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An Erratum to this paper has been published: https://doi.org/10.1134/S0026261721110011 [ABSTRACT FROM AUTHOR]

The abundance and diversity of filamentous fungi in the bottom sediments of the Arctic Ocean seas (the Greenland, Barents, and Kara seas) were studied. Samples of the surface bottom sediments were collected during the 84th (July–August 2021) and 86th (October–November 2021) cruises of RV Akademik Mstislav Keldysh. The taxonomic affiliation of the isolated fungi was determined using polyphasic taxonomy. The isolated fungi belonged to 16 genera of different classes of ascomycetous, basidiomycetous, and zygomycetous fungi. The effect of cultivation temperature and different NaCl concentrations on fungal growth was determined, as well as the effect of cultivation conditions on the fatty acid profile for the strains capable of growth on media with increased osmotic potential. While fatty acid composition was shown to be affected by changes in environmental conditions, the response to osmotic stress differed among the studied cultures from deep-sea sediments. [ABSTRACT FROM AUTHOR]

Although thermokarst alas lakes of Central Yakutia are of great climatic and economic importance, there is currently virtually no information on microbial communities and microbial processes in these lakes. This paper characterizes the hydrochemical features and presents a primary analysis of the diversity of planktonic microbial communities in three alas lakes of Central Yakutia—Tyungulyu, Taby, and Kharyyalakh. It was shown that in terms of the water physicochemical composition, the studied lakes were quite typical for this region; they had increased alkalinity and trophicity, but differed from each other in microbiological indicators. Chemoheterotrophic prokaryotes predominated in the studied planktonic communities, but a significant proportion of the 16S rRNA gene sequences were most similar to uncultured microorganisms whose functional potential is still unknown. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The known approaches to sample preparation have been improved to achieve a more complete detection of microorganisms of the Black Sea bottom sediments using flow cytometry of SYBR Green I-stained cells. Total microbial abundance in the samples from the shelf and deep-sea sediments varied from 0.03 to 1.54 × 108 cells g–1 and from 0.002 to 1.24 × 108 cells g–1 dry weight, respectively. This is comparable to the data reported previously for various areas of the oceans, including the Black Sea. Application of sodium pyrophosphate was shown to be the most universal method for treating sediments of various types; along with this, using hydrofluoric acid is possible for the deep-sea reduced sediments, whereas treatment with methanol was preferable for the sediments of coastal waters with a normal degree of aeration of the bottom layer. For samples of various types, optimal sample preparation procedures were proposed (choice of chemical reagent, mode of ultrasonic processing and centrifugation, and additional washing procedures). These procedures resulted in significantly more efficient enumeration of bacterial cells, while application of flow cytometry ensured rapid determination of the total number of microorganisms in the bottom sediments. [ABSTRACT FROM AUTHOR]

The major substrates for methanogenesis were used for investigation of cultured methanogenic archaea from coastal methane seeps near the Tarkhankut Peninsula, Black Sea. Analysis of the 16S rRNA gene sequences revealed that growth of the classical methanogenic Euryarchaeota occurred in all enrichments but was absent in the controls without the substrates. Enrichments from the seep differed in microbial composition from those from the background point. The most numerous archaea belonged to the genera Methanolobus (medium with methanol and hydrogen), Methanosarcina (trimethylamine and hydrogen), Methanococcoides (trimethylamine), and Methanococcus (hydrogen and CO2). Syntrophic growth of hydrogenotrophic archaea of the genus Methanogenium with clostridia and members of the family Thermotogaceae probably occurred in enrichments with acetate. Relatively low similarity of the recovered 16S rRNA gene sequences with the closest cultured relatives (94% and lower) indicated that the Methanogenium phylotype belonged to a new species. The same was true for the Methanosarcina phylotype revealed in the culture with trimethylamine and hydrogen (97% and less similarity of the 16S rRNA gene sequences to those of the closest cultured relatives). [ABSTRACT FROM AUTHOR]

During long-term cultivation in a laboratory sequencing batch reactor in the phosphorus removal mode, granule-like aggregates of two morphotypes, differing in their physical structure and microbial composition, with predominance of different microbial physiological groups, were formed out of the activated sludge floccules. Phosphate-accumulating bacteria Candidatus "Accumulibacter" prevailed in one morphotype, and glycogen-accumulating bacteria Candidatus "Competibacter," in the other. These are aerobic microorganisms, known to compete for the substrate during the anaerobic period of the anaerobic/aerobic cultivation cycle. Aggregate formation paralleled development of phosphate-accumulating microorganisms, increase in their relative abundance, and higher phosphorus removal efficiency. [ABSTRACT FROM AUTHOR]

