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Nickel (Ni) and cobalt (Co) are widely utilized in various industrial sectors, particularly as components of corrosion-resistant steels and in galvanic production. Pollution of natural environments with these potentially toxic elements is a common consequence of anthropogenic activities. Therefore, understanding the mechanisms underlying microbial resistance to these metals is crucial for their effective remediation. This study provides a comprehensive overview of the current knowledge regarding the molecular genetic mechanisms that enable prokaryotes to resist and actively detoxify Ni and Co. The processes involved in metal uptake, intracellular binding, and energy-dependent efflux of toxic cations are examined in detail. Notably, only a limited number of studies have investigated these mechanisms within the context of genomic interactions (crosstalk) between plants and microbial communities. Furthermore, the potential applications and challenges associated with selecting metal-resistant microbial-plant associations—such as hyperaccumulator plants and rhizosphere bacteria—for induced phytoremediation are thoroughly discussed. To date, no prior literature review has systematically explored the potential of Ni- and Co-resistant microorganisms for remediation purposes. This review critically evaluates the mechanisms of Ni and Co uptake by bacterial cells and emphasizes its role in plant-microbes interactions.

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.

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.

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.

The effect of a coating material containing organic photoluminophore (PL) on the growth and development of mustard Brassica juncea L. plants colonized with beneficial associative bacteria Pseudomonas putida KT2442 and Rhodococcus erythropolis X5 was studied in vitro and in vivo. Plants grown with the use of microbial bacterization in combination with a photoluminophore coating (PLC) had significantly faster growth rates in vitro (2.1 times faster, P. putida; 1.8 times faster, R. erythropolis) than those grown using PLC alone (1.2 times faster). The leaves of plants grown with PLC had higher contents of glucose and fructose (28.4 ± 0.3% more glucose and 60.4 ± 0.3% more fructose accumulated compared to plants grown without PLC). It was found that seed weights and seed number increased 1.9-fold and 1.6-fold, respectively, for plants grown with PLC and colonized with beneficial P. putida KT2442 bacteria. The stimulatory effect of PLC on photosynthetic parameters of Photosystem II (PSII) was observed in colonized plants grown in vitro. For the first time, it was shown that providing plants with a PLC for only 4 weeks may make it possible to support further plant growth without PLC to obtain higher yields in the future. Thus, PLCs that convert shorter-wavelength radiation into red light may induce enhancement of biochemical processes not only in plants but also in microorganisms that supply plants with growth regulators and other active compounds. The results indicate the need for further research to understand the mechanisms of photobiological and photoregulatory systems in the interaction of microbes and plants.

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.

In the Republic of Kazakhstan (one of the top 10 oil-producing countries in the world), the remediation of oil pollution found in unproductive soils under the conditions of a sharply continental arid climate is a highly relevant problem. The aims of this work are to study the biodegradation capacity of the gray soil of the ‘Daulet Asia’ landfill, assess the degradative potential of indigenous oil-degrading strains and changes in the composition of the soil microbial community. Analytical chemistry methods, distillation and chromatographic mass spectrometry were used for oil analysis; gravimetry and IR spectroscopy were used to evaluate oil degradation. Standard microbiological techniques were employed to isolate and cultivate microorganisms and metagenomic sequencing was carried out using Oxford Nanopore technology. Raw data processing and subsequent analysis were performed using modern software packages. Three isolated strains of interest were identified based on the analysis of 16S rRNA gene fragment sequences. The studied soil has low biodegradation capacity (oil loss was 6.2% on day 60), possibly due to the low abundance and weak activity of indigenous hydrocarbon-oxidizing microorganisms. The taxonomic composition of the microbiome in the studied soil suggests some potential for oil degradation. Assessment of the effectiveness of oil degradation by the indigenous microbiome indicates that this potential can be realized only marginally in situ. Isolated oil-degrading strains were identified as belonging to the Rhodococcus and Kocuria genera. Effective oil removal from the studied soil requires the introduction of active microorganisms (e.g., as part of biopreparations). Considering the characteristics of the hot arid climate, for bioremediation of contaminated sierozems of Southern Kazakhstan, it is advisable to use halotolerant oil-degrading microorganisms with a wide temperature range that are capable of degrading hydrocarbons under moisture deficiency.

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.

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.

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.