No 5 (2023)

The diversity of bacteria cultured from the soil of the Negev desert (Israel, sample SN2) and the sedimentary rock of the Sahara Desert (Tunisia, sample Alg) has been studied. To assess the ability of bacteria to metabolize at different levels of moisture availability and to reveal bacterial diversity more fully, culturing was carried out on R2A medium with the addition of glycerol to establish a certain level of water activity (Aw) in range from 1.0 to 0.9 (with a step of 0.01 Aw). After incubation, unique morphotypes of cultured bacteria were isolated, described, identified by 16S rRNA sequencing, and tested for the ability to grow in the Aw gradient in pure cultures. After incubation and isolation, 355 strains were identified and tested. Culturable bacteria were found at Aw 0.95 and higher. With a decrease in Aw from 1 to 0.95, the number of cultured bacteria decreased from 10⁵ and 10⁷ CFU/g in samples SN2 and Alg, respectively, to 2 × 10⁴ CFU/g in both studied samples. As a result of culturing, representatives of 34 genera of bacteria were isolated, mainly representatives of the phylum Actinobacteria; representatives of the genera Arthrobacter, Kocuria, and Pseudarthrobacter dominated. At this, 38 strains with low similarity of nucleotide sequences with databases and, probably, being representatives of previously undescribed species of the genera Agrococcus, Arthrobacter, Bacillus, Brachybacterium, Cellulomonas, Conyzicola, Kocuria, Microbacterium, Okibacterium, Rathayibacter, and Sphingomonas were revealed. Testing the strains for their ability to grow in pure culture in a gradient of Aw values revealed 18 strains of the genera Arthrobacter, Kocuria, Brachybacterium, Serratia, and Leucobacter capable of growing at Aw 0.91. The study confirms the data that desert soils and rocks are a depository of previously undescribed bacterial species and can also be a valuable source of biotechnologically promising strains.

The phylogenetic and functional diversity of a prokaryotic complex with biotechnological potential (carrying out the destruction of biopolymers, hydrocarbons; capable of synthesizing secondary metabolites; nitrogen fixation process) in soil and associated ecosystems has been studied. In order to identify the specifics of 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. The study used molecular biological and bioinformatic approaches. The range of samples studied included modern soils (Volgograd, Tula, Moscow regions, Siberia and the Northern part of Central Kamchatka), relict habitats (Volgograd Region and Central Kamchatka) and permafrost soils of Antarctica (King George Island). The impact of anthropogenic and abiogenic loads on the development of the prokaryotic community was considered. In soils exposed to anthropogenic or abiogenic loads, along with a decrease in the diversity and abundance of prokaryotes, an increase in the number of genes marking the ability of a community to biodegradate xenobiotics, as well as genes encoding nitrogen transformations and the level of metabolism of cofactors and vitamins was found. The bacterial complex is capable of nitrification with high oil contamination of the soil, and its role also increases in the lower layers of the soil profile. Archaea play a leading role in the nitrification process in undisturbed soils. The revealed patterns indicate a high metabolic potential of the prokaryotic component of the objects under consideration and open up opportunities for biotechnological use of strains isolated from relict habitats.

One of the promising approaches to solving the issues of ecosystem resilience to stress is to assess the response of microbial communities of soils performing important ecological and biospheric functions to natural or anthropogenic impacts. In a model experiment with sod-podzolic soil (Eutric Albic Retisols (Abruptic, Loamic), the inhibitory effect of ammonium and the stimulating effect of lanthanum on the oxidation of methane by soil microorganisms were established. The addition of ammonium and lanthanum reduced the taxonomic diversity of the bacterial community of the soil and changed its structure: the relative content of Gram-positive bacteria of the phylum Actinobacteriota and Bacillota decreased, while the proportion of gram-negative bacteria of the phylum Pseudomonadota increased. The introduction of lanthanum significantly, by several orders of magnitude, increases the relative content in the community of methanotrophs of the genus Methylobacter and obligate methylotrophs of the genus Methylotenera. The results of the work can be used to develop approaches for regulating the activity of the soil “methane filter” and the accompanying microbiota.

