Molecular biological techniques and bioinformatic analysis were used to investigate the phylogenetic and functional diversity of the prokaryotic complex of soil microcosms. The dominant organisms of the hydrolytic community were different in the samples from different climatic zones. In the soils subject to anthropogenic or abiogenic load, apart from decreased diversity and abundance of prokaryotes, the number of the genes marking the ability to degrade xenobiotics, as well as those encoding nitrogen conversion and metabolism of vitamins and cofactors, was found to increase. Under heavy oil contamination, the bacterial community was capable of nitrification; its role increased in the lower horizons of the soil profile. The patterns revealed in the work indicate high metabolic potential of the prokaryotic component of the studied soils.

Using luminescent microscopy and real-time PCR, the microbiome of soils and supraglacial objects in the background and oil-contaminated ecosystems of the island was studied Hayes Island, part of the Franz Josef Land archipelago. Biomass of microorganisms ranged from 81 to 666 µg/g of substrate; most of it (up to 88%) is represented by fungi. Length of fungal mycelium reached more than 360 m/g of substrate. The number of prokaryotes varied from 4.0 × 107 to 3.75 × 10⁹ cells/g of substrate; the length of actinomycete hyphae reached 40 m/g of substrate. Up to 78% of the detected prokaryotic cells are represented by small nanoforms, which is typical for extreme ecosystems. Share of viable cells of microorganisms is maximum (74–86%) for surface organogenic horizons and minimum (29–54%) for mineral suprapermafrost layers. Prokaryotic complex was dominated by bacteria (from 5.14×105 to 5.05 × 10¹⁰ 16S rRNA copies/g of soil), but not by archaea, from 8.46 × 10⁵ to 2.28 × 10⁹ 16S rRNA copies/g of substrate. Amount of FJL fungal genetic material ranged from 6.47 × 10⁴ to 8.67 × 10¹⁰ ITS rRNA copies/g soil. Number of copies of the alkB gene (synthesis of alkane monooxygenase for the destruction of hydrocarbon n-alkanes) varied from 1.2 × 10¹ to 1.8 × 10⁵/g of substrate and sharply decreased from the surface horizons to the deep ones. Oil-contaminated soils and supraglacial objects contained a smaller biomass, however, a greater number of ribosomal genes of microorganisms compared to the background ecosystems. An exponential decrease in the analyzed quantitative parameters of microorganisms from surface to deep soil horizons was registered.

The microbiome of soils and supraglacial formations in background and oil-polluted ecosystems of Hayes Island (Franz Josef Land) was studied using the methods of luminescent microscopyreal-time and polymerase chain reaction. The biomass of microorganisms ranged from 81 to 666 μg C/g substrate; its larger part (up to 88

The structure of prokaryotic complexes in microcosms of oil-contaminated and control soil samples (chernozem, Voronezh oblast, gray forest soil, Tula oblast, and chestnut soil, Volgograd oblast) was studied under conditions of different matric potentials of soil water and soil temperatures using molecular biology methods (RT-PCR, metabarcoding, FISH). An increase in the content of functional genes responsible for the synthesis of catechol-2,3-dioxygenase (xylE) and alkane monooxygenase (alkB) marking the initial stage of hydrocarbon degradation was observed in the studied oil-contaminated soils against the background of a decrease in the biomass and diversity of bacteria relative to the control. It was found that an increase in the matric potential of soil water from –800 to –0.1 kPa, simultaneously with an increase in the number of metabolically active representatives of bacteria and the number of alkB gene copies in the oil-contaminated soils incubated at 28°C corresponded to a decrease in the residual content of alkanes to 51

