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Copyright of Stratum Plus Journal is the property of P.P. Stratum plus and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Anaerobic enrichments from hypersaline soda lakes with chitin as substrate yielded five closely related anaerobic haloalkaliphilic isolates growing on insoluble chitin by fermentation at pH 10 and salinities up to 3.5 M. The chitinolytic activity was exclusively cell associated. To better understand the biology and evolutionary history of this novel bacterial lineage, the genome of the type strain ACht1 was sequenced. Analysis of the 2.6 Mb draft genome revealed enzymes of chitin-degradation pathways, including secreted cell-bound chitinases. The reconstructed central metabolism revealed pathways enabling the fermentation of polysaccharides, while it lacks the genes needed for aerobic or anaerobic respiration. The Rnf-type complex, oxaloacetate decarboxylase and sodium-transporting V-type adenosine triphosphatase were identified among putative membrane-bound ion pumps. According to 16 S ribosomal RNA analysis, the isolates belong to the candidate phylum Termite Group 3, representing its first culturable members. Phylogenetic analysis using ribosomal proteins and taxonomic distribution analysis of the whole proteome supported a class-level classification of ACht1 most probably affiliated to the phylum Fibribacteres. Based on phylogenetic, phenotypic and genomic analyses, the novel bacteria are proposed to be classified as Chitinivibrio alkaliphilus gen. nov., sp. nov., within a novel class Chitinivibrione. [ABSTRACT FROM AUTHOR]

Copyright of Stratum Plus Journal is the property of P.P. Stratum plus and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Tuberculosis caused by multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis (MTB) strains is a growing problem in many countries. The availability of the complete nucleotide sequences of several MTB genomes allows to use the comparative genomics as a tool to study the relationships of strains and differences in their evolutionary history including acquisition of drug-resistance. In our work, we sequenced three genomes of Russian MTB strains of different phenotypes – drug susceptible, MDR and XDR. Of them, MDR and XDR strains were collected in Tomsk (Siberia, Russia) during the local TB outbreak in 1998–1999 and belonged to rare KQ and KY families in accordance with IS6110 typing, which are considered endemic for Russia. Based on phylogenetic analysis, our isolates belonged to different genetic families, Beijing, Ural and LAM, which made the direct comparison of their genomes impossible. For this reason we performed their comparison in the broader context of all M. tuberculosis genomes available in GenBank. The list of unique individual non-synonymous SNPs for each sequenced isolate was formed by comparison with all SNPs detected within the same phylogenetic group. For further functional analysis, all proteins with unique SNPs were ascribed to 20 different functional classes based on Clusters of Orthologous Groups (COG). We have confirmed drug resistant status of our isolates that harbored almost all known drug-resistance associated mutations. Unique SNPs of an XDR isolate CTRI-4XDR, belonging to a Beijing family were compared in more detail with SNPs of additional 14 Russian XDR strains of the same family. Only type specific mutations in genes of repair, replication and recombination system (COG category L) were found common within this group. Probably the other unique SNPs discovered in CTRI-4XDR may have an important role in adaptation of this microorganism to its surrounding and in escape from antituberculosis drugs treatment. [ABSTRACT FROM AUTHOR]

Simple Summary: The natural combustion of underground coal deposits leads to the release of large quantities of gases which contain molecular hydrogen and carbon monoxide. In places where hot coal gases are released to the surface, specific communities of thermophilic microorganisms develop. Unlike well-characterized geothermal ecosystems, the thermophiles associated with coal-fire gas vents are largely unexplored. In this work, using molecular genetic methods, we studied the composition and functional potential of bacterial and archaeal communities in the near-surface ground layer of an open quarry in Eastern Siberia, heated by an underground coal fire that began a few decades ago. The communities were dominated by only a few groups of bacteria of the phylum Firmicutes. Genome analysis predicted that they might obtain energy from the oxidation of hydrogen and carbon monoxide in coal gases. All these species were predicted to be spore-forming. Interestingly, closely related bacteria were found in various thermal environments, including burning coal seams, at distances of thousands of kilometers from the studied site. Spores of thermophilic Firmicutes can probably spread over long distances, which allows these microorganisms to colonize these thermal ecological niches. The natural combustion of underground coal seams leads to the formation of gas, which contains molecular hydrogen and carbon monoxide. In places where hot coal gases are released to the surface, specific thermal ecosystems are formed. Here, 16S rRNA gene profiling and shotgun metagenome sequencing were employed to characterize the taxonomic diversity and genetic potential of prokaryotic communities of the near-surface ground layer near hot gas vents in an open quarry heated by a subsurface coal fire. The communities were dominated by only a few groups of spore-forming Firmicutes, namely the aerobic heterotroph Candidatus Carbobacillus altaicus, the aerobic chemolitoautotrophs Kyrpidia tusciae and Hydrogenibacillus schlegelii, and the anaerobic chemolithoautotroph Brockia lithotrophica. Genome analysis predicted that these species can obtain energy from the oxidation of hydrogen and/or carbon monoxide in coal gases. We assembled the first complete closed genome of a member of uncultured class-level division DTU015 in the phylum Firmicutes. This bacterium, 'Candidatus Fermentithermobacillus carboniphilus' Bu02, was predicted to be rod-shaped and capable of flagellar motility and sporulation. Genome analysis showed the absence of aerobic and anaerobic respiration and suggested chemoheterotrophic lifestyle with the ability to ferment peptides, amino acids, N-acetylglucosamine, and tricarboxylic acid cycle intermediates. Bu02 bacterium probably plays the role of a scavenger, performing the fermentation of organics formed by autotrophic Firmicutes supported by coal gases. A comparative genome analysis of the DTU015 division revealed that most of its members have a similar lifestyle. [ABSTRACT FROM AUTHOR]

