Microbiological and biogeochemical investigation of the bottom sediments of semiclosed basins was carried out at the Kislaya Guba tidal power station (Barents Sea) and in Kanda Bay (White Sea). Suppressed tidal water mixing is known to affect the hydrological regime of isolated basins, resulting in the development of oxygen-free sediments. The upper sediments of the studied bays were shown to contain higher concentrations of sulfide and methane, with increased rates of sulfate reduction, methanogenesis, and methane oxidation. The relative abundance of truly marine microorganisms decreased, while microorganisms common in anoxic sediments of meromictic basins developed. The indicator microorganisms with increased relative abundance were archaea of the genera Methanoregula and Methanosaeta. Bacteria of the class Chlorobia, Chloroflexi of the family Anaerolineaceae, and Rhodoferax-related bacteria were indicators of the stagnant seawater. Members of the genus Woeseia were counter-indicators, occurring only in marine water. In our opinion, under reasonably regulated water exchange via the dams, the ecosystems of the Kanda and Kislaya Guba bays may retain the characteristics of marine bays. Otherwise, the studied bays may become stratified basins with anoxic near-bottom water, harboring microbial communities similar to those inhabiting meromictic basins.

Investigations into the microbial community of bottom sediments in the karst Lake Black Kichier were conducted. These sediments exhibited elevated levels of sulfide, dissolved methane, and organic matter. Direct radiotracer experiments revealed substantial rates of microbial processes involved in the decomposition of organic matter. Uncultivated archaea belonging to the phylum Thermoplasmatota were identified within the microbial community. Metagenomic analysis unveiled representatives from five orders: Methanomassiliicoccales, Thermoprofundales (formerly known as Marine Benthic Group D and DHVEG-1), DTX01, SG8-5, and Candidatus Gimiplasmatales (formerly UBA10834). These archaea were previously believed to occur exclusively in deep marine sediments characterized by extreme organic matter scarcity. This discovery reshapes our understanding of the role played by Thermoplasmatota archaea, spanning five orders, in the degradation segment of the carbon cycle.

The data obtained during the recent decades indicate large-scale climatic changes in the Arctic Ocean, especially in the Siberian shelf seas. The impact of shrinking of the Arctic ice cover on marine net primary production (PP) was mostly studied using satellite-derived estimates of chlorophyll-a (Chl a), sea surface temperature, and sea ice concentrations, as well as various modeling approaches. However, no data are available on the quantitative relations between phytoplankton production and heterotrophic bacterioplankton activity in the broadest and shallowest shelf of the World Ocean - the East Siberian Arctic seas (ESAS). In this paper we present a full set of in situ measurements of main PP and microbial heterotrophy characteristics required for better understanding and further validation of the satellite and modeling approaches. In September-October 2011, during the 57th cruise of RV Akademik M.A. Lavrent'ev, PP, bacterioplankton abundance (BA) and bacterioplankton production (BP), as well the rates of dark CO2 assimilation (DCA) were determined in the Chukchi, East Siberian, and Laptev seas and in the Gulf of Anadyr of the Bering Sea (a total of 26 stations) by in situ measurements using radiolabeled bicarbonate. All three important production indicators exhibited significant variance within the studied water areas of the Arctic (PP from 0.98 to 54.7 mu g C L-1 day-1), (BP from 1.1 to 17.1 mu g C L-1 day-1), and (DCA from 0.23 to 8.7 mu g C L-1 day-1). The state of phyto- and bacterioplankton was determined by analysis of the BP/PP and DCA/PP ratios. Active photosynthesis with efficient incorporation of inorganic carbon into the biomass was observed in the Chukchi Sea coastal eastern waters and in the Gulf of Anadyr. On the contrary, the phytoplankton primary production was extremely low in oligotrophic basins of the East Siberian and Laptev seas, while the activity of heterotrophic bacterioplankton consuming organic matter of phytoplankton origin was relatively high. The data of direct measurements can be used for further adjustment of the indirect assessments of production obtained by satellite observations. Glossary East Siberian Arctic seas (ESAS), net primary production (PP), bacterioplankton abundance (BA), bacterial biomass (BB), bacterial production (BP), Arctic Ocean PP (AOPP), organic matter (OM), dissolved organic matter (DOM), colored dissolved organic matter (CDOM), light CO2 assimilation (LCA), dark (heterotrophic + chemotrophic) CO2 assimilation (DCA), production indicators of the surface water layer (PPsurf, DCAsurf, BPsurf), estimated production indicators for the entire depth of the sea (PPint, DCAint, BPint; mg C m- 2 day-1).

