Novel Bioremediation Strategies: Enhancing Polluted Soil and Protecting the Environment through Omics Technologies and Microbial Approaches

Document Type : Invited review paper

Authors

1 Corresponding Author, Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.

2 Department of Systems Biology, Agricultural Research, Education and Extension Organization (AREEO), Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran.

Abstract

Bioremediation is a crucial strategy in combating environmental pollution, particularly in soil. The escalation of industrial and agricultural activities, coupled with the introduction of non-degradable and toxic pollutants, has exacerbated soil contamination. Heavy metals, such as lead and zinc, resistant to degradation over time, potentially accumulating in the food chain and posing persistent threats to both the environment and human health. Similarly, chemical compounds like herbicides and insecticides present challenges due to their prolonged stability and persistence. Although various chemical and physical methods exist for soil remediation, the biological approach gains more attention due to its sustainability and minimal impact on native ecosystems. Bioremediation leverages natural organisms to transform hazardous substances into less harmful forms. Microorganisms play a pivotal role in this process. Furthermore, plants can enhance bioremediation efficiency through symbiotic relationships with bacteria, accelerating the degradation of pollutants and accelerating soil productivity restoration. The use of native plants and microorganisms, especially in countries with high biodiversity such as Iran, is an important step towards the sustainable use of this technology. Native plants and microorganisms have the ability to make better use of environmental conditions and are most efficient with minimal environmental changes. Recent advancements in 'omics' technologies, such as genomics, proteomics, and metabolomics, have opened new avenues for the exploration and application of bioremediation techniques. These advance technologies enable molecular-level studies of organisms by generating big data to identify the most effective microorganisms for specific pollutants. Bioremediation can be applied in two primary ways: in situ or ex situ. In-situ bioremediation addresses contaminated soil directly on-site, whereas ex-situ bioremediation involves the removal of contaminated soil to another location for remediation. Each approach has its advantages and limitations, necessitating careful consideration prior to implementation. The integration of phytoremediation and microbial bioremediation methods can enhance efficiency and reduce costs, making the process economically viable. This study aims to serve as a comprehensive guide to understanding the diverse methodologies in bioremediation. Furthermore, it proposes sustainable and effective strategies to transform non-arable polluted lands into arable areas, offering environmental and economic benefits for future land reuse. Finally, what is ahead of bioremediation is turning bioremediation into a central tool in sustainable development. In addition, from the decomposition of industrial pollutants to the restoration of damaged natural environments, bioremediation can play an important role in providing a better and healthier life for future generations. This multifaceted and expandable approach can be one of the keys to success in sustainable environmental management in the 21st century.

