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An important characteristic of a natural reservoir is the depth distribution of the pigment composition of various groups of photosynthetic organisms and its changes in different seasons, both qualitative and quantitative. In the Arctic zone it is especially important to explore the evolution of natural water bodies under the influence of climate change and the urbanization processes in the region. This paper presents for the first time the study of bacteriochlorophyll (BChl) depth profiles derived from optical measurements accompanied by metagenomic profiling of bacterial communities in two stratified lakes, Trekhtzvetnoe and Elovoe at the Kandalaksha coast of the White Sea. Natural water with microorganisms along with hydrological measurements was sampled from various depths during expedition in March 2021. The metagenomic studies showed that biodiversity indices in both lakes did not appear to significantly diminish with depth. According to the analysis of similarity, differences between samples grouped by the lake of origin were not statistically significant. There were significant differences when samples were grouped by layer of the water column. This suggests that stratification of bacterial communities occurred according to environmental conditions in each part of the water column (oxygenated surface layer; chemocline, and anoxic bottom layers), and was not influenced by the geographical location of the lake. Differences between bacterial communities had strong correlation to changes in redox potential and light penetration, and were weakly correlated with depth and temperature; correlation with salinity and pH was not statistically significant.
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