Microbial and Plant-Based Bioremediation of Petroleum Hydrocarbons: Mechanisms, Strategies and Environmental Applications

Authors

  • Pawan Kumar Kanaujia

    Department of Biotechnology, Faculty of Health and Life Sciences, Mahayogi Gorakhnath University Gorakhpur, Gorakhpur 273007, India

  • Prashant Gupta

    Department of Biotechnology, Faculty of Health and Life Sciences, Mahayogi Gorakhnath University Gorakhpur, Gorakhpur 273007, India

  • Amit Kumar Dubey

    Department of Biotechnology, Faculty of Health and Life Sciences, Mahayogi Gorakhnath University Gorakhpur, Gorakhpur 273007, India

  • Abaidya Nath Singh

    Department of Biotechnology, Faculty of Health and Life Sciences, Mahayogi Gorakhnath University Gorakhpur, Gorakhpur 273007, India

  • Neha Tripathi

    Department of Biotechnology, Faculty of Health and Life Sciences, Mahayogi Gorakhnath University Gorakhpur, Gorakhpur 273007, India

  • Shreya Singh

    Department of Biotechnology, Faculty of Health and Life Sciences, Mahayogi Gorakhnath University Gorakhpur, Gorakhpur 273007, India

DOI:

https://doi.org/10.30564/jees.v8i4.13137
Received: 8 February 2026 | Revised: 5 March 2026 | Accepted: 10 March 2026 | Published Online: 8 April 2026

Abstract

Petroleum hydrocarbon (PH) pollution poses a persistent threat to terrestrial and aquatic ecosystems, with wide‑ranging implications for soil fertility, water quality, and human health. Conventional physicochemical remediation methods, although effective in some contexts, often entail high operational costs, generate secondary waste, and fail to achieve complete mineralization of complex hydrocarbon mixtures. In contrast, microbial bioremediation has emerged as a sustainable, cost‑effective, and ecologically compatible strategy that harnesses the metabolic versatility of indigenous and exogenous bacteria to degrade a broad spectrum of aliphatic, aromatic, and heterocyclic hydrocarbons. Recent advances in biostimulation, bioaugmentation, phytoremediation, and engineered bioreactors have demonstrated field‑scale removal efficiencies of total petroleum hydrocarbons (TPH) exceeding 70–90% within weeks to months, depending on site‑specific conditions and pollutant load. Nevertheless, incomplete degradation, environmental variability, and the potential accumulation of intermediate metabolites constrain the robustness and predictability of bioremediation at scale. Emerging technologies such as nanobioremediation, bioelectrochemical systems, and “omics” driven microbial community engineering offer promising avenues to enhance degradation kinetics, extend substrate range, and mitigate antibiotic resistance gene (ARG) dissemination associated with exposure to contaminated matrices. This review synthesizes current knowledge on the classification, sources, and ecological impacts of petroleum hydrocarbons, critically evaluates the mechanisms and techniques underpinning microbial bioremediation, and identifies key research gaps and regulatory challenges. The article further outlines future perspectives for integrating multi‑process, data‑driven remediation strategies into national and international frameworks for environmental restoration.

Keywords:

Bioremediation; Petroleum Hydrocarbons; Bioaugmentation; Phytoremediation; Bioaccumulative; Antibiotic Resistance Gene and Engineered Bioreactors

References

[1] Varjani, S.J., Upasani, V.N., 2016. Biodegradation of petroleum hydrocarbons by oleophilic strain of Pseudomonas aeruginosa NCIM 5514. Bioresource Technology. 222, 195–201. DOI: https://doi.org/10.1016/j.biortech.2016.10.006

[2] Meckenstock, R.U., Boll, M., Mouttaki, H., et al., 2016. Anaerobic degradation of benzene and polycyclic aromatic hydrocarbons. Journal of Molecular Microbiology and Biotechnology. 26, 92–118. DOI: https://doi.org/10.1159/000441358

[3] Varjani, S.J., Rana, D.P., Jain, A.K., et al., 2015. Synergistic ex-situ biodegradation of crude oil by halotolerant bacterial consortium of indigenous strains isolated from on shore sites of Gujarat, India. International Biodeterioration & Biodegradation. 103, 116–124. DOI: https://doi.org/10.1016/j.ibiod.2015.03.030

[4] Barnes, N.M., Khodse, V.B., Lotlikar, N.P., et al., 2018. Bioremediation potential of hydrocarbon-utilizing fungi from select marine niches of India. 3 Biotech. 8, 21. DOI: https://doi.org/10.1007/s13205-017-1043-8

