Freshwater ecosystems are increasing threatened by climate change and anthropogenic activities. Microorganisms, playing crucial roles in biogeochemical cycles, are key determinants of ecosystem function and stability. Understanding their responses to changing environmental conditions is essential for predicting and mitigating the impacts of abiotic disturbances. This thesis investigated the complex responses of freshwater microbial communities to environmental change, focusing on the underlying mechanisms driving observed shifts in community composition of major microbial groups. By combining laboratory experiments, mesocosm studies, and novel methodological approaches, this work provides valuable insights into how these communities are impacted by changing environmental conditions, particular temperature increases and salinization. This thesis reveals that microbial community dynamics under environmental stress are shaped by several interacting mechanisms.

An important mechanism explored in this thesis is the variation in stress tolerance among individual taxa within a community. I demonstrate that even closely related and morphologically similar nanoflagellate taxa, specifically Spumella rivalis, Pedospumella encystans, and Poteriospumella lacustris, exhibit varying responses to temperature increases, which significantly affected competition between the taxa in mixed cultures. This work also provided evidence that the replacement of functionally redundant taxa, differentially adapted to environmental conditions, can result in shifts in community composition without necessarily altering overall ecosystem function. In a follow-up study, I further explored the influence of biotic factors, such as initial cell densities and prey availability, on dynamics of mix cultures during a simulated heatwave and provide further evidence for the stabilizing effect of functional redundancy among heterotrophic nanoflagellates (HNFs) on their prey populations. Moreover, I investigated how environmental change can alter top-down and bottom-up controls within microbial food webs. Using mesocosm experiments and natural microbial communities, I demonstrated that salinization of freshwater ecosystems can significantly alter feeding behaviour of heterotrophic nanoflagellates, with potential cascading effects on prey community composition. Another study focused on bottom-up effects, investigating how changes in allochthonous organic matter (leaf litter) availability influence benthic bacterial and fungal communities. The results revealed differential sensitivity of fungi and bacteria to changes in resource availability. Additionally, similar gene expression pattern in bacterial and fungal communities suggest the possibility of function redundancy between these two microbial groups.

Varying sensitivity of different microbial groups to environmental stressors is another important aspect investigated in this thesis. I compared the responses of prokaryotic and microeukaryotic communities to heat stress and salinization in both pelagic and benthic habitats. Benthic communities exhibited greater resilience,  likely due to higher diversity and a more stable environment. In the water column, microeukaryotes and prokaryotes were significantly impacted by salinization, with a more pronounced effect on the microeukaryotic community. Interestingly, warmer temperatures alone had no significant effects on microbial community composition but appeared to mitigate the effects of salinization on prokaryotes when communities were exposed to both stressors simultaneously, highlighting the importance of considering multiple stressors when investigating the impact of environmental change on freshwater ecosystems.

Methodological advancements were crucial for this research. Newly designed FISH probes enabled reliable protist identification and quantification, while a semi-automated approach for microscopic image analysis facilitated the investigation of heterotrophic nanoflagellates’ feeding behaviour.

Overall, this thesis demonstrates the complex and multifaceted nature of microbial community responses to environmental change. The interplay of varying stress tolerances, top-down and bottom-up controls, differential group sensitivities, habitat properties, and multiple stressor interactions are all crucial factors shaping these responses. Future research can integrate these findings into predictive models and should further explore the long-term effects of environmental change on microbial communities.