Open-access Use of bacterial preparations for bioremediation of polluted desert areas in the Turkestan Region

Uso de preparados bacterianos para biorremediação de áreas desérticas poluídas na região do Turquestão

Abstract

Soil contamination by oil and petroleum products represents a serious environmental problem that requires effective remediation methods. In recent years, bioremediation using specialized biological products has proven to be a promising, environmentally safe, and cost-effective approach to addressing this issue. Modern studies demonstrate the high efficiency of bioproducts containing specialized bacterial strains in degrading petroleum hydrocarbons. The most commonly used microorganisms include representatives of the genera Pseudomonas, Rhodococcus, and Bacillus, which are capable of metabolizing various components of oil.

Research shows that bioproducts can reduce the concentration of petroleum hydrocarbons in soil by 70-90% within several months, even under harsh climatic conditions and at low temperatures. For example, a new bioproduct developed for the arid conditions of Kazakhstan demonstrated the ability to degrade 70% of crude oil in soil contaminated with 10% oil over six months of field trials.

Keywords:
reclamation; microorganisms; soil; bacteria; arid zone

Resumo

A contaminação do solo por petróleo e derivados representa um grave problema ambiental que exige métodos eficazes de remediação. Nos últimos anos, a biorremediação mediante o uso de produtos biológicos especializados tem se mostrado uma abordagem promissora, ambientalmente segura e economicamente viável para o enfrentamento dessa questão. Estudos modernos demonstram a elevada eficiência de bioprodutos contendo cepas bacterianas especializadas na degradação de hidrocarbonetos de petróleo. Os microrganismos mais comumente empregados incluem representantes dos gêneros Pseudomonas, Rhodococcus e Bacillus, que são capazes de metabolizar diversos componentes do petróleo.

Pesquisas indicam que bioprodutos podem reduzir a concentração de hidrocarbonetos de petróleo no solo em 70-90% em poucos meses, mesmo sob condições climáticas adversas e em baixas temperaturas. Como exemplo, um novo bioproduto desenvolvido para as condições áridas do Cazaquistão demonstrou capacidade de degradar 70% do petróleo bruto em solo contaminado com 10% de petróleo ao longo de seis meses de ensaios de campo.

Palavras-chave:
recuperação; microrganismos; solo; bactérias; zona árida

1. Introduction

Oil is the most widely used raw material for fuel production in the world. Despite modern protection systems for tankers and pipelines during oil transportation, soil remediation and protection remain pressing issues. When oil and petroleum products enter the soil, they inhibit the vital activity of most microorganisms, including their enzymatic activity. Management of oil biodegradation processes should primarily aim at activating microbial communities and creating optimal conditions for their existence (Sozina and Danilov, 2023).

Kazakhstan’s long-term plans include increasing oil production, which in turn leads to the expansion of pipeline networks, a rise in the transportation of oil and petroleum products, and, consequently, the impossibility of completely eliminating the risk of new accidents and oil spills. Once in the soil, petroleum hydrocarbons affect not only the quantity of organic matter but also its qualitative composition. The amount of organic carbon in the humus horizon of a contaminated site increases severalfold (Korshunova and Loginov, 2019). The impact of such an anthropogenic factor as oil cannot be considered unambiguous; it extends in a certain way to the entire studied soil ecosystem (Pashkevich and Bykova, 2022).

Oil contamination alters the composition of soil communities and microbiological populations that maintain soil homeostasis. All processes in soil, including microbiological ones, are interconnected, interdependent, and closely coordinated, ensuring ecosystem balance. The main share of the soil microbiocenosis consists of heterotrophic bacteria, which can account for up to 99.7% of the total number of microorganisms. Microscopic fungi make up to 5.9%, actinomycetes up to 28.2%, and hydrocarbon-oxidizing bacteria no more than 0.01%. The vital activity of microorganisms is one of the most important factors in soil formation, its fertility, and its ability to self-purify from organic pollutants (Tumanyan et al.,2017). When petroleum hydrocarbons enter the soil, they exert a toxic effect on its microflora, slowing development or causing death.