Groundwater, which appears on the surface in the form of springs, is an important ecologically significant component of the aquatic ecosystem, sensitive to changes in environmental conditions. The anthropogenic impact associated with urbanization leads to a change in the characteristics of groundwater, which, in turn, affects the composition of microbial communities in spring waters. Using high-throughput sequencing of the 16S ribosomal RNA gene fragments, we characterized the composition of microbial communities in five natural springs in the city of Moscow in the spring, summer, and winter seasons. The microbial communities of each spring in different seasons were similar to each other and clearly differed from the microbiomes of the other springs. Among the Archaea, which averaged about 20% of the microbial communities, ammonium-oxidizing Crenarchaeota predominated, as well as Nanoarchaeota. Most of the Bacteria belonged to the phyla Proteobacteria, Patescibacteria, Verrucomicrobiota, Chloroflexi, and Bacteroidota. Autotrophic bacteria, including iron-oxidizing bacteria of the family Gallionellaceae and nitrifiers, as well as methanotrophs, accounted for significant proportions in the microbial communities of the springs with a presumably deeper water source. Chemical and molecular analyses did not reveal contamination of spring waters with toxic substances and oil-derived products, as well as the presence of pathogenic microorganisms and indicators of fecal pollution. However, during the spring season, the proportions of halophilic and hydrocarbon-oxidizing bacteria increased in water microbiomes, which may reflect the entry into groundwater after snow thawing of deicing reagents and hydrocarbons, which are successfully biodegraded in the soil. [ABSTRACT FROM AUTHOR]

Copyright of Stratum Plus Journal is the property of P.P. Stratum plus and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Gas hydrates in marine sediments have been known for many years but recently hydrates were found in the sediments of Lake Baikal, the largest freshwater basin in the world. Marine gas hydrates are associated with complex microbial communities involved in methanogenesis, methane oxidation, sulfate reduction and other biotransformations. However, the contribution of microorganisms to the formation of gas hydrates remains poorly understood. We examined the microbial communities in the hydrate-bearing sediments and water column of Lake Baikal using pyrosequencing of 16 S r RNA genes. Aerobic methanotrophic bacteria dominated the water sample collected at the lake floor in the hydrate-bearing site. The shallow sediments were dominated by Archaea. Methanogens of the orders M ethanomicrobiales and M ethanosarcinales were abundant, whereas representatives of archaeal lineages known to perform anaerobic oxidation of methane, as well as sulfate-reducing bacteria, were not found. Affiliation of archaea to methanogenic rather than methane-oxidizing lineages was supported by analysis of the sequences of the methyl coenzyme M reductase gene. The deeper sediments located at 85-90 cm depth close to the hydrate were dominated by Bacteria, mostly assigned to C hloroflexi, candidate division JS1 and C aldiserica. Overall, our results are consistent with the biological origin of methane hydrates in Lake Baikal. [ABSTRACT FROM AUTHOR]

Large areas in the northern hemisphere are covered by extensive wetlands, which represent a complex mosaic of raised bogs, eutrophic fens, and aapa mires all in proximity to each other. Aapa mires differ from other types of wetlands by their concave surface, heavily watered by the central part, as well as by the presence of large-patterned string-flark complexes. In this paper, we characterized microbial diversity patterns in the surface peat layers of the neighboring string and flark structures located within the mire site in the Vologda region of European North Russia, using 16S rRNA gene sequencing. The microbial communities in raised strings were clearly distinct from those in submerged flarks. Strings were dominated by the Alpha- and Gammaproteobacteria. Other abundant groups were the Acidobacteriota, Bacteroidota, Verrucomicrobiota, Actinobacteriota, and Planctomycetota. Archaea accounted for only 0.4% of 16S rRNA gene sequences retrieved from strings. By contrast, they comprised about 22% of all sequences in submerged flarks and mostly belonged to methanogenic lineages. Methanotrophs were nearly absent. Other flark-specific microorganisms included the phyla Chloroflexi, Spirochaetota, Desulfobacterota, Beijerinckiaceae- and Rhodomicrobiaceae-affiliated Alphaproteobacteria, and uncultivated groups env.OPS_17 and vadinHA17 of the Bacteroidota. Such pattern probably reflects local anaerobic conditions in the submerged peat layers in flarks. [ABSTRACT FROM AUTHOR]

Methanotrophic verrucomicrobia of the order Methylacidiphilales are known as extremely acidophilic, thermophilic or mesophilic bacteria that inhabit acidic geothermal ecosystems. The occurrence of verrucomicrobial methanotrophs in other types of acidic environments remains an open question. Notably, Methylacidiphilales-affiliated 16S rRNA gene sequences are commonly retrieved from acidic (pH 3.5–5.5) peatlands. In this study, we compared the patterns of verrucomicrobial diversity in four acidic raised bogs and six neutral fens located in European North Russia. Methylacidiphilales-like 16S rRNA gene reads displaying 83–86% similarity to 16S rRNA gene sequences of currently described verrucomicrobial methanotrophs were recovered exclusively from raised bogs. Laboratory incubation of peat samples with 10% methane for 3 weeks resulted in the pronounced increase of a relative abundance of alphaproteobacterial methanotrophs, while no response was detected for Methylacidiphilales-affiliated bacteria. Three metagenome-assembled genomes (MAGs) of peat-inhabiting Methylacidiphilales bacteria were reconstructed and examined for the presence of genes encoding methane monooxygenase enzymes and autotrophic carbon fixation pathways. None of these genomic determinants were detected in assembled MAGs. Metabolic reconstructions predicted a heterotrophic metabolism, with a potential to hydrolyze several plant-derived polysaccharides. As suggested by our analysis, peat-inhabiting representatives of the Methylacidiphilales are acidophilic aerobic heterotrophs, which comprise a sister family of the methanotrophic Methylacidiphilaceae. [ABSTRACT FROM AUTHOR]

