Mechanism of salt removal from tsunami affected soil by bioremediation

Bioremediation is a waste management technique that involves the use of organisms to remove or neutralize pollutants from a contaminated site.[1] According to the United States EPA, bioremediation is a “treatment that uses naturally occurring organisms to break down hazardous substances into less toxic or non toxic substances”. Technologies can be generally classified as in situ or ex situ. In situ bioremediation involves treating the contaminated material at the site, while ex situ involves the removal of the contaminated material to be treated elsewhere. Some examples of bioremediation related technologies are phytoremediation, bioventing, bioleaching, landfarming, bioreactor, composting, bioaugmentation, rhizofiltration, and biostimulation.

Bioremediation may occur on its own (natural attenuation or intrinsic bioremediation) or may only effectively occur through the addition of fertilizers, oxygen, etc.,that help in enhancing the growth of the pollution-eating microbes within the medium (biostimulation). For example, the US Army Corps of Engineers demonstrated that windrowing and aeration of petroleum-contaminated soils enhanced bioremediation using the technique of landfarming.[2] Depleted soil nitrogen status may encourage biodegradation of some nitrogenous organic chemicals,[3] and soil materials with a high capacity to adsorb pollutants may slow down biodegradation owing to limited bioavailability of the chemicals to microbes.[4] Recent advancements have also proven successful via the addition of matched microbe strains to the medium to enhance the resident microbe population's ability to break down contaminants. Microorganisms used to perform the function of bioremediation are known as bioremediators.

However, not all contaminants are easily treated by bioremediation using microorganisms. For example, heavy metals such as cadmium and lead are not readily absorbed or captured by microorganisms. A recent experiment, however, suggests that fish bones have some success absorbing lead from contaminated soil.[5][6] Bone char has been shown to bioremediate small amounts of cadmium, copper, and zinc.[7] A recent experiment, suggests that the removals of pollutants (nitrate, silicate, chromium and sulphide) from tannery wastewater were studied in batch experiments using marine microalgae.[8] The assimilation of metals such as mercury into the food chain may worsen matters. Phytoremediation is useful in these circumstances because natural plants or transgenic plants are able to bioaccumulate these toxins in their above-ground parts, which are then harvested for removal.[9] The heavy metals in the harvested biomass may be further concentrated by incineration or even recycled for industrial use. Some damaged artifacts at museums contain microbes which could be specified as bio remediating agents.[10] In contrast to this situation, other contaminants, such as aromatic hydrocarbons as are common in petroleum, are relatively simple targets for microbial degradation, and some soils may even have some capacity to autoremediate, as it were, owing to the presence of autochthonous microbial communities capable of degrading these compounds.[11]

The elimination of a wide range of pollutants and wastes from the environment requires increasing our understanding of the relative importance of different pathways and regulatory networks to carbon flux in particular environments and for particular compounds, and they will certainly accelerate the development of bioremediation technologies and biotransformation processes.[12]

Genetic engineering approaches

The use of genetic engineering to create organisms specifically designed for bioremediation has great potential.[13] The bacterium Deinococcus radiodurans (the most radioresistant organism known) has been modified to consume and digest toluene and ionic mercury from highly radioactive nuclear waste.[14] Releasing genetically augmented organisms into the environment may be problematic as tracking them can be difficult; bioluminescence genes from other species may be inserted to make this easier.[15] :135


Mycoremediation is a form of bioremediation in which fungi are used to decontaminate the area. The term mycoremediation refers specifically to the use of fungal mycelia in bioremediation.

One of the primary roles of fungi in the ecosystem is decomposition, which is performed by the mycelium. The mycelium secretes extracellular enzymes and acids that break down lignin and cellulose, the two main building blocks of plant fiber. These are organic compounds composed of long chains of carbon and hydrogen, structurally similar to many organic pollutants. The key to mycoremediation is determining the right fungal species to target a specific pollutant. Certain strains have been reported to successfully degrade the nerve gases VX and sarin.

In one conducted experiment, a plot of soil contaminated with diesel oil was inoculated with mycelia of oyster mushrooms; traditional bioremediation techniques (bacteria) were used on control plots. After four weeks, more than 95% of many of the PAH (polycyclic aromatic hydrocarbons) had been reduced to non-toxic components in the mycelial-inoculated plots. It appears that the natural microbial community participates with the fungi to break down contaminants, eventually into carbon dioxide and water. Wood-degrading fungi are particularly effective in breaking down aromatic pollutants (toxic components of petroleum), as well as chlorinated compounds (certain persistent pesticides; Battelle, 2000).

Two species of the Ecuadorian fungus Pestalotiopsis are capable of consuming Polyurethane in aerobic and anaerobic conditions such as found at the bottom of landfills.[16]

Mycofiltration is a similar process, using fungal mycelia to filter toxic waste and microorganisms from water in soil.


