Bioremediation of Environmental Pollutants: Microbial Tactics for Sustainable Ecosystem Restoration
DOI:
https://doi.org/10.38211/joarps.2026.06.330Keywords:
Bioremediation, Microbial degradation, Environmental pollutants, Nanotechnology and omics toolsAbstract
Environmental pollution from industrial growth, urbanization, and farming has become a serious global issue. Among different cleanup strategies, bioremediation stands out as a sustainable and low-cost approach that uses microorganisms to transform or remove pollutants. This paper reviews the roles of microorganisms such as bacteria, fungi, algae, and yeast in breaking down contaminants under both aerobic and anaerobic conditions. Special attention is given to microbial enzymes such as laccases, peroxidases, and monooxygenases, which play a central role in the degradation of persistent compounds, including pharmaceutical residues. The review also covers in situ and ex situ methods—such as bioventing, composting, and bioreactors—and discusses the environmental factors that affect their efficiency, including pH, pollutant levels, nutrient supply, and soil properties. Bioremediation is a sustainable method for cleaning up the environment. It supports SDG 6 (Clean Water and Sanitation), SDG 12 (Responsible Consumption and Production), and SDG 13 (Climate Action). Using this approach at local, industrial, and global levels shows its ability to reduce pollution, lower chemical waste, and restore ecosystems while promoting sustainable development. Recent developments, including microbial biofilms, bio electrochemical systems, nanomaterials, and omics-based tools, show promise in improving efficiency and extending the range of pollutants that can be treated. Although bioremediation offers clear environmental and economic benefits, it still faces challenges related to speed, specificity, and the formation of harmful byproduct.
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References
Ambaye, T. G., Vaccari, M., Franzetti, A., Prasad, S., Formicola, F., Rosatelli, A., & Ritmi, S. (2023). Microbial electrochemical bioremediation of petroleum hydrocarbons pollution: Recent advances and outlook. Chemical Engineering Journal, 452, 139372. DOI: https://doi.org/10.1016/j.cej.2022.139372
Amobonye, A., Aruwa, C. E., Aransiola, S., Omame, J., Alabi, T. D., & Lalung, J. (2023). The potential of fungi in the bioremediation of pharmaceutically active compounds: A comprehensive review. Frontiers in Microbiology, 14, 1207792. DOI: https://doi.org/10.3389/fmicb.2023.1207792
Andreasen, R., Li, Y., Rehman, Y., Ahmed, M., Meyer, R., & Sabri, A. (2018). Prospective role of indigenous Exiguobacterium profundum PT2 in arsenic biotransformation and biosorption by planktonic cultures and biofilms. Journal of Applied Microbiology, 124(2), 431–443. DOI: https://doi.org/10.1111/jam.13636
Ayilara, M. S., & Babalola, O. O. (2023). Bioremediation of environmental wastes: The role of microorganisms. Frontiers in Agronomy, 5, 1183691. DOI: https://doi.org/10.3389/fagro.2023.1183691
Bala, G. P., Rajnoveanu, R. M., Tudorache, E., Motisan, R., & Oancea, C. (2021). Air pollution exposure: The invisible risk factor for respiratory diseases. Environmental Science and Pollution Research, 28(15), 19615–19628. DOI: https://doi.org/10.1007/s11356-021-13208-x
Becker, D., Rodriguez-Mozaz, S., Insa, S., Schoevaart, R., Barceló, D., De Cazes, M., Belleville, M. P., Sanchez-Marcano, J., Misovic, A., Oehlmann, J., & Wagner, M. (2017). Removal of endocrine disrupting chemicals in wastewater by enzymatic treatment with fungal laccases. Organic Process Research & Development, 21(4), 480–491. DOI: https://doi.org/10.1021/acs.oprd.6b00361
