—A 6-meter core of the Holocene sediments in Lake Dukhovoe is studied. The material composition of the core is heterogeneous and has clear bedding. Lacustrine sediments are represented by the upper 293 cm. Each bed of the sediments is subjected to microbiological analysis. A high total number of heterotrophic bacteria is revealed in the upper (0–15 cm) and deeper (110–150 cm) sapropel intervals. Sulfate-reducing bacteria are identified only in Chrysophyceae cysts. The CaO/Fe2O3 ratio shows the degree of “carbonate content” of bottom sediments. It is low in the lake sapropel (0.2), which indicates the geochemical specificity (carbonate-free sapropel). Na, Mg, Al, Si, Al, Ca, Fe, Mn, Zr, and Cr concentrations in sapropel are within the average concentrations for the Earth’s crust, shale, and oceanic pelagic clays, while U and Mo concentrations exceed them. Phytoplankton is enriched in phosphorus (biogenic element) and chalcophile elements (Zn, Cd, Sn, Sb, Hg, Pb, and Cu), which characterize the pollution of the modern atmosphere of the Baikal region. Diagenetic processes result in the transformation of the pore waters, namely an increase in mineralization as compared to lake water, an increase in the concentrations of biogenic components (HCO3-, NH4+, NO3-, and PO43-) and a decrease in SO42-. Pyrite framboid accumulations are revealed in organomineral sediments below the horizon of 200 cm, and iron phosphates represented by vivianite are identified in sapropel.

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