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Lake microbial communities’ physiological responses to environmental stress and interactions with higher trophic levels can either support ecosystem recovery or contribute to further degradation. These communities are also central to carbon cycling, where lakes act as carbon sinks, and sedimentary organic matter is transformed into carbon dioxide and methane, influencing greenhouse gas emissions. My Master thesis work aims to study the diversity, composition and structure of the microbial communities in the water column, sediment traps, and sediment core from Lake Kassjön (Sweden), along with sediment core from Lake Xiliang (China), using a 16S-18S metabarcoding approach. The aim was to explore how microbial communities vary between lacustrine habitats and with sediment depth, based on two hypotheses: (1) that water column communities are reflected in both sediment traps and cores, and (2) that sediment cores from contrasting lakes show similar taxonomic patterns and vertical variation. In Lake Kassjön, microbial communities in the water and sediment traps were highly similar, while those in the sediment core were distinct. In contrast, the sediment core from Lake Xiliang showed clear vertical structuring of microbial communities, which was not observed in Lake Kassjön. Shared dominant taxonomic groups across lakes included Chloroflexi and Proteobacteria, while Actinobacteria and Acidobacteria were more dominant in Lake Kassjön. These results indicate interlake variability in sediment microbial communities. Future studies should aim to integrate environmental and microbial data to better understand the ecological drivers of microbial community assembly in lake sediments, along with higher quality and quantitative samples from lake water.