The binary asteroids are of current interest in the modern dynamics as there have been up to 50 discoveries of binaries. Estimates are that about 20% of near-Earth asteroids may be binary asteroids. Nevertheless the known asteroids pairs are rather rare objects in the Solar System. There are a number of papers studying the various aspects of asteroid pair dynamics. In this paper we study some stationary motions in the system of binary asteroid. Using the model for the first time suggested in [1], we approximate the bigger asteroid by the dumbbell-shaped rigid body. Moreover we assume that the smaller asteroid has mass close to zero. It was shown in [1] that the motion equations for the considered system have the stationary solutions corresponding to the smaller asteroid's equilibria relative to the axis of the regular precession and the dumbbell rod These equilibria similar to the libration points in the Restricted Circular Problem of Three Bodies (RCP3B). There are two types of such equilibria. The equal distances from the dumbbell endpoints characterize the equilibria of the first type, therefore we shall name them 'the libration points similar to Lagrangian' or 'the triangular libration points' (TLPs) by analogy to a classical problem. At difference with RCP3B there are two or one TLPs or they do not exist. Equilibria of the second type in something are similar to the Eulerian libration points. They belong to the plane containing the bigger asteroid's angular momentum and the dumbbell rod. Moreover, these equilibria belong to the strip bounded by straight lines crossing the dumbbell endpoints and being perpendicular to angular momentum. Therefore we shall name them 'the coplanar libration points'(CLP). The CLPs coordinates are computed by following procedure. Two algebraic equations are deduced. One of these equations determines the curve containing all CLPs. We say that this curve is 'the Geometrical locus of CLPs' (GL). The second equation allows to locate CLPs in GL. Studying evolution of CLPs in GL it can be proved that the number of CLPs varies from 3 up to 7, but if the dumbbell consist of equal spheres then only the odd number of CLPs is possible. However, if the dumbbell is asymmetric then the number of CLPs can be equal 4 or 6 for some rare situations. [ABSTRACT FROM AUTHOR]

Planctomycetes of the family Gemmataceae are strictly aerobic chemo-organotrophs that display a number of hydrolytic capabilities. A member of this family, Telmatocola sphagniphila SP2T, is the first described planctomycete with experimentally proven ability for growth on cellulose. In this study, the complete genome sequence of strain SP2T was obtained and the genome-encoded determinants of its cellulolytic potential were analyzed. The T. sphagniphila SP2T genome was 6.59 Mb in size and contained over 5200 potential protein-coding genes. The search for enzymes that could be potentially involved in cellulose degradation identified a putative cellulase that contained a domain from the GH44 family of glycoside hydrolases. Homologous enzymes were also revealed in the genomes of two other Gemmataceae planctomycetes, Zavarzinella formosa A10T and Tuwongella immobilis MBLW1T. The gene encoding this predicted cellulase in strain SP2T was expressed in E. coli and the hydrolytic activity of the recombinant enzyme was confirmed in tests with carboxymethyl cellulose but not with crystalline cellulose, xylan, mannan or laminarin. This is the first experimentally characterized cellulolytic enzyme from planctomycetes. [ABSTRACT FROM AUTHOR]

A combination of physicochemical and radiotracer analysis, high-throughput sequencing of the 16S rRNA, and particulate methane monooxygenase subunit A (pmoA) genes was used to link a microbial community profile with methane, sulfur, and nitrogen cycling processes. The objects of study were surface sediments sampled at five stations in the northern part of the Barents Sea. The methane content in the upper layers (0–5 cm) ranged from 0.2 to 2.4 µM and increased with depth (16–19 cm) to 9.5 µM. The rate of methane oxidation in the oxic upper layers varied from 2 to 23 nmol CH4 L−1 day−1 and decreased to 0.3 nmol L−1 day−1 in the anoxic zone at a depth of 16–19 cm. Sulfate reduction rates were much higher, from 0.3 to 2.8 µmol L−1 day−1. In the surface sediments, ammonia-oxidizing Nitrosopumilaceae were abundant; the subsequent oxidation of nitrite to nitrate can be carried out by Nitrospira sp. Aerobic methane oxidation could be performed by uncultured deep-sea cluster 3 of gamma-proteobacterial methanotrophs. Undetectable low levels of methanogenesis were consistent with a near complete absence of methanogens. Anaerobic methane oxidation in the deeper sediments was likely performed by ANME-2a-2b and ANME-2c archaea in consortium with sulfate-reducing Desulfobacterota. Sulfide can be oxidized by nitrate-reducing Sulfurovum sp. Thus, the sulfur cycle was linked with the anaerobic oxidation of methane and the nitrogen cycle, which included the oxidation of ammonium to nitrate in the oxic zone and denitrification coupled to the oxidation of sulfide in the deeper sediments. Methane concentrations and rates of microbial biogeochemical processes in sediments in the northern part of the Barents Sea were noticeably higher than in oligotrophic areas of the Arctic Ocean, indicating that an increase in methane concentration significantly activates microbial processes. [ABSTRACT FROM AUTHOR]

An Erratum to this paper has been published: https://doi.org/10.1134/S0026261722120025 [ABSTRACT FROM AUTHOR]

