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Bioremediation is a process used to treat contaminated media, including water, soil and subsurface material, by altering environmental conditions to stimulate growth of microorganisms and degrade the target pollutants. In many cases, bioremediation is less expensive and more sustainable than other remediation alternatives.[1] Biological treatment is a similar approach used to treat wastes including wastewater, industrial waste and solid waste.

Most bioremediation processes involves oxidation-reduction reactions where either an electron acceptor (commonly oxygen) is added to stimulate oxidation of a reduced pollutant (e.g. hydrocarbons) or an electron donor (commonly an organic substrate) is added to reduce oxidized pollutants (nitrate, perchlorate, oxidized metals, chlorinated solvents, explosives and propellants).[2] In both these approaches, additional nutrients, vitamins, minerals, and pH buffers may be added to optimize conditions for the microorganisms. In some cases, specialized microbial cultures are added (bioaugmentation) to further enhance biodegradation. Some examples of bioremediation related technologies are phytoremediation, mycoremediation, bioventing, bioleaching, landfarming, bioreactor, composting, bioaugmentation, rhizofiltration, and biostimulation.


Most bioremediation processes involve oxidation-reduction (Redox) reactions where a chemical species donates an electron (electron donor) to a different species that accepts the electron (electron acceptor). During this process, the electron donor is said to be oxidized while the electron acceptor is reduced. Common electron acceptors in bioremediation processes include oxygen, nitrate, manganese (III and IV), iron (III), sulfate, carbon dioxide and some pollutants (chlorinated solvents, explosives, oxidized metals, and radionuclides). Electron donors include sugars, fats, alcohols, natural organic material, fuel hydrocarbons and a variety of reduced organic pollutants. The redox potential for common biotransformation reactions is shown in the table.

Process Reaction Redox potential (Eh in mV
aerobic O2 + 4e + 4H+ → 2H2O 600 ~ 400
denitrification 2NO3 + 10e + 12H+ → N2 + 6H2O 500 ~ 200
manganese IV reduction MnO2 + 2e + 4H+ → Mn2+ + 2H2O     400 ~ 200
iron III reduction Fe(OH)3 + e + 3H+ → Fe2+ + 3H2O 300 ~ 100
sulfate reduction SO42− + 8e +10 H+ → H2S + 4H2O 0 ~ −150
fermentation 2CH2O → CO2 + CH4 −150 ~ −220


Aerobic bioremediation is the most common form of oxidative bioremediation process where oxygen is provided as the electron acceptor for oxidation of petroleum, polyaromatic hydrocarbons (PAHs), phenols, and other reduced pollutants. Oxygen is generally the preferred electron acceptor because of the higher energy yield and because oxygen is required for some enzyme systems to initiate the degradation process. Numerous laboratory and field studies have shown that microorganisms can degrade a wide variety of hydrocarbons, including components of gasoline, kerosene, diesel, and jet fuel. Under ideal conditions, the biodegradation rates of the low- to moderate-weight aliphatic, alicyclic, and aromatic compounds can be very high. As the molecular weight of the compound increases, so does the resistance to biodegradation.[citation needed]

Common approaches for providing oxygen above the water table include landfarming, composting and bioventing. During landfarming, contaminated soils, sediments, or sludges are incorporated into the soil surface and periodically turned over (tilled) using conventional agricultural equipment to aerate the mixture. Composting accelerates pollutant biodegradation by mixing the waste to be treated with a bulking agent, forming into piles, and periodically mixed to increase oxygen transfer. Bioventing is a process that increases the oxygen or air flow into the unsaturated zone of the soil which increases the rate of natural in situ degradation of the targeted hydrocarbon contaminant[3].

