The self-purification capacity of oil-contaminated soils is largely determined by the metabolic activity of autochthonous oil-oxidizing microorganisms. This study examined three strains of actinobacteria, which are hydrocarbon degraders, isolated from oil-contaminated sierozem soil at the Daulet Asia landfill (Southern Kazakhstan). Functional gene analysis was conducted (genome completeness > 98%, and contamination < 3%), and the phenotypic properties of these bacterial strains were studied to assess their potential for bio- and phytoremediation technologies in the sharply continental arid climate of the Aral Sea region. The isolated strains Rhodococcus kroppenstedtii K18 and MF2 and Kocuria rosea K1 grow on oil (12–22% oil loss after 10 days of cultivation in liquid mineral salt medium) and diesel fuel and can utilize hexadecane and benzoate as the sole source of carbon and energy. Furthermore, Rhodococcus K18 and MF2 utilize dodecane and eicosane, while K. rosea K1 utilizes phenol and gentisate. A significant decrease in surface tension (to 31.4 mN/m) observed during cultivation of strains K18 and MF2 on minimal salt medium indicates the secretion of surfactants that increase the bioavailability of hydrophobic substrates. The studied strains possess a number of properties that promote plant growth: they produce auxins, solubilize calcium hydroxyapatite, and protect plants from infection by the phytopathogenic microorganisms Fusarium oxysporum and Pectobacterium wasabiae. Actinobacteria are compatible when co-cultivated, as no mutual growth inhibition was observed. This study expands our understanding of typical bacterial representatives of desert soil, and this may contribute to the development of bioremediation approaches for the restoration of disturbed biotopes under extreme environmental conditions.

A genomic analysis of the hydrocarbon-oxidizing strain R. qingshengii F2-2 was conducted to characterize the genes responsible for plant growth stimulation and phytopathogen biocontrol. Understanding these mechanisms is vital for developing effective phytoremediation approaches. It was shown that the F2-2 genome consists of a 6.3 Mb chromosome and three plasmids, two of which are linear—pLP156 (155 kb) and pLP337 (337 kb)—and one circular—pCP209 (210 kb). The genes responsible for biosynthesis of phytohormones (auxins, gibberellins, cytokinins), phosphate solubilization, and production of siderophores and antibiotic-active compounds (chloramphenicol and pristinamycin IA) were identified in the strain chromosome. Orthologous genes encoding phenazine antibiotics were found in the linear plasmid pLP156. The phytostimulating properties of the strain, associated with auxin production (2–4 μg/mL); the ability to effectively colonize rapeseed, mustard, and tobacco plants; and protective action against Fusarium spp. under artificial phytopathogenic background conditions, were experimentally confirmed. Thus, the discovered properties of the R. qingshengii F2-2 strain indicate its potential for the phytoremediation of oil-contaminated soils.

Для достижения целей устойчивого развития мирового сообщества необходимо обеспечить защиту, восстановление экосистем и содействие их рациональному использованию, прекращение процесса деградации земель и предотвращение сокращения биологического разнообразия. В обзоре проанализирован большой объем научных публикаций и рассмотрены современные тенденции развития биотехнологических подходов для очистки почвы, воды и воздуха от различных, в том числе устойчивых и опасных, поллютантов. Отдельная глава посвящена утилизации и очистке водных и наземных экосистем от синтетических материалов, включая микропластик. Уделено внимание природоохранным технологиям, применяемым для рекультивации загрязненных военных объектов. Целью данного обзора были анализ и обобщение современных методов, а также характеристика основных направлений современной экологической биотехнологии. To achieve the goals of sustainable development of the world community, it is necessary to ensure the protection, restoration of ecosystems and promotion of their rational use, termination of the process of land degradation and prevention of reduction of biological diversity. The review analyzes a large volume of scientific publications and considers modern trends in the development of biotechnological approaches for cleaning soil, water and air from various pollutants, including persistent and hazardous ones. A separate chapter is devoted to the utilization and cleaning of aquatic and terrestrial ecosystems from synthetic materials, including microplastics. Attention is paid to environmental technologies used for reclamation of contaminated military facilities. The purpose of this review was to analyze and summarize modern methods, as well as to characterize the main directions of modern environmental biotechnology.

