Vol 88, No 6 (2019)

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

Members of the order Thermotogales often occur in high-temperature oilfields. They possess a toga, a characteristic external sheath. Members of the genus Geotoga have been as yet isolated only from oilfields and are represented by three strains with unsequenced genomes. The information on the intraspecific phenotypic diversity is scarce. An enrichment growing anaerobically on oil was obtained from formation water of the Vostochno-Anzirskoe oilfield (Russia). High-throughput sequencing of the V3–V4 region of the 16S rRNA genes revealed the enrichment to contain members of the genera Tangfeifania (51% of the total number of sequences), Halanaerobium (36%), Arcobacter (10%), and Geotoga (3%). Strain HO-Geo1 isolated from this enrichment belonged to the known species Geotoga petraea (99.2% similarity of the 16S rRNA gene sequences). The cells were motile rods surrounded by sheaths. They grew anaerobically, fermented carbohydrates and proteins producing acetate, H₂, and СО₂, and reduced thiosulfate and elemental sulfur to sulfide. In pure culture the strain did not grow on oil. Growth occurred within broad ranges of temperature (24–55°C, optimum at 47–50°C) and salinity (0.2–140 g/L, optimum at 20–40 g/L), which was in agreement with conditions of the low-temperature oilfield with highly mineralized formation water. The genome of strain HO-Geo1 (~2.15 Mb) contained 2057 genes, most of which were involved in protein, amino acid, and carbohydrate metabolism. High salt-tolerance of strain HO-Geo1 depended on the genes of adaptation to hyperosmotic stress. H₂ formation was determined by the presence of the genes encoding all four subunits of NADP-dependent dehydrogenase. In oilfields, members of the genus Geotoga probably utilize microbial biomass and the products of oil biodegradation formed by other microorganisms. They may be involved in corrosion of metal oilfield equipment.

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

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

Wild varieties of plants have stronger stress resistances than their cultivated relatives, and rhizosphere bacteria play an important role in improving the environmental adaptabilities of plants. However, the responses and adaptations of bacterial communities to wild soybean (Glycine soja Sieb. et Zucc) and cultivated soybean (Glycine max L.) have rarely been studied. Thus, the aim of this study was to investigate the differences in the rhizosphere bacterial communities of wild and cultivated soybeans under field and potted conditions using metagenomic analysis. The results showed that the rhizosphere bacterial diversity was higher in wild soybean than that in cultivated soybean in field samples, indicating that domestication leads to a decrease in the rhizosphere bacterial diversity of cultivated soybean. In addition, the higher RAs of beneficial and plant growth-promoting bacteria such as Acidobacteria, Gemmatimonadetes,Bradyrhizobium and Bacillus were in the wild soybean rhizosphere, illustrating that wild soybean has a stronger environmental resistance and adaptation than cultivated soybean. Meanwhile, soil pH, soil organic carbon, total nitrogen, total phosphorus, available phosphorus, and available potassium were significantly correlated with rhizosphere bacteria. Collectively, the rhizosphere bacteria of wild and cultivated soybean were different, wild soybeans increase the numbers of beneficial microbes in the rhizosphere to improve their environmental adaptability, and the utilization of wild resources might be an effective way to improve crop stress resistance.

Soil is not only a habitat of antibiotic-resistant microorganisms and a natural source of antibiotic resistance genes, but also an environment in which clinical determinants of antibiotic resistance may be accumulated and transferred. Quantitative assessment of antibiotic-resistant bacteria in polluted soils used in agriculture and its comparison to the so-called baseline content of resistant bacteria and their resistance genes in the soil is therefore urgent. However, the data on the study of antibiotic-resistant bacteria in pristine soils (with minimal anthropogenic impact) are practically absent. Comparative study was therefore carried out on the spectra of resistance to natural and synthetic antibiotics among gram-negative bacteria isolated from various soils: pristine (Arctic and Antarctic soils); sites with possible pollution (Albic Retisols (IUSS Working Group WRB, 2015) of a woodland park area in the Moscow region), and moderately polluted soils with high mercury content (near the Khaidarkan mercury mine). It was revealed that strains resistant to one or more of the used natural antibiotics, with the exception of tetracycline, were found in all types of biotopes. About one third of the studied strains, both isolated from soils of polar regions with low anthropogenic impact, and from polluted soils near the Khaidarkan mercury mine, exhibited multiple drug resistance. These results suggest that the presence of multiple antibiotic resistance among bacteria is not solely a response to anthropogenic pollution. Bacterial strains with multidrug antibiotic resistance isolated from the biotopes formed in extremely cold conditions belonged mainly to the genera among the representatives of which intrinsic resistance is widespread, due to the specific structure of their cell walls, preventing antibiotic penetration into the cell, and to the presence of various nonspecific efflux systems of release of toxic substances from the cell.

The concepts on the nature of antibiofilm agents and strategies for their search, which exist in modern literature, are analyzed. A new classification of these compounds is proposed, with subdivision into four major classes depending on their mechanism of action. An advanced system of screening for the pro- and antibiofilm agents is proposed, which will make it possible to improve the efficiency of selection and to expand the spectrum of these compounds.

Sulfobacillus thermotolerans predominates in communities of acidophilic chemolithotrophic microorganisms and is of practical importance to biotechnologies for sulfide minerals processing. This is the first report on the presence of the genes encoding a quinone-binding [Fe-Ni] hydrogenase in S. thermotole-rans genome; this microorganism is therefore potentially capable of lithotrophic growth in the presence of molecular hydrogen. Components of the pathways for nitrogen compounds assimilation by S. thermotolerans probably include two assimilatory nitrate reductases, while NO dioxygenase and nitronate monooxygenases are probably involved in detoxication of nitric oxide and nitrocompounds. Research on the pathways of assimilation and detoxication of nitrogen compounds, as well as on alternative electron donors and acceptors in sulfobacilli will improve our understanding of the interactions within acidophilic chemolithotrophic communities in nature and industry.

The T5 group bacteriophages, which infect a number of enterobacterial species and strains, are useful objects for obtaining therapeutic phage preparations with broad specificity. The present work considers the biological properties of T5-related phages responsible for their ability to infect a broad spectrum of bacterial strains in spite of a limited number of known phage receptor proteins. Ability of bacteriophages to recognize bacterial O-antigens specifically enhances their capacity for infection and increases the therapeutic potential of the T5 phages.

In the present work, separation and quantitative assessment of bacteriochlorophylls d and e of green sulfur bacteria (GSB) in lake water was attempted. The method developed reveals the ratio of green- and brown-colored GSB in natural water by measurement of absorption spectra of the pigments in the extracts from environmental samples.