[5] Moustafa, A.M., 2016. Bioremediation of oil spill in Kingdom of Saudi Arabia by using fungi isolated from polluted soils. International Journal of Current Microbiology and Applied Sciences. 5(5), 680–691. DOI: https://doi.org/10.20546/ijcmas.2016.505.069

[6] Maamar, A., Lucchesi, M.-E., Debaets, S., et al., 2020. Highlighting the crude oil bioremediation potential of marine fungi isolated from the Port of Oran (Algeria). Diversity. 12(5), 196. DOI: https://doi.org/10.3390/d12050196

[7] Muhonja, C.N., Makonde, H., Magoma, G., et al., 2018. Biodegradability of polyethylene by bacteria and fungi from Dandora dumpsite Nairobi-Kenya. PLoS One. 13, e0198446. DOI: https://doi.org/10.1371/journal.pone.0198446

[8] Pawłowska, J., Okrasińska, A., Kisło, K., et al., 2019. Carbon assimilation profiles of mucoralean fungi show their metabolic versatility. Scientific Reports. 9, 11864. DOI: https://doi.org/10.1038/s41598-019-48296-w

[9] Chen, T., Xue, L., Chen, T.G.P., et al., 2020. Volatile organic compounds and ozone air pollution in an oil production region in northern China. Atmospheric Chemistry and Physics. 20(11), 7069–7086

[10] Yang, Z., Guo, Z., Qiu, C., et al., 2016. Preliminary analysis showed country-specific gut resistome based on 1267 feces samples. Gene. 581(2), 178–182. DOI: https://doi.org/10.1016/j.gene.2016.01.043

[11] Haritash, A.K., Kaushik, C.P., 2009. Biodegradation aspects of polycyclic aromatic hydrocarbons (PAHs): A review. Journal of Hazardous Materials. 169(1–3), 1–15. DOI: https://doi.org/10.1016/j.jhazmat.2009.03.137

[12] Liu, Y., Hu, H., Zanaroli, G., et al., 2021. A Pseudomonas sp. strain uniquely degrades PAHs and heterocyclic derivatives via lateral dioxygenation pathways. Journal of Hazardous Materials. 403, 123956. DOI: https://doi.org/10.1016/j.jhazmat.2020.123956

[13] Abu Bakar, N., Karsani, S.A., Alias, S.A., 2020. Fungal survival under temperature stress: A proteomic perspective. PeerJ. 8, e10423. DOI: https://doi.org/10.7717/peerj.10423

[14] Xu, X., Liu, W., Tian, S., et al., 2018. Petroleum hydrocarbon-degrading bacteria for the remediation of oil pollution under aerobic conditions: A perspective analysis. Frontiers in Microbiology. 9, 2885. DOI: https://doi.org/10.3389/fmicb.2018.02885

[15] Eliaz, N., Ron, E.Z., Gozin, M., et al., 2018. Microbial degradation of epoxy. Materials. 11(11), 2123. DOI: https://doi.org/10.3390/ma11112123

[16] Patowary, K., Patowary, R., Kalita, M.C., et al., 2017. Characterization of biosurfactant produced during degradation of hydrocarbons using crude oil as sole source of carbon. Frontiers in Microbiology. 8, 279. DOI: https://doi.org/10.3389/fmicb.2017.00279

[17] Varjani, S.J., 2017. Microbial degradation of petroleum hydrocarbons. Bioresource Technology. 223, 277–286.

[18] Wilkes, H., Buckel, W., Golding, B.T., et al., 2016. Metabolism of hydrocarbons in n-alkane-utilizing anaerobic bacteria. Journal of Molecular Microbiology and Biotechnology. 26, 138–151. DOI: https://doi.org/10.1159/000442160

[19] Correa-García, S., Pande, P., Séguin, A., et al., 2018. Rhizoremediation of petroleum hydrocarbons: A model system for plant microbiome manipulation. Microbial Biotechnology. 11(5), 819–832. DOI: https://doi.org/10.1111/1751-7915.13303

[20] Das, P., Tiwari, P., 2018. Valorization of packaging plastic waste by slow pyrolysis. Resources, Conservation and Recycling. 128, 69–77

[21] Al-Dhabaan, F.A., 2021. Mycoremediation of crude oil contaminated soil by specific fungi isolated from Dhahran in Saudi Arabia. Saudi Journal of Biological Sciences. 28(1), 73–77. DOI: https://doi.org/10.1016/j.sjbs.2020.08.033

[22] Abdel-Raouf, M.E., El-Keshawy, M., Hasan, A.M.A., 2022. Green polymers and their uses in petroleum industry, current state and future perspectives. In: Abdel-Raouf, M.E., El-Keshawy, M.H. (Eds.). Crude Oil—New Technologies and Recent Approaches. IntechOpen: London, UK.