Simple Summary: Arctic ecosystems are an extreme habitat characterized by a negative average annual temperature and the presence of permafrost that occupies about 25% of the land. Permafrost can retain viable microorganisms for several million years and therefore it is a source of unique "ancient" microbes. Acinetobacter lwoffii are aerobic chemoorganotrophic bacteria widespread in a variety of natural and artificial environments, and have been reported as hospital pathogens associated with nosocomial infections. Here, we carried out a genome-wide analysis of five strains of A. lwoffii isolated from permafrost aged from 15 thousand to 1.8 million years. Surprisingly, we did not reveal genetic determinants that distinguish them from modern clinical and environmental A. lwoffii isolates. On the phylogenetic tree permafrost strains do not form a separate cluster, but are related to various clinical isolates. The genomes of clinical and permafrost strains contain similar mobile elements and prophages, which indicates an intense horizontal gene transfer. Like clinical isolates, permafrost strains harbored antibiotic resistance genes, although plasmids from the modern strains are enriched with antibiotic resistance genes compared to permafrost ones. The obtained results indicate that thawing of permafrost caused by global warming could release new potentially pathogenic strains of Acinetobacter into the modern biosphere. Microbial life can be supported at subzero temperatures in permafrost up to several million years old. Genome analysis of strains isolated from permafrost provides a unique opportunity to study microorganisms that have not previously come into contact with the human population. Acinetobacter lwoffii is a typical soil bacterium that has been increasingly reported as hospital pathogens associated with bacteremia. In order to identify the specific genetic characteristics of ancient permafrost-conserved strains of A. lwoffii and their differences from present-day clinical isolates, we carried out a genome-wide analysis of five strains of A. lwoffii isolated from permafrost aged from 15 thousand to 1.8 million years. Surprisingly, we did not identify chromosomal genetic determinants that distinguish permafrost strains from clinical A. lwoffii isolates and strains from other natural habitats. Phylogenetic analysis based on whole genome sequences showed that permafrost strains do not form a separate cluster and some of them are most closely related to clinical isolates. The genomes of clinical and permafrost strains contain similar mobile elements and prophages, which indicates an intense horizontal transfer of genetic material. Comparison of plasmids of modern and permafrost strains showed that plasmids from the modern strains are enriched with antibiotic resistance genes, while the content of genes for resistance to heavy metals and arsenic is nearly the same. The thawing of permafrost caused by global warming could release new potentially pathogenic strains of Acinetobacter. [ABSTRACT FROM AUTHOR]

Simple Summary: Corrosion of steel equipment during oil production, transportation, and refining is a big global issue, leading to significant economic losses. The main agents of microbially influenced corrosion (MIC) of steel equipment are sulfate-reducing bacteria (SRB) and archaea (SRA), which reduce sulfate present in the reservoir water to form sulfide. Timely detection of sulfidogens in formations is necessary for the development of measures to suppress their growth. Existing 16S rRNA gene-based molecular methods for the detection of sulfidogens make it possible to identify them in their natural habitat, and the methods based on metagenomic analysis of components of the microbial community make it possible to predict their potential functional activity. However, selection of biocides or other methods for suppressing the growth of sulfidogens requires confirmation of their effectiveness on enrichment and/or pure cultures. In order to establish a collection of sulfidogens inhabiting the oil reservoirs of Tatarstan (Russia), a number of strains of sulfate-reducing bacteria were isolated. This study describes the 5S69T strain, which, based on the physiological and biochemical characteristics and genomic analysis, has been assigned to a new species, Pseudodesulfovibrio methanolicus sp. nov. The strain is able to grow at high salinity, at reservoir temperature, and on media with alcohols or H2/CO2 in the presence of acetate, which indicates its adaptation to environmental conditions and potential in sulfide production in the oil reservoir. The search for the microorganisms responsible for sulfide formation and corrosion of steel equipment in the oil fields of Tatarstan (Russia) resulted in the isolation of a new halotolerant strictly anaerobic sulfate-reducing bacterium, strain 5S69T. The cells were motile curved Gram-negative rods. Optimal growth was observed in the presence of 2.0–4.0% (w/v) NaCl, at pH 6.5, and at 23–28 °C under sulfate-reducing conditions. The isolate was capable of chemoorganotrophic growth with sulfate and other sulfoxides as electron acceptors, resulting in sulfide formation; and of pyruvate fermentation resulting in formation of H2 and acetate. The strain utilized lactate, pyruvate, ethanol, methanol, fumarate, and fructose, as well as H2/CO2/acetate for sulfate reduction. The genome size of the type strain 5S69T was 4.16 Mb with a G + C content of 63.0 mol%. On the basis of unique physiological properties and results of the 16S rRNA gene-based phylogenetic analysis, phylogenomic analysis of the 120 conserved single copy proteins and genomic indexes (ANI, AAI, and dDDH), assigning the type strain 5S69T ((VKM B-3653T = KCTC 25499T) to a new species within the genus Pseudodesulfovibrio, is suggested, with the proposed name Pseudodesulfovibrio methanolicus sp. nov. Genome analysis of the new isolate showed several genes involved in sulfate reduction and its sulfide-producing potential in oil fields with high saline formation water. [ABSTRACT FROM AUTHOR]

