Bioremediation - Treatment of Waste and Pollution

Bacterial

Mycoremediation

Phycoremediation

Phytoremediation

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 involve 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.

Chemistry[edit]

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
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− +10 H+ → H2S + 4H2O	0 ~ −150
fermentation	2CH2O → CO2 + CH4	−150 ~ −220

Aerobic[edit]

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.^[3] 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 aromaticcompounds can be very high. As the molecular weight of the compound increases, so does the resistance to biodegradation.^[3]

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.^[4]

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.^[5]

Anaerobic[edit]

Anaerobic bioremediation can be employed to treat a broad range of oxidized contaminants including chlorinated ethenes (PCE, TCE, DCE, VC), chlorinated ethanes (TCA, DCA), chloromethanes (CT, CF), chlorinated cyclic hydrocarbons, various energetics (e.g., perchlorate,^[6] RDX, TNT), and nitrate.^[7] This process 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. 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.^[7][2]

Heavy Metals[edit]

Heavy metals including cadmium, chromium, lead and uranium are elements so they cannot be biodegraded. However, bioremediation processes can potentially be used to reduce the mobility of these material in the subsurface, reducing the potential for human and environmental exposure. The mobility of certain metals including chromium (Cr) and uranium (U) varies depending on the oxidation state of the material.^[8] Microorganisms can be used to reduce the toxicity and mobility of chromium by reducing hexavalent chromium, Cr(VI) to trivalent Cr (III).^[9] Uranium can be reduced from the more mobile U(VI) oxidation state to the less mobile U(IV) oxidation state.^[10][11] Microorganisms are used in this process because the reduction rate of these metals is often slow unless catalyzed by microbial interactions^[12] Research is also underway to develop methods to remove metals from water by enhancing the sorption of the metal to cell walls.^[12] This approach has been evaluated for treatment of cadmium,^[13] chromium,^[14] and lead.^[15] Phytoextraction processesconcentrate contaminants in the biomass for subsequent removal.

Additives[edit]

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.^[16]

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.^[17]

Limitations[edit]

Bioremediation can be used to completely mineralize organic pollutants, to partially transform the pollutants, or alter their mobility. Heavy metals and radionuclides are elements that cannot be biodegraded, but can be bio-transformed to less mobile forms.^[18][19][20] In some cases, microbes do not fully mineralize the pollutant, potentially producing a more toxic compound.^[20] For example, under anaerobic conditions, the reductive dehalogenation of TCE may produce dichloroethylene (DCE) and vinyl chloride (VC), which are suspected or known carcinogens.^[18] However, the microorganism Dehalococcoides can further reduce DCE and VC to the non-toxic product ethene.^[21] Additional research is required to develop methods to ensure that the products from biodegradation are less persistent and less toxic than the original contaminant.^[20] Thus, the metabolic and chemical pathways of the microorganisms of interest must be known.^[18] In addition, knowing these pathways will help develop new technologies that can deal with sites that have uneven distributions of a mixture of contaminants.^[22]

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.^[22][19] The biological processes used by these microbes are highly specific, therefore, many environmental factors must be taken into account and regulated as well.^[22][18] Thus, bioremediation processes must be specifically made in accordance to the conditions at the contaminated site.^[18] Also, because many factors are interdependent, small-scale tests are usually performed before carrying out the procedure at the contaminated site.^[19] However, it can be difficult to extrapolate the results from the small-scale test studies into big field operations.^[22] In many cases, bioremediation takes more time than other alternatives such as land filling and incineration.^[22][18]

Genetic engineering[edit]

The use of genetic engineering to create organisms specifically designed for bioremediation is under preliminary research.^[23] 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 pollution levels.^[24] 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.^[25]

There are concerns surrounding release and containment of genetically modified organisms into the environment due to the potential of horizontal gene transfer.^[26] Genetically modified organisms are classified and controlled under the Toxic Substances Control Act of 1976 under United States Environmental Protection Agency.^[27] 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.^[26] In addition, the tracking of modified organisms can be made easier with the insertion of bioluminescence genes for visual identification.^[28]

Bioremediation of radioactive waste or bioremediation of radionuclides is an application of bioremediation based on the use of biological agents bacteria, plants and fungi(natural or genetically modified) to catalyze chemical reactions that allow the decontamination of sites affected by radionuclides.^[1] These radioactive particles are by-products generated as a result of activities related to nuclear energy and constitute a pollution and a radiotoxicity problem (with serious health and ecological consequences) due to its unstable nature of ionizing radiation emissions.