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 Microcystisaeruginosa predominated in the photic zone (up to 30% of the total number of the 16S rRNA gene fragments). The sequences of cyanobacteria and freshwater members of the SAR11 clade, which can potentially be involved in aerobic methanogenesis via decomposition of methylphosphonates (MPn), were also detected. The sequences of hydrogenotrophic methanogens of the genus Methanoregula, which are potentially capable of methanogenesis in cooperation with cyanobacteria, were revealed in oxygen-supersaturated water. Hydrogenotrophic and acetoclastic pathways of methanogenesis predominated in reduced sediments. Sequences of methanogens of the orders Methanomicrobiales, Methanobacteriales, Methanosarciniales, and Methanomassiliicoccales were detected there. Cyanobacterial bloom promoted methanogenesis both in the photic zone of Lake Senezh (due to MPn decomposition and anaerobic methanogenesis in association with cyanobacterial aggregates) and in the near-bottom water and sediments (due to oxygen depletion and excessive release of substrates caused by sedimentation and degradation of cyanobacterial mortmass). [ABSTRACT FROM AUTHOR]

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% reads) and considered strictly aerobic. Anaerobic sulfate-reducing Thermodesulfovibrio were also present in the sample. The habitat was characterized by reductive, alkaline conditions. Target-oriented cultivation revealed aerobically growing Meiothermus sp. 1165, which was closely related to Meiothermus cerbereus. An alkaliphilic anaerobic sulfate reducer Thermodesulfovibrio sp. 1176 was also isolated. The rate of sulfate reduction measured in the Belokurikha water using 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Eutrophication of lakes results in the intensification of anaerobic processes, including methanogenesis, and therefore in enhanced emission of methane. A littoral area with its variable oxygen regime is the first to react to eutrophication. The diversity of microbial communities in littoral areas is insufficiently studied, and little data are available concerning the methane cycle microorganisms. In this work, the methanogenesis and methane oxidation were investigated in the littoral site of a freshwater temperate Lake Senezh (Russia). A combination of analytical, microbiological and molecular techniques was used, including physicochemical analyses, high-throughput sequencing, potential activity measurements, and cultivation on selective media. The littoral site was found to be an extremely labile ecological niche, which harbors a diverse community containing aerobic, facultative anaerobic and anaerobic microorganisms, both autotrophs and heterotrophs, which may perform all reactions of the N, S, and CH4 cycles. Methane formation was carried out via hydrogenotrophic, acetoclastic, methylotrophic, and methyl-reducing pathways. Among methanotrophs, type I organisms predominated; type II, nitrate- and nitrite-dependent methanotrophs were also revealed. Comparison of the average rates of methanogenesis and aerobic methane oxidation suggests that all methane, which may potentially be formed in the littoral site of the lake, could simultaneously be oxidized. [ABSTRACT FROM AUTHOR]

Gas seep and fluid flows from the seabed are an environment-forming factor of the aquatic environment, mainly due to their influence on the dissolved gases in the water, including dissolved oxygen. During the summer seasons from 2019 to 2021 in the area of shallow water gas emission site off the southern coast of the Heracles Peninsula, series of vertical probing profiles were carried out to determine hydrological parameters of the water: dissolved oxygen concentration (O2), temperature (T), salinity (S), and flow velocity (U). The study area is an underwater ledge with faults in the form of three canyons composed of dense limestones, two of which contained bubble gas emissions. Significant variability in O2 was identified in canyons where gas emissions are observed: from 1 to 80% saturation in the bottom layer, in contrast to normoxia at the background sites. Hypoxia was observed in the bottom layer above the emission sites in the absence of turbulence at temperature stratification. The values S decreased with depth, and the maximum difference reached 0.4‰. The bubble gas was dominated by methane (68.5–75.5%), and the carbon isotope composition of the bubble methane gas varied from –67.9 to –59.8‰ VPDB in 2019 and 2020, respectively. This generally indicates that the CH4 is of predominantly microbial genesis, was formed under different conditions, and matured in various periods of research during the monitoring period. Bacterial mats (mostly sulfur-oxidizing bacteria) were found in the areas of gas emissions. [ABSTRACT FROM AUTHOR]