Bhatt, P., Verma, A., Gangola, S., Bhandari, G., & Chen, S. (2021). Microbial glycoconjugates in organic pollutant bioremediation: Recent advances and applications. Microbial Cell Factories, 20(1), 72. DOI: https://doi.org/10.1186/s12934-021-01556-9
Dell’Anno, F., Rastelli, E., Sansone, C., Brunet, C., Ianora, A., & Dell’Anno, A. (2021). Bacteria, fungi and microalgae for the bioremediation of marine sediments contaminated by petroleum hydrocarbons in the omics era. Microorganisms, 9(8), 1695. DOI: https://doi.org/10.3390/microorganisms9081695
Dragana, K., Marasović, P., Jugov, N., & Schwarz, I. (2022). Biodegradable nonwoven agrotextile and films: A review. Polymers, 14(11), 2272. DOI: https://doi.org/10.3390/polym14112272
Enerijiofi, K. E., Musa, S. I., Nnachor, E. C., & Ikhajiagbe, B. (2024). Restoration of soil environment for sustained environmental and public health security in the global south. In Sustainable soil systems in global south (pp. 545–572). Springer Nature. DOI: https://doi.org/10.1007/978-981-97-5276-8_20
Eibes, G., Debernardi, G., Feijoo, G., Moreira, M. T., & Lema, J. M. (2011). Oxidation of pharmaceutically active compounds by a ligninolytic fungal peroxidase. Biodegradation, 22(3), 539–550. DOI: https://doi.org/10.1007/s10532-010-9426-0
Giri, B. S., Geed, S., Vikrant, K., Lee, S. S., Kim, K. H., Kailasa, S. K., Vithanage, M., Chaturvedi, P., Rai, B. N., & Singh, R. S. (2021). Progress in bioremediation of pesticide residues in the environment. Environmental Engineering Research, 26, 200446. DOI: https://doi.org/10.4491/eer.2020.446
Gurkok, S. (2021). Important parameters necessary in the bioreactor for the mass production of biosurfactants. In Green sustainable process for chemical and environmental engineering and science (pp. 347–365). Elsevier. DOI: https://doi.org/10.1016/B978-0-12-823380-1.00020-4
Huang, Y., Pan, H., Wang, Q., Ge, Y., Liu, W., & Christie, P. (2019). Enrichment of the soil microbial community in the bioremediation of petroleum-contaminated soil amended with rice straw or sawdust. Chemosphere, 224, 265–271. DOI: https://doi.org/10.1016/j.chemosphere.2019.02.148
Hussain, A., Rehman, F., Rafeeq, H., Waqas, M., Asghar, A., Afsheen, N., Rahdar, A., Bilal, M., & Iqbal, H. M. (2022). In-situ, ex-situ, and nano-remediation strategies to treat polluted soil, water, and air: A review. Chemosphere, 289, 133252. DOI: https://doi.org/10.1016/j.chemosphere.2021.133252
Kango, N., Jana, U. K., & Choukade, R. (2019). Fungal enzymes: Sources and biotechnological applications. In T. Satyanarayana, S. K. Deshpande, & M. V. Deshpande (Eds.), Advancing frontiers (pp. 515–538). Springer. DOI: https://doi.org/10.1007/978-981-13-9349-5_21
Kebede, G., Tafese, T., Abda, E. M., Kamaraj, M., & Assefa, F. (2021). Factors influencing bacterial bioremediation of hydrocarbon contaminants in soil: Mechanisms and impacts. Journal of Chemistry, 2021, 9823362. DOI: https://doi.org/10.1155/2021/9823362
Khalid, F., Hashmi, M. Z., Jamil, N., Qadir, A., & Ali, M. I. (2021). Microbial and enzymatic degradation of PCBs from e-waste-contaminated sites: A review. Environmental Science and Pollution Research, 28(8), 10474–10487. DOI: https://doi.org/10.1007/s11356-020-11996-2
Kharangate-Lad, A., & D’Souza, N. C. (2021). Current approaches in bioremediation of toxic contaminants by microbial cells, biosurfactants and bioemulsifiers of microbial origin. In Rhizobiont bioremediation of hazardous waste (pp. 217–263). Springer. DOI: https://doi.org/10.1007/978-981-16-0602-1_11
Long, C., Jiang, Z., Shangguan, J., Qing, T., Zhang, P., & Feng, B. (2021). Applications of carbon dots in environmental pollution control: A review. Chemical Engineering Journal, 406, 126848. DOI: https://doi.org/10.1016/j.cej.2020.126848