One-hundred-and-fifty strains of streptomycetes have been isolated from gray and dark gray forest soils, as well as from typical chernozem. The isolated strains were analyzed in vitro for antimicrobial activity on nutrient media and in gray forest soil against 23 collection pathogenic test cultures of fungi and bacteria. Four biologically active isolates with a wide action spectrum have been identified and deposited at the All-Russia Collection of Industrial Microorganisms of the National Research Center “Kurchatov Institute” under the following numbers: Streptomyces xiamenensis TB VKPM As-2204, Streptomyces anulatus TG VKPM As-2203, Streptomyces sindenensis TK VKPM As-2205, and Streptomyces flavovirens TT VKPM As-2202. A study of the effect of presowing treatment of wheat seeds with 15-day culture liquids of S. xiamenensis TB VKPM As-2204, S. anulatus TG VKPM As-2203, and S. sindenensis TK VKPM As-2205 for germination rates and levels of infection with F. graminearum has revealed that they inhibited the growth of a pathogenic fungus and improved the seed vigor and germination of wheat. The resulting strains of soil actinomycetes can be used in biotechnology for creating new bioinoculants to combat phytopathogenic bacteria and fungi. The strains can also be used for stimulating the plant growth, as well as for soil bioremediation in organic farming. Based on the HPLC method (high-performance liquid chromatography), we have identified specialized antimicrobial metabolites of monosporous strain suspensions. The identified antibiotics are N-Butylbenzenesulfonamide, 1-(1H-Benzo[d]imidazol-2-yl)ethan-1-ol, 2-[(3S)-1-(Cyclohexylmethyl)-3-pyrrolidinyl]-1H-benzimidazole-5-carbonitrile, Cyclo(leucylprolyl), and Cyclo(phenylalanyl-prolyl). The identified antiseptics are Cetrimonium and Carvone. The identified phytohormone is auxin indole-3-acetic acid (IAA). Observation of the dynamics of development of the introduced actinobacteria in soil samples has shown a high activity of streptomycetes that use chitin. Analysis of the diversity of the prokaryotic complex of the studied soil samples based on high-throughput sequencing of the conserved region of the 16S rRNA gene has revealed its controlling role in the microbial community during the introduction of S. xiamenensis TB VKPM As-2204, which is determined by its antibiotic-forming activity.

The structural and functional components of the microbial complex of chernozem, in particular, its prokaryotic component, were studied in order to assess the possible toxic effect of potassium chloride applied together with mineral nitrogen fertilizers. Soil samples of typical chernozem were taken from the experimental plots with application of nitrogen–phosphorus and nitrogen–phosphorus–potassium fertilizers. To obtain a stable effect of soluble salts on the microbial community of soil, long-term composting of the samples with alternating drying and moistening cycles was performed. During the first two years of composting, the r the suppression of carbon dioxide emission was detected. It was completely leveled out only five years later. The initial reduction in carbon dioxide emissions, as well as denitrification activity, reached twofold values. The negative effect was manifested when the content of chlorides and nitrates in the soil was significantly lower than the level established for slightly saline soils. Long-term composting of the samples treated with potassium chloride led to a decrease in the number and biomass of the metabolically active prokaryotic microorganisms, which confirmed its toxic effect on the microbial community of the soil. Representatives of the prokaryotic complex tolerant and sensitive towards the increased concentrations of chlorides and nitrates in the soil were identified. Almost all representatives of the Bacteria domain, except for Firmicutes and Verrucomicrobia phyla, were sensitive to these salts. Sensitivity to chlorine ions was confirmed at the generic level (Streptomyces and Micromonospora) for some representatives of the phylogenetic group of Actinobacteria. For the Archaea domain, representatives of the Euryarchaeota phylum were identified as the most tolerant towards the presence of chlorides. Thus, the suppression of the microbiological activity of chernozem under the impact of potassium chloride explains the earlier identified decrease in the availability of nutrients.

Natural peatlands represent a wide range of habitats that contribute to the conservation of biodiversity, including microbial biodiversity. Molecular biological methods make it possible to significantly increase the accounting of microbial diversity compared to the cultivation methods. The studies on microbial diversity in minerotrophic peatlands using molecular biological methods lag significantly behind such studies for ombrotrophic peatlands. In this work, we characterized the taxonomic composition and functional potential of the prokaryotic community of the minerotrophic pine swamp (fen) in the Tver region of northwestern Russia using high-throughput sequencing of 16S rRNA gene fragments. This study is unique, since it was carried out not in individual horizons but across the entire fen profile, taking into account the differentiation of the profile into the acrotelm and catotelm. The composition and dominants of bacterial and archaeal communities were determined not only at the level of phyla but also at the level of classes, families, and cultivated genera. The prokaryotic community of the studied fen was shown to have a high taxonomic diversity (28 bacterial and 10 archaeal phyla were identified). The profile differentiation of the taxonomic composition of prokaryotic communities is most clearly manifested in the analysis of the acrotelm and catotelm. In the bacterial communities of the acrotelm, the top three phyla included Acidobacteriota, Alphaproteobacteria, and Actinomycetota, in the catotelm—Betaproteobacteria, Bacteroidota, and Chloroflexota. In archaeal communities of the acrotelm, we discovered the monodominance of Nitrososphaerota, in the catotelm—the dominance of Bathyarchaeota and subdominance of Thermoplasmatota, Halobacterota, and Aenigmarchaeota. The hot spots of microbial diversity in the studied fen profile were found to be the 0–20 cm layer of the acrotelm and the 150–200 cm layer of the catotelm. In contrast to the taxonomic composition, the functional profiles of the prokaryotic communities of the acrotelm and catotelm were generally similar, except for methane metabolism, which was primarily carried out in the catotelm.

