A Review on Environmental Impacts and Risks of Beneficial Microorganisms


  • Shamsudeen Muhammad Muhammad Department of Microbiology, Kebbi State University of Science and Technology, Aliero, Nigeria Author
  • Bilyaminu Garba Jega Department of Microbiology, Kebbi State University of Science and Technology, Aliero, Nigeria Author




microorganisms, bioremediation, agriculture, genetic engineering, environmental safety


The diverse realm of microorganisms, including bacteria, Achaea, fungi, protists, and viruses, plays a crucial role in supporting life on Earth. Microbes are present in various environments, such as Arctic regions and thermal vents, where they participate in vital functions like nutrient cycling, soil formation, pollutant decomposition, and symbiotic interactions with plants. Their positive effects on soil quality, plant development, and animal well-being are a result of their metabolic processes, relationships with other organisms, and utilization in different applications. While beneficial microorganisms present opportunities for improving agriculture, bioremediation, genetic modification, and sustainable biotechnology practices, safety concerns must be addressed. In agriculture, beneficial microorganisms are employed as biopesticides to reduce the use of chemical pesticides, although potential impacts on non-target species need to be considered. Bioremediation, an environmentally friendly method that uses living organisms to break down pollutants, offers benefits with minimal harm to the environment. Nonetheless, challenges such as effectiveness in extreme conditions and the risk of incomplete degradation or unintended ecological disturbances remain significant. Wastewater treatment harnesses beneficial microorganisms to degrade pollutants, leading to reduced chemical usage and the promotion of energy-efficient processes like anaerobic digestion. Yet, issues related to antibiotic resistance development and incomplete remediation are raised. Genetic engineering presents environmental advantages through genetically modified microorganisms (GMMs), assisting in bioremediation, sustainable agriculture, waste management, and bioenergy generation. However, concerns arise regarding potential ecological disruptions caused by altered microbial populations and the dissemination of antibiotic resistance genes. Addressing environmental and safety risks associated with beneficial microorganisms necessitates comprehensive approaches, including thorough risk evaluations, implementation of containment strategies, assurance of ecological harmony, and contemplation of ethical and social consequences. This study aimed to investigate the environmental impacts and safety considerations involved in the application of beneficial microorganisms.


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Fierer J, Looney D, Pechère JC. Nature and Pathogenicity of Micro-organisms. Infectious Diseases. 2017. p. 4-25.e1.

Cotgreave P, Forseth I. Introductory ecology. John Wiley & Sons; 2009.

Cardinale B. Impacts of biodiversity loss. Science (80- ). 2012;336(6081):552–3.

Gupta A, Gupta R, Singh RL. Microbes and Environment. Principles and Applications of Environmental Biotechnology for a Sustainable Future. 2017. p. 43–84.


Kumari M, Ghosh P, Thakur IS. Application of Microbes in Remediation of Hazardous Wastes: A Review BT - Bioremediation: Applications for Environmental Protection and Management. In: Varjani SJ, Agarwal AK, Gnansounou E, Gurunathan B, editors. Singapore: Springer Singapore; 2018. p. 223–41. Available from: https://doi.org/10.1007/978-981-10-7485-1_11

Kumar J, Ramlal A, Mallick D, Mishra V. An overview of some biopesticides and their importance in plant protection for commercial acceptance. Plants. 2021;10(6):1185.

Elnahal ASM, El MT, Ahmed S. growth promotion , and sustainable agriculture : A review The use of microbial inoculants for biological control , plant growth promotion , and sustainable agriculture : A review [Internet]. European Journal of Plant Pathology. Springer Netherlands; 2022. Available from: https://doi.org/10.1007/s10658-021-02393-7

Ezeonu CS, Tagbo R, Anike EN, Oje OA, Onwurah INE. Biotechnological tools for environmental sustainability: prospects and challenges for environments in Nigeria-a standard review. Biotechnol Res Int. 2012;2012:450802.

Tsatsakis AM, Nawaz MA, Kouretas D, Balias G, Savolainen K, Tutelyan VA, et al. Environmental impacts of genetically modified plants: a review. Environ Res. 2017;156:818–33.

