Long-term freshwater time series reveals recurrent and episodic microbial dynamics driven by distinct assembly mechanisms

Background Freshwater bacteria are key contributors to ecosystem stability and resilience, yet their inherent microdiversity and rapid community turnover make interpreting their seasonal dynamics within broader ecological frameworks challenging. Furthermore, the underlying mechanisms of community assembly, driven by deterministic and stochastic processes, remain poorly understood. Results We conducted a five-year time series sampling of microbial communities, alongside key environmental parameters, in an oligo-mesotrophic lake. Seasonal community assembly in this freshwater ecosystem was primarily driven by drift, dispersal limitation, and homogeneous selection, with the relative contributions of these processes varying markedly across months and depths. Six distinct clusters of seasonally recurring microbes shaped the timeline of annual community transitions, while episodic populations sporadically occupied the remaining ecological niches. Network-based reconstruction of microbial dynamics uncovered a highly interconnected structure, where microbial and environmental components exhibited coordinated, time-dependent variation. Conclusions This study highlights the importance of long-term ecological monitoring for resolving microbial dynamics at a fine scale. Our findings establish a foundation for future approaches aiming to apply microbial metrics to freshwater ecosystem assessment and management.