Keywords

Main Subjects


1.Azhar, U., Ahmad, H., Shafqat, H., Babar, M., Munir, H. M. S., Sagir, M., Arif, M., Hassan, A., Rachmadona, N., & Rajendran, S. (2022). Remediation techniques for elimination of heavy metal pollutants from soil: A review. Environmental research. 113918.2.Awa, S. H., & Hadibarata, T. (2020). Removal of heavy metals in contaminated soil by phytoremediation mechanism: a review. Water, Air, & Soil Pollution. 1, 23-47.3.Rajendran, S., Priya, T., Khoo, K. S., Hoang, T. K., Ng, H. S., Munawaroh, H. S. H., Karaman, C., Orooji, Y., & Show, P. L. (2022). A critical review on various remediation approaches for
heavy metal contaminants removal from contaminated soils. Chemosphere. 287, 132-369.4.Wang, L., Rinklebe, J., Tack, F. M., & Hou, D. (2021). A review of green remediation strategies for heavy metal contaminated soil. Soil Use and Management. 37, 936-963.5.Rezaei, H., Shahbazi, K., Saadat, S., & Bazargan, K. (2022). Investigation of Soil Pollution and Agricultural Crops in Iran, Journal of land Management (Soil and Water Sci.) 10, 1.6.Zhang, H., Yuan, X., Xiong, T., Wang, H., & Jiang, L. (2020). Bioremediation of co-contaminated soil with heavy metals and pesticides: Influence factors, mechanisms and evaluation methods. Chemical Engineering Journal. 398, 125657.7.Abbasali, M., Gholipouri, A., Tobeh, A., Khoshkholgh Sima, N. A., & Ghalebi, S. (2017). Identification of drought tolerant genotypes in the Sesame (Sesamum indicum L.) Collection of National Plant Gene Bank of Iran. Iranian Journal of Field Crop Science. 48, 275-289.8.Sharma, I. (2020). Bioremediation techniques for polluted environment: concept, advantages, limitations, and prospects. Trace metals in the environment-new approaches and recent advances. IntechOpen.9.Loni, F., & Khoshkholgh Sima, N. A. (2023). Security agriculture based on plant breeding in non-conventional saline lands. Journal of Biosafety, 15, 0-0.10.Zaghloul, M. (2020). Phytoremediation of heavy metals principles, mechanisms, enhancements with several efficiency enhancer methods and perspectives: A Review. Middle East J. 9, 186-214.11.Kaushik, S., Alatawi, A., Djiwanti, S. R., Pande, A., Skotti, E., & Soni, V. (2021). Potential of extremophiles for bioremediation. Microbial Rejuvenation of Polluted Environment. 1, 293-328.12.DalCorso, G., Fasani, E., Manara, A., Visioli, G., & Furini, A. (2019). Heavy metal pollutions: state of the art and innovation in phytoremediation. International journal of molecular sciences. 20, 3412.13.Bharagava, R. N., Purchase, D., Saxena, G., & Mulla, S. I. (2019). Applications of metagenomics in microbial bioremediation of pollutants: from genomics to environmental cleanup.  Microbial diversity in the genomic era. Elsevier, pp. 459-477.14.Bala, S., Garg, D., Thirumalesh, B. V., Sharma, M., Sridhar, K., Inbaraj, B. S., & Tripathi, M. (2022). Recent strategies for bioremediation of emerging pollutants: a review for a green and sustainable environment. Toxics. 10, 484.15.Jha, A., Narasimhaiah, N. K., Sreekumar, N., Babu, P. A. M., Umashankar, P., Mohan, S., Mahesh, U., Sharief, N. A., Ghatole, K. P., & Dey, P. (2022). Biofiltration techniques in the remediation of hazardous inorganic and organic contaminants. An Innovative Role of Biofiltration in Wastewater Treatment Plants (WWTPs). Elsevier, pp. 137-154.16.Mao, X., Yang, Y., Guan, P., Geng, L., Ma, L., Di, H., Liu, W., & Li, B. (2022). Remediation of organic amendments on soil salinization: Focusing on the relationship between soil salts and microbial communities. Ecotoxicology and Environmental Safety. 239, 113616.17.Sarkar, B., Gupta, A. M., & Mandal, S. (2021). Insights from the comparative genome analysis of natural rubber degrading Nocardia species. Bioinformation. 