Karigar CS, Rao SS. Role of Microbial Enzymes in the Bioremediation of Pollutants : A Review. Enzyme Res. 2011;

Michelini E, Suzuki H, Huang S, Medicine T, Zhang X, Zhang Y. Genetically engineered bacterium : Principles , practices , and prospects. Front Microbiol. 2022;1–15.

Abd-Alla MH, Al-Amri SM, El-Enany AWE. Enhancing Rhizobium–Legume Symbiosis and Reducing Nitrogen Fertilizer Use Are Potential Options for Mitigating Climate Change. Agric. 2023;13(11).

Ojuederie OB, Babalola OO. Microbial and plant-assisted bioremediation of heavy metal polluted environments: a review. Int J Environ Res Public Health. 2017;14(12):1504.

Bala S, Garg D, Thirumalesh BV, Sharma M, Sridhar K, Inbaraj BS, et al. Recent Strategies for Bioremediation of Emerging Pollutants: A Review for a Green and Sustainable Environment. Toxics. 2022 Aug;10(8).

Henze M, van Loosdrecht MCM, Ekama GA, Brdjanovic D. Biological wastewater treatment. IWA publishing; 2008.

Shahid MJ, Al-surhanee AA, Kouadri F, Ali S, Nawaz N, Afzal M, et al. Role of Microorganisms in the Remediation of Wastewater in Floating Treatment Wetlands : A Review. 2020;1–29.

Deckers M, Deforce D, Fraiture MA, Roosens NHC. Genetically modified micro-organisms for industrial food enzyme production: An overview. Foods. 2020;9(3).

Begna T. Major challenging constraints to crop production farming system and possible breeding to overcome the constraints. Int J Res Stud Agric Sci. 2020;6(7):27–46.

Leahy J, Mendelsohn M, Kough J, Jones R, Berckes N. Biopesticide oversight and registration at the U.S. Environmental Protection Agency. ACS Symp Ser. 2014;1172:3–18.

Samada LH, Tambunan USF. Biopesticides as promising alternatives to chemical pesticides: A review of their current and future status. Online J Biol Sci. 2020;20(2):66–76.

Kumar J, Ramlal A, Mallick D, Mishra V. An Overview of Some Biopesticides and Their Importance in Plant Protection for Commercial Acceptance. Plants (Basel, Switzerland). 2021 Jun;10(6).

Daraban GM, Hlihor RM, Suteu D. Pesticides vs. Biopesticides: From Pest Management to Toxicity and Impacts on the Environment and Human Health. Toxics. 2023 Dec;11(12).

De Clercq P, Mason PG, Babendreier D. Benefits and risks of exotic biological control agents. BioControl. 2011;56:681–98.

Koza NA, Adedayo AA, Babalola OO, Kappo AP. Microorganisms in Plant Growth and Development: Roles in Abiotic Stress Tolerance and Secondary Metabolites Secretion. Microorganisms. 2022 Jul;10(8).

Douglas MR, Rohr JR, Tooker JF. Neonicotinoid insecticide travels through a soil food chain, disrupting biological control of non-target pests and decreasing soya bean yield. J Appl Ecol. 2015;52(1):250–60.

Wang G, Ren Y, Bai X, Su Y, Han J. Contributions of Beneficial Microorganisms in Soil Remediation and Quality Improvement of Medicinal Plants. Plants (Basel, Switzerland). 2022 Nov;11(23).

Mendes R, Garbeva P, Raaijmakers JM. The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev. 2013 Sep;37(5):634–63.

Sharma I. Bioremediation Techniques for Polluted Environment: Concept, Advantages, Limitations, and Prospects. In: Murillo-Tovar MA, Saldarriaga-Noreña H, Saeid A, editors. Rijeka: IntechOpen; 2020. p. Ch. 12. Available from: https://doi.org/10.5772/intechopen.90453

Alori ET, Gabasawa AI, Elenwo CE, Agbeyegbe OO. Bioremediation techniques as affected by limiting factors in soil environment. Front Soil Sci [Internet]. 2022;2. Available from: https://www.frontiersin.org/articles/10.3389/fsoil.2022.937186

Azubuike CC, Chikere CB, Okpokwasili GC. Bioremediation techniques–classification based on site of application: principles, advantages, limitations and prospects. World J Microbiol Biotechnol [Internet]. 2016;32(11):180. Available from: https://doi.org/10.1007/s11274-016-2137-x

Kalia A, Sharma S, Semor N, Babele PK, Sagar S, Bhatia RK, et al. Recent advancements in hydrocarbon bioremediation and future challenges: a review. 3 Biotech. 2022 Jun;12(6):135.