A new biopreparation is developed to clean soils from oil pollution in the arid climate of the Republic of Kazakhstan. The biopreparation includes bacterial strains R. qingshengii F2-1, R. qingshengii F2-2, and P. alloputida BS3701. When using the biopreparation in a liquid mineral medium with 15% crude oil, laboratory studies have revealed degradation of 48% n-alkanes and 39% of PAHs after 50 days. The effectiveness of the biopreparation has been demonstrated in field experiments in the soil contaminated with 10% crude oil at the K-Kurylys landfill, Republic of Kazakhstan. During the six-month field experiment, the number of oil degraders reached 107 CFU/g soil, which degraded 70% of crude oil by the end of the experiment.

— Organization and localization of the alkB genes and of alkane 1-monooxygenases they encode in members of the genus Rhodococcus was investigated. All members of a phylogenetic group were found to possess specific types of alkB genes ( alkB1 -type in the operons containing rubredoxin-coding genes, rubredoxin reductase, and a regulatory protein and/or alkB2 -type in the operons lacking the rubredoxin-reductase-coding gene, and additionally, separately located determinants of the alkB3 ‒ alkB8 type). The alkB1 -type genes were present in the chromosomes of bacteria of the groups B1 ( R. aetherivorans, R. ruber ), C ( R. opacus , R. jostii, R. wratislaviensis, R. koreensis ), D ( R. erythropolis , R. qingshengii ), G ( R. triatomae ), and E ( R. fascians ). The alkB2 -type genes occurred in strictly specified loci of the chromosomes of members of the phylogenetic groups A ( R. hoagii / R. equi ), B2 ( R. coprophilus, R. pyridinivorans, R. rhodochrous ), and D ( R. erythropolis , R. qingshengii ). The separately located alkB3 ‒ alkB5 genes were present in the chromosomes of members of the group D ( alkB5 was found only in R. qingshengii ); the alkB6 genes occurred in members of the groups B1 and B2, and alkB7‒alkB8 were present in members of the group E. The proteins encoded by alkB1 and alkB2 genes belonged to three phylogenetic groups. The first one comprised AlkB1-type proteins of members of groups B1 and C and the AlkB2-type proteins of members of the groups D and A. The second one was represented by AlkB2-type proteins of bacteria of the group B2. The third cluster comprised AlkB1-type proteins of members of the groups G and D. Alkane 1-monooxygenases encoded by separately located alkB3 ‒ alkB8 genes were represented by three phylogenetic lineages: AlkB3‒AlkB5, AlkB6, and AlkB7‒AlkB8. In the genome of R. pyridinivorans 5Ap, the alkB2 and alkB6 genes characteristic of group B1 were revealed. It was shown that these determinants are required for biosurfactant synthesis. Emulsifying activity of the mutant with an inactivated alkB2 gene growing at 28 and 42°C was 16 and 3 times lower, respectively, while the amount of trehalose-containing surfactants decreased 7 and 3 times, respectively. Irrespective of the cultivation temperature, the mutant with an inactivated alkB6 gene exhibited 1.2 times lower emulsifying activity and more than twofold decrease in the synthesis of trehalose-containing surfactants. These results suggest that alkB2 plays a key role in biosurfactant synthesis at different cultivation temperatures. The contribution of alkB6 increased at 42°C, probably due to its elevated transcriptional activity.

The aim of our study was to reveal the peculiarities of the adaptation of rhodococci to hydrophobic hydrocarbon degradation at low temperatures when the substrate was in solid states. The ability of actinobacteria Rhodococcus erythropolis (strains X5 and S67) to degrade hexadecane at 10 °C (solid hydrophobic substrate) and 26 °C (liquid hydrophobic substrate) is described. Despite the solid state of the hydrophobic substrate at 10 °C, bacteria demonstrate a high level of its degradation (30–40%) within 18 days. For the first time, we show that specialized cellular structures are formed during the degradation of solid hexadecane by Rhodococcus at low temperatures: intracellular multimembrane structures and surface vesicles connected to the cell by fibers. The formation of specialized cellular structures when Rhodococcus bacteria are grown on solid hexadecane is an important adaptive trait, thereby contributing to the enlargement of a contact area between membrane-bound enzymes and a hydrophobic substrate.