17, 880.18.Song, L., Niu, X., Zhang, N., & Li, T. (2021). Effect of biochar-immobilized Sphingomonas sp. PJ2 on bioremediation of PAHs and bacterial community composition in saline soil. Chemosphere. 279, 130427.19.Medfu Tarekegn, M., Zewdu Salilih, F., & Ishetu, A. I. (2020). Microbes used as a tool for bioremediation of heavy metal from the environment. Cogent Food & Agriculture. 6, 1783174.20.Dangi, A. K., Sharma, B., Hill, R. T., & Shukla, P. (2019). Bioremediation through microbes: systems biology and metabolic engineering approach. Critical reviews in biotechnology, 39, 79-98.21.Garg, S. K., & Tripathi, M. (2017). Microbial strategies for discoloration and detoxification of azo dyes from textile effluents. Research Journal of Microbiology, 12, 1-19.22.Ebadi, A., Ghavidel, A., Sima, N. A. K., Heydari, G., & Ghaffari, M.R. (2021b). New strategy to increase oil biodegradation efficiency by selecting isolates with diverse functionality and no antagonistic interactions for bacterial consortia. Journal of Environmental Chemical Engineering, 9, 106315.23.Muthusaravanan, S., Sivarajasekar, N., Vivek, J., Paramasivan, T., Naushad, M., Prakashmaran, J., Gayathri, V., & Al-Duaij, O. K. (2018). Phytoremediation of heavy metals: mechanisms, methods and enhancements. Environmental chemistry letters. 16, 1339-1359.24.Sima, N. A. K., Ebadi, A., Reiahisamani, N., & Rasekh, B. (2019). Bio-based remediation of petroleum-contaminated saline soils: Challenges, the current state-of-the-art and future prospects. Journal of environmental management. 250, 109476.25.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, 4664.26.Ebadi, A., Ghavidel, A., Sima, N. A. K., Heydari, G., & Ghaffari, M. R. (2021a). Corrigendum to ‘New strategy to increase oil biodegradation efficiency by selecting isolates with diverse functionality and no antagonistic interactions for bacterial consortia’[J. Environ. Chem. Eng.] Journal of Environmental Chemical Engineering. 9, 106535.27.Komaresofla, B. R., Alikhani, H. A., Etesami, H., & Khoshkholgh-Sima,
N. A. (2019). Improved growth and salinity tolerance of the halophyte Salicornia sp. by co–inoculation with endophytic and rhizosphere bacteria. Applied Soil Ecology, 138, 160-170.28.Abatenh, E., Gizaw, B., Tsegaye, Z., & Wassie, M. (2017). The role of microorganisms in bioremediation-A review. Open Journal of Environmental Biology, 2, 38-46.29.Alegbeleye, O. O., Opeolu, B. O., & Jackson, V. A. (2017). Polycyclic aromatic hydrocarbons: a critical review of environmental occurrence
and bioremediation. Environmental management. 60, 758-783.30.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, 1-17.31.Fragkou, E., Antoniou, E., Daliakopoulos, I., Manios, T., Theodorakopoulou, M., & Kalogerakis, N. (2021). In situ aerobic bioremediation of sediments polluted with petroleum hydrocarbons: a critical review. Journal of Marine Science and Engineering. 9, 1003.32.Mupambwa, H. A., & Mnkeni, P. N. S. (2018). Optimizing the vermicomposting of organic wastes amended with inorganic materials for production of nutrient-rich organic fertilizers: a review. Environmental Science and Pollution Research, 25, 10577-10595.33.Cycoń, M., Mrozik, A., & Piotrowska-Seget, Z. (2017). Bioaugmentation as a strategy for the remediation of pesticide-polluted soil: A review. Chemosphere. 172, 52-71.34.Hesham, AE. L., Alrumman, S. A., & ALQahtani, A. D. S. (2018). Degradation of toluene hydrocarbon by isolated yeast strains: molecular genetic approaches for identification and characterization. Russian Journal of Genetics. 54, 933-943.35.Hussain, S., Arshad, M., Saleem, M., & Khalid, A. (2007). Biodegradation of α-and β-endosulfan by soil bacteria. Biodegradation. 