Thermal ecosystems associated with areas of underground burning coal seams are rare and poorly understood in comparison with geothermal objects. We studied the microbial communities associated with gas vents from the coal-fire in the mining wastes in the Kemerovo region of the Russian Federation. The temperature of the ground heated by the hot coal gases and steam coming out to the surface was 58 °C. Analysis of the composition of microbial communities revealed the dominance of Ktedonobacteria (the phylum Chloroflexi), known to be capable of oxidizing hydrogen and carbon monoxide. Thermophilic hydrogenotrophic Firmicutes constituted a minor part of the community. Among the well-known thermophiles, members of the phyla Aquificae, Deinococcus-Thermus and Bacteroidetes were also found. In the upper ground layer, Acidobacteria, Verrucomicrobia, Actinobacteria, Planctomycetes, as well as Proteobacteria of the alpha and gamma classes, typical of soils, were detected; their relative abundancies decreased with depth. The phylum Verrucomicrobia was dominated by Candidatus Udaeobacter, aerobic heterotrophs capable of generating energy through the oxidation of hydrogen present in the atmosphere in trace amounts. Archaea made up a small part of the communities and were represented by thermophilic ammonium-oxidizers. Overall, the community was dominated by bacteria, whose cultivated relatives are able to obtain energy through the oxidation of the main components of coal gases, hydrogen and carbon monoxide, under aerobic conditions. [ABSTRACT FROM AUTHOR]

Two metagenome-assembled genomes (MAGs), obtained from laboratory-scale enhanced biological phosphorus removal bioreactors, were analyzed. The values of 16S rRNA gene sequence identity, average nucleotide identity, and average amino acid identity indicated that these genomes, designated as RT and SSD2, represented two novel species within the genus Thiothrix, 'Candidatus Thiothrix moscowensis' and 'Candidatus Thiothrix singaporensis'. A complete set of genes for the tricarboxylic acid cycle and electron transport chain indicates a respiratory type of metabolism. A notable feature of RT and SSD2, as well as other Thiothrix species, is the presence of a flavin adenine dinucleotide (FAD)-dependent malate:quinone oxidoreductase instead of nicotinamide adenine dinucleotide (NAD)-dependent malate dehydrogenase. Both MAGs contained genes for CO2 assimilation through the Calvin–Benson–Bassam cycle; sulfide oxidation (sqr, fccAB), sulfur oxidation (rDsr complex), direct (soeABC) and indirect (aprBA, sat) sulfite oxidation, and the branched Sox pathway (SoxAXBYZ) of thiosulfate oxidation to sulfur and sulfate. All these features indicate a chemoorganoheterotrophic, chemolithoautotrophic, and chemolithoheterotrophic lifestyle. Both MAGs comprise genes for nitrate reductase and NO-reductase, while SSD2 also contains genes for nitrite reductase. The presence of polyphosphate kinase and exopolyphosphatase suggests that RT and SSD2 could accumulate and degrade polyhosphates during the oxic-anoxic growth cycle in the bioreactors, such as typical phosphate-accumulating microorganisms. [ABSTRACT FROM AUTHOR]

The complete chloroplast genome sequence of Allium obliquum was determined by Illumina single-end sequencing. The complete plastid genome was 152,387 bp in length, containing a large single copy (LSC) of 81,588 bp and a small single copy (SSC) of 18,059 bp, which were separated by a pair of 26,370 bp inverted repeats (IRs). A total of 134 genes were annotated, including 83 protein coding genes, 38 tRNA genes, eight rRNA genes, and five pseudogenes. The overall GC contents of the plastid genome were 36.8%. Unlike A. cepa (onion) and A. sativum (garlic), A. obliquum encodes a functional intact infA gene. [ABSTRACT FROM AUTHOR]

Underground burning of coal seams accompanied by release of gases leads to development of local thermal ecosystems. We investigated the microbial community of the ground heated to 72°C in the release area of hot gases resulting from underground combustion of coal mining waste at the Bungurskiy-Severny coal deposit in the Kemerovo region of Russia. Analysis of the composition of the microbial community by 16S rRNA gene profiling revealed predominance of thermophilic bacteria of the phyla Deinococcus-Thermus, Aquificae, and Firmicutes. As a result of metagenomic analysis, 18 genomes of the main members of the microbial community were assembled, including the complete genomes of Hydrogenobacter thermophiles, a member of the candidate genus UBA11096 of the phylum Aquificae (RBS10-58), Thermoflexus hugenholtzii, and Thermus antranikianii. Analysis of the RBS10-58 genome indicates that this bacterium can autotrophically fix carbon in the reductive tricarboxylic acid cycle and obtain energy via oxidation of hydrogen and sulfur compounds with oxygen or nitrate as electron acceptors. Genome analysis of the two dominant Firmicutes species, Hydrogenibacillus schlegelii and an uncultured member of the class Thermaerobacteria, showed that these bacteria could grow aerobically by oxidizing hydrogen and carbon monoxide. Overall, the community was dominated by aerobic bacteria capable of growing autotrophically and obtaining energy via oxidation of the main components of coal gases, hydrogen and carbon monoxide. Thermus antranikianii, which makes up about a half of the microbial community, probably uses organic matter produced by autotrophic members of Firmicutes and Aquificae. [ABSTRACT FROM AUTHOR]

Telomeres are special DNA-protein structures that are located at the ends of linear eukaryotic chromosomes. The telomere length determines the proliferation potential of cells. Telomerase is a key component of the telomere length maintenance system. While telomerase is inactive in the majority of somatic cells, its activity determines the clonogenic potential of stem cells as a resource for tissue and organism regeneration. Reactivation of telomerase occurs during the process of immortalization in the majority of cancer cells. Telomerase is a ribonucleoprotein that contains telomerase reverse transcriptase and telomerase RNA components. The RNA processing mechanism of telomerase involves exosome trimming or degradation of the primary precursor. Recent data provide evidence that the competition between the processing and decay of telomerase RNA may regulate the amount of RNA at the physiological level. We show that termination of human telomerase RNA transcription is dependent on its promoter, which engages with the multisubunit complex Integrator to interact with RNA polymerase II and terminate transcription of the human telomerase RNA gene followed by further processing. [ABSTRACT FROM AUTHOR]

