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Sustainable Remediation Using Hydrocarbonoclastic Bacteria for Diesel-Range Hydrocarbon Contamination in Soil: Experimental and In Silico Evaluation

Author

Listed:
  • Fernanda Espinosa-López

    (Chemical Sciences School, Universidad La Salle-México, Benjamín Franklin 45, Mexico City 06140, Mexico)

  • Karen Pelcastre-Guzmán

    (Chemical Sciences School, Universidad La Salle-México, Benjamín Franklin 45, Mexico City 06140, Mexico)

  • Anabelle Cerón-Nava

    (Chemical Sciences School, Universidad La Salle-México, Benjamín Franklin 45, Mexico City 06140, Mexico)

  • Alicia Rivera-Noriega

    (Chemical Sciences School, Universidad La Salle-México, Benjamín Franklin 45, Mexico City 06140, Mexico)

  • Marco A. Loza-Mejía

    (Design, Isolation, and Synthesis of Bioactive Molecules Research Group, Universidad La Salle-México, Benjamín Franklin 45, Mexico City 06140, Mexico)

  • Alejandro Islas-García

    (Development and Innovation in Applied Environmental Science and Technology Research Group, Universidad La Salle-México, Benjamín Franklin 45, Mexico City 06140, Mexico)

Abstract

The increasing global oil consumption has led to significant soil contamination by hydrocarbons, notably diesel-range hydrocarbons. Soil bioremediation through bacterial bioaugmentation is an alternative to increase the degradation of organic pollutants such as petroleum products. Bioremediation is a sustainable practice that contributes to the Sustainable Development Goals (SDGs) because it is environmentally friendly, reduces the impact of human activities, and avoids the use of invasive and destructive methods in soil restoration. This study examines the bioremediation potential of hydrocarbonoclastic bacteria isolated from soil close to areas with a risk of spills due to pipelines carrying hydrocarbons. Among the isolated strains, Arthrobacter globiformis , Pantoea agglomerans , and Nitratireductor soli exhibited hydrocarbonoclast activity, achieving diesel removal of up to 90% in short-chain alkanes and up to 60% in long-chain hydrocarbons. The results from in silico studies, which included molecular docking and molecular dynamics simulations, suggest that the diesel removal activity can be explained by the bioavailability of the linear alkanes and their affinity for alkane monooxygenase AlkB present in the studied microorganisms, since long-chain hydrocarbons had lower enzyme affinity and lower aqueous solubility. The correlation of the experimental results with the computational analysis allows for greater insight into the processes involved in the microbial degradation of hydrocarbons with varying chain lengths. Furthermore, this methodology establishes a cost-effective approximation tool for the evaluation of the feasibility of using different microorganisms in bioremediation processes.

Suggested Citation

  • Fernanda Espinosa-López & Karen Pelcastre-Guzmán & Anabelle Cerón-Nava & Alicia Rivera-Noriega & Marco A. Loza-Mejía & Alejandro Islas-García, 2025. "Sustainable Remediation Using Hydrocarbonoclastic Bacteria for Diesel-Range Hydrocarbon Contamination in Soil: Experimental and In Silico Evaluation," Sustainability, MDPI, vol. 17(12), pages 1-18, June.
    • Handle: RePEc:gam:jsusta:v:17:y:2025:i:12:p:5535-:d:1680003
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    References listed on IDEAS

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    1. Oleg S. Sutormin & Andrey S. Goncharov & Valentina A. Kratasyuk & Yuliya Yu. Petrova & Ruslan Ya. Bajbulatov & Aleksandr E. Yartsov & Aleksandr A. Shpedt, 2024. "Effects of Oil Contamination on Range of Soil Types in Middle Taiga of Western Siberia," Sustainability, MDPI, vol. 16(24), pages 1-14, December.
    2. Sang Hwan Lee & Jung Hyun Lee & Woo Chul Jung & Misun Park & Min Suk Kim & Seung Jae Lee & Hyun Park, 2020. "Changes in Soil Health with Remediation of Petroleum Hydrocarbon Contaminated Soils Using Two Different Remediation Technologies," Sustainability, MDPI, vol. 12(23), pages 1-10, December.
    3. Anzhelika M. Eremeeva & Natalia K. Kondrasheva & Artyom F. Khasanov & Ivan L. Oleynik, 2023. "Environmentally Friendly Diesel Fuel Obtained from Vegetable Raw Materials and Hydrocarbon Crude," Energies, MDPI, vol. 16(5), pages 1-12, February.
    4. Wesley Araújo Passos & Meirielly Jesus & Fernando Mata & Millena Souza Menezes & Pablo Omar Lubarino dos Santos & Brenda Lohanny P. Santos & Hortência E. P. Santana & Denise Santos Ruzene & Daniel Per, 2025. "Bioremediation Potential of Sunflower-Derived Biosurfactants: A Bibliometric Description," Sustainability, MDPI, vol. 17(1), pages 1-23, January.
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