For microorganisms, the environment represents not only a set of specific physicochemical habitat conditions but also the presence of other microorganisms. All of this determines the complexity of interactions between microorganisms at various levels of existence and enables them to survive under the most unfavorable conditions due to their ability to adapt to any environmental circumstances, which is their primary survival strategy. In adapting to their habitat, microorganisms use mechanisms at different levels of system organization: supra-organismal level (community structuring, phenotypic heterogeneity and cultural integrity during development, symbiotic interactions, etc.); cellular level (presence of unique structures such as giant vacuoles for nitrate (NO3) storage, capsules, mucous formations, and sheaths); ecophysiological level (ability to adhere and colonize, production of physiologically active substances, synthesis of antibiotics, siderophores, etc.). Microorganisms are capable of forming population structures characterized by the following ecological properties (Babaev, 2019; Zhuniszhan et al., 2024; Yessentayeva et al.,2024).

Many bacteria, including Pseudomonas, during the process of growth are capable of dissociation into variants that differ in physiological, biochemical, and morphological characteristics, including colony morphology, resistance to external stress factors, ability to synthesize industrially valuable compounds, intensity of xenobiotic and hydrocarbon degradation, and nutritional requirements of the growth medium (Gussenov etal., 2023; Nurzhanova et al., 2020).

According to literature data, cyanobacterial communities have been identified in natural and technogenic sites (oil-contaminated soils in the vicinity of drilling wells in Kalmykia, treatment facilities of a gas-chemical complex, and storage reservoirs of oil-sludge wastewater) located in arid climate zones. These communities include representatives of several trophic levels (photosynthetic organisms, bacteria, and protozoa) involved in the transformation of pollutants.

For soil remediation, the application of radical sanitation methods, such as removal of the contaminated soil layer, is unacceptable, as it leads to degradation of the topsoil and its subsequent loss. Phytoremediation is one of the less efficient but environmentally gentle methods for soil restoration (Mikolasch et al., 2020). The effectiveness of phytoremediation is limited by high oil concentrations (not exceeding 1.5%), soil hydrophobicity, and the need to select plant species according to the specific contamination scenario (Mikolasch et al., 2020). Increased soil hydrophobicity results in reduced plant growth and development due to disruption of cellular water exchange processes in the photosynthetic apparatus, as well as in stems and root systems (Nurzhanova et al., 2025). Therefore, phytoremediation is recommended to be combined with other remediation approaches.

1.1. Aim of the research

To study the state of soil microflora in oil-contaminated soils of Southern Kazakhstan and isolate active strains of hydrocarbon-oxidizing microorganisms from oil-contaminated these soils, obtain an ecological biological product for soil purification from petroleum hydrocarbons.

2. Materials and Methods

2.1. Weather and climatic conditions of the Turkistan Region

The territory of the region is distinguished by a diversity of relief and is divided into four clearly expressed parts: the northern and south-western parts are plains; the southern part is plain; the south-eastern part is mountainous. In geographical terms, the region includes the south-eastern part of the sandy desert of the Muyunkum sands, the valleys of the middle course of the Shu River, the western part of the clay desert Betpakdala, the greater part of the Karatau ridge, and a number of ridges of the Western Tien Shan. Owing to its location deep within the continent, the studied region is considerably remote from large water bodies. Therefore, the climate of the region is characterized by sharp continentality and aridity. The prevailing clear and dry weather in the winter period is caused by the influence of the Asian anticyclone.

In laboratory investigations, soils collected from the industrial zone of PetroKazakhstan Oil Products LLP (“PKOP”) were used and represent typical medium-loamy sierozems with different contents of petroleum products. The oil-contaminated and control soils selected did not differ from each other in their main parameters.

2.2. Oil and petroleum products

The objects of our investigations were: Kumkol oil, diesel fuel, and fuel oil (mazut). The oil is characterized by the following indicators: pour point 10°C; content of silica-gel resins 19.2%; carbenes and carboids 5.82%; asphaltenes 5.4%; paraffin 7.5%; sulfur 0.064%. At a temperature of 20 °C it had a density of 0.850 g/cm3. Diesel fuel fractions are low-sulfur; their acidity does not exceed 3%. At 20 °C it has a density of 0.804 g/cm3. A high content of n-alkanes (24%) allows them to be considered as promising raw material for the production of liquid paraffins. Fuel oil is characterized by an actual pour point between 25-42 °C. At 20 °C it has a density of 0.890-0.899 g/cm3. Viscosity at 80°C is not more than 16; sulfur content not higher than 0.5%; mechanical impurities not more than 1%.