[23] Abdel-Shafy, H.I., Mansour, M.S.M., 2016. A review on polycyclic aromatic hydrocarbons: Source, environmental impact, effect on human health and remediation. Egyptian Journal of Petroleum. 25(1), 107–123

[24] Abdulqader, M.A., Syed-Hassan, S.S.A., Jawad, A.H., et al., 2021. Characterization study of oily sludge produced from North Refineries Company Baiji to determine the suitability for conversion into solid fuel. Egyptian Journal of Chemistry. 64(6), 2775–2781.

[25] Abdulqawi, M., Ibrahim, A., Embong, R., et al., 2023. Development of a hybrid technique of solvent extraction and freeze-thaw for oil recovery from petroleum sludge. Materials Today: Proceedings. DOI: https://doi.org/10.1016/j.matpr.2023.04.661

[26] Abdulraheim, M.A.H., Mohamed, E.A.-A., et al., 2021. Ionic liquids as demulsifiers for petroleum emulsions: Review. Trends in Chemical Engineering Journal. 19, 1–17.

[27] Adewunmi, A.A., Amao, A.O., Kamal, M.S., et al., 2020. Demulsification and breaking mechanism of variable quartz concentrates obtained from sand. Journal of Petroleum Science and Engineering. 192, 107263

[28] Adigwe, C.C., Nwaogazie, I.L., Ugwoha, E., et al., 2022. Sludge pollution control from crude oil tank cleaning. Journal of Water Resource Protection. 14(9), 632–649

[29] Abdullah, S.R.S., Al-Baldawi, I.A., Almansoory, A.F., et al., 2020. Plant-assisted remediation of hydrocarbons in water and soil: Application, mechanisms, challenges and opportunities. Chemosphere. 247, 125932. DOI: https://doi.org/10.1016/j.chemosphere.2020.125932

[30] Ahmed, F., Fakhruddin, A., 2018. A review on environmental contamination of petroleum hydrocarbons and its biodegradation. International Journal of Environmental Sciences and Natural Resources. 11(3), 555811.

[31] Aliku, C.B., Madu, C.N., Aliku, O., 2021. Organic stimulants for enhancing phytoremediation of crude oil polluted soil: A study on cowpea. Environmental Pollution. 287, 117674. DOI: https://doi.org/10.1016/j.envpol.2021.117674

[32] Alotaibi, F., Hijri, M., St-Arnaud, M., 2021. Overview of approaches to improve rhizoremediation of petroleum hydrocarbon-contaminated soils. Applied Microbiology. 1(2), 329–351

[33] Balogh, J.C., Watson, J.R., 2020. Role and conservation of water resources. In Golf Course Management & Construction: Environmental Issues. CRC Press: Boca Raton, FL, USA, pp. 39–104

[34] Banet, G., Turaani, A., Farber, R., et al., 2021. The effects of biostimulation and bioaugmentation on crude oil biodegradation in two adjacent terrestrial oil spills of different age, in a hyper-arid region. Journal of Environmental Management. 286, 112248. DOI: https://doi.org/10.1016/j.jenvman.2021.112248

[35] Cai, B., Ma, J., Yan, G., et al., 2016. Comparison of phytoremediation, bioaugmentation and natural attenuation for remediating saline soil contaminated by heavy crude oil. Biochemical Engineering Journal. 112, 170–177

[36] Charles, F., Salami, S., Dashak, D., et al., 2021. An analytical investigation study of potential human health risks caused by petroleum-contaminated surface water containing various toxic heavy metals at the Okpoka creek, Niger-delta, Nigeria. International Research Journal of Pure and Applied Chemistry. 22(2), 1–11

[37] Colcord, D.E., Shilling, A.M., Freeman, K.H., et al., 2019. Aquatic biomarkers record Pleistocene environmental changes at Paleolake Olduvai, Tanzania. Palaeogeography, Palaeoclimatology, Palaeoecology. 524, 250–261

[38] Connellan, S.J., 2017. Lung diseases associated with hydrocarbon exposure. Respiratory Medicine. 126, 46–51. DOI: https://doi.org/10.1016/j.rmed.2017.03.021

[39] Dupuis, A., Ucan-Marin, F., 2015. Research Documents. 2015/007: A Literature Review on the Aquatic Toxicology of Petroleum Oil: An Overview of Oil Properties and Effects to Aquatic Biota. Canadian Science Advisory Secretariat (CSAS): Ottawa, ON, Canada.

