Seasonal Dynamics of Freshwater Bacterial Communities in Continental and Mediterranean Lakes

Lakes are highly dynamic freshwater ecosystems where complex interactions between environmental factors and microbial communities regulate biogeochemical cycling and ecosystem stability. Seasonal dynamics of rare and dominant bacterial taxa, as well as the links between dominant taxa and environmental drivers in freshwater ecosystems across Croatia’s contrasting climatic regions, remain insufficiently explored. To address this gap, this study investigated six deep karstic lakes across both regions. Amplicon-based 16 S rRNA gene sequencing coupled with FAPROTAX-based functional predictions revealed that microbial community structure and inferred functional potential were strongly influenced by environmental variability. Dissolved organic carbon (DOC) was identified as the primary driver of community composition. Typical freshwater bacterial genera, including hgcl, Cyanobium PCC-6307, and Luteolibacter, dominated across all lakes. Mediterranean lakes exhibited greater heterogeneity in inferred functional potential across seasons, with variable enrichment in predicted pathways associated with carbon, nitrogen, and sulfur cycling. By contrast, continental lakes showed more stable inferred functional potential with less pronounced seasonal fluctuations. Overall, this study highlights how environmental and climatic variability shape the taxonomic composition and inferred functional potential of microbial communities in freshwater systems, emphasizing the ecological dynamics of dominant bacterial taxa, while also revealing seasonal and regional differences between dominant and rare bacterial taxa across contrasting climatic regions.