Microbiological examination of oil-contaminated sites was carried out according to generally accepted methods in microbiological practice. Isolation of soil microorganisms was performed on MPA and Voroshilova-Dianova media by the Koch method various fractions of petroleum products were used as carbon sources for microbial nutrition. The taxonomic affiliation of the isolated strains of hydrocarbon-oxidizing microorganisms (HOM) was determined in the Laboratory of Microbial Ecology of the Institute of Microbiology and Virology according to generally accepted methodology.

The scheme of reclamation of oil-contaminated soil had the following sequence: loosening, application of HOM biomass, watering with water with the addition of biogenic elements – 1% ammophos, subsequently – watering with water. Repeated loosening of the soil was carried out not less than once a month; watering was performed once every 7-10 days. The moisture content of the soil being purified was maintained at the level of 50-60% of its total moisture capacity. Sawdust used for immobilization of HOM was applied in the amount of 2-10 t/ha depending on the type and degree of oil contamination.

When carrying out bioreclamation of oil-contaminated soils using weather-climatic conditions, agrotechnical measures began in autumn (October, early November), when microorganisms of the biopreparation immobilized on sawdust were introduced. After application of the biopreparation into the soil and its moistening, the work was suspended until the end of February-beginning of March. At the same time, soil moisture was maintained due to natural moistening, i.e., precipitation (rain, snow). The time of completion of reclamation works after this period at each tested site was determined by the result of analysis for petroleum product content in the reclaimed soil.

Soil samples for petroleum product content were collected once a month and analyzed according to the appropriate methodology (Kumar and Kaur, 2018).

3. Results and Discussion

In some cases, oil stimulates the growth of certain soil fungi (Paecilomyces, Fusarium); certain species of Coluobasidium have been detected and inhabit only soils saturated with petroleum products. On the other hand, massive oil contamination of soil, occurring during accidental spills, is accompanied by an acute toxic effect of oil on living organisms. The latter manifests most clearly immediately after the pollutant enters the soil. The microbial system of soils under various types of anthropogenic contamination responds in a similar manner by changing the composition of actively functioning populations within the microbial community. The response of microorganisms depends on the quantity and quality of the contaminant [8, 9]. The hazard of oil lies in the fact that it contains nearly 3,000 ingredients, most of which are readily oxidizable. In oils of different origin, light, medium, and heavy fractions are distinguished.

A comparative analysis of the state of soil heterotrophic microflora in uncontaminated (the area near the checkpoint and near the plant) and soils contaminated with various fractions of petroleum products showed that the number of major groups of heterotrophic bacteria in oil-contaminated soils was reduced by 58-68%, the number of hydrocarbon-oxidizing microorganisms by 71%, and spore-forming microorganisms by 68%, due to the toxic effect of petroleum products on the vital activity of microorganisms.

At the same time, as a result of chronic toxic effects, the composition of the microflora is quite homogeneous and is represented by such genera as Pseudomonas, Micrococcus and a number of Gram-positive rod-shaped bacteria. In case of accidental oil product spills (at sites 1 and 2), a sharp decrease in the number of heterotrophic microorganisms was observed, however, on 3-5 days the titer of the natural microflora increases, which is probably due to the end of the period of adaptation of the soil microbiota to the changed physico-chemical environmental conditions.

During the research work, spontaneously occurring hydrocarbon-oxidizing bacteria in the soil were taken into account (Table 1). According to the table data, it can be concluded that the titer of spontaneous HOM in oil-contaminated soils is sufficiently high. The results of the studies show that the main quantity of heterotrophic microflora is concentrated in the 0-10 cm soil horizon, which is fully explained by ecological factors favorable to the vital activity of this group of microorganisms: oxygen availability, sufficient moisture, and gas-air regime. As the sampling depth increases to 20-30 cm and 30-40 cm, the titer of heterotrophic microorganisms decreases by 1-2 orders of magnitude. Somewhat contradictory data regarding the number of HOM in the 10-20 cm horizon may be explained by the layered alternation of uncontaminated and contaminated soil strata.