The rates of oxygenic and anoxygenic photosynthesis, the microorganisms responsible for these processes, and the hydrochemical characteristics of the sulfide-containing karst lakes, Black Kichier and Big Kichier (Mari El Republic), were investigated. In these lakes, a plate of anoxygenic phototrophic bacteria (APB) is formed at the upper boundary of sulfide occurrence in the water. The phototrophic community of the chemocline zone was analyzed using a combination of high-throughput sequencing of the 16S rRNA gene fragments and light and electron microscopic techniques. Green-colored Chlorobium clathratiforme were absolutely predominant in both lakes. The minor components included green sulfur bacteria (GSB) Chlorobium spp., symbiotic consortia Chlorochromatium magnum and Pelochromatium roseum, purple sulfur bacteria (PSB) Chromatium okenii, and unidentified phylotypes of the family Chromatiaceae, as well as members of the Chloroflexota: Chloronema sp. and Oscillochloris sp. Based on the results of the molecular analysis, the taxonomic status of Ancalochloris perfilievii and other prosthecate GSB, as well as of the PSB Thiopedia rosea, which were visually revealed in the studied freshwater lakes, is discussed.

Depending on the season, the primary production of planktonic communities determined by radiotracer analysis varied within a broad range, from 6 to 314 µg C/(L h). Primary production in cyanobacterial mats was 4.2‒10.9 × 103 µg C/(dm3 h), and Chl a content varied from 6‒13 to 132‒140 mg Chl a/m2. For the plankton, the highest values were revealed in summer (25‒46 mg Chl a/m3), with the maximum in August (223 mg Chl a/m3). High abundance of bacterioplankton (0.3‒7.4 × 106 cells/mL) and massive growth of diatoms (0.15 × 106 cells/mL) with predominance of the genus Chaetoceros were found. Sulfate reduction rates varied from 0.037 µmol S/(dm3 h) in the upper reach to 61.87 µmol S/(dm3 h) in the river mouth.

Microbial communities of terrestrial mud volcanoes are involved in aerobic and anaerobic methane oxidation, but the biological mechanisms of these processes are still understudied. We have investigated the taxonomic composition, rates of methane oxidation, and metabolic potential of microbial communities in five mud volcanoes of the Taman Peninsula, Russia. Methane oxidation rates measured by the radiotracer technique varied from 2.0 to 460 nmol CH4 cm−3 day−1 in different mud samples. This is the first measurement of high activity of microbial methane oxidation in terrestrial mud volcanos. 16S rRNA gene amplicon sequencing has shown that Bacteria accounted for 65–99% of prokaryotic diversity in all samples. The most abundant phyla were Pseudomonadota, Desulfobacterota, and Halobacterota. A total of 32 prokaryotic genera, which include methanotrophs, sulfur or iron reducers, and facultative anaerobes with broad metabolic capabilities, were detected in relative abundance >5%. The most highly represented genus of aerobic methanotrophs was Methyloprofundus reaching 36%. The most numerous group of anaerobic methanotrophs was ANME-2a-b (Ca. Methanocomedenaceae), identified in 60% of the samples and attaining relative abundance of 54%. The analysis of the metagenome-assembled genomes of a community with high methane oxidation rate indicates the importance of CO2 fixation, Fe(III) and nitrate reduction, and sulfide oxidation. This study expands current knowledge on the occurrence, distribution, and activity of microorganisms associated with methane cycle in terrestrial mud volcanoes.

