Preliminary Approach to Reimagining of Polluted Soil Ecosystem: Identification and Utilization of Autochthonous Hydrocarbon Degrading Bacteria
DOI:
https://doi.org/10.33003/fjs-2026-1008-5048Keywords:
Bioremediation, biotechnology, ecosystem restoration, hydrocarbon utilizing bacteria, Isolates’ characterizationAbstract
Crude-oil Pollution negatively impacts the ecosystems. This study sought to recover crude-oil impacted soil ecosystem, by isolating, screening and identifying indigenous bacteria in a microcosm experiment. Samples of agricultural soil, were thoroughly blended with bonny light crude-oil and allowed to equilibrate for three weeks. Physiochemical parameters (pH, Moisture content, Electrical Conductivity, heavy metals, Polycyclic Aromatic Hydrocarbons (PAHs) and Total Petroleum Hydrocarbons (TPH) of the control and contaminated soils were assessed using standard laboratory methods and Gas Chromatography-Mass Spectrometry (GC-MS). Hydrocarbon-utilizing bacteria (HUB) were isolated from the impacted soil using Bacto Bushnell Haas broth supplemented with 1% crude-oil as the nutrient medium. Isolates’ Morphological, Biochemical and molecular characterization, as well as degradation screening were done. Physical parameters for the control and impacted soils differed significantly (P<0.05). The soil sample had a mean value of 47.5 x 109 cfu/ml count for Total Heterotrophic Bacteria. Bacteria isolates characterized, belonged to the genera; Klebsiella, staphylococcus, Enterobacter, Acinetobacter, Aeromonas and Kurthia. The population of HUB consisted Staphylococcus spp. (30%), Klebsiella spp. (20%), Aeronomas spp. (10%), Enterobacter spp., Acinetobacter spp. (10%), (10%) and Kurthia spp. (20%). Acinetobacter spp. showed the highest biodegradation capacity; with 2,6-dichlorophenol indophenols (DCPIP) indicator. Kurthia spp, a novel hydrocarbon degrader, was discovered. The study found that different isolates of native bacteria differ in degradation abilities and are effective for remediating polluted soils. The findings promote sustainable environmental management practices by harnessing naturally occurring bacteria for remediation, and supports the development of green technologies that align with global sustainability goals
References
Kanungo, J., Sahoo, T., Swain, L. P., & Behera, I. D. (2024). Toxicity of persistent hydrocarbon pollutants, sources and sustainable remediation process. In Impact of petroleum waste on environmental pollution and its sustainable management through circular economy (pp. 39-65). Cham: Springer Nature Switzerland.
Sayed, K., Baloo, L., & Sharma, N. K. (2021). Bioremediation of total petroleum hydrocarbons (TPH) by bioaugmentation and biostimulation in water with floating oil spill containment booms as bioreactor basin. International Journal of Environmental Research and Public Health, 18(5), 2226. https://doi.org/10.3390/ijerph18052226
Hasan, A. M., Nassar, A. M., Nassar, I., Maysour, N., & Abdel-Raouf, M. E. (2025). Environmental impacts for the transportation of crude oil and refined products. Environmental Science and Pollution Research, 32(30), 17869–17896.
Akinwumiju, A. S., Adelodun, A. A., & Ogundeji, S. E. (2020). Geospatial assessment of oil spill pollution in the Niger Delta of Nigeria: An evidence-based evaluation of causes and potential remedies. Environmental Pollution, 267, 115545.
Faboya, O. L., Sojinu, O. S., & Otugboyega, J. O. (2023). Preliminary investigation of polycyclic aromatic hydrocarbons (PAHs) concentration, compositional pattern, and ecological risk in crude oil-impacted soil from Niger Delta, Nigeria. Heliyon, 9(4), e15508. https://doi.org/10.1016/j.heliyon.2023.e15508
Energy Information Administration. (2015). Country analysis brief: Nigeria. http://www.eia.gov/beta/international/analysis_includes/countries_long/Nigeria/nigeria.pdf
Ahiamadu, N. M., Nwaogazie, I. L., & Momoh, Y. O. L. (2021). Assessment of polycyclic aromatic hydrocarbons in crude oil spill sites in Emohua Local Government Area of Rivers State, Nigeria. American Journal of Engineering Research, 10(6), 175–187.