Approaches for oxygen addition below the water table include recirculating aerated water through the treatment zone, addition of pure oxygen or peroxides, and air sparging. Recirculation systems typically consist of a combination of injection wells or galleries and one or more recovery wells where the extracted groundwater is treated, oxygenated, amended with nutrients and reinjected. However, the amount of oxygen that can be provided by this method is limited by the low solubility of oxygen in water (8 to 10 mg/L for water in equilibrium with air at typical temperatures). Greater amounts of oxygen can be provided by contacting the water with pure oxygen or addition of hydrogen peroxide (H2O2) to the water. In some cases, slurries of solid calcium or magnesium peroxide are injected under pressure through soil borings. These solid peroxides react with water releasing H2O2 which then decomposes releasing oxygen. Air sparging involves the injection of air under pressure below the water table. The air injection pressure must be great enough to overcome the hydrostatic pressure of the water and resistance to air flow through the soil.[citation needed]


Typical contaminated groundwater systems contain high amounts of organic and inorganic contaminants, and high levels of anaerobic microorganisms.[4] The anaerobic microorganisms that dominate these environments are widely beneficial due to the difficulty in using aerobic microorganisms in the presence of highly reducing sediment material. Anaerobic bioremediation involves the addition of an electron donor to: 1) deplete background electron acceptors including oxygen, nitrate, oxidized iron and manganese and sulfate; and 2) stimulate the biological and/or chemical reduction of the oxidized pollutants. This approach can be employed to treat a broad range of contaminants including chlorinated ethenes. (PCE, TCE, DCE, VC), chlorinated ethanes (TCA, DCA), chloromethanes (CT, CF), chlorinated cyclic hydrocarbons, various energetics (e.g., perchlorate,[5] RDX, TNT), and nitrate. Hexavalent chromium (Cr[VI]) and uranium (U[VI]) can be reduced to less mobile and/or less toxic forms (e.g., Cr[III], U[IV]). Similarly, reduction of sulfate to sulfide (sulfidogenesis) can be used to precipitate certain metals (e.g., zinc, cadmium). The choice of substrate and the method of injection depend on the contaminant type and distribution in the aquifer, hydrogeology, and remediation objectives. Substrate can be added using conventional well installations, by direct-push technology, or by excavation and backfill such as permeable reactive barriers (PRB) or biowalls. Slow-release products composed of edible oils or solid substrates tend to stay in place for an extended treatment period. Soluble substrates or soluble fermentation products of slow-release substrates can potentially migrate via advection and diffusion, providing broader but shorter-lived treatment zones. The added organic substrates are first fermented to hydrogen (H2) and volatile fatty acids (VFAs). The VFAs, including acetate, lactate, propionate and butyrate, provide carbon and energy for bacterial metabolism.[citation needed]


Toxic heavy metals pose an array of dangers for species in over 10% of the world's farmlands and can be traced back to human activities 90% of the time.[6] One heavy metal that requires much attention is cadmium. Cadmium is an extremely dangerous heavy metal partially due to its long half-life of over twenty years.[7] These dangers can be felt by plants and animals alike resulting in diseases and ailments such as lung cancer, homeostatic disruption, growth inhibition, and damage to the reproductive, cardiovascular, renal, and hepatic systems.[7] Although the vast majority of microorganisms are sensitive to heavy metal toxicity, in the recent decades, studies have found seventy different species of bacterium which are resistant to the toxic effects of cadmium.[6] Studies have been done in order to test the effectiveness of biosorption and bioaccumulation of cadmium when put to use in the field in order to immobilize it from biological influence. Biosorption has been found to be a favorable technique when trying to immobilize cadmium and similar heavy metals, because it is specific to the metal that one is aiming to secure.[8] These studies have found that there are two specific biological pathways for resistance to toxic metals in microorganisms including metal-binding proteins and efflux systems.[9] The efflux system of gram-positive bacterium for cadmium is often a single protein known as the CadA protein which binds to the cadmium atom/molecule and removes it from the cell.[9] In gram-negative bacterium, the mechanisms for ridding toxic metals like cadmium is often a network of multiple proteins which transport the toxic metals out of the cell.[9]


Hexavalent uranium contamination is a large global problem in areas such as near uranium mines, and near weapon crafting facilities. The typical, very costly, method for removing uranium from ground water is to pump the water out, treat it above ground, then pump it back to its original location. Some ways that have been attempted to remediate the contaminates are biosorption and bioaccumulation[10], a third option has been shown to have a more stable outcome, which is reduction of uranium (VI) to uranium (IV) which is immobile in solution and settles to the bottom[11]. A wide range of microorganisms have shown to be able to utilize uranium for this reaction including Pseudomonas sp., Pantoea sp., Enterobacter sp., several Geobacter species, and Thermus scotoductus[11]. The difficulties with this method are determining what methods and conditions are optimal for this type of bioremediation, including pH, type of substrate (electron donor), and salt concentrations.