The article summarizes the results of recent research by the staff of Soil Biology Department Faculty of Soil Science of Lomonosov Moscow State University in the field of assessing the genetic potential of microbial communities of soils and their application in the development of fundamental soil and environmental technologies. Promising areas of further work related to the use of the microbial potential of soils for the purpose of bioremediation territories from ecotoxicants, the development of technologies for selfpurification of soils based on the stimulation of natural communities of microorganisms, as well as the use of microbial cultures for biodegradation of petroleum products, pesticides and synthetic polymers. Another important direction is related to the development of scientific basis for the indication of biological objects in the environment and space objects. Within the framework of this direction, genomic analysis of uncultivated microorganisms from the Arctic, Antarctic and other extreme habitats is carried out, and the knowledge gained apply as a model of alien life. Another relevant direction for the Department of Soil Biology is the development of agrobiotechnologies based on the management of the natural soil microbiome, the creation of microbial preparationsstimulators of plant growth and development, microbiological ways to increase the proportion of biological nitrogen in plant nutrition, application of microbial plant endosymbionts and bioinsecticides. An equally important aspect is the search of producers of biologically active substances, such as phytohormones, antibiotics, enzymes, probiotics, hydrolytics of natural and artificial polymers. The considered areas of research in the field of soil biology are important for improving land management, environmental protection and the development of environmental technologies.

The effect of nitrate and potassium chloride salts, on the structure of the metabolically active prokaryotic community of oil-contaminated chernozem has been studied. Molecular biological approaches and bioinformatic methods of analysis were used in the study. The objects of the study were samples of chernozem selected in the Voronezh region (N 51°1′41″, E 40°43′31″). The phylogenetic and functional diversity of the prokaryotic complex of oil-contaminated chernozem was considered when introducing nitrate and potassium chloride under conditions of a slightly alkaline reaction of the medium. Contamination of chernozem with oil in an amount of 5% of the soil mass led to alkalinization of the medium from 7.1 to 7.9. The introduction of nitrate and potassium chloride, both separately and together in a total dose of 2 mmol/100 g of soil removed this negative effect. The combined addition of nitrate and potassium chloride led to a more than twofold increase in the biomass of metabolically active prokaryotic cells and the number of copies of functional genes responsible for the synthesis of alkanmonooxygenase enzymes involved in the decomposition of oil. In the presence of oil, the formation of a specific complex of bacteria was revealed, in which representatives of A-ctinobacteria (Rhodococcus erythropolis) and Alphaproteobacteria (Bradyrhizobium japonicum) prevailed. Rhodococcus erythropolis and Bradyrhizobium japonicum, being autochthonous organisms in uncontaminated soil, began to occupy dominant positions in oil-contaminated samples, and the introduction of nitrates enhanced this effect.

