Tatyana V. Pogodaeva

Microbial communities of the discharge zone of oil- and gas-bearing fluids in low-mineral Lake Baikal

At the site of natural ingress of oil, microbial diversity in the Central Baikal bottom sediments differing in the chemical composition of pore waters was studied by molecular biological techniques. The sediments saturated with oil and methane were found to contain members of 10 bacterial and 2 archaeal phyla. The oxidized sediment layer contained methanotrophic bacteria belonging to the Alphaproteobacteria, which had a specific structure of the pmoA gene and clustered together with uncultured methanotrophs from cold ecosystems. The upper sediment layer also contained oil-oxidizing bacteria and the alkB genes most closely related to those of Rhodococcus. The microbial community of reduced sediments exhibited lower diversity and was represented mostly by the organisms involved in hydrocarbon biodegradation.

Sequentially sampled gas hydrate water, coupled with pore water and bottom water isotopic and ionic signatures at the Kukuy mud volcano, Lake Baikal: ambiguous deep-rooted source of hydrate-forming water

The isotopic and ionic composition of pure gas hydrate (GH) water was examined for GHs recovered in three gravity cores (165–193 cm length) from the Kukuy K-9 mud volcano (MV) in Lake Baikal. A massive GH sample from core St6GC4 (143–165 cm core depth interval) was dissociated progressively over 6 h in a closed glass chamber, and 11 sequentially collected fractions of dissociated GH water analyzed. Their hydrogen and oxygen isotopic compositions, and the concentrations of Cl– and HCO3– remained essentially constant over time, except that the fraction collected during the first 50 minutes deviated partly from this pattern. Fraction #1 had a substantially higher Cl– concentration, similar to that of pore water sampled immediately above (135–142 cm core depth) the main GH-bearing interval in that core. Like the subsequent fractions, however, the HCO3– concentration was markedly lower than that of pore water. For the GH water fractions #2 to #11, an essentially constant HCO3–/Cl– ratio of 305 differed markedly from downcore pore water HCO3–/Cl– ratios of 63–99. Evidently, contamination of the extracted GH water by ambient pore water probably adhered to the massive GH sample was satisfactorily restricted to the initial phase of GH dissociation. The hydrogen and oxygen isotopic composition of hydrate-forming water was estimated using the measured isotopic composition of extracted GH water combined with known isotopic fractionation factors between GH and GH-forming water. Estimated δD of −126 to −133‰ and δ18O of −15.7 to −16.7‰ differed partly from the corresponding signatures of ambient pore water (δD of −123‰, δ18O of −15.6‰) and of lake bottom water (δD of −121‰, δ18O of −15.8‰) at the St6GC4 coring site, suggesting that the GH was not formed from those waters. Observations of breccias in that core point to a possible deep-rooted water source, consistent with published thermal measurements for the neighboring Kukuy K-2 MV. By contrast, the pore waters of core St6GC4 and also of the neighboring cores GC2 and GC3 from the Kukuy K-9 MV show neither isotopic nor ionic evidence of such a source (e.g., elevated sulfate concentration). These findings constrain GH formation to earlier times, but a deep-rooted source of hydrate-forming water remains ambiguous. A possible long-term dampening of key deep-water source signatures deserves further attention, notably in terms of diffusion and/or advection, as well as anaerobic oxidation of methane.

Diversity of Archaea in Bottom Sediments of the Discharge Areas With Oil- and Gas-Bearing Fluids in Lake Baikal

ABSTRACT Using massively parallel sequencing (the Roche 454 platform) we have studied the diversity of archaeal 16S rRNA gene sequences in oxic and anoxic sediments at six sites in Lake Baikal with oil- and gas-bearing fluids discharge. Archaeal communities appeared to be represented mainly by five phyla: Euryarchaeota, Crenarchaeota, Thaumarchaeota, Bathyarchaeota (miscellaneous Crenarchaeotic group), and Woesearchaeota (deep sea hydrothermal vent group 6). Among them we detected sequences of methanogens of the orders Methanomicrobiales, Methanosarsinales, Methanococcales, as well as representatives of the following uncultured archaeal lineages: Group C3, Marine Benthic Group D, and Terrestrial Miscellaneous Group. We have also identified sequences of ammonia-oxidizing archaea of the phyla Crenarchaeota and Thaumarchaeota. Phylogenetic analysis showed the presence ANME-2d-related sequences. However, the analysis of mcrA genes libraries has not revealed typical representatives of ANME groups. Comparison of amplicon libraries 16S rRNA gene fragments from different samples proved the widespread presence of previously detected Baikal archaeal lineages, which are members of the phylum Crenarchaeota and Thaumarchaeota (formerly Group C3 of Crenarchaeota).

Production of gaseous hydrocarbons by microbial communities of Lake Baikal bottom sediments

Production of gaseous hydrocarbons by the microbial community of the Posolsky Bank methane seep bottom sediments (southern Baikal) was studied at 4°C. Formation of both methane and a heavier gaseous hydrocarbon, ethane, was detected in enrichment cultures. The highest methane concentrations (6.15 and 4.51 mmol L−1) were revealed in enrichments from the sediments from 55-cm depth incubated with sodium acetate and H2/CO2 gas mixture, respectively. A decrease in activity of aceticlastic methanogens and a decrease in methane concentration produced by hydrogenotrophic archaea occurred with depth. The highest concentration of ethane was revealed in enrichments from the microbial community of the layer close to gas hydrates (75 cm) incubated with CO2 as a substrate. According to analysis of the 16S rRNA gene fragments from the clone library, these enrichments were found to contain members of the phylum Crenarchaeota forming a separate cluster with members of the class Thermoprotei. The phylum Euryarchaeota was represented by nucleotide sequences of the organisms homologous to members of the orders Methanococcales, Methanosarcinales, and Thermoplasmatales.