Numbere, A. O., Jude, K., Chuku, S. B., Uzoma, M. C., Obanye, C., Ohia, P., ... & Dick-Abbey, I. W. (2024). The impact of unsustainable development and climate change on agriculture and forestry in Nigeria: Predictions, solutions, and management. In Ecosystem management: Climate change and sustainability (pp. 541–579).
Kebede, G., Tafese, T., Abda, E. M., Kamaraj, M., & Assefa, F. (2021). Factors influencing the bacterial bioremediation of hydrocarbon contaminants in the soil: Mechanisms and impacts. Journal of Chemistry, 2021, Article 9823362. https://doi.org/10.1155/2021/9823362
Okoh, E., Yelebe, Z. R., Oruabena, B., et al. (2020). Clean-up of crude oil-contaminated soils: Bioremediation option. International Journal of Environmental Science and Technology, 17, 1185–1198. https://doi.org/10.1007/s13762-019-02605-y
Kalia, A., Sharma, S., Semor, N., et al. (2022). Recent advancements in hydrocarbon bioremediation and future challenges: A review. 3 Biotech, 12(6), 135. https://doi.org/10.1007/s13205-022-03199-y
Kanwal, M., Ullah, H., Gulzar, A., et al. (2022). Biodegradation of petroleum hydrocarbons and the factors effecting rate of biodegradation. American Journal of Biomedical Science & Research, 16(1). https://doi.org/10.34297/AJBSR.2022.16.002182
Bala, S., Garg, D., Thirumalesh, B. V., et al. (2022). Recent strategies for bioremediation of emerging pollutants: A review for a green and sustainable environment. Toxics, 10(8), 484. https://doi.org/10.3390/toxics10080484
Osburn, E. D., Yang, G., Rilling, M. C., & Strickland, M. S. (2023). Evaluating the role of bacterial diversity in supporting soil ecosystem functions under anthropogenic stress. SME Communications, 3(1). https://doi.org/10.1038/s43705-023-00273-1
Alegbeleye, O. O., Opeolu, B. O., & Jackson, V. (2017). Bioremediation of polycyclic aromatic hydrocarbon (PAH) compounds: (acenaphthene and fluorene) in water using indigenous bacterial species isolated from the Diep and Plankenburg rivers, Western Cape, South Africa. Brazilian Journal of Microbiology, 48, 314–325. https://doi.org/10.1016/j.bjm.2016.07.027
Umar, S. A., Dhakar, R., Sa'idu, M., Sulaiman, M., Wudil, A. A., Shitu, A. S., Abdullahi, A. R., Saminu, S. M., Teli, P. K., & Aliyu, U. A. (2025). Bioremediation of water pollutants from wastewater. FUDMA Journal of Sciences, 9(1), 163–179. https://doi.org/10.33003/fjs-2025-0901-2988
Hopton, C. M., Nienow, P., & Cockell, C. S. (2025). Growth, physiology, and metabolism of Halomonas meridiana in aqueous ammonium sulfate with implications for icy moon astrobiology. Frontiers in Microbiology, 16, 1642998.
Khadka, D., Amgain, R., Joshi, S., & Shrestha, S. (2021). Evaluation of distilled water pH measurement with electrolyte methods in cultivated soils of Nepal. AgroChemistry Soil Science, 92, 52–61. https://doi.org/10.31073/acss92-06
Falodun, T. O., Boisa, N., Ideriah, T. J. K., & Konne, J. L. (2023). Oral bioaccessibility of polycyclic aromatic hydrocarbons in fly ash derived from incineration of petroleum products and waste motor tyres. International Research Journal of Pure and Applied Chemistry, 24(3), 20–30
American Public Health Association. (1998). Standard methods for the examination of water and wastewater (20th ed.). American Public Health Association.
