—We discuss the results of a model experiment on cultivation of the microbial community from the area of the Khoboy mud volcano (Akademichesky Ridge) conducted under conditions typical of the hydrocarbon generation zone (80 °C, 5 MPa). The cultivation under conditions of biomass enrichment with the Baikal diatom Synedra acus changed the composition of organic matter. The transformation degree of organic matter in the sediment after the experiment was 16%, whereas the concentration of phenanthrenes relative to methyl-substituted homologues, including retene, decreased, and the concentration of dibenzothiophenes relative to normal alkanes increased. We have identified tri- and monoaromatic steroids, including 17-dismethyl, 23-methyl monoaromatic steroids C27. An increase in the concentration of tri- and monoaromatic steroids in the sediments after the experiment might indicate that the biomass of the Baikal diatom S. acus was destructed, which led to an increase in the steroid concentration. In the control (sterile) sediment, we detected no changes in the composition of organic matter. Representatives of various taxa capable of surviving in anaerobic thermophilic conditions have been identified in the microbial community by molecular genetic methods. Their presence in the surface sediments might be due to the inflow of deep-seated mineralized fluids and breccia from deep-seated sedimentary rocks.