on the microbial dark matter. Aquatic environments, such as groundwater and marine ecosystems, the archaeal branch gained a broad range of new representatives, predominantly within the DPANN branch. Candidatus Altiarchaeum (Ca.) is a globally widespread DPANN archaeon found in, e.g., geysers and subsurface aquifers of diverse chemical properties and with varying bio-processible compounds. Previous metagenomic analyses revealed a CRISPR system, known as immune systems of microorganisms, encoded in population genomes of Ca. Altiarchaeum as well as an association with an episymbiont of the DPANN branch Ca. Huberiarchaeum. Yet the type and complexity of the CRISPR systems of Ca. Altiarchaeum and the respective targets were unknown. This thesis aims to analyze the potential targets of the CRISPR systems and to compare expression rates of conserved core metabolic functions in ecosystems around the globe in order to delineate the focus of metabolic functions of Ca. Altiarchaeum. The analyses of the CRISPR interference with spacers derived from the hosts’ CRISPR array revealed targeting of viral sequences, the hosts’ own genome and genomic regions of the episymbiont. By mapping metagenomic reads to the targeted sites, decreases in coverage indicated that the CRISPR system cleaves the genomic DNA of the host via self-targeting and the episymbiont within gene coding regions. Transferring the reported results to publicly available archaeal genomes on NCBI revealed that spacer acquisition of genomic DNA from divergent archaeal lineages might be an widespread phenomenon, particularly within extreme subsurface environments. The results suggest that CRISPR targeting alters symbiotic relationship and might result in shifts from parasitic to mutualistic behaviors based on necessary metabolic complementation between archaea. Moreover, the differential expression rates of core metabolic functions from Ca. Altiarchaea were analyzed in ecosystems with and without its episymbiont. Although the compared ecosystems have significantly different chemical compositions and available bio-processable molecules, the shared core metabolic functions suggest that Ca. Altiarchaea are in one ecosystem influenced by viral attacks and, in the other, affected by environmental stressors. The combined results indicate that Ca. Altiarchaea, as a player in carbon fixation in the deep subsurface, is affected by viral attacks and symbiotic relationship dependent on the ecosystems. Compared to other known DPANN archaea–archaea host-symbiont associations, the symbiosis of Ca. Altiarchaea and Ca. Huberiarchaea provides new insights into microbial interactions via CRISPR-Cas interference. In general, this thesis sheds light onto the potential diversity of CRISPR interference in DPANN archaea of aquatic subsurface ecosystems and expands the knowledge about uncultivated archaeal symbiotic partners. Furthermore, the comparison of expression rates of core metabolic functions of the DPANN archaeon Ca. Altiarchaeum gives an insight into the variety of the archaeal metabolism dependent on the aquatic subsurface ecosystems.