Environmental drivers of microbial assembly and stability in lakes across biogeographical regions

• Stratification and mixing events shaped distinct microbial distribution patterns across lakes. • Oligotrophic Alpine lakes showed higher community stability than mesotrophic Mediterranean lakes. • Salinity fluctuations in Lake Crniševo drive stronger selection pressures and community divergence. • Free-living and particle-associated bacteria exhibit distinct responses to stratification and mixing events. • Deterministic processes dominated microbial community assembly in all investigated lakes. Freshwater lake ecosystems play a crucial role in the global carbon cycle, acting as both carbon sinks and sources while providing essential ecosystem services. Within these ecosystems, planktonic microorganisms drive nutrient cycling and energy transfer in aquatic food webs. Due to their rapid response to environmental fluctuations, microbial communities serve as indicators of ecosystem change. In stratified lakes, thermal layering restricts energy and nutrient exchange, creating distinct microbial niches across depths. Microbial communities can be classified into free-living (FL) and particle-associated (PA) bacteria, which exhibit divergent metabolic strategies and responses to environmental change. Ecological theory suggests that PA bacteria are more influenced by deterministic factors (e.g., nutrient availability, oxygen gradients), whereas FL bacteria experience greater stochasticity (e.g., ecological drift). However, the stability and assembly mechanisms of these microbial fractions in dynamic lake environments remain poorly understood. In this study, we analyzed FL and PA bacterial communities in four karstic lakes in Croatia over two years, capturing both stratified and mixed conditions. Our results revealed that stratification and mixing events drove distinct microbial distribution patterns, with environmental gradients shaping niche partitioning between FL and PA bacteria. Contrary to the ecological theory, deterministic processes dominated community assembly in all lakes and fractions, though stochastic processes played a role, particularly in PA communities. Lakes with more stable conditions, such as Plitvice Lakes, exhibited resilient microbial networks, while more dynamic environments, like Baćina Lakes, supported less stable communities. In Lake Crniševo, seasonal salinity fluctuations created strong selection pressures, contributing to community divergence over time. These findings underscore the importance of environmental drivers in shaping microbial assembly and stability, highlighting the distinct ecological roles of FL and PA bacteria. Understanding these dynamics is crucial for predicting microbial responses to environmental change and enhancing biomonitoring strategies for freshwater ecosystem management.