Aerobic methanotrophic bacteria are prokaryotic microorganisms possessing methane monooxygenases, unique enzymes that determine their ability to utilize methane (CH4) as a growth substrate. This metabolic capability makes methanotrophs attractive objects for biotechnological applications aimed at utilizing methane for production of microbial cell protein and various target metabolites. The current raise of interest to these biotechnologies is driven by high availability of methane, which is a major component of natural gas, as well as of the biogas produced in anaerobic fermentation processes. Since aerobic methanotrophs oxidize methane at the ambient temperature and pressure, they represent natural cell factories for converting CH4 into various value-added products. Further development of biotechnologies based on methane utilization requires application of genome editing techniques to obtain producer strains with improved characteristics. For a long time, the progress in metabolic engineering of methanotrophs was hampered by their specific metabolic properties and the difficulties of handling these bacteria. Here, we present an overview of the latest achievements in the field of metabolic engineering of methanotrophic bacteria and identify the potential targets as well as the currently available tools for genome editing of these microorganisms. These techniques open up the possibility of constructing strains with biotechnologically relevant characteristics and conducting in-depth research of the metabolic features of aerobic methanotrophs. [ABSTRACT FROM AUTHOR]

A microbial community enriched with phosphate-accumulating organisms (PAO) was obtained in a laboratory sequencing batch reactor after 150 days of cultivation. Analysis of phosphate dynamics in the medium and the results of Raman scattering spectroscopy indicated the cycle of phosphate consumption and release during cultivation under oxic and anoxic conditions, respectively, which was typical of PAO. The highest content of intracellular phosphorus was 16.5 ± 0.15% of the dry ash-free biomass. Molecular genetic analysis and FISH revealed the taxonomic diversity of the microbial community, in which members of the "Ca. Аccumulibacter" group were the major PAO. [ABSTRACT FROM AUTHOR]

An isolate of prosthecate bacteria was isolated from the takyr soil of a rice field on the Akdala massif (Kazakhstan) and designated as strain 22T. Strain 22T was represented by gram-negative, aerobic, motile, oxidase and catalase-positive bacteria. Cells of this strain formed numerous prosthecae extending in different directions from the cell surface. Bacteria had a dimorphic life cycle, with two different morphological types of cells. The prosthecae may be short (i.e., less than 1.0 µm long) or long (i.e., more than 2.0 µm long). Cells reproduced by budding and grew within the pH range of 6.5–8.5 and at 28–30°C. Major cellular fatty acids were C18:1 ω7, C16:0, C19:1 branched, and C16:1 ω7. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain 22T shared the highest gene sequence similarity with Prosthecomicrobium hirschii 16T (99.9%) and formed a common branch on the phylogenomic tree with P. hirschii 16T and Siculibacillus lacustris SA-279T. This branch was only distantly related to the phylogenetic lineage defined by the type species of the genus Prosthecomicrobium, P. pneumaticum ATCC 23633T, thus indicating a polyphyletic nature of the genus Prosthecomicrobium. The average nucleotide identity (ANI) and in silico DNA–DNA hybridization (dDDH) values between strain 22T and the most closely related species P. hirschii 16T were 93.6 and 47.6%, respectively, and were below the threshold accepted for species demarcation. Based on the results of phylogenetic analysis, strains 22T and 16T should be assigned to the Ancalomicrobiaceae family, with introduction of a novel genus Prosthecodimorpha gen. nov. The G + C content of the genome of strain 22T was 61.9%. Strain 22T represented a novel species in a novel genus, for which the name Prosthecodimorpha staleyi gen. nov., sp. nov. is proposed, with the type strain 22T (=VKM B-3576T = UQM 41461T = DSMZ 113594T). [ABSTRACT FROM AUTHOR]

The transition process caused by an abruptly increased ammonium load (2.5-fold) on the microbial community of a sequential batch reactor carrying out nitrogen removal from the water via nitritation-anammox was studied. The community developed in the bioreactor at incoming ammonium concentration of 200 mg N/L removed 76.5% of the inflowing nitrogen and was satisfactorily described by the BioWin mathematical simulator with corrected coefficients. Abrupt increase of nitrogen load from 200 to 500 mg N/L resulted in ammonium concentration at the reactor outlet increasing from 27 to 280–290 mg N/L, with nitrogen removal efficiency dropping to 40%. The calculation using the BioWin simulator showed that the efficiency of the nitritation-anammox process should increase in the course of a month and stabilize at the level close to the original one (76.5%). However, experimental data did not support this calculation: no increase in efficiency was observed during this period. Changes in the structural and functional characteristics of the biofilms and aggregates, which were not accounted for in the model, were probably responsible for discrepancies between the experimental and calculated data. [ABSTRACT FROM AUTHOR]

