The possibility of using microbiological indicators of soil “health” to assess soils has been considered. The fundamental possibility of quantitative characterization of the functional potential of the microbial system with the assessment of ecological services has been shown. It has been shown that thermodynamic criteria of natural microbial system (exergy and specific exergy) allow carrying out diagnostics of soil condition with direct estimation of degradation and damage. System characteristics of soil microbiota have been shown to be necessary for the solution of many topical problems of functional soil science.

This article contains an analysis of structural and functional parameters of bacterial complexes taken for examination from complete profiles of fens assigned to the Klyukvennoe and Karbyshevskoe wetlands in Tomsk oblast. Bacteria in the fens are revealed throughout the entire profile. Their number determined by a direct method of fluorescence microscopy is high and varies from 27 to 78 × 109 cells/g of dry peat. The high number of saprotrophic bacteria (to 108–109 CFU/g of dry peat) is detected by the plate method. An increase in the number of saprotrophic bacteria down the fen profile is revealed. These data enable us to conclude for the first time that index k (a dimensionless universal characteristic of natural prokaryotic communities) in fen profiles decreases with depth. The bacterial cultures isolated from the fens studied are assigned to ten taxa: Bacillus, Streptomyces, Arthrobacter, Microbacterium, Pseudomonas, Flavobacterium, Dyadobacter, Janthinobacterium, Pedobacter, and Myxobacteriales. The acrotelm is dominated by bacterial cultures represented by genera Bacillus and Streptomyces; and Pseudomonas, Dyadobacter, and Arthrobacter are the dominants of the catotelm. The functions of bacterial genera and species identified by molecular biological methods are described. The study of nitrogen fixation, denitrification, and methanogenesis has shown that bacteria are viable and active throughout the entire peat profile.

This paper describes symbiotic relationships at various succession stages of a meadow phytocoenosis using the example of vesicular–arbuscular mycorrhiza of Trifolium pratense L. It is established that the functional potential of symbiotic relationships changes in the course of the succession, and it is fully realized in undisturbed climax communities. It is shown that discriminant analysis of biometric parameters of a single leguminous plant performed taking into account its symbiotic potential can be used for biological diagnostics of the phytocoenosis state (i.e., succession stage).

The known conceptions of resistome as a complex of all the antibiotic resistance genes in the genomes of all the microorganisms, pathogenic and nonpathogenic ones, in nature are considered. The data on the origin, evolution and distribution of antibiotic resistance genes and possible approaches to the resistance distribution control are presented.

Application of molecular biological techniques in environmental studies provides a more complete information concerning the taxonomic diversity and potential hydrolytic activity of soil microbial complexes that exist in a wide range of environmental factors. Among the key environmental parameters that determine the functional activity of the hydrolytic complex of soil layer, the most significant one is moisture. Moisture levels providing maximum activity of a hydrolytic microbial complex depend on the soil type. At high levels of moisture and temperature, the role of prokaryotic organisms, mainly actinomycetes, in the microbial complex significantly increases. It was discovered a new functional activity of actinomycetes in the hydrolytic prokaryotic complex: their controlling influence on the respiratory level of the complex in a wide range of parameters (moisture, organic matter, successional time).At the optimum for the life of most microorganisms levels of moisture (60% of field capacity) and temperature (27°C), representatives of Firmicutes and Actinobacteria phylums stand out among chitinolytic and pectinolytic dominants of the studied soils within the Bacteria domain. With increasing moisture and decreasing temperature the proportion of Proteobacteria increases. With decreasing moisture and increasing temperature, there is an increase in the amount of unicellular actinobacteria.

The paper presents a comparative analysis of the structural and functional characteristics of microbial communities of gray forest soil of fallow and intensively cultivated areas. The long-term anthropogenic impact with massive annual mineral fertilization when growing a monoculture of potatoes has led to degradation of the soil microbial system. A catastrophic decrease in the functional potential of the microbial system (environmental services) is shown using eco-exergy as a thermodynamic indicator of soil “health”.

The review considers some problems of soil microbial system management, as well as the possibilities, constraints, and risks caused by environmental and food security problems. A natural microbial system, which obeys its own dynamic laws, is considered a required condition for the existence of a biosphere. Ignorance and disregard of these laws can lead to catastrophic consequences for the higher hierarchical system in which humanity acts.

Four previously isolated methanogenic anaerobic consortia, which were originally cultivated on a cellulose-containing substrate (filter paper), were used as inocula for the anaerobic conversion of the biomass of Anabaena variabilis into biogas at 55°C. The cumulative methane yield in the biogas produced by the most active consortia reached 64%. However, the biotransformation was only efficient in the course of the single inoculation and pretreatment of the cyanobacterial biomass by its concentration and freeze-thawing. The DGGE analysis of the structure of the selected microbial consortia, cultivated on the filter paper, revealed qualitative variations in the biodiversity of predominant Bacteria, showing differences in band number and intensity. The composition of methanogenic Archaea in these consortia was similar, with the presence of the genera Methanoculleus and Methanosarcina. The efficiency of the microbial consortia selection, and the role of the various microbial trophic groups in bioconversion of the substrates, such as cellulose and the biomass of phototrophic microorganisms are discussed.

