In this work, we compare the resolution of V2-V3 and V3-V4 16S rRNA regions for the purposes of estimating microbial community diversity using paired-end Illumina MiSeq reads, and show that the fragment, including V2 and V3 regions, has higher resolution for lower-rank taxa (genera and species). It allows for a more precise distance-based clustering of reads into species-level OTUs. Statistically convergent estimates of the diversity of major species (defined as those that together are covered by 95% of reads) can be achieved at the sample sizes of 10000 to 15000 reads. The relative error of the Shannon index estimate for this condition is lower than 4%.

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The ability to compare the composition and metabolic potential of microbial communities inhabiting the subsurface sediment in geographically distinct locations is one of the keys to understanding the evolution and function of the subsurface biosphere. Prospective areas for study of the subsurface biosphere are the sites of hydrocarbon discharges on the bottom of the Lake Baikal rift, where ascending fluxes of gas-saturated fluids and oil from deep layers of bottom sediments seep into near-surface sediment. The samples of surface sediments collected in the area of the Posolskaya Bank methane seep were cultured for 17 months under thermobaric conditions (80°C, 5 MPa) with the addition of complementary organic substrate, and a different composition for the gas phase. After incubation, the presence of intact cells of microorganisms, organic matter transformation and the formation of oil biomarkers was confirmed in the samples, with the addition of Baikal diatom alga Synedra acus detritus, and gas mixture CH4:H2:CO2. Taxonomic assignment of the 16S rRNA sequence data indicates that the predominant sequences in the enrichment were Sphingomonas (55.3%), Solirubrobacter (27.5%) and Arthrobacter (16.6%). At the same time, in heat-killed sediment and in sediment without any additional substrates, which were cultivated in a CH4 atmosphere, no geochemical changes were detected, nor the presence of intact cells and 16S rRNA sequences of Bacteria and Archaea. This data may suggest that the decomposition of organic matter under culturing conditions could be performed by microorganisms from low-temperature sediment layers. One possible explanation of this phenomenon is migration of the representatives of the deep thermophilic community through fault zones in the near surface sediment layers, together with gas-bearing fluids.

We analysed the relationship between the chemical complex (concentration of dissolved ions, nutrients, pH) and biological parameters (primary production, biomass of phytoplankton, abundance and activity of bacterial communities) at estuaries of rivers and coastal waters of Southern Baikal during the under-ice period. Correlation network analysis revealed CO2 to be the main limiting factor for the development of algae and microbial communities in the coastal zone of Lake Baikal. This study indicates that primarily reverse synthesis of bicarbonate and carbonate ions associated with the development of phytoplankton and accumulation of dissolved CO2 during photosynthesis regulates pH in the Baikal water. We did not detect the anthropogenic factors that influence the change in pH and acidification. Near the Listvyanka settlement (Lake Baikal, Listvennichnaya Bay), there was a great number of organotrophs and thermotolerant bacteria with low bacterioplankton activity and high concentration of organic carbon. This evidences eutrophication due to the influx of organic matter having an anthropogenic source. Nutrients produced during the bacterial destruction of this matter may explain the changes in bottom phytocenoses of Listvennichnaya Bay.

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Although in sediments of Lake Baikal process of anaerobic oxidation methane was revealed by radioisotope techniques, by of the methane profile we know a little about the microorganisms carrying out this process. Here we studied diversity of archaeal communities in different types geological structures (methane seeps and mud volcano) on Lake Baikal with different composition of pore waters and the discharged fluid. In investigate were used different methods molecular biology including of high-throughput sequencing of gene 16S rRNA and PCR analysis different genes of AOM (mcrA). Molecular analysis did not reveal methane-oxidizing archaea ANME-1, -2, or -3, which are responsible for anaerobic oxidation of methane in marine sediments. Hydrogenotrophic methanogenic archaea representatives of the orders Methanomicrobiales, Methanococcales, as well as acetoclastic methanogens of the order Methanosarsinales were abundant in a mud volcano at Lake Baikal. In investigation sites we found divers M. nitroreducens-like archaea (ANME-2d subcluster) both in deep sediments of a methane seeps and in a mud volcanoes. Their closest homologues involved in process anaerobic oxidation of methane in different freshwater systems, bioreactors, paddy field soils.

—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.