Primary production (PP) and the chlorophyll-a concentration (chl-a) in the European Arctic in the summer of 2020–2021, where continued climatic warming and increased “Atlantification” accelerate the sea ice losses, are discussed. The maximum integrated PP and the total chl-a content were observed in the marginal ice zone (MIZ) of the Barents Sea under weakened stratification of the water column and reached 1109 mgC m–2 day–1 and 118 mg m–2. Near the ice edge in the Nansen Basin, the main part of PP formed in the upper mixed layer and did not exceed 469 mgC m–2 day–1; the chl-a content reached 56 mg m–2. The early and late stages of phytoplankton bloom in the MIZ were characterized by the leading role of picophytoplankton in carbon fixation. Large centric diatoms, microphytoplankton, were recorded to dominate in the MIZ at the stage of peak bloom in 2020 under the dense ice cover of the Nansen Basin. A similar phenomenon was observed earlier only in the Arctic shelf seas and was not recorded in the high-latitude basins of the Arctic Ocean. With the sparse ice cover of the Nansen Basin in 2021, the main primary producers were pico- and nanophytoplankton. The low variability of assimilation numbers (1.7 ± 0.3 mgC mg chl-a–1 h–1) at all bloom stages indicates indirectly the acclimatization of different species of phytoplankton to the environmental changes. The ecological flexibility of the primary production link of the MIZ ecosystems in the studied seas of the European Arctic during the period of climate changes is confirmed.

— Formation of the Kanda Bay resulted from construction of a railway dam (1916) and subsequent isolation of the sea lagoon from the main basin of the Kandalaksha Gulf, White Sea. Decreased action of tidal flows, which mix the water column of the lagoon, altered the hydrological regime of the basin. Decreased water exchange resulted in formation of oxygen-depleted near-bottom water and to sulfide contamination. A freshwater lake was, however, preserved in the southern part of the Kanda Bay. The composition of microbial communities was studied for the near-bottom water horizons at different sides of the Kanda Bay. The oxygen regime in this layer was found to change, with increasing concentrations of sulfide and methane and active processes of sulfate reduction and methane oxidation. The composition of the microbial community changed noticeably, with lower abundance of true marine and freshwater microorganisms and development of bacteria and archaea predominant in microbial communities of anoxic water in meromictic basins. Among the microbial diversity, indicator species with increased abundance were revealed. These are archaea of the genera Methanoregula and Methanosaeta (phylum Halobacterota ). The sulfur cycle microorganisms, which were the indicators of stagnant marine water, included anoxygenic phototrophic bacteria of the class Chlorobia , ( Chlorobium phaeovibrioides, Pelodictyon phaeoclathratiforme ), Chloroflexi of the genus Chloronema , nonsulfur purple bacteria related to the genus Rhodoferax , colorless sulfur bacteria of the family Beggiatoaceae , and sulfur oxidizers of the genus Thiobacillus . Archaea of the genus Nitrosopumilus (phylum Crenarchaeota ) and bacteria of the genus Woeseia may be considered opposites to the indicator microorganisms, since they were found only in the open sea water. In our opinion, stable water exchange through the dam will result in the stable composition of the Kanda Bay microbial community, with only seasonal variations and year-to-year fluctuations. The negative scenario supports prediction of conversion of the Kanda Bay into a stratified basin with anoxic near-bottom water and the microbial community similar to that found in meromictic lakes.

Bottom sediments at methane discharge sites of the Laptev Sea shelf were investigated. The rates of microbial methanogenesis and methane oxidation were measured, and the communities responsible for these processes were analyzed. Methane content in the sediments varied from 0.9 to 37 µmol CH4 dm−3. Methane carbon isotopic composition (δ13C-CH4) varied from −98.9 to −77.6‰, indicating its biogenic origin. The rates of hydrogenotrophic methanogenesis were low (0.4–5.0 nmol dm−3 day−1). Methane oxidation rates varied from 0.4 to 1.2 µmol dm−3 day−1 at the seep stations. Four lineages of anaerobic methanotrophic archaea (ANME) (1, 2a–2b, 2c, and 3) were found in the deeper sediments at the seep stations along with sulfate-reducing Desulfobacteriota. The ANME-2a-2b clade was predominant among ANME. Aerobic ammonium-oxidizing Crenarchaeota (family Nitrosopumilaceae) predominated in the upper sediments along with heterotrophic Actinobacteriota and Bacteroidota, and mehtanotrophs of the classes Alphaproteobacteria (Methyloceanibacter) and Gammaproteobacteria (families Methylophilaceae and Methylomonadaceae). Members of the genera Sulfurovum and Sulfurimonas occurred in the sediments of the seep stations. Mehtanotrophs of the classes Alphaproteobacteria (Methyloceanibacter) and Gammaproteobacteria (families Methylophilaceae and Methylomonadaceae) occurred in the sediments of all stations. The microbial community composition was similar to that of methane seep sediments from geographically remote areas of the global ocean.