Lueangjaroenkit, P., Teerapatsakul, C., Sakka, K., Sakka, M., Kimura, T., Kunitake, E., Chitradon, L., & Poompuan, P. (2019). Two manganese peroxidases and a laccase of Trametes polyzona KU-RNW027 with novel properties for dye and pharmaceutical product degradation in a redox mediator-free system. Mycobiology, 47(3), 217–229. DOI: https://doi.org/10.1080/12298093.2019.1589900
Mahmoud, G. A. E. (2021). Microbial scavenging of heavy metals using bioremediation strategies. In Rhizobiont bioremediation of hazardous waste (pp. 265–289). Springer. DOI: https://doi.org/10.1007/978-981-16-0602-1_12
Medfu Tarekegn, M., Zewdu Salilih, F., & Ishetu, A. I. (2020). Microbes used as a tool for bioremediation of heavy metals from the environment. Cogent Food & Agriculture, 6(1), 1783174. DOI: https://doi.org/10.1080/23311932.2020.1783174
Methneni, N., Morales-Gonzalez, J. A., Jaziri, A., Mansour, H. B., & Fernandez-Serrano, M. (2021). Persistent organic and inorganic pollutants in the effluents from textile dyeing industries: Ecotoxicology appraisal via a battery of biotests. Environmental Research, 196, 110956. DOI: https://doi.org/10.1016/j.envres.2021.110956
Mishra, M., Singh, S. K., & Kumar, A. (2021). Environmental factors affecting the bioremediation potential of microbes. In Microbe mediated remediation of environmental contaminants (pp. 47–58). Elsevier. DOI: https://doi.org/10.1016/B978-0-12-821199-1.00005-5
Mori, T., Ohno, H., Ichinose, H., Kawagishi, H., & Hirai, H. (2021). White-rot fungus Phanerochaete chrysosporium metabolizes chloropyridinyl-type neonicotinoid insecticides by an N-dealkylation reaction catalyzed by two cytochrome P450s. Journal of Hazardous Materials, 402, 123831. DOI: https://doi.org/10.1016/j.jhazmat.2020.123831
Narayanan, M., Ali, S. S., & El-Sheekh, M. (2023). A comprehensive review on the potential of microbial enzymes in multipollutant bioremediation: Mechanisms, challenges, and future prospects. Journal of Environmental Management, 334, 117532. DOI: https://doi.org/10.1016/j.jenvman.2023.117532
Ndeddy Aka, R. J., & Babalola, O. O. (2017). Identification and characterization of Cr-, Cd-, and Ni-tolerant bacteria isolated from mine tailings. Bioremediation Journal, 21(1), 1–19. DOI: https://doi.org/10.1080/10889868.2017.1282933
Patel, A. K., Singhania, R. R., Albarico, F. P. J. B., Pandey, A., Chen, C. W., & Dong, C. D. (2022). Organic wastes bioremediation and its changing prospects. Science of the Total Environment, 824, 153889. DOI: https://doi.org/10.1016/j.scitotenv.2022.153889
Persson, L., Carney Almroth, B. M., Collins, C. D., Cornell, S., De Wit, C. A., Diamond, M. L., Fantke, P., Hassellöv, M., MacLeod, M., Ryberg, M. W., Søgaard Jørgensen, P., Villarrubia-Gómez, P., Wang, Z., & Hauschild, M. Z. (2022). Outside the safe operating space of the planetary boundary for novel entities. Environmental Science & Technology, 56(3), 1510–1521. DOI: https://doi.org/10.1021/acs.est.1c04158
Ren, X., Zeng, G., Tang, L., Wang, J., Wan, J., Wang, J., Deng, Y., Liu, Y., & Chen, D. (2018). The potential impact on the biodegradation of organic pollutants from composting technology for soil remediation. Waste Management, 72, 138–149. DOI: https://doi.org/10.1016/j.wasman.2017.11.032
Saikia, S., Yadav, M., Hoque, R. A., & Yadav, H. S. (2022). Bioremediation mediated by manganese peroxidase: An overview. Biocatalysis and Biotransformation, 41(3), 161–173. DOI: https://doi.org/10.1080/10242422.2022.2113517
Sales da Silva, I. G., Gomes de Almeida, F. C., Padilha da Rocha e Silva, N. M., Casazza, A. A., Converti, A., & Asfora Sarubbo, L. (2020). Soil bioremediation: Overview of technologies and trends. Energies, 13(18), 4664. DOI: https://doi.org/10.3390/en13184664
Santosa, I., Grossman, M. J., Sartoratto, A., Ponezi, A. N., & Durrant, L. R. (2012). Degradation of the recalcitrant pharmaceuticals carbamazepine and 17α-ethinylestradiol by ligninolytic fungi. Chemical Engineering Journal, 41, 161–173.