The poultry industry is generating a significant amount of waste from chicken droppings that are abundant in microbes as well as macro- and micronutrients suitable for manure. It has the potential to improve the microbial activity and nutrient dynamics in the soil, ultimately improving soil fertility. The present study aimed to investigate the effect of chicken droppings manure (CDM) on the diversity of the soil microbiome in the free walking chicken’s area located in Stefanidar, Rostov Region, Russia. The data obtained were compared with 16 s rRNA from control samples located not far from the chicken's free-walking area, but not in direct contact with the droppings. Effect of CDM on the physicochemical characteristics of the soil and changes in its microbial diversity were assessed by employing the metagenomic approaches and 16 s rRNA-based taxonomic assessment. The alpha and beta diversity indices revealed that the application of the CDM significantly improved the soil microbial diversity. The 16S taxonomical analysis confirmed Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Planctomycetes as abundant bacterial phylum. It also revealed the increase in the total number of the individual operational taxonomic unit (OTU) species, a qualitative indicator of the rich microbial community. The alpha diversity confirmed that the significant species richness of the soil is associated with the CDM treatment. The increased OTUs represent the qualitative indicator of a community that has been studied up to the depth of 5–20 cm of the CDM treatment range. These findings suggested that CDM-mediated microbial richness are believed to confer the cycling of carbon, nitrogen, and sulfur, along with key soil enzymes such as dehydrogenases and catalase carbohydrate-active enzymes. Hence, the application of CDM could improve soil fertility by nutrient cycling caused by changes in soil microbial dynamics, and it could also be a cost-effective sustainable means of improving soil health.

The possibility of using the microorganisms Pseudomonas sp. 7p-81, Pseudomonas putida BS394(pBS216), Rhodococcus erythropolis s67, Rhodococcus pyridinivorans 5Ap, Rhodococcus erythropolis X5, Rhodococcus pyridinivorans F5 and Pseudomonas veronii DSM 11331T as the basis of a biosensor for the phenol index to assess water environments was studied. The adaptation of microorganisms to phenol during growth was carried out to increase the selectivity of the analytical system. The most promising microorganisms for biosensor formation were the bacteria P. putida BS394(pBS216). Cells were immobilized in redox-active polymers based on bovine serum albumin modified by ferrocenecarboxaldehyde and based on a composite with a carbon nanotube to increase sensitivity. The rate constants of the interaction of the redox-active polymer and the composite based on it with the biomaterial were 193.8 and 502.8 dm3/(g·s) respectively. For the biosensor created using hydrogel bovine serum albumin-ferrocene-carbon nanotubes, the lower limit of the determined phenol concentrations was 1 × 10−3 mg/dm3, the sensitivity coefficient was (5.8 ± 0.2)∙10−3 μA·dm3/mg, Michaelis constant KM = 230 mg/dm3, the maximum rate of the enzymatic reaction Rmax = 217 µA and the long-term stability of the bioanalyzer was 11 days. As a result of approbation, it was found that the urban water phenol content differed insignificantly, measured by creating a biosensor and using the standard photometric method.

Hydrocarbon-decomposing microorganisms identified as representatives of the genera Pseudomonas, Rhodococcus, Acinetobacter, Kocuria, Raoultella, and Candida have been isolated from the oil-contaminated soil samples of the Middle Ob region. They have been screened for the ability to decompose various classes of hydrocarbons in a wide temperature range (6–37°C), in acid media (up to pH 4), and at increased salinity (up to 3%), for the ability to produce biosurfactants, and for the presence of genes encoding enzymes responsible for hydrocarbon decomposition. A microbial consortium has been suggested as the basis of a biological preparation for bioremediation of oil-contaminated soils in the Middle Ob region, including strains of Candida fluviatilis 24p-51, Rhodococcus erythropolis 24-44, Acinetobacter calcoaceticus 7-43, and Pseudomonas extremaustralis 7-31. The modes of cultivation and lyophilization of biomass have been determined for these microorganisms. The efficiency of degradation of oil hydrocarbons by the developed microbial consortium has been evaluated in laboratory model systems. The degree of oil degradation by the microbial consortium in the liquid mineral medium was 56%; in the model soil, 22% in 10 days at 24°C.