Table 1
Dynamics of the Spontaneous Microflora Population.

It was established that the distribution of hydrocarbon-oxidizing microorganisms (HOM) across soil horizons is uneven and correlates with the molecular weight of the contaminating petroleum products. On plots Nº 1, 3, and 4, contaminated with oil, fuel oil, and sludge-like wastes containing asphaltenes and maltenes, the highest concentration of HOM was found in the 10-20 cm and 20-30 cm horizons. Analysis of petroleum product content in soil samples collected from different horizons showed that the highest concentrations occur in the 10-20 cm layer and below. In contrast, on plots contaminated with diesel fuel (mainly containing maltenes), both the petroleum product content and the microorganism titer were highest in the 0-10 cm horizon.

For the implementation of bioremediation activities, it was necessary to isolate new microbial cultures with high metabolic activity. Accordingly, over a long period, 255 microbial cultures were isolated from various oil-contaminated plots of JSC “PKOP.” Among the isolated cultures, 4 strains demonstrated the ability for active growth – B1Ag8G, B1Ag16G, B1Ag6G, and G 311/1.

Thus, it was found that the titer of the soil hydrocarbon-oxidizing microflora correlates with both the concentration of petroleum products and the qualitative composition of oil pollution. In the real production conditions of PKOP, the most favorable conditions for the vital activity of hydrocarbon-oxidizing microflora: humidity, aeration, and carbon nutrition are created in the horizon of 0-10 cm, where their highest titer is determined.

As a result of the oxidative activity of the native microflora, 22.1% of hydrocarbons were degraded within 2 months in the control variant, with the degradation of oil hydrocarbons occurring at the lowest rate of 2.2 mg/kg of soil per day. Under optimized conditions, with aeration achieved by regular soil loosening (once every 10 days), the percentage of oil degradation increased to 28.9%, with an average degradation rate of 2.9 mg/kg per day. When regular loosening was combined with enrichment of the soil with biogenic elements (1% ammonium phosphate solution), 30.8% of oil hydrocarbons were degraded, with an average degradation rate of 3.0 mg/kg per day.

With increased aeration, the addition of mineral nitrogen and phosphorus salts, and the use of wood chips as a sorbent, the level of hydrocarbon degradation reached 45%. Using bentonite clay as an immobilizer, combined with the introduction of HOM biomass and maintenance of the bioremediation methods, up to 59% of hydrocarbons were degraded. Finally, with regular loosening, addition of ammonium phosphate as a source of nitrogen and phosphorus, and the use of wood chips as a sorbent supplemented with HOM biomass, up to 72% of oil hydrocarbons were degraded, at a rate of 8.7 mg/kg per day (Figure 1).

Figure 1
Oil content depending on soil treatment.

Semi-industrial tests were carried out on the territory of JSC PKOP near reservoirs E and D, where soil contamination was 5.4 and 9.8%. In section E, two adjacent sections were analyzed: the experimental and the control (without bio-treatment). Sawdust was soaked with an aqueous mixture, including an association of microorganisms with a density of 106-108 cells per 1 ml. (the amount of biomass is 6 g / l) and a 1% solution of ammophos, and then introduced into contaminated soils at the rate of 2.5 kg per 1 m2, the rest of the solution of ammophos was irrigated with the studied area. The decrease in petroleum products in the soil of the studied site occurred on average at a rate of 0.13 g/100g per day, for 30 days from 5.4g/100g of soil to 1.3 g/100g of soil, i.e. the degree of purification was 74%.

The reduction of petroleum products in the soil of the studied plot occurred at an average rate of 0.13 g/100 g per day. Over 30 days, the oil content decreased from 5.4 g/100 g of soil to 1.3 g/100 g of soil, i.e., the degree of purification reached 74%. In the control plot, where only soil turning was performed without the addition of microorganisms or biogenic nutrients, about 9% of hydrocarbons were degraded, as shown in Figure 2.

Figure 2
Effect of microorganisms on the dynamics of petroleum hydrocarbon reduction in soil.