The diversity and activity of sulfate-reducing bacteria (SRB) in the camel gut remains largely unexplored. An abundant SRB community has been previously revealed in the feces of Bactrian camels (Camelus bactrianus). This study aims to combine the 16S rRNA gene profiling, sulfate reduction rate (SRR) measurement with a radioactive tracer, and targeted cultivation to shed light on SRB activity in the camel gut. Fresh feces of 55 domestic Bactrian camels grazing freely on semi-arid mountain pastures in the Kosh-Agach district of the Russian Altai area were analyzed. Feces were sampled in early winter at an ambient temperature of −15 °C, which prevented possible contamination. SRR values measured with a radioactive tracer in feces were relatively high and ranged from 0.018 to 0.168 nmol S cm−3 day−1. The 16S rRNA gene profiles revealed the presence of Gram-negative Desulfovibrionaceae and spore-forming Desulfotomaculaceae. Targeted isolation allowed us to obtain four pure culture isolates belonging to Desulfovibrio and Desulforamulus. An active SRB community may affect the iron and copper availability in the camel intestine due to metal ions precipitation in the form of sparingly soluble sulfides. The copper-iron sulfide, chalcopyrite (CuFeS2), was detected by X-ray diffraction in 36 out of 55 analyzed camel feces. In semi-arid areas, gypsum, like other evaporite sulfates, can be used as a solid-phase electron acceptor for sulfate reduction in the camel gastrointestinal tract.

Burning coal seams, characterized by massive carbon monoxide (CO) emissions, the presence of secondary sulfates, and high temperatures, represent suitable environments for thermophilic sulfate reduction. The diversity and activity of dissimilatory sulfate reducers in these environments remain unexplored. In this study, using metagenomic approaches, in situ activity measurements with a radioactive tracer, and cultivation we have shown that members of the genus Desulfofundulus are responsible for the extremely high sulfate reduction rate (SRR) in burning lignite seams in the Altai Mountains. The maximum SRR reached 564 ± 21.9 nmol S cm−3 day−1 at 60°C and was of the same order of magnitude for both thermophilic (60°C) and mesophilic (23°C) incubations. The 16S rRNA profiles and the search for dsr gene sequences in the metagenome revealed members of the genus Desulfofundulus as the main sulfate reducers. The thermophilic Desulfofundulus sp. strain Al36 isolated in pure culture, did not grow at temperatures below 50°C, but produced spores that germinated into metabolically active cells at 20 and 15°C. Vegetative cells germinating from spores produced up to 0.738 ± 0.026 mM H2S at 20°C and up to 0.629 ± 0.007 mM H2S at 15°C when CO was used as the sole electron donor. The Al36 strain maintains significant production of H2S from sulfate over a wide temperature range from 15°C to 65°C, which is important in variable temperature biotopes such as lignite burning seams. Burning coal seams producing CO are ubiquitous throughout the world, and biogenic H2S may represent an overlooked significant flux to the atmosphere. The thermophilic spore outgrowth and their metabolic activity at temperatures below the growth minimum may be important for other spore-forming bacteria of environmental, industrial and clinical importance.

— Preliminary microbiological investigation of the Barguzin Valley terrestrial hydrotherms did not elucidate the composition of the community of sulfate-reducing prokaryotes (SRP) responsible for high sulfide concentrations in the Kuchiger and Umkhei springs. Measurement of sulfate reduction rate (SRR) with labeled sulfate in the samples collected together with those for determination of community composition by 16S rRNA gene profiling revealed that, while not numerous, the SRP consisting of Desulfobacterota and Thermodesulfovibrio was responsible for a highly active process. SRR in the sediments of the Umkhei and Kuchiger springs was up to 12.7 ± 0.2 and 2.05 ± 0.08 mg S dm –3 day –1 , respectively.