The technology of single-cell protein production from natural gas is based on using thermotolerant methanotrophic bacteria with high growth rates on methane. So far, the spectrum of strains used for industrial purposes was restricted to members of the genus Methylococcus. This poses limitations to further development of this technology and fuels the search for new cultures of fast-growing methanotrophs. The later task was addressed in the present work by analyzing the sediment samples of the Chernaya River, Crimea. Molecular analysis of the microbial community composition in the sediment revealed Gammaproteobacteria as the predominant group (33‒42% of all retrieved 16S rRNA gene fragments), as well as Chloroflexi, Actinobacteria, Alphaproteobacteria, Bacteroidota, and Acidobacteria as other numerically significant community members. The methanotrophic enrichment culture obtained from the sediment contained bacteria of the genus Methylomonas as the major component, with the relative abundance of up to 60% of all 16S rRNA gene fragments. The use of various strategies for methanotroph isolation resulted in obtaining three isolates of target bacteria of the genera Methylomonas, Methylomagnum and Methylocystis. The optimal growth temperatures of these isolates were 25, 35, and 40°С, respectively. The highest specific growth rate in batch culture, 0.21 h−1, was determined for Methylocystis sp. Kr9, which displayed 99.22 and 99.13% 16S rRNA gene sequence similarity to the type strains of two Methylocystis species, Methylocystis echinoides IMET 10491T and Methylocystis parvus OBBPT, respectively. [ABSTRACT FROM AUTHOR]

A new, highly efficient xanthan-producing strain, Xanthomonas campestris M 28, was obtained. It produces up to 28 g/L of the polysaccharide on a molasses medium, which is almost two times higher than the productivity of the NRRL B-1459 strain. Whole-genome sequencing of the strain was performed with the Illumina method and nanopore sequencing. The genome of X. campestris M 28 contained one chromosome of 5 102 828 nucleotides with an average G + C content of 65.03%. The structure and physicochemical and rheological properties of the obtained xanthan were studied. It was found that the addition of xanthan to the bentonite dispersion led to the formation of primary clay particles (70 nm) and aggregates of ~190 nm without the formation of a precipitate. This indicated the interaction of macromolecules with particles and aggregates with the formation of polymer-clay bridging structures. This ensures the stability of clay dispersions and makes it possible to achieve the required rheological properties of drilling fluids based on xanthan obtained in a molasses medium, thereby reducing its cost. [ABSTRACT FROM AUTHOR]

Methane oxidation rates and diversity of methane-oxidizing microorganisms were studied in the upper sediment layers of the Laptev Sea (methane seep area, Lena fore-delta, shelf, and upper slope not affected by seeps and river flow). The highest methane concentrations and methane oxidation rates (up to 1.16 µmol СН4 dm−3 day−1) were revealed at the seep stations. Carbon dioxide was the main product of methane oxidation at all stations. Sequencing of the 16S rRNA gene fragments revealed microorganisms of the class Gammaproteobacteria, order Methylococcales. Since the share of methanotrophs was high at the sites of constant gas seepage (up to 1.93% of the total read number), they could be detected by sequencing of the native samples. Phylogenetic diversity of methane-oxidizing bacteria was not high, and all detected microorganisms belonged to the Deep-Sea 1 cluster. On the phylogenetic tree, the sequences formed a cluster together with the genus Methyloprofundus. Members of the genera Methylomonas and Methylobacter related to methanotrophs inhabiting freshwater ecosystems were revealed in enrichments from the coastal stations sediment samples. [ABSTRACT FROM AUTHOR]

Comparative study of methanogen diversity and potential activity of different methanogenic pathways in the sediments of young thermokarst and mature polygenetic Yamal lakes was carried out. The hydrogenotrophic pathway of methanogenesis played an important role in methane formation in thermokarst lakes. The acetoclastic and methylotrophic pathways were also revealed there. In a polygenetic lake with a dissolved organic matter content closest to that of the thermokarst lakes, methanogenesis proceeded more intensively, and the relative abundance of methanogens, especially acetoclastic ones, was higher than in thermokarst lakes. The activity of methyl-reducing methanogens was also assumed there. Methanogens of the genera Methanothrix and Methanoregula, as well as representatives of the family Methanomassiliicoccaceae were identified in the sediments of all lakes. Methane-oxidizing bacteria (Methylobacter, Candidatus "Methylomirabilis") and archaea (Ca. "Methanoperedens") were also detected. [ABSTRACT FROM AUTHOR]

