Shared stream–lake patterns in diversity, rRNA-based activity and community assembly of bacteria and microeukaryotes under distinct hydrological regimes

Freshwater systems are shaped by hydrological connectivity, yet distinct microbial communities persist between lotic and lentic habitats. While bacterial biogeography across aquatic habitats has been widely explored, less is known about the spatiotemporal links of microeukaryotes to bacterial communities. Here, we investigated microbial diversity, rRNA-based activity and community assembly within a stream-lake network in Sweden under contrasting hydrological regimes. Using amplicon sequencing of both rRNA genes and transcripts, we found parallel patterns in bacterial and microeukaryotic alpha and beta diversity, with lower richness in lakes than in inlet streams. Bacterial phenotypic diversity, assessed by flow cytometry, captured biogeographic trends comparable to sequencing-based methods. Bacteria and microeukaryotes also appeared to be structured by similar assembly mechanisms, with environmental selection having a higher relative importance in lakes compared to streams. During low-flow periods, the catchment outlet became increasingly distinct from upstream communities, demonstrating dispersal limitation from lakes. Finally, phantom taxa, undetected in rRNA genes, were predominantly rare and exhibited disproportionately high RNA: DNA ratios compared to active taxa, underscoring the need for their careful handling. Our findings revealed habitat-driven microbial dynamics, despite pronounced seasonal shifts in hydrology.