18, 731-740.36.Sayqal, A., & Ahmed, O. B. (2021). Advances in heavy metal bioremediation: An overview. Applied bionics and biomechanics 2021.37.Bhandari, S., Poudel, D. K., Marahatha, R., Dawadi, S., Khadayat, K., Phuyal, S., Shrestha, S., Gaire, S., Basnet, K., & Khadka, U. (2021). Microbial enzymes used in bioremediation. Journal of Chemistry. 2021, 1-17.38.Priyadarshanee, M., & Das, S. (2021). Biosorption and removal of toxic heavy metals by metal tolerating bacteria for bioremediation of metal contamination: A comprehensive review. Journal of Environmental Chemical Engineering. 9, 104686.39.Bell, C. H., Wong, J., Parsons, K., Semel, W., McDonough, J., & Gerber, K. (2022). First Full‐Scale In Situ Propane Biosparging for Co‐Metabolic Bioremediation of 1, 4‐Dioxane. Groundwater Monitoring & Remediation. 42, 54-66.40.Sattar, S., Hussain, R., Shah, S. M., Bibi, S., Ahmad, S. R., Shahzad, A., Zamir, A., Rauf, Z., Noshad, A., & Ahmad, L. (2022). Composition, impacts, and removal of liquid petroleum waste through bioremediation as an alternative clean-up technology: A review. Heliyon.41.Ebadi, A., Sima, N. A. K., Olamaee, M., Hashemi, M., & Nasrabadi, R. G. (2018b). Remediation of saline soils contaminated with crude oil using the halophyte Salicornia persica in conjunction with hydrocarbon-degrading bacteria. Journal of environmental management. 219, 260-268.42.Ebadi, A., Olamaee, M., Khoshkholgh Sima, N. A., Ghorbani Nasrabadi, R., & Hashemi, M. (2018a). Isolation and characterization of biosurfactant producing and crude oil degrading bacteria from oil contaminated soils. Iranian Journal of Science and Technology, Transactions A: Science. 42, 1149-1156.43.Ebadi, A., Sima, N. A. K., Olamaee, M., Hashemi, M., & Nasrabadi, R. G. (2017). Effective bioremediation of a petroleum-polluted saline soil by a surfactant-producing Pseudomonas aeruginosa consortium. Journal of advanced research. 8, 627-633.44.Raimondo, E. E., Aparicio, J. D., Bigliardo, A. L., Fuentes, M. S., & Benimeli, C. S. (2020). Enhanced bioremediation of lindane-contaminated soils through microbial bioaugmentation assisted by biostimulation with sugarcane filter cake. Ecotoxicology and environmental safety. 190, 110143.45.Khodabakhshi Soureshjani, M., & Zytner, R. G. (2023). Developing a Robust Bioventing Model. Mathematical and Computational Applications. 28, 76.46.Anekwe, I. M. S., & Isa, Y. M. (2021). Comparative evaluation of wastewater and bioventing system for the treatment of acid mine drainage contaminated soils. Water-Energy Nexus, 4, 134-140.47.Katyal, A. K. (2022). Improving separate phase hydrocarbon recovery with bioslurping. Hazardous and Industrial Waste Mid-Atlantic Conference. CRC Press, pp. 622-631.48.Varshney, K. (2019). Bioremediation of pesticide waste at Proceedings, 29th
contaminated sites. Journal of Emerging Technologies and Innovative Research. 6, 128-134.49.Abena, M. T. B., Li, T., Shah, M. N., & Zhong, W. (2019). Biodegradation of total petroleum hydrocarbons (TPH) in highly contaminated soils by natural attenuation and bioaugmentation. Chemosphere. 234, 864-874.50.Alishahi, F., Alikhani, H. A., Khoshkholgh-Sima, N. A., & Etesami, H. (2020). Mining the roots of various species of the halophyte Suaeda for halotolerant nitrogen-fixing endophytic bacteria with the potential for promoting plant growth. International Microbiology, 23, 415-427.51.Sutherland, D. L., & Ralph, P. J. (2019). Microalgal bioremediation of emerging contaminants-Opportunities and challenges. Water research 164, 114921.52.Jaain, R., & Patel, A. (2019). Bioremediation of Gurugram–Faridabad Dumpsite at Bandhwari. Waste Valorisation and Recycling: 7th IconSWM-ISWMAW 2017, 2, 433-440.53.Zhang, K., Wang, S., Guo, P., & Guo, S. (2021). Characteristics of organic carbon metabolism and bioremediation of petroleum-contaminated soil by a mesophilic aerobic biopile system. Chemosphere. 264, 128521.54.Chen, M., Xu, P., Zeng, G., Yang, C., Huang, D., & Zhang, J. (2015). Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols
and heavy metals by composting: applications, microbes and future research needs. Biotechnology advances. 33, 745-755.55.Ren, X., Zeng, G., Tang, L., Wang, J., Wan, J., Wang, J., Deng, Y., Liu, Y., & Peng, B. (2018). The potential impact on the biodegradation of organic pollutants from composting technology for soil remediation. Waste management. 72, 138-149.56.Mupambwa, H. A., Haulofu, M., Nciizah, A. D., & Mnkeni, P. N. (2022). Vermicomposting technology: A sustainable option for waste beneficiation. Handbook of Waste Biorefinery: Circular Economy of Renewable Energy. Springer, pp. 583-600.57.Iturbe-Espinoza, P., Brown, D. M., Weedon, J. T., Braster, M., Brandt, B. W., Bonte, M., & van Spanning, R. J. (2023). Microbial communities associated with landfarming amendments during bioremediation of crude oil in Niger Delta soils. Applied Soil Ecology. 191, 105058.58.Lukwambe, B., Zhao, L., Nicholaus, R., Yang, W., Zhu, J., & Zheng, Z. (2019). Bacterioplankton community in response to biological filters (clam, biofilm, and macrophytes) in
an integrated aquaculture wastewater bioremediation system. Environmental Pollution. 254, 113035.59.Yang, L., Li, X., Chu, Z., Ren, Y., & Zhang, J. (2014). Distribution and genetic diversity of the microorganisms in the biofilter for the simultaneous removal of arsenic, iron and manganese from simulated groundwater. Bioresource Technology. 156, 384-388.60.Maurya, K. L., Swain, G., Sonwani, R. K., Verma, A., & Singh, R. S. (2021). Bioremediation of Congo red in an anaerobic moving bed bioreactor: Process optimization and kinetic modeling. Bioresource Technology Reports. 16, 100843.61.Noori, F., Etesami, H., Zarini, H. N., Khoshkholgh-Sima, N. A., Salekdeh, G. H., & Alishahi, F. (2018). Mining alfalfa (Medicago sativa L.) nodules
for salinity tolerant non-rhizobial bacteria to improve growth of alfalfa under salinity stress. Ecotoxicology and Environmental Safety. 162, 129-138.62.Farzi, A., Borghei, S. M., & Vossoughi, M. (2017). The use of halophytic plants for salt phytoremediation in constructed wetlands. International journal of phytoremediation. 19, 643-650.63.Malik, G., Arora, R., Chaturvedi, R., & Paul, M. S. (2021). Implementation of genetic engineering and novel omics approaches to enhance bioremediation: a focused review. Bulletin of environmental contamination and toxicology. pp. 1-8.64.Chandran, H., Meena, M., & Sharma, K. (2020). Microbial biodiversity and bioremediation assessment through omics approaches. Frontiers in Environmental Chemistry. 1, 570326.65.Shah, M. P. (2020). Microbial bioremediation & biodegradation. Springer.66.Abdullah, K., Wilkins, D., & Ferrari, B. C. (2023). Utilization of-Omic technologies in cold climate hydrocarbon bioremediation: a text-mining approach. Frontiers in Microbiology, 14, 1113102.67.López, A. M. Q., & dos Santos Silva,
A. L. (2023). Proteomics and Bioremediation Using Prokaryotes. Genomics Approach to Bioremediation: Principles, Tools, and Emerging Technologies. pp. 485-502.68.Vázquez-Núñez, E., Molina-Guerrero, C. E., Peña-Castro, J. M., Fernández-Luqueño, F., & de la Rosa-Álvarez, M. G. (2020). Use of nanotechnology for the bioremediation of contaminants: A review. Processes. 8, 826.69.Kahrizi, H., Bafkar, A., & Farasati, M. (2016). Effect of nanotechnology on heavy metal removal from aqueous solution. Journal of Central South University. 23, 2526-2535.70.Mallikarjunaiah, S., Pattabhiramaiah, M., & Metikurki, B. (2020). Application of nanotechnology in the bioremediation of heavy metals and wastewater management. Nanotechnology for food, agriculture, and environment. pp. 297-321.