The taxonomic diversity and metabolic activity of microbial communities in the Laptev Sea water column above and outside the methane seep field were studied. The concentrations of dissolved methane in the water column at both stations were comparable until the depth of the pycnocline (25 m). At this depth, local methane maxima were recorded, with the highest concentration (116 nM CH4) found at the station outside the methane seep field. Results of the 16S rRNA gene sequencing and measurements of the rates of hydrogenotrophic methanogenesis indicated the absence of methanogenesis caused by the methanogenic archaea in the pycnocline and in other horizons of the water column. The 16S rRNA-based analysis of microbial phylogenetic diversity, as well as radiotracer analysis of the rates of primary production (PP), dark CO2 assimilation (DCA), and methane oxidation (MO), indicated the functioning of a diverse community of pelagic microorganisms capable of transforming a wide range of organic compounds under oligotrophic conditions of the Arctic basin. Hydrochemical prerequisites and possible microbial agents of aerobic methane production via demethylation of methylphosphonate and decomposition of dimethylsulfoniopropionate using dissolved organic matter synthesized in the PP, DCA, and MO processes are discussed. [ABSTRACT FROM AUTHOR]

Formation of a community of phosphate-accumulating microorganisms in a laboratory sequential batch reactor (SBR) ensuring alternated aerobic and anaerobic conditions during periodic removal and addition of the medium were investigated. The bioreactor removed 50% phosphorus from the incoming medium after 22 days from the start-up. Microscopy and X-ray microassay revealed the of cells of diverse morphology that contained phosphorus-enriched granules. High-throughput sequencing of the 16S rRNA gene fragments carried out on days 0, 8, 15, and 22 showed changes in the community composition and its decreasing diversity. On day 22, approximately twofold increase of the relative abundances of Bacteroidetes (up to 43% of the 16S rRNA gene sequences) and Proteobacteria of the classes alpha (up to 15%) and beta (up to 27%) was observed. While at the onset of the reactor operation, typical PAOs related to "Candidatus Accumulibacter" (class Betaproteobacteria) constituted 0.2% of the community, they were not detected on day 22. The most likely PAO candidates were beta-proteobacteria of the genus Dechloromonas, the share of which increased from 0.7 to 11% by the time of the highest phosphorus removal from the inflowing medium. The relative abundance of heterotrophs of the genus Zoogloea (family Rhodocyclaceae) increased from 0.1 to 11.5%. [ABSTRACT FROM AUTHOR]

Analysis of the taxonomic structure of prokaryotic microbial complexes of the saline soils in the Lake Elton area and their comparative characteristics were carried out for a soil catena along the Khara River flowing into the hypersaline Lake Elton. High-throughput pyrosequencing detected 11 bacterial and 2 archaeal phyla. Comparative analysis of community structure revealed the differences between Solonchaks located at the river flood land and Kastanozems at the slope and top of the river terrace. The patterns of occurrence were described for six predominant phyla (Euryarchaeota, Thaumarchaeota, Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria). For the floodplain soils, the relations between the distribution of Euryarchaeota, Thaumarchaeota, Firmicutes, Actinobacteria, Proteobacteria and soil salinity as well as soil pH were described. Occurrence of members of the phyla Euryarchaeota, Thaumarchaeota, Firmicutes, Actinobacteria, and Proteobacteria in flood land soils was shown to depend on the soil salinity and pH. Members of the phyla Actinobacteria and Firmicutes were shown to predominate in Gleyic Kastanozems. Cloning of the 16S rRNA gene revealed high diversity within the genus Streptomyces (Actinobacteria). A number of the isolated streptomycete clones were homologous to the known antibiotic producers, which indicates that soils of this area are promising for further biotechnological screening. [ABSTRACT FROM AUTHOR]

