18S rRNA V9 metabarcoding of zooplankton communities from the Lake Baikal littoral zone

This study presents the first metabarcoding-based assessment of zooplankton diversity in the littoral zone of Lake Baikal. Zooplankton samples were collected from eight nearshore stations in June and September 2021 using a Juday net (75 um mesh). DNA was extracted from ethanol-fixed aliquots and the V9 region of the 18S rRNA gene was amplified with primers 1389F and 1510R. Amplicons were sequenced on an Illumina MiSeq platform (2x250 bp). After quality filtering and clustering at 99% similarity, a total of 795 OTUs were obtained, including both microeukaryotes and metazooplankton. The dominant copepod Epischura baikalensis was represented by over 200 OTUs, likely reflecting intragenomic variation. This dataset reveals seasonal shifts and spatial heterogeneity in zooplankton communities and highlights the strengths and limitations of DNA metabarcoding compared to traditional microscopy. Correlation analyses were performed between OTU read counts and biomass estimates for major zooplankton taxa. The dataset supports future biodiversity monitoring and reference library development for Lake Baikal endemic taxa.