The techniques of bioremediation of environmental areas as soil, water and sediments contaminated by radionuclides are diverse and currently being set up as an ecological and economic alternative to traditional procedures. Physico-chemical conventional strategies are based on the extraction of waste by excavating and drilling, with a subsequent long-range transport for their final confinement. These works and transport have often unacceptable estimated costs of operation that could exceed a trillion dollars in the US and 50 million pounds in the UK.^[2]

The species involved in these processes have the ability to influence the properties of radionuclides such as solubility, bioavailability and mobility to accelerate its stabilization. Its action is largely influenced by electron donors and acceptors, nutrient medium, complexation of radioactive particles with the material and environmental factors. These are measures that can be performed on the source of contamination (in situ) or in controlled and limited facilities in order to follow the biological process more accurately and combine it with other systems (ex situ).^[3][4]

Areas contaminated by radioactivity[edit]

Main article: Radioactive contamination

Typology of radionuclides and polluting waste[edit]

Main article: Radioactive waste

The presence of radioactive waste in the environment may cause long-term effects due to the activity and half-life of the radionuclides, leading their impact to grow with time.^[2] These particles exist in various oxidation states and are found as oxides, coprecipitates, or as organic or inorganic complexes, according to their origin and ways of liberation. Most commonly they are found in oxidized form, which makes them more soluble in water and thus more mobile.^[4] Unlike organic contaminants, however, they cannot be destroyed and must be converted into a stable form or extracted from the environment.^[5]

The sources of radioactivity are not exclusive of human activity. The natural radioactivity does not come from human sources: it covers up to ¾ of the total radioactivity in the world and has its origins in the interaction of terrestrial elements with high energy cosmic rays (cosmogenic radionuclides) or in the existing materials on Earth since its formation (primordial radionuclides). In this regard, there are differences in the levels of radioactivity throughout the Earth's crust. India and mountains like the Alps are among the areas with the highest level of natural radioactivity due to their composition of rocks and sand.^[6]

The most frequent radionuclides in soils are naturally radium-226 (²²⁶Ra), radon-222 (²²²Rn), thorium-232 (²³²Th), uranium-238 (²³⁸U) and potassium-40 (⁴⁰K). Potassium-40 (up to 88% of total activity), carbon-14 (¹⁴C), radium-226, uranium-238 and rubidium-87 (⁸⁷Rb) are found in ocean waters. Moreover, in groundwater abound radius radioisotopes such as radium-226 and radium-228 (²²⁸Ra).^[7][8] They are also habitual in building materials radionuclides of uranium, thorium and potassium (the latter common to wood).^[8]

At the same time, anthropogenic radionuclides (caused by humans) are due to thermonuclear reactions resulting from explosions and nuclear weapons tests, discharges from nuclear facilities, accidents deriving from the reprocessing of commercial fuel, waste storage from these processes and to a lesser extent, nuclear medicine.^[9] Some polluted sites by these radionuclides are the US DOE facilities (like Hanford Site), the Chernobyl and Fukushima exclusion zones and the affected area of Chelyabinsk Oblast due to the Kyshtym disaster.

In ocean waters, the presence of tritium (³H), cesium-137 (¹³⁷Cs), strontium-90 (⁹⁰Sr), plutonium-239 (²³⁹Pu) and plutonium-240 (²⁴⁰Pu) has significantly increased due to anthropogenic causes.^[10][11] In soils, technetium-99 (⁹⁹Tc), carbon-14, strontium-90, cobalt-60 (⁶⁰Co), iodine-129 (¹²⁹I), iodine-131 (¹³¹I), americium-241 (²⁴¹Am), neptunium-237(²³⁷Np) and various forms of radioactive plutonium and uranium are the most common radionuclides.^[2][8][9]

The classification of radioactive waste established by the International Atomic Energy Agency (IAEA) distinguishes six levels according to equivalent dose, specific activity, heatreleased and half-life of the radionuclides:^[13]

• Exempt waste (EW): Waste that meets the criteria for exclusion from regulatory control for radiation protection purposes.
• Very short lived waste (VSLW): Waste with very short half-lives (often used for research and medical purposes) that can be stored over a limited period of up to a few years and subsequently cleared from regulatory control.
• Very low level waste (VLLW): Waste like soil and rubble (with low levels of activity concentration) that may also contain other hazardous waste.
• Low level waste (LLW): Waste that is above clearance levels and requires robust isolation and containment for periods of up to a few hundred years and is suitable for disposal in engineered near surface facilities. LLW include short lived radionuclides at higher levels of activity concentration and also long lived radionuclides, but only at relatively low levels of activity concentration.
• Intermediate level waste (ILW): Waste with long lived radionuclides that requires a greater degree of containment and isolation at greater depths.
• High level waste (HLW): Waste with large amounts of long lived radionuclides that need to be stored in deep, stable geological formations usually several hundred metres or more below the surface.