The article summarizes the results of recent research on assessment of the genetic potential of microbial communities of soils and their application to the development of fundamental soil science and environmental technologies carried out by the staff of the Soil Biology Department of the Faculty of Soil Science, Moscow State University. Future promising lines of work are formulated with respect to the use of the microbial potential of soils for the purpose of bioremediation of territories due to ecotoxicants and the creation of technologies for self-purification of soils based on stimulation of the natural communities of microorganisms, as well as the use of microbial cultures for biodegradation of petroleum products, pesticides, and synthetic polymers. Another important area lies in constructing the scientific bases of the bioindication in the environment and space objects. Genomic analysis of nonculturable microorganisms from the Arctic, Antarctica, and other extreme habitats is performed within the framework of this direction, while the derived knowledge is used to model life on other planets. Development of agrobiotechnologies based on the management of the natural soil microbiome is another up-to-date research line at the Department of Soil Biology, as well as the creation of microbial formulations, specifically, plant-growth promoters and microbiological ways to increase a proportion of biological nitrogen in plant nutrition and the use of microbial plant endosymbionts and bioinsecticides. Search for the producers of biologically active substances, such as phytohormones, antibiotics, enzymes, probiotics, and hydrolytics of naturally occurring and artificial polymers, is an equally important aspect of the research work. The considered areas of research in the field of soil biology are essential for improving land management, environmental protection, and development of environmental technologies.

The phylogenetic and functional diversity of the prokaryotic complex with a biotechnological potential (decomposing biopolymers and hydrocarbons; capable of synthesizing secondary metabolites; and involved in nitrogen fixation) in soils and associated ecosystems has been studied. In order to identify the specific features in the development of metabolically active prokaryotes with biotechnological potential, the patterns of their distribution and the dependence of functional activity on the main environmental factors have been established using molecular biological and bioinformatics approaches. The range of the studied samples includes modern soils (Volgograd, Tula, and Moscow oblasts; Siberia; and the northern part of Central Kamchatka), relict habitats (Volgograd oblast and Central Kamchatka), and permafrost soils of the Antarctic (King George Island). The impact of anthropogenic and abiogenic loads on the development of the prokaryotic community is considered. Along with a decrease in the diversity and abundance of prokaryotes, the number of genes marking the ability of community to biodegrade xenobiotics increases in the soils exposed to anthropogenic or abiogenic loads, as well as of the genes coding for nitrogen transformations and the level of metabolism of cofactors and vitamins. The bacterial complex is capable of nitrification at a high oil pollution of soil and its role increases in the lower layers of the soil profile. Archaea play a leading role in the nitrification in undisturbed soils. The observed patterns suggest a high metabolic potential of the prokaryotic component in the examined objects and open up the opportunities for biotechnological use of the strains isolated from relict habitats.

The evaluation of antibiotic and chitinolytic activity in actinomycetes isolated from soddy-podzolic soil (Albic Retisol (Loamic)) was carried out in Moscow region (56°07′15″ N, 37°30′54″ E). Isolated strains were classified as Streptomyces avidinii INA 01467 and Micromonospora aurantiaca INA 01468 on the basis of cultural and morphological features and analysis of the 16S rRNA gene. Evaluation of the antibiotic activity of isolated actinomycete cultures showed that the strains exhibit both antibacterial activity against gram-positive bacteria and antifungal activity against the collection strains of fungi Sac. cerevisiae INA 01042, C. albicans ATCC 14053, and F. oxysporum VKPM F-148. The ability to synthesize antifungal compounds increased when growing on a medium with chitin by the Streptomyces avidinii INA 01467 strain, including the phytopathogenic Fusarium oxysporum VKPM F-148 strain. Using the Real-Time PCR (Real-Time-PCR) method, the presence of functional genes shitA, responsible for the synthesis of group A chitinase enzymes, was found in the studied bacterial strains of Streptomyces and Micromonospora. The largest amount of the gene was found in the strain Streptomyces avidinii INA 01467, when growing on chitin, and reaches about 15 × 103 copies per mL. The results demonstrated the presence of chitinase and antibiotic activity in the studied strains, including the activity against phytopathogenic fungi, and this allows using these strains in plant protection technologies and soil bioremediation.