The problem of eliminating petroleum pollution and its consequences is currently very relevant for Kazakhstan, which is among the ten largest oil-producing countries. The specifics of natural conditions—the sharply continental arid climate—necessitate the development and application of adequate technologies for the restoration of oil-contaminated territories and the Caspian seashore. The key factors (temperature, moisture, alkalinity, salinity, low mineral and organic matter content) affect the self-purification processes and microbiological status of oil-contaminated soils of Kazakhstan. The assessment of taxonomic diversity and characteristics of oil-degrading microorganisms isolated from samples of soils and reservoirs contaminated with hydrocarbons are given. The review of biopreparations and biotechnologies developed and used in Kazakhstan for cleaning environments from oil pollution is made, and their effectiveness is shown. The analysis of the current state of research in the field of biodegradation of hazardous pollutants and bioremediation of oil-contaminated areas allows us to identify promising areas of further work and approaches to the development and improvement of technologies for environmental protection.

Polycyclic aromatic hydrocarbons (PAHs) are chemically recalcitrant carcinogenic and mutagenic compounds with primarily anthropogenic origin. The investigation of the effects of emissions from energy enterprises on soil microbiomes is of a high priority for modern soil science. In this study, metagenomic profiling of technogenic contaminated soils was carried out based on bioinformatic analysis of shotgun metagenome data with PAH-degrading genes identification. The use of prokaryotic consortia has been often used as one of the bio-remediation approaches to degrade PAHs with different molecular weight. Since the process of PAH degradation predominantly includes non-culturable or yet-to-be cultured species, metagenomic approaches are highly recommended for studying the composition and metabolic abilities of microbial communities. In this study, whole metagenome shotgun sequencing of DNA from two soils with varying PAH levels was performed. In the control site, the total content of 12 priority PAHs was 262 µg kg−1. The background soil levels in the polluted site for PAHs with 3 or more rings exceeded this, at 800 µg kg−1. The abundance of genes and taxa associated with PAH degradation in these two sites were estimated. Despite differences in PAH concentrations up to 1200 µg kg−1, individual and operon-organized PAH degradation genes were almost equally abundant and diverse in pristine and highly contaminated areas. The most numerous taxa in both spots were actinobacteria from Terrabacteria group. In addition to well-known PAH degraders such as Gordonia and Rhodococcus, genes corresponding to the PAH degradation were found in Azoarcus, Burkholderia and Variovorax. The data shows non-specificity and multifunctionality of metabolic pathways encoded in the genes of PAH-degrading microorganisms.

The All-Russian Scientific Research Institute of Reclaimed Lands has developed organic solid-phase biologic means for crop production and agriculture – multi-purpose compost (KMN) and fermentation product (PF). A characteristics of KMN and PF allows them to be use for bioremediation of oil-contaminated soil as activators of the native microflora and as sorbents of strains of oil destructive microorganisms. As source of oil destructing microorganisms the MikroBak preparation was used. Suspensed MikroBak was added to the PF and KMN in the process of their production – at the stage of ripening, based on the final content of oil destructors in the soil 105 CFU / 1 g of soil. It was established that three days after the MikroBak introduction, samples of solid-phase biological means had the highest microbiological activity, in particular, the number of microorganisms utilizing oil increased 2.5–7.5 times. To study the effectiveness of new biological means for remediation of oil-contaminated soils, a model experiment lasting 4 months was laid. Sod-podzolic light loamy soil was artificially contaminated with oil at the rate of 5 % of oil pollution, taking into account the mass of applied biological means. New biological means, prepared both on the basis of PF and MikroBak, and on the basis of KMN and MikroBak, combine two methods of bioremediation – stimulation of native microorganisms and the introduction of active microorganisms-destructors. After 2 weeks from the start of the experiment, the greatest destruction of oil was revealed in the variants using new biological means based on KMN and MikroBak, as well as PF and MikroBak – 29.8 and 24.3 %, respectively. In a month, the maximum destruction was observed in the variant with the use of the MikroBak – 36 %. At the end of the experiment, the degree of oil destruction and the number of microorganisms utilizing crude oil were in a linear relationship, the correlation coefficient r = 0.76. It was established that the use of the MikroBak biopreparation at the stage of maturation of the PF contributed to obtaining the most optimal, effective biological mean, which in 4 months provided a degree of oil destruction of 60.6 %.

The strain Pseudomonas putida BS3701 was isolated from soil contaminated with coke by-product waste (Moscow Region, Russian Federation). It is capable of degrading crude oil and polycyclic aromatic hydrocarbons (PAHs). The P. putida BS3701 genome consists of a 6,337,358-bp circular chromosome and two circular plasmids (pBS1141 with 107,388 bp and pBS1142 with 54,501 bp).