Ecological and human health consequences[edit]

Deformity of hand due to an X-ray burn.

Radioactive contamination is a potential danger for living organisms and results in external hazards, concerning radiation sources outside the body, and internal dangers, as a result of the incorporation of radionuclides inside the body (often by inhalation of particles or ingestion of contaminated food).^[14]

In humans, single doses from 0.25 Sv produce first anomalies in the amount of leukocytes. This effect is accentuated if the absorbed dose is between 0.5 and 2 Sv, in whose first damage, nausea and hair loss are suffered. The strip ranging between 2 and 5 Sv is considered the most serious and include bleeding, ulcers and risk of death; values exceeding 5 Sv involve immediate death.^[14] If radiation, likewise, is received in small doses over long periods of time, the consequences can be equally severe. It is difficult to quantify the health effects for doses below 10 mSv, but it has been shown that there is a direct relationship between prolonged exposure and cancer risk (although there is not a very clear dose-response relationship to establish clear limits of exposure).^[15]

The information available on the effect of natural background radiation with respect anthropogenic pollution on wildlife is scarce and refers to very few species. It is very difficult to estimate from the available data the total doses that can accumulate during specific stages of the life cycle (embryonic development or reproductive age), in changes in behavior or depending on environmental factors such as seasonality.^[16] The phenomena of radioactive bioaccumulation, bioconcentration and biomagnification, however, are especially known to sea level. They are caused by the recruitment and retention of radioisotopes by bivalves, crustaceans, corals and phytoplankton, which then amounted to the rest of the food chain at low concentration factors.^[17]

Radiobiological literature and IAEA establish a safe limit of absorbed dose of 0.001 Gy/d for terrestrial animals and 0.01 Gy/d for plants and marine biota, although this limit should be reconsidered for long-lived species with low reproductive capacity.^[18]

1909 study in which the effect of exposure to radioactive radium on lupins is shown. The radiological activity was the same for all seedlings, but not the duration of exposure (descending from left to right, the fourth as control). Those exposed for longer suffered more damage and higher growth and germination deficiences.^[19]

Radiation tests in model organisms that determine the effects of high radiation on animals and plants are:^[18]

• Chromosomal aberrations.
• DNA damage.
• Cancer, particularly leukemia.^[2]
• Leukopenia.
• Growth reduction.
• Reproductive deficiencies: sterility, reduction in fecundity, and occurrence of developmental abnormalities or reduction in viability of offspring
• Reduced seed germination.
• Burned tissues exposed to radiation.
• Mortality, including both acute lethality and long-term reduction in life span.

The effects of radioactivity on bacteria are given, as in eukaryotes, by ionization of water and production of reactive oxygen species. These compounds mutate DNA strands and produce genetic damage, inducing newly lysis and subsequent cell death.^[20][21]

Its action on viruses, on the other hand, results in damaged nucleic acids and viral inactivation.^[22] They have a sensory threshold ranging between 1000 and 10,000 Gy (range occupying most biological organisms) which decreases with increasing genome size.^[23]

Bacterial bioremediation[edit]

The biochemical transformation of radionuclides into stable isotopes by bacterial species significantly differs from the metabolism of organic compounds coming from carbon sources. They are highly energetic radioactive forms which can be converted indirectly by the process of microbial energy transfer.^[1]

Radioisotopes can be transformed directly through changes in valence state by acting as acceptors or by acting as cofactors to enzymes. They can also be transformed indirectly by reducing and oxidizing agents produced by microorganisms that cause changes in pH or redox potential. Other processes include precipitation and complexation of surfactants, or chelating agents that bind to radioactive elements. Human intervention, on the other hand, can improve these processes through genetic engineering and omics, or by injection of microorganisms or nutrients into the treatment area.^[1][5]

Bioreduction[edit]

Main article: Biotransformation

According to the radioactive element and the specific site conditions, bacteria can enzymatically immobilize radionuclides directly or indirectly. Their redox potential is exploited by some microbial species to carry out reductions that alter the solubility and hence, mobility, bioavailability and radiotoxicity. This waste treatment technique called bioreduction or enzymatic biotransformation is very attractive because it can be done in mild conditions for the environment, does not produce hazardous secondary waste and has potential as a solution for waste of various kinds.^[4]