— This is the first report on the application of metagenomic analysis of the microbiome of Lake Baikal bottom sediments in order to assess the community structure and metabolic potential of the microorganisms inhabiting the upper sediment horizon at the site of a deep-water station. Compared to the metagenome of near-bottom water, relative abundance of the phyla Methylomirabilota, Chloroflexota , and Acidobacterota was found to increase, as well as that of the genes for the pathways of methane, sulfur, and thiosulfate oxidation and of nitrate reduction. Genomes of members of 12 phyla forming the basis of the studied microbiome were assembled. Reconstruction of the metabolic pathways indicated the possible coexistence of microorganisms capable of gaining carbon and energy due to oxidation of carbohydrates, methane, thiosulfate, and ammonia, as well as via anaerobic processes of fermentation, denitrification, and (to a lesser degree) sulfate reduction.

Research on the microorganisms inhabiting deep aquifers is based on sampling the water released from deep wells and is seldom concerned with the physicochemical processes of the water-rock system. The issue of metabolism of aerobic prokaryotes revealed in deep habitats by molecular techniques remains unclear. Cultivation is required for direct determination of relation of prokaryotes to oxygen. In the present work, aerobic and anaerobic bacteria, which were revealed in thermal radon baths of the Belokurikha resort by molecular techniques, were isolated. Profiling by the 16S rRNA gene revealed predominance of members of the Deionococcus-Thermus group belonging to the genus Meiothermus (17.6 Na_2^ 35SO_4 yielded the value of 41.4 ± 1.06 µg Sred L–1 day–1, or 1.29 nmol S mL–1 day–1. Analysis of the genome of strain 1176 revealed the presence of various mechanisms responsible for its relative resistance to oxygen and oxidative stress, which included superoxide reductase, rubredoxin, a Fe-Mn family superoxide dismutase, a KatG catalase-peroxidase, and a cytochrome bd ubiquinol oxidase. The low redox potential and intense anaerobic sulfate reduction provide evidence for the generally reduced conditions in the Belokurikha deep horizons. Spatial separation of aerobes and anaerobes in the water-rock system, similar to the one occurring in the terrestrial microbial mats, may be hypothesized, as well as occurring of aerobic processes in microniches.

Over the last half-century, microbial communities of the Kamchatka hot springs have been largely studied using molecular, radioisotopic, and cultural approaches. Generally, these results were obtained for mixed samples of water with sediments, for only hydrothermal water, or for only sediment samples. Simultaneous comparative analysis of the microbial communities of water and sediments was performed for only one Kamchatka hot spring with circumneutral pH. Here, the microbial communities of both sediments and water (separately) of hot spring #4229 (the Uzon Caldera, Kamchatka) with a temperature of 50–56 °C and pH of 3.2 were analyzed by 16S rRNA gene V4 fragment amplicon sequencing. It was revealed that the microbial community of sediments was represented by uncultured phylogenetically deep-branching lineages of archaea, such as ARK-15 within Thermoplasmatota and ‘Ca. Marsarchaeales’ from the Thermoproteota phyla. Metagenome analysis showed that these archaea most probably carried out the degradation of organic matter. The microbial community of the hot water is represented by thermoacidophilic, (micro)aerobic, chemolithoautotrophic, hydrogen- and sulfur-oxidizing bacteria of the genera Hydrogenobaculum (phylum Aquificota) and Acidithiobacillus (phylum Pseudomonadota). Radioisotopic tracing and DNA-stable-isotope probing techniques proved their role as primary producers in the hot spring. The experiment revealed significant differences in the composition and functions of the microbial communities of sediments and water through the example of a typical acidic hot spring in Kamchatka.

Methane oxidation rates and diversity of methane-oxidizing microorganisms in the Kara Sea upper sediments at the sites of conserved gas prospecting wells were investigated. Analysis of the 16S rRNA gene sequences revealed members of the class Gammaproteobacteria , order Methylococcales . All samples exhibited similar diversity of the methane filter microorganisms, comprising mainly of methanotrophs related to the genus Methyloprofundus and of uncultured methanotrophic bacteria detected previously in the upper sediments of the Arctic seas. Molecular identification of methane-oxidizing bacteria of this community by high-throughput sequencing of the pmoA gene encoding particulate methane monooxygenase confirmed the similar structure of the methane filter in the upper sediments impaired by drilling and at the reference sites at significant distance from the wells. The sediments at the conserved well drilled less than two years earlier were shown to have the characteristics of a methane seep, i.e., elevated level of dissolved methane and high rates of microbial methane oxidation. No indication of methane seepage was observed for the wells conserved more than two years earlier; abundance of methane-oxidizing bacteria in their vicinity was below the detection threshold.

