Abstract
Plankton play a key role in biogeochemical cycles in aquatic environments, and their abundance and composition vary spatially and seasonally. We characterised the seasonal dynamics and environmental preferences of freshwater bacteria and microeukaryotes from four pelagic sites in the oligotrophic Lake Baikal and examined the spatio‐seasonal niche of closely related taxa. Based on spatio‐seasonal patterns, the amplicon sequence variants (ASVs) of bacterial 16S rRNA gene, microeukaryote 18S rRNA gene, and zooplankton 18S rRNA gene were divided into ubiquitous, seasonal (spring or summer‐autumn), and episodic groups. Co‐occurrence networks for each of the dominant bacteria (Iluma, acI, Cyanobium , Flavobacterium , Verrucomicrobiae) or microeukaryotes (Chrysophyceae, Chlorophyta, Cryptophyceae, Dinophyceae, Ciliophora) contained ubiquitous, seasonally similar, or divergent closely related ASVs. In co‐occurrence networks of bacterial or microeukaryotic ASVs, related taxa showed more positive correlations with each other, whereas distantly related or unrelated ASVs showed more negative correlations. This study revealed the coexistence of closely related taxa for some bacterial or microeukaryotic groups and spatio‐seasonal differentiation for others in a temperate freshwater environment.