Depiction of direct enzymatic reduction. Microorganisms use organic compounds as lactate, acetate or formate as electron donors to reduce and leave radionuclides in insoluble form.^[2][24]

Direct enzymatic reduction is the change of radionuclides of a higher oxidation state to a lower one made by facultative and obligate anaerobes. The radioisotope interact with binding sites of metabolically active cells and is used as terminal electron acceptor in the electron transport chainwhere compounds such as ethyl lactate act as electron donors under anaerobic respiration.^[4]

The periplasm plays a very important role in these bioreductions. In the reduction of uranium (VI) to insoluble uranium (IV), made by Shewanella putrefaciens, Desulfovibrio vulgaris, Desulfovibrio desulfuricans and Geobacter sulfurreducens, the activity of periplasmic cytochromes is required. The reduction of technetium (VII) to technetium (IV) made by S. putrefaciens, G. sulfurreducens, D. desulfuricans, Geobacter metallireducens and Escherichia coli, on the other hand, requires the presence of the complex formate hydrogenlyase, also placed in this cell compartment.^[2]

Other radioactive actinides such as thorium, plutonium, neptunium and americium are enzymatically reduced by Rhodoferax ferrireducens, S. putrefaciens and several species of Geobacter, and directly form an insoluble mineral phase.^[2]

The phenomenon of indirect enzymatic reduction is carried out by sulfate-reducing and dissimilatory metal-reducing bacteria on excretion reactions of metabolites and breakdown products. There is a coupling of the oxidation of organic acids —produced by the excretion of these heterotrophic bacteria— with the reduction of iron or other metals and radionuclides, which forms insoluble compounds that can precipitate as oxide and hydroxide minerals. In the case of sulfate-reducing bacteria hydrogen sulfide is produced, promoting increased solubility of polluting radionuclides and their bioleaching (as liquid waste that can then be recovered).^[2][4]

There are several species of reducing microorganisms that produce indirect sequestering agents and specific chelators, such as siderophores. These sequestering agents are crucial in the complexation of radionuclides and increasing their solubility and bioavailability. Microbacterium flavescens, for example, grows in the presence of radioisotopes such as plutonium, thorium, uranium or americium and produces organic acids and siderophores that allow the dissolution and mobilization of radionuclides through the soil. It seems that siderophores on bacterial surface could also facilitate the entry of these elements within the cell as well. Pseudomonas aeruginosa also secretes chelating agents out that meet uranium and thorium when grown in a medium with these elements. In general, it has also been found that enterobactin siderophores are extremely effective in solubilizing actinide oxides of plutonium.^[2][4]

Citrate complexes[edit]

Citrate is a chelator which binds to certain transition metals and radioactive actinides. Stable complexes such as bidentate, tridentate (ligands with more than one atom bound) and polynuclear complexes (with several radioactive atoms) can be formed with citrate and radionuclides, which receive a microbial action. Anaerobically, Desulfovibrio desulfuricans and species of the genera Shewanella and Clostridium are able to reduce bidentate complexes of uranyl-citrate (VI) to uranyl-citrate (IV) and make them precipitate, despite not being able to degrade metabolically complexed citrate at the end of the process.^[2] In denitrifying and aerobic conditions, however, it has been determined that it is not possible to reduce or degrade these uranium complexes. Bioreduction do not get a head when they are citrate complex mixed metal complexes or when they are tridentate, monomeric or polynuclear complexes, since they become recalcitrant and persistent in the environment.^[4][25] From this knowledge exists a system that combines the degradation of radionuclide-citrate complex with subsequent photodegradation of remaining reduced uranyl-citrate (previously not biodegradated but sensitive to light), which allows for stable precipitates of uranium and also of thorium, strontium or cobalt from contaminated lands.^[4]

Biosorption, bioaccumulation and biomineralization[edit]

Biosorption, bioaccumulation and biomineralization strategies with a specific role for each cell compartment.^[3]

Main articles: Biosorption, Bioaccumulation, and Biomineralization

The set of strategies that comprise biosorption, bioaccumulation and biomineralization are closely related to each other, because one way or another have a direct contact between the cell and radionuclide. These mechanisms are evaluated accurately using advanced analysis technologies such as electron microscopy, X-ray diffraction and XANES, EXAFS and X-ray spectroscopies.^[1][26]