Methane oxidation rates and diversity of methane-oxidizing microorganisms in the upper sediment layers of the Crimean Peninsula coastal regions (Black Sea) were investigated. Analysis of the 16S rRNA gene sequences revealed microorganisms of the class Gammaproteobacteria, order Methylococcales. At the sites of continuous gas seepage, the percentage of methanotrophs in the bacterial community was high (up to 2.1% of the total read number), which made it possible to detect them by sequencing of the native samples. At the sites of intermittent gas seepage formed during summer and autumn, methanotrophs were minor components of the communities and could be detected only after incubation of the sediment samples in the presence of methane. Low similarity between their 16S rRNA sequences and those of the known methanotrophs indicates that some organisms probably belong to new taxa of the species and genus levels. [ABSTRACT FROM AUTHOR]

The stages of formation and development of activated sludge biofilm carrying out the anammox process in a laboratory sequencing batch reactor (SBR) with complete biomass retention on the carrier were investigated using light, epifluorescence, and electron microscopy. Light microscopy revealed biofilm formation on the carrier to occur within one week. Rod-shaped and filamentous microorganisms were the first to attach on the carrier and acted as a skeleton for biofilm formation, thus playing an important role in colonization of the carrier. Epifluorescence microscopy revealed physiologically active anammox bacteria of the genera Candidatus "Brocadia" and Ca. "Jettenia" in the biofilms. Selective autofluorescence of the colonies of anammox bacteria Ca. "Jettenia" was observed. This autofluorescence was probably caused by specific proteins in the extracellular polymeric substances (EPS), their synthesis and/or amount depending on the colony age and the physiological state of the cells. Structural organization of the colonies of anammox bacteria was investigated by electron microscopy. High-throughput sequencing of the 16S rRNA gene fragments revealed the presence of sequences affiliated with members of the phyla Chloroflexi, Bacteroidetes, Planctomycetes, and Proteobacteria in the biofilms. Apart from anammox bacteria, anaerobic and facultatively anaerobic organotrophs, stage I nitrifiers, denitrifiers, and sulfate reducers were detected. Members of the genus Ca. "Brocadia" were predominant among the anammox bacteria, probably due to better adhesion of their cells to the carrier or to their competitive advantage over Ca. "Jettenia" in the presence of organic acids (acetate and formate) in the medium. [ABSTRACT FROM AUTHOR]

Mutant strains of the halotolerant type-I methanotroph Methylotuvimicrobium alcaliphilum 20Z with an inactivated sps gene, which encodes sucrose phosphate synthase, and the deletion of a gene cluster for the synthesis and degradation of glycogen were obtained. Blockage of the synthesis of sucrose and glycogen increased the protein content in cells but slightly reduced the growth rate of the methanotroph grown on methane. It is shown that relatively stable methanotroph growth is possible without synthesis of the storage carbon compounds. [ABSTRACT FROM AUTHOR]

The composition of the microbial community formed in the course of long-term (over 60 days) continuous cultivation of an obligate methanotroph Methylococcus sp. Concept-8 on natural gas in a 50-L bioreactor at 42°C and pH 5.6 was monitored. Stable growth with high optical density of the culture (average OD540 = 13.5), specific growth rate of 0.2 h–1, and biomass yield of 4.0–4.5 g dry matter L–1 continued for 50 days. During the subsequent period of regime instability, optical density decreased sharply, down to OD540 = 4. Formate, acetate, and a number of unidentified fatty acids derived from oxidation of methane homologs were detected in the culture liquid. Microscopy revealed the highest share of satellite bacteria (10–15% of the total cell number) during the period of stable growth, while it dropped to 4.5% during growth decline. Molecular profiling of the community composition based on 16S rRNA gene sequence analysis revealed members of the genera Cohnella, Brevibacillus,Azospirillim, Thermomonas, Cupriavidus, and Paenibacillus among the major microbial satellites responsible for utilization of metabolites and the products of lysis of the methanotroph cells. During the phase of growth instability, the relative abundance of Brevibacillus decreased drastically; these organisms were most likely responsible for acetate oxidation. Isolates obtained by means of cultivation represented only a minor part of microbial diversity revealed in the community by molecular analysis. Isolation of the cultures of Brevibacillus and Cupriavidus species representing the functionally important components of the community opens the way for targeted construction of associations with strain Concept-8, which will display high productivity and stable growth. [ABSTRACT FROM AUTHOR]