[40] Eltoukhy, A., Jia, Y., Nahurira, R., et al., 2020. Biodegradation of endocrine disruptor Bisphenol A by Pseudomonas putida strain YC-AE1 isolated from polluted soil, Guangdong, China. BMC Microbiology. 20(1), 11. DOI: https://doi.org/10.1186/s12866-020-1699-9

[41] Fenibo, E.O., 2021. Suitability of bacteria in bioremediation techniques common for petroleum-related pollution. Asia Journal of Applied Microbiology. 8(1), 1–18.

[42] MacLean, R.C., Millan, A.S., 2019. The evolution of antibiotic resistance. Science. 365(6458), 1082–1083. DOI: https://doi.org/10.1126/science.aax3879

[43] Baquero, F., Cantón, R., 2017. Evolutionary biology of drug resistance. In: Mayers, D.L., Sobel, J.D., Ouellette, M., et al. (Eds.). Antimicrobial Drug Resistance, Vol. 1: Mechanisms of Drug Resistance. Springer International Publishing: Cham, Switzerland. pp. 9–32.

[44] Hiltunen, T., Virta, M., Anna-Liisa, L., 2017. Antibiotic resistance in the wild: An eco-evolutionary perspective. Philosophical Transactions of the Royal Society B: Biological Sciences. 372(1712), 20160039. DOI: https://doi.org/10.1098/rstb.2016.0039

[45] Martínez, J.L., Coque, T.M., Baquero, F., 2015. What is a resistance gene? Ranking risk in resistomes. Nature Reviews Microbiology. 13, 116–123. DOI: https://doi.org/10.1038/nrmicro3399

[46] Andersson, D.I., 2015. Improving predictions of the risk of resistance development against new and old antibiotics. Clinical Microbiology and Infection. 21(10), 894–898. DOI: https://doi.org/10.1016/j.cmi.2015.05.012

[47] Munck, C., Albertsen, M., Telke, A., et al., 2015. Limited dissemination of the wastewater treatment plant core resistome. Nature Communications. 6, 8452. DOI: https://doi.org/10.1038/ncomms9452

[48] Baquero, F., Lanza, V.F., Cantón, R., et al., 2015. Public health evolutionary biology of antimicrobial resistance: Priorities for intervention. Evolutionary Applications. 8(3), 223–239. DOI: https://doi.org/10.1111/eva.12235

[49] Christaki, E., Marcou, M., Tofarides, A., 2020. Antimicrobial resistance in bacteria: Mechanisms, evolution, and persistence. Journal of Molecular Evolution. 88, 26–40. DOI: https://doi.org/10.1007/s00239-019-09914-3

[50] Van Goethem, M.W., Pierneef, R., Bezuidt, O.K.I., et al., 2018. A reservoir of “historical” antibiotic resistance genes in remote pristine Antarctic soils. Microbiome. 6, 40. DOI: https://doi.org/10.1186/s40168-018-0424-5

[51] Al-Zahrani, R.M., Al-Otibi, F., Marraiki, N., et al., 2022. Biodegradation of petroleum hydrocarbons by Drechsleraspicifera isolated from contaminated soil in Riyadh, Saudi Arabia. Molecules. 27(19), 6450. DOI: https://doi.org/10.3390/molecules27196450

[52] Hasan, A.M.A., Kamal, R.S., Farag, R.K., et al., 2024. Petroleum sludge formation and its treatment methodologies: A review. Environmental Science and Pollution Research International. 31(6), 8369–8386. DOI: https://doi.org/10.1007/s11356-023-31674-3

[53] Fierer, N., Wood, S.A., de Mesquita, C.P.B., 2021. How microbes can, and cannot, be used to assess soil health. Soil Biology and Biochemistry. 153, 108111.

[54] Kumari, B., Singh, S., Singh, D., 2016. Induced degradation of crude oil mediated by microbial augmentation and bulking agents. International Journal of Environmental Science and Technology. 13, 1029–1042.

[55] Kurylenko, V., Izosimova, O., 2016. Study of the impact of petroleum hydrocarbons on sea organisms. Journal of Ecological Engineering. 17(1), 26–29.