Sahota NK, Sharma R. Bioremediation: Harnessing Natural Forces for Solid Waste Management BT - Handbook of Solid Waste Management: Sustainability through Circular Economy. In: Baskar C, Ramakrishna S, Baskar S, Sharma R, Chinnappan A, Sehrawat R, editors. Singapore: Springer Nature Singapore; 2022. p. 1077–108. Available from: https://doi.org/10.1007/978-981-16-4230-2_107

Alaidaroos BA. Advancing Eco-Sustainable Bioremediation for Hydrocarbon Contaminants: Challenges and Solutions. Vol. 11, Processes. 2023.

Bajić B, Vučurović D, Vasić Đ, Jevtić-Mučibabić R, Dodić S. Biotechnological Production of Sustainable Microbial Proteins from Agro-Industrial Residues and By-Products. Vol. 12, Foods. 2023.

Zhang M, Yoshikawa M. Bioremediation: Recent Advancements and Limitations BT - Sustainable Environmental Geotechnics. In: Reddy KR, Agnihotri AK, Yukselen-Aksoy Y, Dubey BK, Bansal A, editors. Cham: Springer International Publishing; 2020. p. 21–9.

Ball AS. The intentional release of micro-organisms into the environment: challenges to commercial use. Biosaf Environ uses micro-organisms Conf proceedings, OECD Publ Paris. 2015;115–26.

Saravanan A, Kumar PS, Jeevanantham S, Karishma S, Tajsabreen B, Yaashikaa PR, et al. Effective water/wastewater treatment methodologies for toxic pollutants removal: Processes and applications towards sustainable development. Chemosphere. 2021;280:130595.

Rani N, Sangwan P, Joshi M, Sagar A, Bala K. Wastewater Treatment [Internet]. Microbial Wastewater Treatment. Elsevier Inc.; 2019. 83–102 p. Available from: http://dx.doi.org/10.1016/B978-0-12-816809-7.00005-1

Akpor OB, Otohinoyi DA, Olaolu DT, Aderiye BI. Pollutants in wastewater effluents: impacts and remediation processes. Int J Environ Res Earth Sci. 2014;3(3):50–9.

Mahmoud GAE. Microbial scavenging of heavy metals using bioremediation strategies. Rhizobiont bioremediation Hazard waste. 2021;265–89.

Manyi-Loh CE, Mamphweli SN, Meyer EL, Okoh AI, Makaka G, Simon M. Microbial anaerobic digestion (bio-digesters) as an approach to the decontamination of animal wastes in pollution control and the generation of renewable energy. Int J Environ Res Public Health. 2013 Sep;10(9):4390–417.

Liu FH, Wang SB, Zhang JS, Zhang J, Yan X, Zhou HK, et al. The structure of the bacterial and archaeal community in a biogas digester as revealed by denaturing gradient gel electrophoresis and 16S rDNA sequencing analysis. J Appl Microbiol. 2009;106(3):952–66.

Amarasiri M, Sano D, Suzuki S. Understanding human health risks caused by antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG) in water environments: Current knowledge and questions to be answered. Crit Rev Environ Sci Technol. 2020;50(19):2016–59.

Karkman A, Do TT, Walsh F, Virta MPJ. Antibiotic-resistance genes in waste water. Trends Microbiol. 2018;26(3):220–8.

Ojha N, Karn R, Abbas S, Bhugra S. Bioremediation of industrial wastewater: A review. In: IOP Conference Series: Earth and Environmental Science. IOP Publishing; 2021. p. 12012.

Prakash D, Verma S, Bhatia R, Tiwary BN. Risks and Precautions of Genetically Modified Organisms. ISRN Ecol. 2011;2011:1–13.