The seasonally ice-covered marine region of the European Arctic has experienced warming and sea ice loss in the last two decades. During expeditions in August 2020 and 2021, new data on size-fractioned primary production (PP), chlorophyll a concentration, phytoplankton biomass and composition and carbon fixation rates in the dark were obtained in the marginal ice zone (MIZ) of the Barents Sea, Nansen Basin and Greenland Sea to better understand the response of Arctic ecosystems to ongoing climate changes. Four different situations were observed in the study region: (i) a bloom of the large-cell diatom Podosira glacialis, whose biomass was trapped in a strong halocline at the edge of a dense ice cover; (ii) a bloom of the chain-like colonies of Thalassiosira diatoms on the shelf in mixed waters in fields of shallow ice that could be supported by “fresh” elements in the polynya condition, as well as by terrestrial run-off and drifting ices; at the late stage, this bloom was accompanied by intensive growth of Phaeocystis pouchetti; (iii) dominance of small-cell phytoplankton under weakened stratification and the significant influence of the Atlantic water, depleted of microelements and silicates; (iv) dominance of dinoflagellates of eutrophic water in the contact zone between the water masses of Arctic origin and Atlantic origin in clear water under conditions of increased light intensity. The >10 µm phytoplankton cell size group increased its relative contribution to PP as a response to stratification, light and nutrient load associated with sea ice conditions. Small phytoplankton with sizes < 2 µm formed the basis of total PP in the MIZ regardless of the state of the sea ice.

The microbial community of subsurface environments remains understudied due to limited access to deep strata and aquifers. Coal-bed methane (CBM) production is associated with a large number of wells pumping water out of coal seams. CBM wells provide access to deep biotopes associated with coal-bed water. Temperature is one of the key constraints for the distribution and activity of subsurface microorganisms, including sulfate-reducing prokaryotes (SRP). The 16S rRNA gene amplicon sequencing coupled with in situ sulfate reduction rate (SRR) measurements with a radioactive tracer and cultivation at various temperatures revealed that the SRP community of the coal bed water of the Kuzbass coal basin is characterized by an overlapping mesophilic-psychrophilic boundary. The genus Desulfovibrio comprised a significant share of the SRP community. The D. psychrotolerans strain 1203, which has a growth optimum below 20 °C, dominated the cultivated SRP. SRR in coal bed water varied from 0.154 ± 0.07 to 2.04 ± 0.048 nmol S cm −3 day −1 . Despite the ambient water temperature of ~ 10–20 °C, an active thermophilic SRP community occurred in the fracture water, which reduced sulfate with the rate of 0.159 ± 0.023 to 0.198 ± 0.007 nmol S cm −3 day −1 at 55 °C. A novel moderately thermophilic “ Desulforudis audaxviator ”-clade SRP has been isolated in pure culture from the coal-bed water.

Seasonal cyanobacterial blooms have a negative impact on freshwater ecosystems. The role of cyanobacteria in methane production and their relationship with methanogenic archaea are not yet well understood. The goal of the present work was to identify the features of methanogenesis in the water column and sediments of a profundal part of the freshwater Lake Senezh (Moscow oblast) during a period of cyanobacterial over-bloom. Analytical, radiotracer, microscopic, molecular biological, and incubation techniques were used. Alkalization and oxygen oversaturation of the 0‒2-m water layer were caused by intensive photosynthesis. The near-bottom water (4 m) was pH-neutral and hypoxic; the sediments were reduced. Methane was detected throughout the water column; its concentration in the surface water was an order of magnitude lower than in the near-bottom water and 4 orders of magnitude lower than in the sediments. Cyanobacteria of the species Microcystis aeruginosa predominated in the photic zone (up to 30