Thus, it was established that regular soil loosening and the application of mineral salts of nitrogen and phosphorus contribute to the enhancement of petroleum hydrocarbon degradation. However, the greatest reduction in hydrocarbon content occurs due to the use of wood chips immobilized on the biomass of hydrocarbon-oxidizing microorganisms (HOM) as a sorbent, supplemented with additional nutrients, as this sharply increases the rate of oil degradation up to 74%.

Literature data on bioremediation of soils with petroleum hydrocarbon content above 7-8% are practically absent. Therefore, it was decided to utilize not only the oxidative capabilities of the biopreparation but also to stimulate the native microbial flora. For this purpose, the necessary aeration conditions were created by regular soil loosening (once every 10 days) (Photo 2) and the addition of biogenic elements via 1% ammonium phosphate. After 30 days, visual observations (Photo 3) indicated changes in organoleptic properties: the soil became hydrophilic and loose, the petroleum odor disappeared, and the color of the soil changed from dark brown to light.

After the introduction of the microbial consortium into the soil, the population of native microflora increased by several orders of magnitude (Table 2). Before treatment with the hydrocarbon-oxidizing microorganism suspension (HOM biomass), microbial counts in control and oil-contaminated soils were approximately 104-105 cells/g. Within two months, microbial counts in the control soil increased to 105-106, whereas in oil-contaminated soils treated with HOM suspension, counts rose to 107-109 during the first month and to 109-1010 cells/g during the second month of reclamation.

Table 2
Effect of HOM suspension application on the titer of native microflora in soil.

The study of reclamation potential for oil-contaminated soils, initially containing 47,300 mg/kg of hydrocarbons, revealed that agronomic interventions such as soil loosening (to increase oxygen contact) and ammonium phosphate addition (to narrow the C:N ratio) were effective. The biopreparation “PEROIL” (BP) was applied to the soil at two dilutions: 1:100 and 1:1000. Additionally, for reclamation purposes, a suspension of hydrocarbon-oxidizing microbial biomass (BM), cultivated in an aeration tank, was introduced. The experiment lasted two months.

One month of aeration resulted in 15.2% hydrocarbon degradation, with microbial counts remaining low (~106). The addition of ammonium phosphate (to improve nitrogen nutrition of microorganisms) increased microbial titers to ~107. A sharp increase in petroleum degradation was achieved by applying the “PEROIL” biopreparation. Within one month, 60.6-65.5% of hydrocarbons were degraded with a 1:100 dilution of PEROIL. Reducing the microbial inoculum tenfold (1:1000 dilution) decreased the degradation percentage to 44.1%. Correspondingly, microbial counts in soil reached 109-1010 at 1:100 dilution and decreased to 108 at 1:1000 dilution.

After two months of reclamation using PEROIL at 1:100 dilution, hydrocarbon degradation reached 92.8-98.9%, while at 1:1000 dilution, it reached 77.6%. Hydrocarbon-oxidizing bacteria titers were 1010 at 1:100 dilution and 109 at 1:1000 dilution.

A significant difference in fuel oil hydrocarbon degradation persists between the application of PEROIL at 1:100 dilution and the introduction of hydrocarbon-oxidizing bacteria cultivated in an aeration tank. The microbial counts in soil were approximately the same (~109) in both cases.

In two months, the number of microorganisms in the control soil increased to 105-106, while in soils contaminated with petroleum products and treated with UOM suspension, the number of microorganisms increased in the first month to 107-109, and in the second month of reclamation to 109-1010 cells per 1g of soil.

A month of contact with air resulted in 15.2% degradation of petroleum products, the number of microorganisms in the soil remained at a low level of -106, the introduction of ammophos (narrowing the ratio with:N) in order to improve the nitrogen nutrition of microorganisms, it led to an increase in their titer. But a sharp increase in the decomposition of petroleum products in the soil was achieved by introducing the drug "Peroil" into the soil. In one month, 60.6 - 65.5% of hydrocarbons decomposed when applying the preparation "Peroil" in a dilution of 1:100; It was necessary to introduce hydrocarbon-oxidizing bacteria in 10 times less quantity (dilution 1:1000), as the percentage of degradation dropped to 44.1%. Also, the number of microorganisms in the soil when the drug was applied at a dilution of 1:100 was 109-1010, and at a dilution of 1:1000 it dropped to 108.