The aim of our work was to study the colonization of potato, tomato, rapeseed and camelina by associative microorganisms Methylobacterium mesophilicum, Pseudomonas aureofaciens BS1393 and Pseudomonas putida BS3701; examine the resistance of colonized plants to biotic (phytopathogens Erwinia carotovora and Sclerotinia sclerotiorum) and abiotic (naphthalene, oil) stressors. Colonized plants were characterized by an increased growth rate (1.5–2.0 times higher) compared to non-colonized ones; flower-bud formation, flowering and fructification of the colonized plants also started earlier. An increased resistance of colonized plants to phytopathogens, naphthalene (100 mµ/ml) and oil (0.7 %) was noted, too. The level of superoxide dismutase (SOD) in control plants on a medium with naphthalene or oil increased by 160–150%; in colonized plants – by 20–18 %. Colonized plants were more viable because of the presence of P. putida BS3701 on the roots.

Исследовано распространение антибиотикоустойчивых микроорганизмов и генов резистентности к антибиотикам в очистных сооружениях г. Пущино. Обнаружены и охарактеризованы плазмиды резистентности к антибиотикам как возможные векторы для распространения генов устойчивости в окружающей среде. Продемонстрирована роль катаболических плазмид в биодеградации углеводородов нефти. Исследован горизонтальный перенос плазмид в лабораторных условиях и в открытой окружающей среде в процессе утилизации полициклических ароматических углеводородов. Исследованы ризосферные бактерии рода Pseudomonas, относящиеся к уникальной группе PGPR. Штаммы продуцируют широкий спектр биологически активных метаболитов, включая сидерофоры, феназины, 2,4-диацетилфлороглюцин, пиолютеорин, пирролнитрин, оомицин А, цианогенные гликозиды, синтезируют фитогормоны, включая индолил-3-уксусную кислоту (ИУК) и стимулируют корнеобразование у растений. На основе одного из таких штаммов P. chlororaphis (ранее P. aureofaciens) BS1393 разработан биопрепарат «Псевдобактерин-2», обладающий высокой эффективностью против целого ряда заболеваний растений. The dissemination of antibiotic-resistant microorganisms and antibiotic resistance genes in treatment facilities of Pushchino was studied. The antibiotic resistance plasmids were isolated and characterized as possible vectors for the spread of resistance genes in the environment. The role of catabolic plasmids in the biodegradation of oil hydrocarbons was demonstrated. The horizontal transfer of plasmids was studied under laboratory conditions and in an open environment during the utilization of polycyclic aromatic hydrocarbons. The rhizospheric bacteria of the genus Pseudomonas belonging to the unique PGPR group were studied. The strains produce a wide range of biologically active metabolites, including siderophores, phenazines, 2,4-diacetylphloroglucin, pyoluteorin, pyrrolnitrin, oomycin A, hydrocyanic acid, synthesize phytohormones, including indolyl-3-acetic acid (IAA), and stimulate root formation in plants. Based on one of these strains of P. chlororaphis (formerly P. aureofaciens) BS1393, the biopreparation Pseudobacterin-2 was developed, which is highly effective against a number of plant diseases.

A thermotolerant bacterial strain 1D isolated from refinery oil-contaminated soil was identified as Gordonia sp. based on the analysis of 16S rRNA and gyrB gene sequences. The strain was found to utilize crude oil, diesel fuel, and a wide spectrum of alkanes at temperatures up to 50 °C. Strain 1D is the first representative of Gordonia amicalis capable of utilizing alkanes of chain length up to С36 at a temperature of 45–50 °C. The degree of crude oil degradation by Gordonia sp. 1D at 45 °C was 38% in liquid medium and 40% in soil (with regard to abiotic loss). There are no examples of so effective hydrocarbon-oxidizing thermotolerant Gordonia in the world literature. The 1D genome analysis revealed the presence of two alkane hydroxylase gene clusters, genes of dibenzothiophene cleavage, and the cleavage of salicylate and gentisate – naphthalene metabolism intermediates. The highly efficient thermotolerant strain Gordonia sp. 1D can be used in remediation of oil-contaminated soils in hot climates.