30In this study, we explored the diversity and community composition of bacteria along a 31 vertical gradient in Lake Issyk Kul, Kyrgyzstan, one of the largest and deepest brackish lakes 32 in in the world. We identified 4904 bacterial ASVs based on analysis of 16S rRNA gene 33 sequences and determined significant changes in the composition responding mainly to the 34 variables depth and salinity. A higher abundance of Proteobacteria and Bacteroidetes was 35 observed in the surface waters and the lake tributaries. Cyanobacteria were more abundant in 36 the deep chlorophyll maximum (28.5 to 128 m), while Planctomycetes and Chloroflexi were 37 dominant at depths between 128 to 600 m. According to our machine learning analysis used 38 for identifying the most critical environmental factors, depth and temperature revealed the 39 strongest effect on members of Proteobacteria, Planctomycetes, and Chloroflexi, while 40 oxygen is associated with the variations in Cyanobacteria. Also, a notable increase in alpha 41 diversity estimations was observed with increasing water depth. This work evidences 42 significant differences in the structure of bacterial communities along the depth gradient in 43 deep, transparent lake ecosystems. Notably, there is a dominance of Planctomycetes and 44

We explored the diversity and community composition of bacteria along a vertical gradient in Lake Issyk Kul, Kyrgyzstan, one of the world's largest and deepest brackish lakes. We identified 4904 bacterial amplicon sequence variants based on the 16S rRNA gene analysis and determined significant changes in the composition, responding mainly to depth and salinity. A higher abundance of Proteobacteria and Bacteroidetes was observed in the surface waters and lake tributaries. Cyanobacteria were more abundant in the deep chlorophyll maximum from 28.5 to 128 m, while Planctomycetes and Chloroflexi were dominant in the deepest layers, from 128 to 600 m. According to our machine learning analyses, depth and temperature were the most critical environmental factors, with strong effects on Proteobacteria, Planctomycetes and Chloroflexi, while oxygen was associated with the variations in Cyanobacteria. We also observed that with increasing depth, the alpha diversity values increased. The dominance of Planctomycetes and Chloroflexi in the deepest layers can only be seen in a few lakes of the world. However, the lake is facing increasing anthropogenic and climatic pressure. There is an urgent need to understand better the ecological role and function of these unique deep-water microbial communities.