Bentonite clays have a large specific surface area and a large Vume of pore space, which determines their high sorption capacity and allows them to be used as one of the barriers in the construction of deep geological repositories (DGR). It is expected that DGR will function for thousands of years, so the problem of forecasting changes that may occur during this time is relevant. During the functioning of DGR, bentonites can change their properties due to microbiological effects. In this work was analyzed the microbial community structure of two bentonites from 10th Khutor and Taganskoye disposal at different temperatures (25 and 60°C) of incubation. In bentonite from the 10th Khutor deposit, 10 phyla and 92 genera of bacteria were identified during incubation at 60°С, while 12 phyla and 94 genera were identified during incubation at 25°С. In bentonite from the Taganskoye deposit, 14 phyla and 87 genera were identified during incubation at 60°С, and 15 phyla and 123 genera were identified during incubation at 25°С. Samples were dominated with bacteria of Proteobacteria and Firmicutes phyla. It was concluded that is the main factor influencing the formation of the microbial in the studied bentonites community is temperature, and not the chemical and mineral composition of examined bentonites.

The soil actinobiota of various climatic zones are a rich source of bioactive natural products, including novel drugs. A complex of soil actinomycetes in the upper horizon of the grumusols (Vertisols) on the western coast of Lake Kinneret in the vicinity of Tiberias (Lower Galilee, Israel) was studied. The screening of the antagonistic activity of 26 isolates using on a dual reporter system revealed the bacterial strain 3IZ-6, which had the ability to inhibit protein synthesis. Strain 3IZ-6 was assigned to Streptomyces rochei by polyphase taxonomy approach. The active substance of S. rochei 3IZ-6 was isolated and purified using solid-phase extraction and HPLC. Toe-print analysis and mass spectrometry data allowed to establish, that active compound is a known inhibitor of protein biosynthesis, borrelidin. S. rochei 3IZ-6 can be used as a producer of borrelidin in biocontrol against phytopathogens and weeds.

In a model laboratory experiment on infertile arable soil with low biological activity, it was found that the introduction of glyphosate leads to a short-term change in the intensity of the main processes of microbial transformation of nitrogen in the soil. When incubating soil with glyphosate at the maximum recommended dose of 8 l/ha for 22 days, there is an increase in nitrogen-fixing and denitrifying activity by 30–80% and 300% and a decrease in the nitrification process by 20–40%. The effects are of a short-term nature and do not reflect the entire complex of ongoing microbiological processes: no effect of glyphosate was detected on the emission of CO₂, which is an integral indicator of biological activity. At the end of incubation in the soil with the introduced glyphosate, there was an increase in the number of bacteria by 40% and a decrease in the number of micromycetes by 70%. In general, under the selected conditions, the introduction of glyphosate led to a marked deterioration in the biological activity of the soil. By the method of multisubstrate testing, it was shown that under the action of the herbicide there is an increase in the value of the coefficient of rank diversity of the consumption spectra of substrates d, accompanied by a decrease in the specific metabolic work W and the integral vitality index G. It was shown for the first time that when glyphosate is introduced into soil with low biological activity and availability of phosphorus and the herbicide is degraded along the sarcosine pathway with a break in the C–P bond, excluding the formation of toxic metabolites, there is a pronounced negative effect of glyphosate on soil microorganisms, which leads to inhibition of wheat plant growth.