During two months of reclamation, when using the Peroil biologics at a dilution of 1:100, the percentage of hydrocarbon degradation reached 92.8-98.9%, and at a dilution of 1:1000 – 77.6%. The titer of hydrocarbon-oxidizing bacteria at a dilution of 1:100 is 1010, and at a dilution of 1:1000 - 109.

There remains a significant difference in the decomposition of fuel oil hydrocarbons when the Peroil preparation is introduced into the soil at a dilution of 1:100 and the same hydrocarbon-oxidizing bacteria grown in an aerotank.

In a month, it decomposed in the soil when applying the drug in dilution 1:100 - 60,6-65,6%, and the biomass of hydrocarbon-oxidizing bacteria grown in an aerotank is 28.3-36.7%. Two months of reclamation of fuel oil-contaminated soil with biomass of hydrocarbon-oxidizing bacteria grown in an aerotank produced 65.4 - 68.5% decomposition of hydrocarbons, which is 70% of the decomposition of hydrocarbons by the preparation.

It is possible that the activity of cultures of hydrocarbon-oxidizing microorganisms grown in an aerotank on wastewater is significantly reduced due to a number of environmental factors, which include: instability of weather and climatic conditions; fluctuations in the C:N:O ratio in the composition of wastewater; changes in the ecological balance of the biocenosis of activated sludge in aerotanks.

Thus, evaluating the results of the conducted studies, it is possible to note the high efficiency of the Peroil biological product, while the degree of effectiveness correlates with the amount of microorganisms introduced into the oil-contaminated soil. The best indicators for soil purification were obtained by using a bacterial solution obtained by diluting freeze-dried biomass in a ratio of 1:100, regular loosening and moistening (1 time per decade of the month), the introduction of 1% of ammonium.

Within one month, hydrocarbon degradation in soil reached 60.6-65.6% when treated with the microbial consortium at a 1:100 dilution, whereas the biomass of hydrocarbon-oxidizing bacteria cultivated in the aeration tank achieved 28.3-36.7%. Two months of reclamation of fuel oil-contaminated soil using the biomass of hydrocarbon-oxidizing bacteria grown in the aeration tank resulted in 65.4-68.5% hydrocarbon degradation, which corresponds to 70% of the degradation achieved with the biopreparation.

During the preliminary analyses, it was visually noted that oil pollution in the soils is unevenly represented. The soil horizon A and A1 (0-10, 10-20 cm) in the areas inside RP L, near RP M and near N looks relatively clean, the soil is light brown in color with a faint odor of petroleum products. Organoleptic parameters change when sampling from a depth of more than 15-20 cm, where the soil turns dark brown to black with a pungent odor of petroleum products. The clay castle of site K is a sludge-like waste, where hydrophobic heavily smeared black areas are marked in places. The height of the ground at this point ranges from 15 to 40 cm.

As a result of the microbiological examination, it was found that the titer of microorganisms in the studied soils is significant and closely depends on the nature of oil pollution.

It was found that the content of microorganisms in the soil varies between: heterotrophic microorganisms - 106-107 cells/g, hydrocarbon-oxidizing - 105-106 cells/g, which indicates that most of the heterotrophic microorganisms are represented by hydrocarbon-oxidizing forms.

4. Conclusion

Oil production and refining in Kazakhstan increase each year. However, the intensification of these processes is accompanied by environmental pollution, particularly of soils.

The ecological niche vacated due to the death of oil-sensitive microorganisms is occupied by hydrocarbon-oxidizing bacteria. Their numbers increase with contamination, with their share in the 0-10 cm soil horizon reaching 45% of the total microbial population, while the background level exceeds 0.1%.

For the development of a microbiological technology for soil remediation from petroleum contamination, the activity of hydrocarbon-oxidizing microorganisms (HOM) should be taken into account. There are two approaches to activating HOM: creating favorable conditions in the soil for the activity of hydrocarbon-oxidizing microorganisms; selecting highly active HOM strains and developing ecological biopreparations.

Data Availability Statement

Research data is only available upon request.

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Edited by

  • Editor:
    Takako Matsumura Tundisi

Publication Dates

  • Publication in this collection
    24 Aug 2026
  • Date of issue
    2026

History

  • Received
    07 May 2026
  • Accepted
    26 June 2026
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