Lead is commonly found in wastewaters as it is released from manufacturing facilities that utilize the metal or that recycle it. Lead as an environmental contaminant can cause many adverse health effects in animals and humans, and higher cases in young children in developing countries . Multiple species of bacteria have been shown to utilize different methods for removing lead from soils or ground water including biosorption, biofilm-mediated, and cell surface hydrophobicity[11]. The removal of lead from water and soils has many difficulties such as an increased energy consumption, introduction of additional chemicals, and pollution from byproducts. The use of Microorganisms for bioremediation is an environmentally friendly process that can reach the goals of removing the contaminant from the environment. Pseudomonas aeruginosa in a previous study was shown to be able to adsorb 61.2% of lead from a water source in optimal conditions indicating that it could be useful for bioremediation of lead[11]. This species of Pseudomonas was also shown to be able to remove soil bound lead showing more versatility than only that of water containing lead[11].


Chromium is the second largest heavy metal in contaminated environmental systems like soil and water. It can be introduced into the environment from human activities and through natural processes. Chromium can exist in nature in two forms, Trivalent Chromium (Cr III) and Hexavalent Chromium (Cr VI) with Cr (VI) being the most toxic as it can denature proteins and has mutagenic effects[12]. Many strategies have been used to remove Chromium from environmental systems. Many methods involve high prices, high energy requirements, and generation of dangerous byproducts[12]. The eco-friendly way to remediate the system from the Chromium is a method known as bioadsorption as the heavy metal has an affinity for cell wall components. Two species of bacterial organisms with the highest adsorption are Psuedomonas and Aeromonas cavisiae[12]. The bioremedation of chromium from contaminated systems can take two paths for the most effective route. At concentrations of 50 mg/L of Cr (VI) or lower, biological reduction of Cr (VI) to Cr (III) predominates, at concentrations above 50 mg, bioadsorption dominates[12]. The adsorption method showed a reduction of 70% for concentrations of 5-500 mg/L with a maximum of 94% at 100 mg/L. The biological reduction pathway had a maximum reduction at 60 mg/L at initial concentrations of 250 mg/L[12].


In the event of biostimulation, adding nutrients that are limited to make the environment more suitable for bioremediation, nutrients such as nitrogen, phosphorus, oxygen, and carbon may be added to the system to improve effectiveness of the treatment.[13]

Many biological processes are sensitive to pH and function most efficiently in near neutral conditions. Low pH can interfere with pH homeostasis or increase the solubility of toxic metals. Microorganisms can expend cellular energy to maintain homeostasis or cytoplasmic conditions may change in response to external changes in pH. Some anaerobes have adapted to low pH conditions through alterations in carbon and electron flow, cellular morphology, membrane structure, and protein synthesis.[14]


Only biodegradable contaminants can be transformed using bioremediation processes.[15] Some compounds, such as highly chlorinated compounds, heavy metals, and radionuclides are not readily biodegradable.[16][17][18] Also, microbes sometimes do not fully biodegrade a pollutant and may end up producing a more toxic compound.[18] For example, under anaerobic conditions, the reductive dehalogenation of TCE may produce vinyl chloride, which is a known carcinogen.[16] Therefore, more research is required to see if the products from biodegradation are less persistent and less toxic than the original contaminant.[18] Thus, the metabolic and chemical pathways of the microorganisms of interest must be known.[16] In addition, knowing these pathways will help develop new technologies that can deal with sites that have uneven distributions of a mixture of contaminants.[15]

Also, for biodegradation to occur, there must be a microbial population with the metabolic capacity to degrade the pollutant, an environment with the right growing conditions for the microbes, and the right amount of nutrients and contaminants.[15][17] The biological processes used by these microbes are highly specific, therefore, many environmental factors must be taken into account and regulated as well.[15][16] Thus, bioremediation processes must be specifically made in accordance to the conditions at the contaminated site.[16] Also, because many factors are interdependent, small-scale tests must be performed before carrying out the procedure at the contaminated site.[17] However, it is difficult to extrapolate the results from the small-scale test studies into big field operations.[15] Lastly, the process of bioremediation is longer and can be more expensive than other conventional options such as land filling and incineration.[15][16]