Metagenomic Analysis of Microbial Communities of the Sediments of the Kara Sea Shelf and the Yenisei Bay

Microbial diversity in the sediments of the Kara Sea shelf and the southern Yenisei Bay, differing in pore water mineralization, was studied using massive parallel pyrosequencing according to the 454 (Roche) technology. Members of the same phyla (Cyanobacteria, Verrucomicrobia, Actinobacteria, Proteobacteria, and Bacteroidetes) predominated in bacterial communities of the sediments, while their ratio and taxonomic composition varied within the phyla and depended on pore water mineralization. Increasing salinity gradient was found to coincide with increased share of the γ-Proteobacteria and decreased abundance of α- and β-Proteobacteria, as well as of the phyla Verrucomicrobia, Chloroflexi, Chlorobi, and Acidobacteria. Archaeal diversity was lower, with Thaumarchaeota predominant in the sediments with high and low mineralization, while Crenarchaeota predominated in moderately mineralized sediments. Microbial communities of the Kara Sea shelf and Yenisei Bay sediments were found to contain the organisms capable of utilization of a broad spectrum of carbon sources, including gaseous and petroleum hydrocarbons.

Phylogenetic diversity of microbial communities of the Posolsk Bank bottom sediments, Lake Baikal

Massive parallel sequencing (the Roche 454 platform) of the 16S rRNA gene fragments was used to investigate microbial diversity in the sediments of the Posolsk Bank cold methane seep. Bacterial communities from all sediment horizons were found to contain members of the phyla Actinobacteria, Bacteroidetes, Deinococcus-Thermus, Firmicutes, Nitrospirae, Chloroflexi, Proteobacteria, and the candidate phyla Aminicenantes (OP8) and Atribacteria (OP9). Among Bacteria, members of the Chloroflexi and Proteobacteria were the most numerous (42 and 46%, respectively). Among archaea, the Thaumarchaeota predominated in the upper sediment layer (40.1%), while Bathyarchaeota (54.2%) and Euryarchaeota (95%) were predominant at 70 and 140 cm, respectively. Specific migration pathways of fluid flows circulating in the zone of gas hydrate stability (400 m) may be responsible for considerable numbers of the sequences of Chloroflexi, Acidobacteria, and the candidate phyla Aminicenantes and Atribacteria in the upper sediment layers and of the Deinococcus-Thermus phylum in deep bottom sediments.

Substrate Specificity of Methanogenic Communities from Lake Baikal Bottom Sediments Associated with Hydrocarbon Gas Discharge

Methane production by microbial communities from Lake Baikal bottom sediments with different chemical composition of pore water was studied. Methane production was more active in the media supplemented with H2: CO2 and H2 + CH3COONa, rather than on media with acetate as the sole source of carbon and energy. Addition of methanol stimulated methane production only in the case of microbial communities from upper silts. Ability of the communities to produce methane correlated reliably with the concentrations of the NO3–, SO42−, Cl–, and CH3COO– ions in the pore water of the relevant sediments. Cultivation of communities from the mud volcano sediments resulted in development of methanogenic archaea of the family Methanocellaсеае in the media supplemented with H2: CO2 and H2 + CH3COONa, while methanogenic archaea in the communities cultivated without additional substrates belonged to the genera Methanoregula, Methanobacterium, and Methanosaeta.

Anaerobic Methane Oxidation in Enrichment Cultures from Deep Sediments of a Mud Volcano Peschanka (South Baikal)

Under laboratory conditions, the microbial communities of bottom sediments of a mud volcano Peschanka (Lake Baikal) were found to carry out anaerobic methane oxidation (AOM). After 16 days of anaerobic cultivation of the enrichment cultures, methane content in the gas phase decreased, and microbial consortia were established. The content of carbon, nitrogen, and oxygen determined by energy dispersive X-ray spectroscopy (EDS) was higher than in the nearby sediment particles. The presence of bacteria of the NC10 phylum and archaea of the ANME-2d cluster was established by fluorescent in situ hybridization (FISH).

Authigenic rhodochrosite from a gas hydrate-bearing structure in Lake Baikal

Early diagenetic carbonates are rare in Lake Baikal. Siderite (Fe carbonate) concretions in the sediments were discovered only recently. Here, we discuss the first finding of rhodochrosite concretions (Mn carbonate) discovered in the near-bottom sediments of the gas hydrate-bearing seepage structure St. Petersburg-2 in the deep water environment of the Central Baikal Basin. The crystal lattice of rhodochrosite contains iron and calcium substituting to manganese. Based on pore water geochemistry and of δ13C values of rhodochrosite (− 23.3 and − 29.4‰), carbon dioxide (+ 3.8 to − 16.1‰) and methane (− 63.2 to − 67.8‰), we show that carbonate crystallization most likely occurred during microbial anaerobic oxidation of organic matter, and that part of the oxygen making up the rhodochrosite seems to be derived from the 18O-rich water released from dissociating gas hydrates.

The Ability of Microbial Community of Lake Baikal Bottom Sediments Associated with Gas Discharge to Carry Out the Transformation of Organic Matter under Thermobaric Conditions.

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.