The actinomycete complexes of eutrophic peatlands differing by genesis were studied in order to broaden the knowledge of microorganisms' biodiversity in wetland ecosystems and to detect microorganisms with a high potential for antagonistic action. The research sites included eutrophic peatlands of lacustrine, forest, and floodplain origins in Tver and Tomsk regions, Russia. Samples from the 3-m-thick peatlands were taken layer-by-layer with due account for the botanical composition of peat in September 2019. The length and biomass of the mycelium of actinomycetes were determined by luminescent microscopy; and the number of culturable actinomycetes was determined by plate method. The actinomycetes species were identified by their morphological and cultural features and the analysis of 16S rRNA fragments. The antagonistic activity of streptomycetes was analyzed by the method of agar blocks. The actinomycetic mycelium was found throughout the peatland profiles. Its length varied from 700 to 3000 m/g dry peat and its biomass was from 22 to 140 mg/g dry peat. A reliable correlation between the abundance of actinomycetic mycelium and the botanical composition of peat was determined for the first time. It was also found that the abundance of actinomycetic mycelium depends on the degree of decomposition of profile-forming peat. The actinomycete complex included representatives of the Streptomyces, Micromonospora, Streptosporangium, and Streptoverticillium genera. Representatives of Streptomyces were dominant according to their occurrence frequency and were assigned to 19 species from 9 series and 5 sections. About 70% of the studied actinomycetes demonstrated the ability for microaerophilic growth. This fact indicated that these actinomycetes are adapted to the oxygen deficiency in the deep layers of peatlands. Antibacterial activity was found in 89% of the isolates. S. avicenniae and S. caeruleus proved to be the most active strains with antibacterial activity and multiple resistance to antibiotics.

An Erratum to this paper has been published: https://doi.org/10.1134/S0026261722300142

In 1995–1998 and 2013–2016, we measured methane fluxes (1Q-median-3Q, mgC m−2 h−1) in the Petushikha black alder swamp of the boreo-nemoral zone of European Russia. At microelevations (EL sites), flat surfaces (FL), microdepressions (DEP), and water surfaces of streams and channels (STR) sites, the fluxes comprised 0.01–0.03–0.09, 0.02–0.06–0.19, 0.04–0.14–0.43, and 0.10–0.21–0.44, respectively. The biggest uncertainty of methane fluxes was caused by seasonal variability (the level of relative variability of fluxes is a nonparametric analogue of the coefficient of variation) which comprised 144%, then by spatial variability—105%, and the smallest by interannual variability—75%. Both spatial and temporal variability of methane fluxes at different elements of the microrelief is heterogeneous: the most variable are communities that are “unstable” in terms of hydrological conditions, such as FL and DEP, and the least variable are the most drained EL and the most moistened STR (“stable” in terms of hydrological conditions). The obtained data on the fluxes and their spatial and temporal variability are consistent with the literature data and can be used to optimize the process of planning studies of the methane budget of “sporadic methane sources”, such as waterlogged forests. This is especially relevant for an adequate assessment of the role of methane fluxes in the formation of the waterlogged forests carbon budget and a changing climate.

Actinomycetes are an important group of bioactive hydrolytic bacteria in any ecosystem. However, the actinomycete biodiversity in tropical ecosystems, particularly in Vietnam, is still underexplored. The aim of this article is to analyze the abundance, taxonomic structure and ecophysiological features of actinomycete complexes of soils and litter in Vietnam’s protected areas. A total of 41 samples of soils, plant litter and suspended soils were collected from six of Vietnam’s national parks and nature reserves. The direct inoculation technique showed that the total abundance of actinomycetes varied from 2.0 × 104 to 1.0 × 108 CFU/g. According to the luminescent microscopy with acridine orange dye, the length of the actinomycete mycelium was as long as 1000 m/g in the litter of Xuan Son National Park. A total of 80 strains were isolated and tested for antagonistic activity against Bacillus subtilis, Aspergillus niger and Candida albicans. Inoculation on Getchinson’s medium showed high cellulolytic activity. The most active strains were isolated from alluvial brown soil, plant litter and suspended soil of the Pu Hoat Nature Reserve. In these samples, actinomycetes adapted to high temperatures and low pH were found to be predominant. High-throughput sequencing of the V3–V4 region of the 16S rRNA gene and bioinformatic analysis confirmed the high taxonomic diversity and high hydrolytic activity of actinomycete complexes of the Pu Hoat Nature Reserve samples.