Shekhar, S. K., Godheja, J., & Modi, D. R. (2015). Hydrocarbon bioremediation efficiency by five indigenous bacterial strains isolated from contaminated soils. International Journal of Current Microbiology and Applied Sciences, 4(3), 892–905.
Okoye, A. U., Chikere, C. B., & Okpokwasili, G. C. (2020). Isolation and characterization of hexadecane degrading bacteria from oil-polluted soil in Gio Community, Niger Delta, Nigeria. Scientific African. https://doi.org/10.1016/j.sciaf.2020.e00340
Mulet, M., Sanchez, D., Rodriguez, A. C., Nogales, B., Bosch, R., Busquets, A., Gomila, M., Lalucat, J., & Garcia-Valdes, E. (2018). Pseudomonas gallaeciensis sp. nov., isolated from crude-oil-contaminated intertidal sand samples after the Prestige oil spill. Systematic and Applied Microbiology, 41(4), 340–347.
Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35, 1547–1549.
Ogundolie, F. A. (2022). Optimization and production of extracellular Bacillus megaterium (ISA 08) alpha-amylase isolated from cassava dumpsite soil. Archives of Science and Technology, 3(1), 92–104.
Ejairu, K. O., & Okiotor, M. E. (2022). Effect of oil spill on physicochemical properties of soil spilled sites in Kokori, Ethiope East Local Government Area, Delta State, Nigeria. Journal of Applied Science and Environmental Management, 26(11), 1869–1872.
Solomon, M. P., Agbagwa, I., & Osuji, L. C. (2023). Status of oil quality in the vicinity of artisanal refining sites in Rivers State. Asian Journal of Environment and Ecology, 22(4), 63–67.
Li, X., Wang, X., Zhang, Y., et al. (2016). Salinity and conductivity amendment of soil enhanced the bioelectrochemical degradation of petroleum hydrocarbons. Scientific Reports, 6, 32861. https://doi.org/10.1038/srep32861
Bankole, A. O., Ogunkeyede, A. O., Agboro, H., Ekhorutomwen, P. A., Otuomagie, O. I., Isimekhai, K. A., Fadairo, E. A., & Isuruku, E. J. (2024). Heavy metal levels and ecological risk in crude oil-contaminated soils from Okpare-Olomu, Niger Delta, Nigeria. Journal of Environmental Protection, 15, 415–438. https://doi.org/10.4236/jep.2024.154024
Otugboyega, J. O., Madu, F. U., Otugboyega, O. O., Ojo, A. M., Adeyeye, A. J., & Ajayi, J. A. (2023). Biomonitoring and biomathematical modeling of health risks associated with dumpsite grown vegetables in Lagos State. Biological Trace Element Research, 202(7), 3333–3348. https://doi.org/10.1007/s12011-023-03903-w
Samuel-Osamaka, F. C., Arotupin, D. J., Olaniyi, O. O., & Banat, I. M. (2021). Crude oil degrading bacteria obtained from unpolluted soils. Fuoye Journal of Physics and Applied Sciences, 6(2).
Zhang, H., Liu, W., Xiong, Y., Li, G., Cui, J., Zhao, C., & Zhang, L. (2024). Effects of dissolved organic matter on distribution characteristics of heavy metals and their interactions with microorganisms in soil under long-term exogenous effects. Science of the Total Environment, 947, 174565.
Yu, Y., Zhang, Y., Zhao, N., Guo, J., Xu, W., Ma, M., & Li, X. (2020). Remediation of crude-oil polluted soil by the bacterial rhizosphere community of Suaeda salsa revealed by 16S RNA genes. International Journal of Environmental Research and Public Health, 17(5), 1471. https://doi.org/10.3390/ijerph17051471
Chattopadhyay, S., & Ghosh Sachan, S. (2023). Biodegradation of polycyclic aromatic hydrocarbons and the impact of various genes for their enhanced degradation. Letters in Applied Microbiology, 76(2), ovac062.