Godwill EA. Genetic engineering on microorganism : the ecological and bioethical implications. Eur J Biotechnol Biosci. 2014;1(3):27–33.

Hughes AR, Inouye BD, Johnson MTJ, Underwood N, Vellend M. Ecological consequences of genetic diversity. Ecol Lett. 2008;11(6):609–23.

Sayler GS, Ripp S. Field applications of genetically engineered microorganisms for bioremediation processes. Curr Opin Biotechnol [Internet]. 2000;11(3):286–9. Available from: https://www.sciencedirect.com/science/article/pii/S0958166900000975

Rafeeq H, Afsheen N, Rafique S, Arshad A, Intisar M, Hussain A, et al. Genetically engineered microorganisms for environmental remediation. Chemosphere [Internet]. 2023;310:136751. Available from: https://www.sciencedirect.com/science/article/pii/S0045653522032441

Amarger N. Genetically modified bacteria in agriculture. 2002;84:1061–72.

Ghosh S, Sarkar B, Khumphon J, Thongmee S. Genetically Modified Microbe Mediated Metal Bioaccumulation: A Sustainable Effluent Treatment Strategy BT - Industrial Wastewater Reuse: Applications, Prospects and Challenges. In: Shah MP, editor. Singapore: Springer Nature Singapore; 2023. p. 215–29. Available from: https://doi.org/10.1007/978-981-99-2489-9_11

Bhatt A, Shandilya J, Singal SK, Prajapati SK. Application of Genetically Modified Microorganisms for Bioremediation of Heavy Metals from Wastewater. In: Genomics Approach to Bioremediation [Internet]. 2023. p. 295–320. Available from: https://doi.org/10.1002/9781119852131.ch16

Patel HK, Dobariya JB, Patel PS. Genetic Engineering: An Optimism for Sustainable Biofuel Production BT - Bio-Clean Energy Technologies: Volume 1. In: Chowdhary P, Khanna N, Pandit S, Kumar R, editors. Singapore: Springer Nature Singapore; 2022. p. 133–53. Available from: https://doi.org/10.1007/978-981-16-8090-8_6

Kassen R, Rainey P. The Ecology and Genetics of Microbial Diversity. Annu Rev Microbiol. 2004 Feb 1;58:207–31.

Singh K, Chaube R. Chapter 3 - Enrichment of drug resistance genes in human pathogenic bacteria showing antimicrobial resistance. In: Pal D, Kumar ABTAR in W and HH, editors. Antimicrobial Resistance in Wastewater and Human Health [Internet]. Academic Press; 2023. p. 41–60. Available from: https://www.sciencedirect.com/science/article/pii/B9780323961240000088

Ezinne O, Okeke O, Irefin MO, Ezeala HI, Amadi C. Environmental Impact Assessment and Environmental Risk Assessment: Review of Concepts, Steps and Significance. IIARD Int J Geogr Environ Manag. 2023 Sep 2;9:25–51.

Kobinger GP, Croyle M, Feldmann H. Chapter 20 - Ebola and Marburg. In: Barrett ADT, Stanberry LRBTV for B and E and ND, editors. London: Academic Press; 2009. p. 325–37. Available from: https://www.sciencedirect.com/science/article/pii/B9780123694089000202

Hoffmann SA, Diggans J, Densmore D, Dai J, Knight T, Leproust E, et al. Safety by design: Biosafety and biosecurity in the age of synthetic genomics. iScience [Internet]. 2023;26(3):106165. Available from: https://www.sciencedirect.com/science/article/pii/S2589004223002420

Mandell DJ, Lajoie MJ, Mee MT, Takeuchi R, Kuznetsov G, Norville JE, et al. Biocontainment of genetically modified organisms by synthetic protein design. Nature. 2015 Feb;518(7537):55–60.




How to Cite

Muhammad Muhammad S, Jega BG. A Review on Environmental Impacts and Risks of Beneficial Microorganisms. IRABCS [Internet]. 2024 Jul. 2 [cited 2024 Jul. 20];2(1):13-20. Available from: https://irabcs.com/ojs/article/view/31

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