Although dissimilatory sulfate reduction (DSR) is an important microbial process in subterranean aquifers, its geochemical consequences in this ecosystem remain insufficiently studied. The absence of data on the process rate under in situ conditions prevents quantitative estimation of the sulfur reservoir. This research is aimed at investigation of microbial sulfate reduction in subterranean aquifers associated with the Severnaya coal mine in Kuzbass. Water samples were collected from an artesian borehole broaching the underground horizons of the flooded mine. During over 10 years of sampling the water temperature fluctuated within a narrow range (10–13°C); the water was anoxic (–112 to –174 mV) and contained up to 6 mg/L sulfide. Analysis by high-throughput sequencing of the 16S rRNA genes showed that sulfur-oxidizing bacteria Sulfurovum, Sulfuricurvum, Sulfurospirillum, and Thiothrix predominated in the community. No phylotypes with known ability to carry out DSR were detected. Measurement of sulfate reduction rates with showed the process to be relatively active, resulting in up to 178 g of reduced sulfur per year at the borehole discharge. Two organisms representing minor components of the community, a psychrophilic and acidophilic Desulfomicrobium sp. DI and a moderately thermophilic Desulfotomaculum LL1, were isolated in pure culture by varying the cultivation condition in a bioreactor. These members of the "rare biosphere" may be responsible for production of reduced sulfur species, which are used by a diverse and numerous sulfur-oxidizing community. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The results of field studies of the species composition and productive parameters (biomass, photosynthesis rate, chlorophyll a content, and assimilation numbers) of microalgae in the plankton and the interstitial icy waters of Lake Baikal southern littoral area obtained in March 2018 are presented. A comprehensive study of the ice and phytoplankton algae showed that their productive activity was relatively low at most stations. Their higher values observed near river mouths with significant anthropogenic pollution were caused by both the additional nutrient input and development of small-sized algae, primarily of phytoflagellates, which indicate water pollution by organic matter inflowing to Lake Baikal with its tributaries. Using the principal component method, we failed to reveal reliable correlation between the primary producers and the microorganisms decomposing organic matter into mineral substances (the correlation coefficient was 0.49). The differences between the stations subject to anthropogenic impact and the reference ones indicate that access to easily mineralized organic matter promoted the massive development of phytoflagellates. Although large-cell diatoms common in the lake were absent, primary production at these sites reached 100 to 280 mg C m−2, which was comparable with the values obtained for abundant diatom blooms during the under-ice period. High functional potential of the algae at the areas subject to anthropogenic impact results in significant biomass accumulation, which leads eutrophication of the littoral zone and may lead to increased primary production of the pelagic zone. [ABSTRACT FROM AUTHOR]

The complete genome sequence of a thermotolerant obligate methanotroph Methylococcus sp. Concept-8 was determined and analyzed. This strain was obtained by long-term storage, selection, and purification of an industrial culture of Methylococcus capsulatus BSV-874, which was used for methane-based protein biosynthesis in the Soviet Union. The size of the Concept-8 genome is 3.46 Mb. Genome annotation identified 3266 open reading frames that encode proteins. The closest phylogenetic relative of strain Concept-8 is Methylococcus capsulatus Bath (98.7% identity of 16S rRNA gene sequences). Comparison of the genomic sequences of these methanotrophs revealed 88.39% average nucleotide sequence identity, indicating that Concept-8 represents a novel species of the genus Methylococcus. The genomes of the strains Bath and Concept-8 both contain two copies of rRNA operons and pmoBAC operons for particulate methane monooxygenase, as well as a single copy of the soluble methane monooxygenase operon mmoXYBZDC. Growth on methanol was possible due to the presence of two complementary methanol dehydrogenases: MxaFJGIRACKLD and XoxF. The two methanotrophs also possess highly similar sets of genes encoding enzymes of the major pathways of the metabolism of C1 compounds. The genome of Methylococcus sp. Concept-8 was found to contain two regions associated with prophages of the family Siphoviridae. The prophage regions detected in the genome of Mc. capsulatus Bath are also homologous to viral sequences of the family Siphoviridae but differ from those identified in the genome of Concept-8. [ABSTRACT FROM AUTHOR]

The review examines the microbiological aspects of the biological phosphorus removal from wastewater. The history of the development of biotechnology and the discovery of the physiological group of phosphate-accumulating organisms (PAOs), which biologically remove phosphorus via the phosphate uptake and storage in the form of intracellular polyphosphates, is briefly described. PAOs are characterized by a cyclic type of metabolism that occurs when the anaerobic/aerobic conditions cyclically change. Under anaerobic conditions, PAOs uptake and store organic compounds through the energy of degradation of intracellular polyphosphates. When anaerobic conditions change to aerobic or an alternative electron acceptor appears, PAOs uptake phosphates and synthesize intracellular polyphosphates using the intracellular polymeric sources of carbon and energy accumulated under anaerobic conditions. The main representatives of the PAOs, their metabolic models, and physiological characteristics are described. The basic principles of the implementation of biotechnology used in the practice of wastewater treatment for phosphorus and other nutrients are considered. [ABSTRACT FROM AUTHOR]