There are a number of cost/efficiency advantages to bioremediation, which can be employed in areas that are inaccessible without excavation.[17] For example, hydrocarbon spills (specifically, petrol spills) or certain chlorinated solvents may contaminate groundwater, and introducing the appropriate electron acceptor or electron donor amendment, as appropriate, may significantly reduce contaminant concentrations after a long time allowing for acclimation. This is typically much less expensive than excavation followed by disposal elsewhere, incineration or other ex situ treatment strategies, and reduces or eliminates the need for "pump and treat", a practice common at sites where hydrocarbons have contaminated clean groundwater. Using archaea for bioremediation of hydrocarbons also has the advantage of breaking down contaminants at the molecular level, as opposed to simply chemically dispersing the contaminant.[18]

Monitoring bioremediation

The process of bioremediation can be monitored indirectly by measuring the Oxidation Reduction Potential or redox in soil and groundwater, together with pH, temperature, oxygen content, electron acceptor/donor concentrations, and concentration of breakdown products (e.g. carbon dioxide). This table shows the (decreasing) biological breakdown rate as function of the redox potential.

ProcessReactionRedox 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

This, by itself and at a single site, gives little information about the process of remediation.

  1. It is necessary to sample enough points on and around the contaminated site to be able to determine contours of equal redox potential. Contouring is usually done using specialised software, e.g. using Kriging interpolation.
  2. If all the measurements of redox potential show that electron acceptors have been used up, it is in effect an indicator for total microbial activity. Chemical analysis is also required to determine when the levels of contaminants and their breakdown products have been reduced to below regulatory limits.
  3. Chemical analysis should also be carried out for assessing transformations in inorganic contaminants (e.g. heavy metals, radionuclides). Unlike organic pollutants, inorganic pollutants cannot be degraded[19] and remediation processes can both increase and decrease their solubility and bio-availability. An increase in heavy metal mobility can occur, even in reductive conditions, during in-situ bioremediation.[20]

See also


  2. Mann, D. K., T. M. Hurt, E. Malkos, J. Sims, S. Twait and G. Wachter. 1996. Onsite treatment of petroleum, oil, and lubricant (POL)-contaminated soils at Illinois Corps of Engineers lake sites. US Army Corps of Engineers Technical Report No. A862603 (71pages).
  3. Sims, G.K. (2006). "Nitrogen Starvation Promotes Biodegradation of N-Heterocyclic Compounds in Soil". Soil Biology & Biochemistry. 38: 2478–2480. doi:10.1016/j.soilbio.2006.01.006.
  4. O'Loughlin, E. J; Traina, S. J.; Sims, G. K. (2000). "Effects of sorption on the biodegradation of 2-methylpyridine in aqueous suspensions of reference clay minerals". Environ. Toxicol. and Chem. 19: 2168–2174. doi:10.1002/etc.5620190904.
  5. Kris S. Freeman (January 2012). "Remediating Soil Lead with Fishbones". Environmental Health Perspectives.
  7. Huan Jing Ke Xue (February 2007). "Chemical fixation of metals in soil using bone char and assessment of the soil genotoxicity".
  8. Adam s. "marine Biology and ocenography".
  9. Meagher, RB (2000). "Phytoremediation of toxic elemental and organic pollutants". Current Opinion in Plant Biology. 3 (2): 153–162. doi:10.1016/S1369-5266(99)00054-0. PMID 10712958.
  10. Francesca Cappitelli; Claudia Sorlini (2008). "Microorganisms Attack Synthetic Polymers in Items Representing Our Cultural Heritage". Applied and Environmental Microbiology. 74: 564–9. doi:10.1128/AEM.01768-07. PMC 2227722Freely accessible. PMID 18065627.
  11. Olapade, OA; Ronk, AJ (2014). "Isolation, Characterization and Community Diversity of Indigenous Putative Toluene-Degrading Bacterial Populations with Catechol-2,3-Dioxygenase Genes in Contaminated Soils". Microbial Ecology. 69: 59–65. doi:10.1007/s00248-014-0466-6. PMID 25052383.
  12. Diaz E (editor). (2008). Microbial Biodegradation: Genomics and Molecular Biology (1st ed.). Caister Academic Press. ISBN 1-904455-17-4.
  13. Lovley, DR (2003). "Cleaning up with genomics: applying molecular biology to bioremediation". Nature Reviews Microbiology. 1 (1): 3544. doi:10.1038/nrmicro731. PMID 15040178.
  14. Brim H, McFarlan SC, Fredrickson JK, Minton KW, Zhai M, Wackett LP, Daly MJ (2000). "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments". Nature Biotechnology. 18 (1): 8590. doi:10.1038/71986. PMID 10625398.
  15. Robert L. Irvine; Subhas K. Sikdar. Bioremediation Technologies: Principles and Practice.
  16. "Biodegradation of Polyester Polyurethane by Endophytic Fungi". Applied and Environmental Microbiology. July 2011.
  17. "Why Bioremediation". JRW Bioremediation. Retrieved 2016-05-02.
  18. "Archaea Effectiveness, Benefits - Akaya". Akaya. Retrieved 2015-09-10.
  19. "Developments in Bioremediation of Soils and Sediments Polluted with Metals and Radionuclides – 1. Microbial Processes and Mechanisms Affecting Bioremediation of Metal Contamination and Influencing Metal Toxicity and Transport". Reviews in Environmental Science and Bio/Technology. 4: 115–156. August 2005. doi:10.1007/s11157-005-2169-4.
  20. "Bioremediation of contaminated marine sediments can enhance metal mobility due to changes of bacterial diversity". Water Research. January 2015.

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