The microbiota of chicken litter remains largely unexplored, despite its leading role in the formation of volatile odorants and unpleasant odors. One of the main components of the odor is hydrogen sulfide, which may be formed as a result of microbial sulfate reduction. The composition of the microbial community of poultry plant waste was investigated. Samples were collected at the Mezheninovskaya large poultry farm, 15 km from the city of Tomsk, Russia. The 16S rRNA gene profiling revealed sulfate-reducing Desulfovibrionaceae in the microbial community. Both their share in the community and sulfide production increased upon incubation of the waste in the medium with sulfate and lactate. The possible sulfate sources in the waste are gypsum and the feed additives introduced as sulfates, such as lysine sulfate. [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]

Complete nucleotide sequence of the 27,266 bp mitochondrial genome of the сephalosporin C producing fungus Acremonium chrysogenum have been determined using whole genome shotgun sequencing approach. The circular mapping molecule encodes a usual set of mitochondrial proteins and RNA genes, including large and small ribosomal RNAs, 19 proteins and 26 tRNA genes and contains 2 introns. All structural genes are located on one strand and are apparently transcribed in one direction. Comparative analysis of this and previously sequenced Pezizomycotina mtDNAs revealed more extensive similarity between A. chrysogenum genome and those of Fusarium clade and specific synthenic patterns characteristic of Hypocrealean mitogenomes. Phylogenetic analysis based on catenated mitochondrial protein sequences confirmed current taxonomic position of A. chrysogenum within Hyprocreales and related taxa. [ABSTRACT FROM AUTHOR]

Filamentous iron oxides accumulating bacteria Sphaerotilus natans subsp. natans and S. natans subsp. sulfidivorans were described as subspecies based on 99.7% identity of their 16S rRNA sequences, in spite of important physiological difference. The ANI between their genomes was 94.7%, which indicate their assignment to different species. S. natans subsp. sulfidivorans and S. montanus possess genes for a complete SOX system, while S. natans subsp. natans encode only SoxYZ. There are genes for the Calvin cycle in the genomes of S. hippei DSM 566T, S. natans subsp. sulfidivorans D-501T, and S. montanus HST. Lithoautotrophy on reduced sulfur compounds is probably possible for S. natans subsp. sulfidivorans and S. montanus, but not for S. natans subsp. natans. Considering significant differences in the genome characteristics and metabolic potential of S. natans subsp. sulfidivorans and S. natans subsp. natans, we propose their classification as different species, S. natans and S. sulfidivorans sp. nov. [ABSTRACT FROM AUTHOR]

The candidate phylum Riflebacteria was described based on analysis of genomes assembled from the metagenomes of various anaerobic ecosystems; however, to date, no member of Riflebacteria has been isolated in a pure culture. In this work, the genome of a new member of Riflebacteria was obtained from the metagenome of the microbial community of a deep subsurface thermal aquifer in Western Siberia. Phylogenetic analysis indicates that this bacterium, designated Ch46, represents a new genus of the phylum Riflebacteria, distinct from the previously described Candidatus Ozemobacter. The genome of Ch46 was found to encode putatively secreted alpha-amylases and various sugar and peptide transporters. Reconstruction of central metabolic pathways suggests that Ch46 is an anaerobic organotroph capable of fermenting sugars and proteinaceous substrates. The bacterium lacks the genes of the known pathways of autotrophic carbon fixation, as well as the aerobic respiratory chain. The transmembrane ion gradient can be generated by an Rnf complex, as well as by a sodium-transporting NADH‒quinone oxidoreductase. The presence of multiheme c-type cytochromes indicates the possibility of dissimilatory Fe(III) reduction. The pathways of dissimilatory reduction of sulfate, nitrate, nitrite, arsenate, and sulfur were not detected. In the subsurface aquifer, Riflebacteria probably utilize starch and similar polysaccharides, as well as low-molecular-weight organic compounds. Based on the results of phylogenetic and genomic analysis, it is proposed to classify the novel bacterium as 'Candidatus Rifleibacterium amylolyticum.' [ABSTRACT FROM AUTHOR]

The goal of the present work was to determine the effect of different concentrations of an organic carbon source (molasses) on the biooxidation of gold-bearing pyrite−arsenopyrite flotation concentrate, as well as on the composition of microbial populations that formed during the biooxidation process. Biooxidation activity increased with increasing molasses concentration in the medium. Concentration of molasses had a greater effect on the total number of microorganisms, while the relative numbers of microorganisms of different groups did not differ significantly. Thus, it was shown that the use of cheap organic substrates is promising to increase the efficiency of biohydrometallurgical processes. [ABSTRACT FROM AUTHOR]

Ethyl carbamate, a potential carcinogen, is formed in wine as a result of a chemical reaction between ethanol and urea during fermentation and storage. Using genome editing methods, a modified strain of wine yeast Saccharomyces cerevisiae was constructed, with a deletion of the CAR1 arginase gene, leading to a decrease in the formation of urea from arginine. Transcriptome analysis by high-throughput sequencing identified 738 genes whose transcription level reliably changed more than twofold as a result of deletion of the CAR1 gene. Expression of most genes of the central metabolic pathways in the CAR1 deletion strain was decreased; increased transcription levels were observed for the Map kinase signaling cascades. Among the genes of arginine metabolism pathways, the level of transcription of the ornithine aminotransferase gene CAR2 increased significantly. The wine material obtained using a strain with a deletion of the CAR1 gene under micro-winemaking conditions contained 25% less urea than in the case of using an unmodified strain. The resulting strain of wine yeast, having lower urea levels, may be promising for winemaking. [ABSTRACT FROM AUTHOR]