Biosorption and bioaccumulation are two metabolic actions that are based on the ability to concentrate radionuclides over a thousand times the concentration of the environment. They consist of complexation of radioactive waste with phosphates, organic compounds and sulfitesso that they become insoluble and less exposed to radiotoxicity. They are particularly useful in biosolids for agricultural purposes and soil amendments, although most properties of these biosolids are unknown.^[27]

Biosorption method is based on passive sequestration of positively charged radioisotopes by lipopolysaccharides (LPS) on the cell membrane (negatively charged), either live or dead bacteria. Its efficiency is directly related to the increase in temperature and can last for hours, being a much faster method than direct bioreduction. It occurs through the formation of slimesand capsules, and with a preference for binding to the phosphate and phosphoryl groups (although it also occurs with carboxyl, amine or sulfhydryl groups). Firmicutes and other bacteria like Citrobacter freudii have significant biosorption capabilities; Citrobacter does it through electrostatic interaction of uranium with phosphates of their LPS.^[2][3]

Quantitative analyzes determine that, in the case of uranium, biosorption may vary within a range between 45 and 615 milligrams per gram of cell dry weight. However, it is a technique that requires a high amount of biomass to affect bioremediation; it presents problems of saturation and other cations that compete for binding to the bacterial surface.^[3]

Bioaccumulation refers to uptake of radionuclides into the cell, where they are retained by complexations with negatively charged intracellular components, precipitation or granulesformations. Unlike biosorption, this is an active process: it depends on an energy-dependent transport system.^[24] Some metals or radionuclides can be absorbed by bacteria accidentally because of its resemblance to dietary elements for metabolic pathways. Several radioisotopes of strontium, for example, are recognized as analogs of calcium and incorporated within Micrococcus luteus.^[4] Uranium, however, has no known function and is believed that its entry into the cell interior may be due to its toxicity (it is able to increase membrane permeability).^[3]

Chernikovite and meta-autunite, radioactive minerals result of possible biomineralization.

Furthermore, biomineralization —also known as bioprecipitation— is the precipitation of radionuclides through the generation of microbial ligands, resulting in the formation of stable biogenic minerals. These minerals have a very important role in the retention of radioactive contaminants. A very localized and produced enzymatically ligand concentration is involved and provides a nucleation site for the onset of biomineral precipitation.^[28] This is particularly relevant in precipitations of phosphatase activity-derivate biominerals, which cleavage molecules such as glycerol phosphate on periplasm. In Citrobacter and Serratia genera, this cleavage liberates inorganic phosphates (HPO₄²⁻) that precipitates with uranyl ion (UO₂²⁺) and cause deposition of polycrystalline minerals around the cell wall.^[2][29] Serratia also form biofilms that promote precipitation of chernikovite (rich in uranium) and additionally, remove up to 85% of cobalt-60 and 97% of cesium-137 by proton substitution of this mineral.^[26] In general, biomineralization is a process in which the cells do not have limitations of saturation and can accumulate up to several times its own weight as precipitated radionuclides.^[4]

Investigations of terrestrial and marine bacterial isolates belonging to the genera Aeromonas, Bacillus, Myxococcus, Pantoea, Pseudomonas, Rahnella and Vibrio have also demonstrated the removal of uranium radioisotopes as phosphate biominerals in both oxic and anoxic growth conditions.^[26]

Biostimulation and bioaugmentation[edit]

Main articles: Biostimulation and Bioaugmentation

Evolution of the Old Rifle UMTRA Site (Colorado, US) from 1957 (above) until 2008 (below), in which biostimulation tasks were carried out.^[30]

Aside from bioreduction, biosorption, bioaccumulation and biomineralization, which are bacterial strategies for natural attenuation of radioactive contamination, there are also human methods that increase the efficiency or speed of microbial processes. This accelerated natural attenuation involves an intervention in the contaminated area to improve conversion rates of radioactive waste, which tend to be slow. There are two variants: biostimulation and bioaugmentation.^[31]

Biostimulation is the addition of nutrients with trace elements, electron donors or electron acceptors to stimulate activity and growth of natural indigenous microbial communities.^[4][31] It can range from simple fertilization or infiltration (called passive biostimulation) to more aggressive injections to the ground, and is widely used at US DOE sites.^[27] Nitrate is used as nutrient to biostimulate the reduction of uranium, because it serves as very energetically favorable electron acceptor for metal-reducing bacteria. However, many of these microorganisms (Geobacter, Shewanella or Desulfovibrio) exhibit resistance genes to heavy metals that limit their ability to bioremediate radionuclides. In these particular cases, a carbon source such as ethanol is added to the medium to promote the reduction of nitrate at first, and then of uranium. Ethanol is also used in soil injection systems with hydraulic recirculations: it raises the pH and promotes the growth of denitrifying and radionuclide-reducing bacteria, that produce biofilms and achieve almost 90% decrease in the concentration of radioactive uranium.^[2]