The loss of soil organic matter (SOM) due to agricultural land use has a negative impact on soil properties and is one of the major contributors to the increase in atmospheric CO₂ concentrations. An appropriate way for simultaneous restoration of POM stocks and deposition of sequestered carbon is the straw application to the soil. The aim of the study was to evaluate the effect of straw on the quantitative indicators of different groups of microorganisms in sod-podzolic soil (Umbric Retisol) in a long-term field experiment. Introduction of straw increased microbial biomass carbon (Cmic) by 1.25–2 times, with the greatest increase in microbial biomass observed in the variants without fertilizer. Basal respiration and respiration coefficient (qCO₂) increased in the row: control < NPK < NPK + straw < straw. Application of straw increased the gene copy number of fungi and bacteria up to 2 times and archaea up to 1.5 times. Mineral fertilizer application without straw reduced qCO₂, fungi biomass and archaeal gene copy number by 1.5–3.0 times. The fungi/bacteria ratio varied from 4 to 15 determined by fluorescent microscopy and from 0.17 to 0.33 by quantitative PCR. The lowest values of fungi/bacteria ratios were found in soils with the application of mineral fertilizers, and the highest – with the incorporation of straw. Thus, the regular introduction of fresh organic matter of straw is an important technological procedure to increase the microbiological activity of soil and leveling the negative impact of mineral fertilizers on soil microbiota.

The complex (quantitative and qualitative) characteristics of prokaryotic communities of solid atmospheric fallouts (dust aerosol) and soils in the territory of Moscow in areas with different intensity of anthropogenic load have been done. The total number of bacteria in the studied samples of solid atmospheric fallouts (SAF) was lower than the number of bacteria in soil samples; actinomycete mycelium was not found in the dust samples, although it was found in soil samples. The number of culturable saprotrophic bacteria in dust samples was an order of magnitude lower than in Urbic Technosols taken from the same plots. Representatives of the genus Micrococcus dominated among cultivated bacteria in the dust aerosols, while representatives of the phylum Proteobacteria dominated in soils. Representatives of the Enterobacteriaceae family were found in the dust samples, among which there are species that are potential human pathogens. The maximum biodiversity of bacteria of the Enterobacteriaceae family was recorded in the dust samples taken in areas with increased anthropogenic and transport load. The sanitary-indicative bacterium Escherichia coli was found in all samples of the dust and Urbic Technosols, its content varied (from 10 to 100 CFU/g), according to the degree of epidemic danger it characterizes dust and soils as moderately dangerous. Ecological indices calculated for prokaryotic communities in situ (barcoding of the 16S rRNA gene) indicate a lower taxonomic diversity of SAF prokaryotic communities compared to communities of closely spaced Urbic Technosols.

The microbial parameters in Albic Podzol soil were analyzed along the pollution gradient (3, 16, 30, 50 km) with Pechenganickel plant emissions (Murmansk region). The amount and structure of the prokaryotes and fungi biomass were assessed by the method of luminescent microscopy; the content of microorganism’s ribosomal genes copies was determined by real-time PCR; the taxonomic diversity and abundance of culturable soil microfungi were studied. An increase in the number of genes copies of bacteria, archaea, and fungi close the source of emissions compared to remote areas was revealed. In all plots, the highest number of ribosomal genes copies was found for bacteria (from 3.21 × 10¹⁰ to 12 × 10¹⁰ per g of soil). For fungi and archaea, the number varied from 0.53 × 10¹⁰ to 1.59 × 10¹⁰ per g of soil and from 0.55 × 10¹⁰ to 11.41 × 10¹⁰ gene copies/g of soil, respectively. A significant increase in the actinomycetes biomass close the plant was noted, while the biomass of bacteria and fungi remained practically unchanged at different distances from the emission source. Mycelium and fungal spores in all areas are mainly represented by small forms with a diameter of 2–3 microns. The length of the fungal mycelium varied from 51.2 m/g near the plant to 397 m/g in remote areas, with no regularities in its distribution along the contamination gradient. A decrease in the diversity of soil microfungi at the level of genera and higher taxa along the pollution gradient with plant emissions was noted. A change in the structure of communities from polydominant (background site) to monodominant (near the plant) was revealed. The species Penicillium raistrickii dominated in all plots. Fungi Trichoderma viride, dark-colored yeasts Torula lucifuga (3 km) and Aureobasidium pullulans (16 km) also dominated in the zone 16 km from the emission source. In the background area, representatives of the orders Mucorales and Umbelopsidales were dominant.