[56] Luke, M.E., Odokuma, L.O., 2021. Acute toxicity of crude oil from NNPC and artisanal refineries in Niger Delta on selected aquatic biota. GSC Biological and Pharmaceutical Sciences. 15(3), 16–24.

[57] Maddela, N.R., Scalvenzi, L., Venkateswarlu, K., 2017. Microbial degradation of total petroleum hydrocarbons in crude oil: A field-scale study at the low-land rainforest of Ecuador. Environmental Technology. 38(20), 2543–2550. DOI: https://doi.org/10.1080/09593330.2016.1270356

[58] Mafiana, M.O., Kang, X.-H., Leng, Y., et al., 2021. Petroleum contamination significantly changes soil microbial communities in three oilfield locations in Delta State, Nigeria. Environmental Science and Pollution Research. 28, 31447–31461. DOI: https://doi.org/10.1007/s11356-021-12955-1

[59] Mai, C.T.N., Linh, N.V., Lich, N.Q., et al., 2021. Advanced materials for immobilization of purple phototrophic bacteria in bioremediation of oil-polluted wastewater. Chemosphere. 278, 130464. DOI: https://doi.org/10.1016/j.chemosphere.2021.130464

[60] Mansur, A.A., Pannirselvam, M., Al-Hothaly, K.A., et al., 2015. Recovery and characterization of oil from waste crude oil tank bottom sludge from Azzawiya oil refinery in Libya. Journal of Advanced Chemical Engineering. 5(1), 118.

[61] Kalia, A., Sharma, S., Semor, N., et al., 2022. Recent advancements in hydrocarbon bioremediation and future challenges: A review. 3 Biotech. 12(6), 135. DOI: https://doi.org/10.1007/s13205-022-03199-y

[62] Macchi, M., Festa, S., Nieto, E., et al., 2021. Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics. Biotechnology Reports. 29, e00588. DOI: https://doi.org/10.1016/j.btre.2021.e00588

[63] Imam, A., Suman, S.K., Ghosh, D., et al., 2019. Analytical approaches used in monitoring the bioremediation of hydrocarbons in petroleum-contaminated soil and sludge. Trends in Analytical Chemistry. 118, 50–64. DOI: https://doi.org/10.1016/j.trac.2019.05.023

[64] Mekonnen, B.A., Aragaw, T.A., Genet, M.B., 2024. Bioremediation of petroleum hydrocarbon contaminated soil: A review on principles, degradation mechanisms, and advancements. Frontiers in Environmental Science. 12, 1354422. DOI: https://doi.org/10.3389/fenvs.2024.1354422

[65] Baghaie, A.H., Keshavarzi, M., 2025. Strategies to enhance bioremediation of petroleum hydrocarbon degradation in contaminated environments: A review. Journal of Human Environment and Health Promotion. 11, 138–150.

[66] Larsson, D.G.J., Flach, C.F., 2022. Antibiotic resistance in the environment. Nature Reviews Microbiology. 20(5), 257–269. DOI: https://doi.org/10.1038/s41579-021-00649-x

[67] Kumar, M., Jaiswal, S., Sodhi, K.K., et al., 2019. Antibiotics bioremediation: Perspectives on its ecotoxicity and resistance. Environment International. 124, 448–461. DOI: https://doi.org/10.1016/j.envint.2018.12.065

[68] Apreja, M., Sharma, A., Balda, S., et al., 2022. Antibiotic residues in environment: Antimicrobial resistance development, ecological risks, and bioremediation. Environmental Science and Pollution Research. 29, 3355–3371. DOI: https://doi.org/10.1007/s11356-021-17374-w

[69] Hussain, I., Puschenreiter, M., Gerhard, S., et al., 2018. Rhizoremediation of petroleum hydrocarbon-contaminated soils: Improvement opportunities and field applications. Environmental and Experimental Botany. 147, 202–219. DOI: https://doi.org/10.1016/j.envexpbot.2017.12.016

Downloads

How to Cite

Kanaujia, P. K., Gupta, P., Kumar Dubey, A., Nath Singh, A., Tripathi, N., & Singh, S. (2026). Microbial and Plant-Based Bioremediation of Petroleum Hydrocarbons: Mechanisms, Strategies and Environmental Applications. Journal of Environmental & Earth Sciences, 8(4), 55–87. https://doi.org/10.30564/jees.v8i4.13137

Issue

Article Type

Review (This article belongs to the Topical Collection "Monitoring and Control of Urban Environmental Pollution")