A prokaryotic heterotrophic mesophilic community was studied in volcanic soil samples from Kamchatka. A phylogenetic and physiological characterization of the prokaryotic complex of modern and buried soils of the Kamchatka Peninsula is given. Volcanic Paleolithic soils (2500 and 11,300 years old) and their modern equivalents were investigated. It was found that the biomass of metabolically active prokaryotes in modern volcanic and Paleolithic soils reached 50 and 40 µg/g, respectively. The proportion of archaea in the metabolically active prokaryotic complex varied from 20% to 30% and increased in variants with the application of the nitrogen-containing biopolymer chitin. The application of the additional resource to paleovolcanic soils led to an incremental increase in the proportion of metabolically active prokaryotes, which reached 50% of the total prokaryotic biomass detected, indicating the high metabolic potential of the considered soils. Phylogenetic structure characteristics of the prokaryotic metabolically active component of modern and buried volcanic soil were established by molecular biology methods (metagenomic analysis, FISH method). The phylum Proteobacteria (74%), Acidobacteria, and Actinobacteria (14% combined) were dominant in modern soils; phylum Acidobacteria (51.8%) was dominant in paleosoils, whereas Chloroflexi (21%) and Proteobacteria (9%) were subdominant. It was determined that the potential activity of the microbial hydrolytic community, as measured by the relative response to the added resource (chitin), was found to increase in a series from modern to paleovolcanic soil. It was demonstrated that several key genes of the nitrogen cycle responsible for the processes of molecular nitrogen fixation, nitrification, and denitrification (nifH, amoA, nirK) were present in both modern and buried horizons.

The quantitative and qualitative characteristics are given of the soil prokaryotic communities in the Dystric Fluvisol, litter, and "suspended soil" in epiphyte baskets. The number of bacteria (direct luminescence method) varied from 1.1 to 2.6 billion cells/g soil and was the highest in the suspended soil sample and lower in the litter and A and AB horizons of Dystric Fluvisol (brown meadow alluvial soil). Proteobacteria, Actinobacteria, and Acidobacteria predominated in the prokaryotic community (at the phylum level); Chloroflexi, Firmicutes, and Verrucomicrobia were found in smaller amounts; the content of Nitrospirae, Planctomycetes, and Gemmatimonadetes was even lower. Representatives of the Archaea domain were found in the A horizon and in the suspended soil. Their content was significantly lower than that of the Bacteria domain and did not exceed 1%. Archaea were represented by the Thaumarchaeota and Euryarchaeota phyla in the A horizon and by Thaumarchaeota and Woesearchaeota phyla in the suspended soil. Based on the calculated ecological indices (alpha and beta diversity, measures of similarity by Bray-Curtis metrics and weighted UniFrac), it was shown that the microbiome of the suspended soil was closer to the microbiome of A horizon of Dystric Fluvisol than to the microbiome of litter. The metabolically active part of the prokaryotic community represented by the Proteobacteria, Actinobacteria, and Acidobacteria phyla reached its maximum in the suspended soil and was lower in the litter and A horizon of Dystric Fluvisol, and this correlated with the high abundance of these phyla and the significant taxonomic diversity of bacteria in this locus. Functional genes (nifH and alkB) were detected in all studied substrates. The number of copies of functional genes was the highest in the suspended soil sample, which makes this locus promising for isolating the strains with high biotechnological potential.

Previously conducted space missions revealed the presence of perchlorates, which are known to have a high oxidizing potential in Martian regolith, at the level of 0.5%. Due to hygroscopic properties and crystallization features of perchlorate-containing solutions, assumptions leading to the possibility of the existence of liquid water in the form of brines, which can contribute to the vital activity of microorganisms, have been made. At the same time, high concentrations of perchlorates can inhibit the growth of microorganisms and cause their death. Previously performed studies have discovered the presence of highly diverse microbial communities in terrestrial perchlorate-containing soils and have also demonstrated the stability and activity of some prokaryotes cultured on highly concentrated perchlorates media (over 10%). Nevertheless, the limits of microbial tolerance to perchlorates and whether microbial communities are able to withstand the effects of high concentrations of perchlorates remain uncertain. The aim of this research was to study the reaction of microbial communities of hot-arid and cryo-arid soils and sedimentary rocks to the adding of a highly concentrated solution of sodium perchlorate (5%) in situ. An increase in the total number of prokaryotes, the number of metabolically active Bacteria and Archaea, and the variety of the consumed substrates were revealed. It was observed that in samples incubated with sodium perchlorate, a high taxonomic diversity of the microbial community is preserved at a level comparable to control sample. The study shows that the presence of high concentrations of sodium perchlorate (5%) in the soil does not lead to the death or significant inhibition of microbial communities.