Methanotrophs are ubiquitous organisms in the environment, acting as a biofilter for the potent greenhouse gas methane in many methane emitting environments, being the only guild of organisms capable of methane oxidation. Many studies have investigated methanotrophs in various environments, but few have taken the methanotrophic interactome, i.e., the methanotroph-associated non-methanotrophic organisms, into account. Methanotrophs do not live in seclusion, being influenced, both positively and negatively, by non-methanotrophic organisms. Thus, the methanotrophic interactome may contribute to methanotrophic community functioning and promote stress response.In this thesis, a novel strategy applies co-occurrence network analyses to infer methanotroph-related trophic interaction networks. A pre-selection of the active and metabolizing community was facilitated by DNA-stable isotope probing to avoid overestimation of such networks that can occur otherwise. This work further provides insights into the site-specificity of methanotrophic networks and community-related stressor impacts. The former was revealed by comparing the methanotrophic interactome of five different methane-emitting environments, as the same trophically interacting taxa were seldom found in multiple environments. The latter was demonstrated by applying a mild and severe stressor to methane-emitting environments, and the impact on the methanotrophic interactome was determined. While mild desiccation / re-wetting stress applied to paddy soil had a minor impact on the methanotrophic interactome and potentially strengthened the interacting community, a severe stressor, such as peatland mining and restoration, had a significant impact on the interactome, which in turn likely impairs the system’s stress response to future stressors. Changes in the interactome were not reflected in the methanotrophic activity and abundance, which weakens these parameters as indicators of soil functional restoration. Lastly, the influence of biotic and biotic parameters on the re-colonization of gamma-irradiated soil was analyzed, indicated by methanotrophic activity and community development. To an extent, the initial community composition affects methanotrophic community succession, while edaphic properties mainly influence methanotrophic activity.Altogether, the methanotrophic interactome was site-specific, and the influence of stressors on the methanotrophic interactome may be dependent on abiotic and biotic parameters. Even though the soil functions recovered after disturbance, the co-occurrence networks remained impaired.