Azevedo, M. A., do Nascimento, L. P., dos Remédios Vieira-Neta, M., & Duarte, I. C. S. (2023). Production of biosurfactant by bacteria from extreme environments: Biotechnological potential and applications. In Multifunctional microbial biosurfactants (pp. 129–156). Springer Nature Switzerland.
Ali, M. F., Ridha, M. J., & Taly, A. H. (2018). Optimization kerosene bio-degradation by a local soil bacterium isolate Klebsiella pneumoniae Sp. Pneumonia. Journal of Pure and Applied Microbiology, 12(4), 2049–2057.
Rajkumari, J., Singha, L. P., & Pandey, P. (2018). Genomic insight of aromatic hydrocarbon degrading Klebsiella pneumoniae AWD5 with plant growth promoting attributes: A paradigm of soil isolates with elements of biodegradation. 3 Biotech, 8(2). https://doi.org/10.1007/s13205-018-1341
Zhang, G., Wu, Y., Qian, X., & Meng, Q. (2005). Biodegradation of crude oil by Pseudomonas aeruginosa in the presence of rhamnolipids. Journal of Zhejiang University Science B, 6(8), 725–730. https://doi.org/10.1631/jzus.2005.B0725
Medić, A., Lješević, M., Inui, H., Beskoski, V., Kojic, I., Stojanovic, K., & Karadžić, I. (2020). Efficient biodegradation of petroleum n-alkanes and polycyclic aromatic hydrocarbons by polyextremophilic Pseudomonas aeruginosa SAN AI with multidegradative capacity. RSC Advances, 10(24), 14060–14070. https://doi.org/10.1039/C9RA1037F
Das, S., Das, N., Choure, K., & Pandey, P. (2023). Biodegradation of asphaltene by lipopeptide-biosurfactant producing hydrocarbonoclastic, crude-oil degrading Bacillus spp. Bioresource Technology, 382, 129198. https://doi.org/10.1016/j.biortech.2023.129198
Bisht, S., Pandey, P., Sood, A., Sharma, S., & Bisht, N. S. (2010). Biodegradation of naphthalene and anthracene by chemotactically active rhizobacteria of Populus deltoides. Brazilian Journal of Microbiology, 41(4), 922–930.
Kumar, R., & De, M. (2023). Enhanced degradation of petroleum hydrocarbons by Klebsiella michiganensis RK and Acinetobacter baumannii IITG19 isolated from local soil sources. International Journal of Environmental Science and Technology, 20, 13387–13398. https://doi.org/10.1007/s13762-023-04790-3
Cai, Y., Wang, R., Rao, P., Wu, B., Yan, L., Hu, L., Park, S., Ryu, M., & Zhou, X. (2021). Bioremediation of petroleum hydrocarbons using Acinetobacter sp. SCYY-5 isolated from contaminated oil sludge: Strategy and effectiveness study. International Journal of Environmental Research and Public Health, 18(2), 819. https://doi.org/10.3390/ijerph18020819
Sharma, A., Dubey, V., Sharma, R., Devnath, K., Gupta, V. K., Akhter, J., Bhando, T., Verma, A., Ambatipudi, K., Sarkar, M., & Pathania, R. (2018). The unusual glycine-rich C terminus of the Acinetobacter baumannii RNA chaperone Hfq plays an important role in bacterial physiology. Journal of Biological Chemistry, 293(35), 13377–13388. https://doi.org/10.1074/jbc.RA118.002921
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Copyright (c) 2026 JOSEPH Otugboyega, OLAIDE OLUWAYEMISI Otugboyega, ITUNNU O. AYO, KAMORU T. ALIU
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