Genetic Engineering Applications

The use of genetic engineering to create organisms specifically designed for bioremediation has great potential.[19] Two category of genes can be inserted in the organism: degradative genes which encode proteins required for the degradation of pollutants, and reporter genes that are able to monitor pollutant levels.[20] An example of a degradation gene is biphenyl dioxygenase, which has been transformed in E.Coli to degrade PCB (polychlorinated biphenyl).[20] An example of a reporter gene is lux, which can act as a biosensor for detecting the Hg2+ concentration in E.Coli.[20] Numerous members of Pseudomonas have also been modified with the lux gene, but for the detection of the polyaromatic hydrocarbon naphthalene. A field test for the release of the modified organism has been successful on a moderately large scale.[21]

There are concerns surrounding release and containment of genetically modified organisms into the environment due to the potential of horizontal gene transfer.[22] Genetically modified organisms are classified and controlled under the Toxic Substances Control Act of 1976 under United States Environmental Protection Agency.[23] Measures have been created to address these concerns. Organisms can be modified such that they can only survive and grow under specific sets of environmental conditions. Outside of environmental conditions they were designed for, they lose their biodegradation ability or undergo self destruction.[22] To survive, a signal (the pollutant) is required. In the absence of the signal, a suicide gene is expressed which will lead to cell apoptosis.[22] In addition, the tracking of modified organisms can be made easier with the insertion of bioluminescence genes for visual identification.[24]