Saxena, G., & Bharagava, R. N. (Eds.). (2020). Bioremediation of industrial waste for environmental safety: Volume I – Industrial waste and its management. Springer. DOI: https://doi.org/10.1007/978-981-13-1891-7
Shahi Khalaf Ansar, B., Kavusi, E., Dehghanian, Z., Pandey, J., Asgari Lajayer, B., Price, G. W., & Astatkie, T. (2023). Removal of organic and inorganic contaminants from the air, soil, and water by algae. Environmental Science and Pollution Research, 30(55), 116538–116566. DOI: https://doi.org/10.1007/s11356-022-21283-x
Sharma, I. (2020). Bioremediation techniques for polluted environment: Concept, advantages, limitations, and prospects. In Trace metals in the environment: New approaches and recent advances. IntechOpen. DOI: https://doi.org/10.5772/intechopen.90453
Sharma, J. (2019). Advantages and limitations of in situ methods of bioremediation. Recent Advances in Biology and Medicine, 5, 955923. DOI: https://doi.org/10.18639/RABM.2019.955923
Sharma, P., Singh, S. P., Parakh, S. K., & Tong, Y. W. (2022). Health hazards of hexavalent chromium (Cr VI) and its microbial reduction. Bioengineered, 13(3), 4923–4938. DOI: https://doi.org/10.1080/21655979.2022.2037273
Suda, T., Hata, T., Kawai, S., Okamura, H., & Nishida, T. (2012). Treatment of tetracycline antibiotics by laccase in the presence of 1-hydroxybenzotriazole. Bioresource Technology, 103, 498–501. DOI: https://doi.org/10.1016/j.biortech.2011.10.041
Tegene, B., & Tenkegna, T. (2020). Mode of action, mechanism and role of microbes in bioremediation service for environmental pollution management. Journal of Biotechnology and Bioinformatics Research, 1–18. DOI: https://doi.org/10.47363/JBBR/2020(2)116
Tripathi, S., Sanjeevi, R., Anuradha, J., Chauhan, D. S., & Rathoure, A. K. (2022). Nano-bioremediation: Nanotechnology and bioremediation. In Research anthology on emerging techniques in environmental remediation (pp. 135–149). IGI Global. DOI: https://doi.org/10.4018/978-1-6684-3714-8.ch007
Vaksmaa, A., Guerrero-Cruz, S., Ghosh, P., Zeghal, E., Hernando-Morales, V., & Niemann, H. (2023). Role of fungi in bioremediation of emerging pollutants. Frontiers in Marine Science, 10, 1070905. DOI: https://doi.org/10.3389/fmars.2023.1070905
Wen, X., Jia, Y., & Li, J. (2009). Degradation of tetracycline and oxytetracycline by crude lignin peroxidase prepared from Phanerochaete chrysosporium. Chemosphere, 75(8), 1003–1007. DOI: https://doi.org/10.1016/j.chemosphere.2009.01.052
Yunusa, Y. R., & Umar, Z. D. (2021). Effective microbial bioremediation via the multi-omics approach: An overview of trends, problems and prospects. UMYU Journal of Microbiological Research, 6, 127–145. DOI: https://doi.org/10.47430/ujmr.2161.017
Xiao, M., Long, Z. E., Fu, X., & Zou, L. (2024). Versatile applications and mechanisms of genus Exiguobacterium in bioremediating heavy metals and organic pollutants: A review. International Biodeterioration & Biodegradation, 194, 105884. DOI: https://doi.org/10.1016/j.ibiod.2024.105884
Freyria, N. J., Lirette, A. O., O’Connor, B. R. W., Greer, C. W., & Whyte, L. G. (2025). Transcriptomic analyses unveil hydrocarbon degradation mechanisms in a novel polar Rhodococcus sp. strain R1B_2T from a high Arctic intertidal zone exposed to ultra-low sulphur fuel oil. Environmental Microbiology Reports, 17(5), e70218. DOI: https://doi.org/10.1111/1758-2229.70218
Chandramouli, K., & Qian, P. Y. (2009). Proteomics: Challenges, techniques and possibilities to overcome biological sample complexity. Human Genomics and Proteomics, 2009, 239204. DOI: https://doi.org/10.4061/2009/239204
Qiu, S., Cai, Y., Yao, H., Lin, C., Xie, Y., Tang, S., & Zhang, A. (2023). Small molecule metabolites: Discovery of biomarkers and therapeutic targets. Signal Transduction and Targeted Therapy, 8(1), 132. DOI: https://doi.org/10.1038/s41392-023-01399-3
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Copyright (c) 2026 Mazia Amber, Maryam Iqbal, Umm E Habiba, Mehral Aslam, Sabah Mansoor, Sadia Noor, Samia Faiz
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