A number of geophysical techniques have been used to monitor the effects of in situ biostimulation trials including measurement of: spectral ionization potential, self potentials, current density, complex resistivity and also reactive transport modelling (RTM), which measures hydrogeological and geochemical parameters to estimate chemical reactions of the microbial community.^[3]

Bioaugmentaton, on the other hand, is the deliberated addition to the environment of microorganisms with desired traits to accelerate bacterial metabolic conversion of radioactive waste. They are often added when necessary species for bioremediation do not exist in the treatment place.^[4][31] This technique has shown in field trials over the years that it does not offer better results than biostimulation; neither it is clear that introduced species can be distributed effectively through the complex geological structures of most subsurface environments or that can compete long term with the indigenous microbiota.^[1][27]

Genetic engineering and omics[edit]

Deinococcus radiodurans has much interest in genetic engineering for bioremediation of radioactive waste.

Main articles: Genetic engineering and Omics

Omics, especially genomics and proteomics, allow identifying and evaluating genes, proteins and enzymes involved in radionuclide bioremediation, apart from the structural and functional interactions that exist between them and other metabolites. Genome sequencing of various microorganisms has uncovered, for example, that Geobacter sulfurreducens possess more than 100 coding regions for c-type cytochromes involved in bioremediation radionuclide, or that NiCoT gene is significantly overexpressed in Rhodopseudomonas palustris and Novosphingobium aromaticivorans when grown in medium with radioactive cobalt.^[1][2]

From this information, different genetic engineering and recombinant DNA techniques are being developed to generate specific bacteria for bioremediation. Some constructs expressed in microbial species are phytochelatins, polyhistidines and other polypeptides by fusion-binding domains to outer-membrane-anchored proteins.^[2] Some of these genetically modified strains are derived from Deinococcus radiodurans, one of the most radiation-resistant organisms. D. radiodurans is capable to resist oxidative stress and DNA damage from radiation, and reduces technetium, uranium and chromium naturally as well. Besides, through insertion of genes from other species it has been achieved that it can also precipitates uranyl phosphates and degrades mercury by using toluene as an energy source to grow and stabilize other priority radionuclides.^[1][3]

Directed evolution of bacterial proteins related to bioremediation of radionuclides is also a field research. YieF enzyme, for example, naturally catalyzes the reduction of chromium with a very wide range of substrates. Following protein engineering, however, it has also been able to participate in uranyl ion reduction.^[32]

Plant bioremediation[edit]

Main article: Phytoremediation

Phytoremediation processes. Radionuclides can not be phytodegraded but converted to more stable or less toxic forms.

The use of plants to remove contaminants from the environment or to render them less harmful is called phytoremediation. In the case of radionuclides, it is a viable technology when decontamination times are long and waste are scattered at low concentrations.^[33][34]

Some plant species are able to transform the state of radioisotopes (without suffering toxicity) concentrating them in different parts of their structure, making them rush through the roots, making them volatile or stabilizing them on the ground. As in bacteria, plant genetic engineering procedures and biostimulation —called phytostimulation— have improved and accelerate these processes, particularly with regard to fast-growing plants.^[34] The use of Agrobacterium rhizogenes, for example, is quite widespread and significantly increases radionuclide uptake by the roots.^[35]

Phytoextraction[edit]

Main article: Phytoextraction

In phytoextraction (also phytoaccumulation, phytosequesteration or phytoabsorption)^[36] plants carry radioactive waste from the root system to the vascular tissue and become concentrated in the biomass of shoots. It is a technique that removes radionuclides without destroying the soil structure, with minimal impact on soil fertility and valid for large areas with a low level of radioactivity. Its efficiency is evaluated through bioaccumulation coefficient(BC) or total removal of radionuclides per m², and is proven to attract cesium-137, strontium-90, technetium-99, cerium-144, plutonium-240, americium-241, neptunium-237 and various radioisotopes of thorium and radium.^[34] By contrast, it requires large biomass production in short periods of time.^[35]

Species like common heather or amaranths are able to concentrate cesium-137, the most abundant radionuclide in the Chernobyl Exclusion Zone. In this region of Ukraine, mustard greens could remove up to 22% of average levels of cesium activity in a single growing season. In the same way, bok choy and mustard greens can concentrate 100 times more uranium than other species.^[34]

Rhizofiltration[edit]

Connected pond system at River Dearne(England).