The possibility of using the method of exhaustion (removal sampling) applied to determine the absolute number of Bacteria and Archaea populations in soil based on accounting data for quantitative fluorescence in situ hybridization has been shown.

DNA isolation from soil samples and amplification of fragment of a key gene of nitrification, archaeal and bacterial amoA, revealed presence of the product in all investigated soil samples. Characteristics of ammonia-oxidizing microbial communities in agrocenoses and undisturbed soil were determined. Bacteria were predominant in agrocenoses (at circum-neurtal pH), whereas the share of representatives of domain Archaea (phylum Thaumarchaeota) increased in prokaryotic ammonia-oxidizing complexes of undisturbed forest ecosystems (at low pH). It was demonstrated that the contribution of taumarhaea in nitrous oxide emission from gray forest soil may reach 20–25%.

Streptomycetes or mycelial microorganisms are able to form biofilms under the natural, industrial and clinical conditions. The controlled use of biofilms in various industrial processes is much more efficient vs. the cultivation of plankton suspended cells. Optimization of biotechnological processes with the use of streptomycete biofilms is advisable in production of lactic acid and detoxication of the liquor in pyrolysis of plant biomass. Streptomycete biofilms are used in water purification systems. It is recommended to use biofilms for detoxication of wastes and bioremediation of soils contaminated with hard metals. The use of biofilms of streptomycetes producing biologically active substances is of special interest. High yields of antibiotics and actinomycin D in particular was observed with cultivation of antibioc-producing streptomycetes as biofilms in bioreactors of unique design.

Streptomycetes, soil-dwelling mycelial bacteria, can form biofilms as indigenous components of the environment. The biofilms formed by streptomycetes exist in different ecological niches, in natural, medical, industrial environments. The biofilm-forming streptomycetes affect water quality, human health, associate with deterioration of artworks and historical monuments. The review should be of interest for researchers of the biofilm mode of streptomycetes growth.

Установлена высокая численность (до сотен тысяч и миллионов КОЕ/г почвы) мицелиальных бактерий (актиномицетов), выделяемых из засоленных почв аридных территорий Украины, России, Туркменистана. Среди всех изученных почв достоверно меньшее (тысячи и десятки тысяч КОЕ/г почвы) количество актиномицетов выделяется из соровых и содовых солончаков, формирующихся на дне пересыхащих соленых озер в Бурятии и в дельте Аму-Дарьи. Актиномицеты представлены в исследуемых почвах родами Streptomyces, Micromonospora, Nocardiopsis. Выявлено, что на активность потребления субстратов культурами актиномицетов в значительной степени влияют условия предынкубирования, что, очевидно, связано с перестройкой метаболизма актиномицетов как одного из механизмов адаптации к повышенной осмолярности среды. Экспериментально установлена алкалотолерантность галотолерантных актиномицетов, выделенных из почв засоленных территорий.

A high population density (up to hundreds of thousands or millions CFU/g soil) of mycelial bacteria (actinomycetes) is determined in salt-affected soils of arid territories of Ukraine, Russia, and Turkmenistan. Of all the studied soils, the lowest amounts of actinomycetes (thousands and tens of thousands CFU/g soil) are isolated from sor (playa) and soda solonchaks developed on the bottoms of drying salt lakes in Buryatia and in the Amu Darya Delta. Actinomycetes of the Streptomyces, Micromonospora , and Nocardiopsis genera were recorded in the studied soils. It is found that conditions of preincubation greatly affect the activity of substrate consumption by the cultures of actinomycetes. This could be attributed to changes in the metabolism of actinomycetes as a mechanism of their adaptation to the increased osmotic pressure of the medium. The alkali tolerance of halotolerant actinomycetes isolated from the salt-affected soils is experimentally proved.

Streptomycetes or mycelial microorganisms are able to form biofilms under the natural, industrial and clinical conditions. The controlled use of biofilms in various industrial processes is much more efficient vs. the cultivation of plankton suspended cells. Optimization of biotechnological processes with the use of streptomycete biofilms is advisable in production of lactic acid and detoxication of the liquor in pyrolysis of plant biomass. Streptomycete biofilms are used in water purification systems. It is recommended to use biofilms for detoxication of wastes and bioremediation of soils contaminated with hard metals. The use of biofilms of streptomycetes producing biologically active substances is of special interest. High yields of.antibiotics and actinomycin D in particular was observed with. cultivation of antibioc-producing streptomycetes as biofilms in bioreactors of unique design.