Flow Velocity and Anthropogenic Stressors Drive Microbial Community Dynamics in Riverine Ecosystems

Microbial communities in riverine ecosystems are essential drivers of biogeochemical cycling, mediating nutrient transformation and energy flow. However, they are substantially affected by anthropogenic stressors such as pollution, alteration in flow regime and land-use change and, which can alter their composition and functionality, leading to ecosystem degradation. Here, we performed metagenomic analyses of sediment samples from four different flow-through stream mesocosm setups in Germany, Ireland and New Zealand encompassing a total of 254 mesocosms. Our results revealed differential responses of microbial communities to altered flow velocity, an important stressor identified in previous research. Microbial communities from two riverine ecosystems showed significant compositional shifts at slower flow in the mesocosms, whereas the other two showed only minor changes, suggesting a resilience that we infer to be linked to higher microbial diversity. We also identified significant differences in encoded metabolic gene profiles between the microbial communities of the European and New Zealand experiments, particularly in genes associated with nitrogen, methane and sulfur cycling. To further investigate this difference, we selected one stream ecosystem substantially affected by reduced flow velocity and performed in-depth metatranscriptomic analyses revealing up-regulation of, e.g., heat-shock proteins across multiple community members. Notably, a combination of elevated water temperature and flow velocity reduction showed an antagonistic effect at transcription level, highlighting the complexity of stressor interactions associated with river ecosystems. This study stresses the importance of understanding anthropogenic impacts on river microbial communities to mitigate the consequences of these stressors.