Main article: Rhizofiltration

Rhizofiltration is the adsorption and precipitation of radionuclides in plant roots or absorption thereof if soluble in effluents. It has great efficiency in the treatment of cesium-137 and strontium-90, particularly by algae and aquatic plants, such as Cladophora and Elodeagenera, respectively. It is the most efficient strategy for bioremediation technologies in wetlands,^[36] but must have a continuous and rigorous control of pH to make it an optimal process.^[35]

From this process, some strategies have been designed based on sequences of ponds with a slow flow of water to clean polluted water with radionuclides. The results of these facilities, for flows of 1000 liters of effluent are about 95% retention of radiation in the first pond (by plants and sludge), and over 99% in three-base systems.^[34]

The most promising plants for rhizofiltration are sunflowers. They are able to remove up to 95% of uranium of contaminated water in 24 hours, and experiments in Chernobyl have demonstrated that they can concentrate on 55 kg of plant dry weight all the cesium and strontium radioactivity from an area of 75 m² (stabilized material suitable for transfer to a nuclear waste repository).^[34]

Phytovolatilization[edit]

Main article: Phytovolatilization

Phytovolatilization involves the capture and subsequent transpiration of radionuclides into the atmosphere. It does not remove contaminants but releases them in volatile form (less harmful). Despite not having too many applications for radioactive waste, it is very useful for the treatment of tritium, because it exploits plants' ability to transpire enormous amounts of water.^[34][36]

The treatment applied to tritium (shielded by air produces almost no external radiation exposure, but its incorporation in water presents a health hazard when absorbed into the body) uses polluted effluents to irrigate phreatophytes. It becomes a system with a low operation cost and low maintenance, with savings of about 30% in comparison to conventional methods of pumping and covering with asphalt.^[34]

Phytostabilization[edit]

Main article: Phytostabilization

Phytostabilization is an specially valid strategy for radioactive contamination based on the immobilization of radionuclides in the soil by the action of the roots. This can occur by adsorption, absorption and precipitation within root zone, and ensures that radioactive waste can not be dispersed because soil erosion or leaching. It is useful in controlling tailings from strip and open pit uranium mines, and guarantees to retrieve the ecosystem.^[34][36] However, it has significant drawbacks such as large doses of fertilizer needed to reforest the area, apart from radioactive source (which implies long-term maintenance) remaining at the same place.^[35]

Fungal bioremediation[edit]

Radiotrophic fungi growth has been described in reactor 4 at the Chernobyl Nuclear Power Station.

Main article: Mycoremediation

Several fungi species have radioactive resistance values equal to or greater than more radioresistant bacteria; they perform mycoremediation processes. It was reported that some fungi had the ability of growing into, feeding, generating spores and decomposing pieces of graphite from destroyed reactor No. 4 at the Chernobyl Nuclear Power Station, which is contaminated with high concentrations of cesium, plutonium and cobalt radionuclides. They were called radiotrophic fungi.^[37]

Since then, it has been shown that some species of Penicillium, Cladosporium, Paecilomyces and Xerocomus are able to use ionizing radiationas energy through the electronic properties of melanins.^[37][38] In their feeding they bioaccumulate radioisotopes, creating problems on concretewalls of deep geological repositories.^[39] Other fungi like oyster mushrooms can bioremediate plutonium-239 and americium-241.^[40]

Ways of research[edit]

Current research on bioremediation techniques is fairly advanced and molecular mechanisms that govern them are well known. There are, however, many doubts about the effectiveness and possible adversities of these processes in combination with the addition of agrochemicals. In soils, the role of mycorrhizae on radioactive waste is poorly described and sequestration patterns of radionuclides are not known with certainty.^[41]

Longevity effects of some bacterial processes, such as maintenance of uranium in insoluble form because of bioreductions or biomineralizations, are unknown. There are not clear details about the electronic transfer from some radionuclides with these bacterial species either.^[3]

