Streams are diverse ecosystems, serving as hydrological connections that link mountains, urbanized areas, and the sea. Despite streams’ importance for the environment and human civilization, they are under severe anthropogenic stress. As part of the global freshwater biodiversity crisis caused by anthropogenic stressors, for example only 28% of analyzed North American streams were found to contain healthy biological communities. The microbes as the major part of the microbiome and their metabolic activity in stream ecosystems like the surface water or hyporheic sediment are essential for ecosystem functioning and provision of ecosystem services to humans. Today, it is widely acknowledged that stream microbiomes are an integral part of stream ecosystems and face severe anthropogenic stress. However, a mechanistic understanding of processes governing degradation and recovery of stream microbiomes is still missing. 
This thesis aims at unraveling the structural and functional responses of stream microbiomes to multiple anthropogenic stressors. Obtained results of microbial stressor responses are put into context with the importance of distinct stream ecosystems and their positions within fluvial networks. A comprehensive insight into the ecological processes of stream microbiomes under stress was achieved by leveraging factorial mesocosm experiments and continent-spanning field samples. The response of targeted stream microbiomes to stress was analyzed via genome-resolved metagenomics and metatranscriptomics. Results of this thesis revealed a great sensitivity of microbiomes to anthropogenic stressors, e.g., to treated wastewater in case of surface water, or to lowered flow velocity and to increased temperature in hyporheic zone sediments. While a full-factorial mesocosm experiment indicated mostly antagonistic stressor interactions on community level, finer taxonomic resolution shed light on a complex community response composed of sensitive and resistant microbial lineages for applied stressor combinations. Despite a community shift caused by applied stressors, altered microbiomes were forced to upregulate their stress response to applied stressors like lowered flow velocity or increased temperature. By contrast, encoded metabolic functions were found to be resilient to applied stressors and the community structure was able to recover after stressor removal indicating a high resilience of stream microbiomes. In combination with a continent-spanning field study which confirmed response mechanisms detected in mesocosm systems, the results hereby presented suggest that resilience to anthropogenic stressors in streams is at least partially governed by two processes: a universal stress response to disturbances which intensified as a consequence of human activities, and a stream-specific response based on the exposure history to purely anthropogenic stressors like wastewater.
In summary, this thesis advances multiple-stressor research of stream microbiomes by integrating meta-omic approaches with large-scale mesocosm experiments and field studies. Obtained results verified the previously hypothesized substantial importance of individual tolerances of microbes to stressors during stressor application. Additionally, new hypotheses for processes governing recovery of microbiomes after stressor removal were posed. In future studies, these hypotheses could be tested with a modified mesocosm system ExStream SIGMA which was designed within this doctoral project. Acknowledging the accelerating degradation of streams, this thesis provides results and suggestions that can serve as guidelines for future multiple-stressor research of stream microbiomes and renaturation efforts of stressed stream microbiomes.