Bioremediation

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Overview

Bioremediation can be defined as any process that uses microorganisms, fungi, green plants or their enzymes to return the environment altered by contaminants to its original condition. Bioremediation may be employed to attack specific soil contaminants, such as degradation of chlorinated hydrocarbons by bacteria. An example of a more general approach is the cleanup of oil spills by the addition of nitrate and/or sulfate fertilisers to facilitate the decomposition of crude oil by indigenous or exogenous bacteria.

Overview and applications

Naturally-occurring bioremediation and phytoremediation have been used for centuries. For example, desalination of agricultural land by phytoextraction has a long tradition. Bioremediation technology using microorganisms was reportedly invented by George M. Robinson. He was the assistant county petroleum engineer for Santa Maria, California. During the 1960's, he spent his spare time experimenting with dirty jars and various mixes of microbes.

Bioremediation 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 technologies are bioventing, landfarming, bioreactor, composting, bioaugmentation, rhizofiltration, and biostimulation.

Not all contaminants, however, are easily treated by bioremediation using microorganisms. For example, heavy metals such as cadmium and lead are not readily absorbed or captured by organisms. The assimilation of metals such as mercury into the food chain may worsen matters. Phytoremediation is useful in these circumstances, as many plants are able to bioaccumulate these toxins in their above-ground parts, which are then harvested for removal. The heavy metals in the harvested biomass may be further concentrated by incineration.

Microbial Biodegradation

Interest in the microbial biodegradation of pollutants has intensified in recent years as mankind strives to find sustainable ways to clean up contaminated environments.^[1] These bioremediation and biotransformation methods endeavour to harness the astonishing, naturally occurring, microbial catabolic diversity to degrade, transform or accumulate a huge range of compounds including hydrocarbons (e.g. oil), polychlorinated biphenyls (PCBs), polyaromatic hydrocarbons (PAHs), pharmaceutical substances, radionuclides and metals. Major methodological breakthroughs in recent years have enabled detailed genomic, metagenomic, proteomic, bioinformatic and other high-throughput analyses of environmentally relevant microorganisms providing unprecedented insights into key biodegradative pathways and the ability of organisms to adapt to changing environmental conditions.

The elimination of a wide range of pollutants and wastes from the environment is an absolute requirement to promote a sustainable development of our society with low environmental impact. Biological processes play a major role in the removal of contaminants and they take advantage of the astonishing catabolic versatility of microorganisms to degrade/convert such compounds. New methodological breakthroughs in sequencing, genomics, proteomics, bioinformatics and imaging are producing vast amounts of information. In the field of Environmental Microbiology, genome-based global studies open a new era providing unprecedented in silico views of metabolic and regulatory networks, as well as clues to the evolution of degradation pathways and to the molecular adaptation strategies to changing environmental conditions. functional genomic and metagenomic approaches are 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.^[1]

Genetic engineering approaches

The use of genetic engineering to create organisms specifically designed for bioremediation has great potential.^[2] 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.^[3]

Advantages

There are a number of cost/efficiency advantages to bioremediation, which can be employed in areas that are inaccessible without excavation. 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 lag 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 common practice at sites where hydrocarbons have contaminated groundwater.

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.

Process	Reaction	Redox potential (E_h in mV)
aerobic:	O₂ + 4e^- + 4H⁺ → 2H₂O	600 — 400
anaerobic:
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^- +10H⁺ → 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.

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.
if all the measurements of redox potential show is that electron acceptors have been used up, it's 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.

References

↑ ^1.0 ^1.1 Diaz E (editor). (2008). Microbial Biodegradation: Genomics and Molecular Biology (1st ed. ed.). Caister Academic Press. ISBN 978-1-904455-17-2.CS1 maint: Extra text (link)
↑ Lovley, DR (2003). "Cleaning up with genomics: applying molecular biology to bioremediation". NATURE REVIEWS. MICROBIOLOGY. 1 (1): 35 &ndash, 44. PMID 15040178.
↑ 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): 85 &ndash, 90. PMID 16645051.

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[Diaz-1] 1.0 ^1.1 Diaz E (editor). (2008). Microbial Biodegradation: Genomics and Molecular Biology (1st ed. ed.). Caister Academic Press. ISBN 978-1-904455-17-2.CS1 maint: Extra text (link)

[2] Lovley, DR (2003). "Cleaning up with genomics: applying molecular biology to bioremediation". NATURE REVIEWS. MICROBIOLOGY. 1 (1): 35 &ndash, 44. PMID 15040178.

[3] 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): 85 &ndash, 90. PMID 16645051.

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