Bacteria of the candidate phylum Bipolaricaulota, previously known as OP1 and Acetothermia, have been identified in various terrestrial and marine ecosystems as a result of molecular analysis of microbial communities. To date, none of the members of Bipolaricaulota has been isolated in a pure culture. We assembled the complete closed genome sequence of the bacterium of this phylum from the metagenome of a subsurface thermal aquifer and used the genomic data to analyze the phylogenetic position and metabolic potential of this bacterium. Analysis of the genome of this bacterium, designated Ch78, revealed various transporters of sugars and peptides and limited capacities for the extracellular hydrolysis of polysaccharides. Reconstruction of the central metabolic pathways suggested that the bacterium Ch78 is an anaerobic organotroph capable of fermenting sugars and proteinaceous substrates. Known pathways of aerobic and anaerobic respiration, as well as of autotrophic carbon fixation, were not found in the Ch78 genome. In the subsurface aquifer Bipolaricaulota probably consume low-molecular weight organic compounds and produce hydrogen and acetate. Based on the results of phylogenetic and genomic analysis, classification of the novel bacterium as "Candidatus Bipolaricaulis sibiricus" is proposed. [ABSTRACT FROM AUTHOR]

Methanogenesis is the main source of biogenic methane in the atmosphere and therefore plays an important role in climate change. While all methanogens known until recently belonged to the phylum Euryarchaeota, potential methanogens were recently found among two uncultured archaeal phyla, Bathyarchaeota and Verstraetearchaeota. Analysis of the genomes of several members of Verstraetearchaeota revealed their ability to use methylated compounds for methanogenesis; however, all these genomes were incomplete, which prevents an unequivocal reconstruction of their metabolic pathways. The present work reports the complete genome of a new member of Verstraetearchaeota from the metagenome of the microbial community of a deep subsurface reservoir of thermal waters in Western Siberia. Phylogenetic analysis revealed the new archaeon to belong to a new species of the genus 'Candidatus Methanosuratus', for which the name 'Candidatus Methanosuratus subterraneum' was proposed. The possibility of methyl-reducing methanogenesis was indicated by the presence of the methyl coenzyme M reductase complex and of the genes required for methane production using methanol as the methyl group donor, while the genes required for the oxidation of methyl group to CO2 were missing. Genome analysis showed that 'Ca. Methanosuratus subterraneum' has the metabolic pathways required for growth by fermentation of proteinaceous substrates. Analysis of the global distribution of 'Ca. Methanosuratus' revealed the 16S rRNA gene sequences assigned to this genus in hot springs, underground waters, and oil reservoirs, which makes it possible to consider this genus as a representative of the subsurface biosphere. [ABSTRACT FROM AUTHOR]

Simple Summary: A significant amount of residual oil is located in oil reservoirs with high-salinity formation water levels. Microorganisms are capable of producing a number of oil-displacing metabolites, such as volatile acids, alcohols, biosurfactants, biopolymers, and others. The application of microbial-enhanced oil recovery (MEOR) methods is possible after a detailed study of the microbial community of the oil reservoir. The aim of this study was to elucidate the biodiversity of microorganisms in oil reservoirs of Tatarstan (Russia) with high saline formation water in order to select suitable MEOR technologies for these reservoirs. Using metagenomic and cultural methods, it was shown that fermentative and sulfate-reducing bacteria predominate in reservoirs with high-sulfate formation water, whereas in oil reservoirs with low-sulfate water, in the community of Methanohalophilus methanogens predominated. A total of 20 pure bacterial cultures were isolated from oil reservoirs. The isolated fermentative bacteria were able to produce oil-displacing metabolites from sugar-containing and protein substrates. However, fermentation products stimulate the growth of sulfidogenic bacteria that form sulfide, which reduces the quality of oil and causes the corrosion of steel equipment. Thus, when choosing MEOR technology, it is necessary to take into account the possibility of activation of fermentative prokaryotes with simultaneous suppression of the growth of sulfidogens in the oil reservoir. The reserves of light conditional oil in reservoirs with low-salinity formation water are decreasing worldwide, necessitating the extraction of heavy oil from petroleum reservoirs with high-salinity formation water. As the first stage of defining the microbial-enhanced oil recovery (MEOR) strategies for depleted petroleum reservoirs, microbial community composition was studied for petroleum reservoirs with high-salinity formation water located in Tatarstan (Russia) using metagenomic and culture-based approaches. Bacteria of the phyla Desulfobacterota, Halanaerobiaeota, Sinergistota, Pseudomonadota, and Bacillota were revealed using 16S rRNA-based high-throughput sequencing in halophilic microbial communities. Sulfidogenic bacteria predominated in the studied oil fields. The 75 metagenome-assembled genomes (MAGs) of prokaryotes reconstructed from water samples were assigned to 16 bacterial phyla, including Desulfobacterota, Bacillota, Pseudomonadota, Thermotogota, Actinobacteriota, Spirochaetota, and Patescibacteria, and to archaea of the phylum Halobacteriota (genus Methanohalophilus). Results of metagenomic analyses were supported by the isolation of 20 pure cultures of the genera Desulfoplanes, Halanaerobium, Geotoga, Sphaerochaeta, Tangfeifania, and Bacillus. The isolated halophilic fermentative bacteria produced oil-displacing metabolites (lower fatty acids, alcohols, and gases) from sugar-containing and proteinaceous substrates, which testify their potential for MEOR. However, organic substrates stimulated the growth of sulfidogenic bacteria, in addition to fermenters. Methods for enhanced oil recovery should therefore be developed, combining the production of oil-displacing compounds with fermentative bacteria and the suppression of sulfidogenesis. [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]