See also


  1. ^ "Green Remediation Best Management Practices: Sites with Leaking Underground Storage Tank Systems. EPA 542-F-11-008" (PDF). EPA. June 2011. 
  2. ^ Introduction to In Situ Bioremediation of Groundwater (PDF). US Environmental Protection Agency. 2013. p. 30. 
  3. ^ Frutos, F. Javier García; Escolano, Olga; García, Susana; Babín, Mar; Fernández, M. Dolores (2010-11). "Bioventing remediation and ecotoxicity evaluation of phenanthrene-contaminated soil". Journal of Hazardous Materials. 183 (1-3): 806–813. doi:10.1016/j.jhazmat.2010.07.098. ISSN 0304-3894.  Check date values in: |date= (help)
  4. ^ Coates JD, Anderson RT (October 2000). "Emerging techniques for anaerobic bioremediation of contaminated environments". Trends in Biotechnology. 18 (10): 408–12. doi:10.1016/S0167-7799(00)01478-5. PMID 10998506. 
  5. ^ Coates J, Jackson W (2008). "Principles of perchlorate treatment". In Stroo H, Ward CH. In situ bioremediation of perchlorate in groundwater. New York: Springer. pp. 29–53. doi:10.1007/978-0-387-84921-8_3. ISBN 978-0-387-84921-8. 
  6. ^ a b Tripathi M, Munot HP, Shouche Y, Meyer JM, Goel R (May 2005). "Isolation and functional characterization of siderophore-producing lead- and cadmium-resistant Pseudomonas putida KNP9". Current Microbiology. 50 (5): 233–7. doi:10.1007/s00284-004-4459-4. PMID 15886913. 
  7. ^ a b Hu Q, Dou MN, Qi HY, Xie XM, Zhuang GQ, Yang M (2007). "Detection, isolation, and identification of cadmium-resistant bacteria based on PCR-DGGE". Journal of Environmental Sciences. 19 (9): 1114–9. doi:10.1016/S1001-0742(07)60181-8. PMID 17966518. 
  8. ^ Ansari MI, Malik A (November 2007). "Biosorption of nickel and cadmium by metal resistant bacterial isolates from agricultural soil irrigated with industrial wastewater". Bioresource Technology. 98 (16): 3149–53. doi:10.1016/j.biortech.2006.10.008. PMID 17166714. 
  9. ^ a b c Saluja B, Sharma V (2013). "Cadmium Resistance Mechanism in Acidophilic and Alkalophilic Bacterial Isolates and their Application in Bioremediation of Metal-Contaminated Soil". Soil and Sediment Contamination: An International Journal. 23: 1–17. doi:10.1080/15320383.2013.772094. 
  10. ^ Williams KH, Bargar JR, Lloyd JR, Lovley DR (June 2013). "Bioremediation of uranium-contaminated groundwater: a systems approach to subsurface biogeochemistry". Current Opinion in Biotechnology. 24 (3): 489–97. doi:10.1016/j.copbio.2012.10.008. PMID 23159488. 
  11. ^ a b c d e Kalita D, Joshi SR (December 2017). "Study on bioremediation of Lead by exopolysaccharide producing metallophilic bacterium isolated from extreme habitat". Biotechnology Reports. 16: 48–57. doi:10.1016/j.btre.2017.11.003. PMC 5686426Freely accessible. PMID 29167759. 
  12. ^ a b c d e Durán U, Coronado-Apodaca KG, Meza-Escalante ER, Ulloa-Mercado G, Serrano D (May 2018). "Two combined mechanisms responsible to hexavalent chromium removal on active anaerobic granular consortium". Chemosphere. 198: 191–197. Bibcode:2018Chmsp.198..191D. doi:10.1016/j.chemosphere.2018.01.024. PMID 29421729. 
  13. ^ Adams, Omokhagbor (February 28th, 2015). "Bioremediation, Biostimulation and Bioaugmentation: A Review". Internation Journal of Environmental Bioremediation and Biodegredation. Volume 3, No. 1: 28–39 – via Research Gate.  Check date values in: |date= (help)
  14. ^ Slonczewski, J.L. (2009). "Stress Responses: pH". In Schaechter, Moselio. Encyclopedia of microbiology (3rd ed.). Elsevier. pp. 477–484. doi:10.1016/B978-012373944-5.00100-0. ISBN 978-0-12-373944-5. 
  15. ^ a b c d e f Vidali, M. (2001). "Bioremediation. An overview" (PDF). Pure and Applied Chemistry. 73 (7): 1163–72. doi:10.1351/pac200173071163. 
  16. ^ a b c d e f Juwarkar AA, Singh SK, Mudhoo A (2010). "A comprehensive overview of elements in bioremediation". Reviews in Environmental Science and Bio/Technology. 9 (3): 215–88. doi:10.1007/s11157-010-9215-6. 
  17. ^ a b c Boopathy, R (2000). "Factors limiting bioremediation technologies". Bioresource Technology. 74: 63–7. doi:10.1016/S0960-8524(99)00144-3. 
  18. ^ a b c Wexler, editor-in-chief, Philip (2014). Encyclopedia of toxicology (3rd ed.). San Diego, Ca: Academic Press Inc. p. 489. ISBN 9780123864543. 
  19. ^ Lovley DR (October 2003). "Cleaning up with genomics: applying molecular biology to bioremediation". Nature Reviews. Microbiology. 1 (1): 35–44. doi:10.1038/nrmicro731. PMID 15040178. 
  20. ^ a b c Menn F, Easter JP, Sayler GS (2001). "Genetically Engineered Microorganisms and Bioremediation". Biotechnology Set. pp. 441–63. doi:10.1002/9783527620999.ch21m. ISBN 978-3-527-62099-9. 
  21. ^ Ripp S, Nivens DE, Ahn Y, Werner C, Jarrell J, Easter JP, Cox CD, Burlage RS, Sayler GS (2000). "Controlled Field Release of a Bioluminescent Genetically Engineered Microorganism for Bioremediation Process Monitoring and Control". Environmental Science & Technology. 34 (5): 846–53. Bibcode:2000EnST...34..846R. doi:10.1021/es9908319. 
  22. ^ a b c Davison J (December 2005). "Risk mitigation of genetically modified bacteria and plants designed for bioremediation". Journal of Industrial Microbiology & Biotechnology. 32 (11-12): 639–50. doi:10.1007/s10295-005-0242-1. PMID 15973534. 
  23. ^ Sayler GS, Ripp S (June 2000). "Field applications of genetically engineered microorganisms for bioremediation processes". Current Opinion in Biotechnology. 11 (3): 286–9. doi:10.1016/S0958-1669(00)00097-5. PMID 10851144. 
  24. ^ Shanker R, Purohit HJ, Khanna P (1998). "Bioremediation for Hazardous Waste Management: The Indian Scenario". In Irvine RL, Sikdar SK. Bioremediation Technologies: Principles and Practice. pp. 81–96. ISBN 978-1-56676-561-9. 

External links

  • Phytoremediation, hosted by the Missouri Botanical Garden
  • To remediate or to not remediate?
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