Abstract—Biotechnologies involving phosphate-accumulating organisms, which collect inorganic phosphates from the medium as polyphosphates during cyclic growth under aerobic and anaerobic conditions, are presently applied for phosphorus removal from wastewater. Betaproteobacteria of the candidate genus 'Candidatus Accumulibacter' carry out phosphate accumulation in most systems for wastewater treatment. However, no member of 'Ca. Accumulibacter' has been isolated in pure culture. Metagenomic analysis of the microbial consortium formed in a laboratory setup for phosphate removal from wastewater and removing up to 80% phosphorus from the medium was carried out. Members of the phyla Proteobacteria (82.5%), Bacteroidetes (10.5%), and Chloroflexi (1.6%) predominated in the community. Among the proteobacteria, Betaproteobacteria were revealed, among which 'Ca. Accumulibacter' predominated, as well as Gammaproteobacteria (26.8%), which mainly belonged to the family 'Ca. Competibacteraceae.' Metagenomic data were used to obtain the genome of the dominant phosphate-accumulating bacterium, which belonged to a new 'Ca. Accumulibacter' species. The studied community was promising both for further basic research on metabolism of phosphate-accumulating organisms and for improvement of existing biotechnologies for phosphorus removal from wastewater. [ABSTRACT FROM AUTHOR]

Thermokarst lakes are formed as a result of thawing of ice-rich permafrost, causing development of land depressions which in flat areas are filled with water in the case of positive water balance. Activation of the thermokarst process is one of the possible indicators of permafrost degradation under the conditions of global warming. Thermokarst lakes occur in the areas of continuous, discontinuous, and sporadic permafrost, i.e., in Siberia, Alaska, Canada, and northern Scandinavia. Specific microbial communities adapted to long-term exposure to low temperatures develop in such lakes. They vary in the rates of aerobic and anaerobic metabolism depending on the mineral composition of bottom sediments, availability of organic matter, limnological and hydrological features of the lakes. High rates of methane emission are characteristic of a number of thermokarst lakes. Recent studies of thermokarst lakes revealed active methane formation via various methanogenic pathways, as well as aerobic and anaerobic methane oxidation by diverse methanogenic and methanotrophic bacteria and archaea. The question of what mechanisms and microorganisms are involved in anaerobic methane oxidation, which may be responsible for up to 80% of methane consumption in thermokarst lakes, remains, however, open. The microorganisms actively functioning beneath the ice during the long winter season, while highly important for northern aquatic ecosystems, also remain insufficiently studied. Almost no serious microbiological research on thermokarst lakes has been carried out in Russia, although permafrost occupies up to 65% of its territory, thermokarst process is common, and thermokarst lakes are numerous. [ABSTRACT FROM AUTHOR]

In March 2018, we analyzed water, ice, and snow cover in the estuaries and estuarine basins of the rivers of the southeastern and southwestern parts of Lake Baikal, as well as in two reference stations in the lake pelagic zone. The parameters determined in melted ice cores and estuarine waters were chemical composition, total microbial counts (TMC), dark CO2 assimilation (DCA) as well as the overall abundance of organotrophs and bacteria of sanitary importance. Our results indicated ice acidification in the basins of the Rivers Pereemnaya, Krestovka, and Bolshaya Cheremshanaya due to the effect of atmospheric precipitation enriched with the exhaust of nearby coal power plants and the river bottom. These processes had no negative effects on TMC, the abundance of organotrophic bacteria, and production characteristics. DCA measurements revealed the higher activity of ice microbial communities in the rivers and estuarine basins of the southeastern part of the lake (0.43 µg C L–1 day–1) compared to those of southwestern Baikal (0.26 µg C L–1 day–1). Microbiological parameters of the water samples exhibited a correlation with the levels of biogenic elements, total ions, and dissolved organic matter; a positive correlation was also observed between TMC and pH (r = 0.66). Low activity of microbial communities observed at high TMC at the estuaries of Lake Baikal rivers could result from the anthropogenic impact on microbial productive potential. [ABSTRACT FROM AUTHOR]