Two metagenome-assembled genomes (MAGs), GKL-01 and GKL-02, related to the family Thiotrichaceae have been assembled from the metagenome of bacterial mat obtained from a sulfide-rich thermal spring in the North Caucasus. Based on average amino acid identity (AAI) values and genome-based phylogeny, MAG GKL-01 represented a new genus within the Thiotrichaceae family. The GC content of the GKL-01 DNA (44%) differed significantly from that of other known members of the genus Thiothrix (50.1–55.6%). We proposed to assign GKL-01 to a new species and genus 'Candidatus Thiocaldithrix dubininis' gen. nov., sp. nov. GKL-01. The phylogenetic analysis and estimated distances between MAG GKL-02 and the genomes of the previously described species of the genus Thiothrix allowed assigning GKL-02 to a new species with the proposed name 'Candidatus Thiothrix putei' sp. nov. GKL-02 within the genus Thiothrix. Genome data first revealed the presence of both Na+-ATPases and H+-ATPases in several Thiothrix species. According to genomic analysis, bacteria GKL-01 and GKL-02 are metabolically versatile facultative aerobes capable of growing either chemolithoautotrophically or chemolithoheterotrophically in the presence of hydrogen sulfide and/or thiosulfate or chemoorganoheterotrophically. [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]

Acidobacteriota are one of the major prokaryotic groups in soils and peatlands. They are especially abundant in acidic peat bogs, where representatives of the well-characterized class Acidobacteriia predominate. The diversity and metabolic potential of Acidobacteriota inhabiting fens with neutral pH have been studied less thoroughly. We analyzed the composition of acidobacterial communities in four peat bogs and six fens of the Vologda region. The Acidobacteriota-affiliated 16S rRNA gene sequences comprised 30–42 and 7–22% of all reads retrieved from the peat bogs and fens, respectively. The acidobacteria of peat bogs were represented by the orders Acidobacteriales and Bryobacterales of the class Acidobacteriia, while the classes Vicinamibacteria and Blastocat•ellia predominated in fens. Genomes of four uncultured bacteria of Blastocatellia (family Pyrinomonadaceae, two genomes), Vicinamibacteria (family UBA2999), and Thermoanaerobaculia (order UBA5066) were assembled from the metagenomes of peat fens. Genome analysis revealed key pathways of aerobic heterotrophic metabolism in all four microorganisms, including the Embden–Meyerhof pathway, gluconeogenesis, the non-oxidative stage of the pentose phosphate pathway, the tricarboxylic acid cycle, and the electron transport chain of aerobic respiration, including terminal cytochrome c oxidases. All genomes encoded molybdopterin oxidoreductases of the CISM family and multiheme cytochromes c, indicating the possibility of dissimilatory reduction of sulfur compounds and Fe(III) under anaerobic conditions. Probable growth substrates may be amino acids, peptides, and fatty acids. Members of the Pyrinomonadaceae can also use various carbohydrates, including polysaccharides, and are likely involved in the degradation of various biopolymers in peat bogs. Members of Thermoanaerobaculia and Vicinamibacteria lacked the genes for secreted glycosyl hydrolases and probably could only use a limited range of simple sugars. The genome of a bacterium of the class Vicinamibacteria contained a set of genes encoding bacterial microcompartments (metabolosomes) that have not previously been described in acidobacteria and are probably involved in the metabolism of L-rhamnose. [ABSTRACT FROM AUTHOR]

Representatives of the genus Thiothrix are filamentous, sulfur-oxidizing bacteria found in flowing waters with counter-oriented sulfide and oxygen gradients. They were first described at the end of the 19th century, but the first pure cultures of this species only became available 100 years later. An increase in the number of described Thiothrix species at the beginning of the 21st century shows that the classical phylogenetic marker, 16S rRNA gene, is not informative for species differentiation, which is possible based on genome analysis. Pangenome analysis of the genus Thiothrix showed that the core genome includes genes for dissimilatory sulfur metabolism and central metabolic pathways, namely the Krebs cycle, Embden–Meyerhof–Parnas pathway, glyoxylate cycle, Calvin–Benson–Bassham cycle, and genes for phosphorus metabolism and amination. The shell part of the pangenome includes genes for dissimilatory nitrogen metabolism and nitrogen fixation, for respiration with thiosulfate. The dispensable genome comprises genes predicted to encode mainly hypothetical proteins, transporters, transcription regulators, methyltransferases, transposases, and toxin–antitoxin systems. [ABSTRACT FROM AUTHOR]

Microbial communities in wastewater treatment plants (WWTPs) play a key role in water purification. Microbial communities of activated sludge (AS) vary extensively based on plant operating technology, influent characteristics and WWTP capacity. In this study we performed 16S rRNA gene profiling of AS at nine large-scale WWTPs responsible for the treatment of municipal sewage from the city of Moscow, Russia. Two plants employed conventional aerobic process, one plant—nitrification/denitrification technology, and six plants were operated with the University of Cape Town (UCT) anaerobic/anoxic/oxic process. Microbial communities were impacted by the technology and dominated by the Proteobacteria, Bacteroidota and Actinobacteriota. WWTPs employing the UCT process enabled efficient removal of not only organic matter, but also nitrogen and phosphorus, consistently with the high content of ammonia-oxidizing Nitrosomonas sp. and phosphate-accumulating bacteria. The latter group was represented by Candidatus Accumulibacter, Tetrasphaera sp. and denitrifiers. Co-occurrence network analysis provided information on key hub microorganisms in AS, which may be targeted for manipulating the AS stability and performance. Comparison of AS communities from WWTPs in Moscow and worldwide revealed that Moscow samples clustered together indicating that influent characteristics, related to social, cultural and environmental factors, could be more important than a plant operating technology. [ABSTRACT FROM AUTHOR]