A Five-Year Time Series Reveals Recurrent and Episodic Microbial Community Dynamics in an Oligotrophic Lake

Microbial community dynamics are central to the functioning of freshwater ecosystems, yet short-term surveys fail to capture long-term ecological trajectories. Here, we present a five-year monthly time series of microbial communities and environmental variables in Lake Soyang, a model oligotrophic freshwater ecosystem in South Korea. We identified six distinct clusters of seasonally recurring microbes that drive a predictable annual microbial cycle, which operates alongside episodic populations that transiently occupy ephemeral niches. Crucially, the genome-streamlined acI and acIVclades of Actinomycetota exhibited extensive spatiotemporal niche differentiation, with recurring lineages partitioning into previously undescribed low-oxygen- and winter-associated subgroups, while specific members emerged as episodic bloomers, thereby expanding our understanding of their ecological versatility. Network analysis further revealed dense interconnectivity among diverse populations, indicative of finely coordinated, time-dependent succession. By linking short-term fluctuations to multiyear trends, this study highlights the value of long-term monitoring and offers a baseline for incorporating microbial indicators into freshwater management and conservation.