Another important aspect is the change of ex situ or laboratory scale processes to their real application in situ, in which soil heterogeneity and environmental conditions generate reproduction deficiencies of optimal biochemical status of the used species, a fact that decreases the efficiency. This implies finding what are the best conditions in which to carry out an efficient bioremediation with anions, metals, organic compounds or other chelating radionuclides that can compete with the uptake of interest radioactive waste.^[2] Nevertheless, in many cases research is focused on the extraction of soil and water and its ex situ biological treatment to avoid these problems.^[4]

Finally, the potential of GMOs is limited by regulatory agencies in terms of responsibility and bioethical issues. Their release require support on the action zone and comparability with indigenous species. Multidisciplinary research is focused on defining more precisely necessary genes and proteins to establish new free-cell systems, which may avoid possible side effects on the environment by the intrusion of transgenic or invasive species.^[2]

Microbial biodegradation

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Microbial biodegradation is the use of bioremediation and biotransformation methods to harness the naturally occurring ability of microbial xenobiotic metabolism to degrade, transform or accumulate environmental pollutants, including hydrocarbons (e.g. oil), polychlorinated biphenyls (PCBs), polyaromatic hydrocarbons (PAHs), heterocyclic compounds(such as pyridine or quinoline), pharmaceutical substances, radionuclides and metals.

Interest in the microbial biodegradation of pollutants has intensified in recent years,^[1][2] and recent major methodological breakthroughs have enabled detailed genomic, metagenomic, proteomic, bioinformatic and other high-throughput analyses of environmentally relevant microorganisms, providing new insights into biodegradative pathways and the ability of organisms to adapt to changing environmental conditions.

Biological processes play a major role in the removal of contaminants and take advantage of the catabolic versatility of microorganisms to degrade or convert such compounds. In environmental microbiology, genome-based global studies are increasing the understanding of metabolic and regulatory networks, as well as providing new information on the evolution of degradation pathways and molecular adaptation strategies to changing environmental conditions.

Contents

• 1Aerobic biodegradation of pollutants
• 2Anaerobic biodegradation of pollutants
• 3Bioavailability, chemotaxis, and transport of pollutants
• 4Oil biodegradation
• 5Cholesterol biodegradation
• 6Analysis of waste biotreatment
• 7Metabolic engineering and biocatalytic applications
• 8Fungal biodegradation
• 9See also
• 10References

Aerobic biodegradation of pollutants[edit]

The increasing amount of bacterial genomic data provides new opportunities for understanding the genetic and molecular bases of the degradation of organic pollutants. Aromatic compounds are among the most persistent of these pollutants and lessons can be learned from the recent genomic studies of Burkholderia xenovorans LB400 and Rhodococcus sp. strain RHA1, two of the largest bacterial genomes completely sequenced to date. These studies have helped expand our understanding of bacterial catabolism, non-catabolic physiological adaptation to organic compounds, and the evolution of large bacterial genomes. First, the metabolic pathways from phylogenetically diverse isolates are very similar with respect to overall organization. Thus, as originally noted in pseudomonads, a large number of "peripheral aromatic" pathways funnel a range of natural and xenobioticcompounds into a restricted number of "central aromatic" pathways. Nevertheless, these pathways are genetically organized in genus-specific fashions, as exemplified by the b-ketoadipate and Paa pathways. Comparative genomic studies further reveal that some pathways are more widespread than initially thought. Thus, the Box and Paa pathways illustrate the prevalence of non-oxygenolytic ring-cleavage strategies in aerobic aromatic degradation processes. Functional genomic studies have been useful in establishing that even organisms harboring high numbers of homologous enzymes seem to contain few examples of true redundancy. For example, the multiplicity of ring-cleaving dioxygenases in certain rhodococcal isolates may be attributed to the cryptic aromatic catabolism of different terpenoids and steroids. Finally, analyses have indicated that recent genetic flux appears to have played a more significant role in the evolution of some large genomes, such as LB400's, than others. However, the emerging trend is that the large gene repertoires of potent pollutant degraders such as LB400 and RHA1 have evolved principally through more ancient processes. That this is true in such phylogenetically diverse species is remarkable and further suggests the ancient origin of this catabolic capacity.^[3]

Anaerobic biodegradation of pollutants[edit]

Anaerobic microbial mineralization of recalcitrant organic pollutants is of great environmental significance and involves intriguing novel biochemical reactions.^[4] In particular, hydrocarbons and halogenated compounds have long been doubted to be degradable in the absence of oxygen, but the isolation of hitherto unknown anaerobic hydrocarbon-degrading and reductively dehalogenating bacteria during the last decades provided ultimate proof for these processes in nature. While such research involved mostly chlorinatedcompounds initially, recent studies have revealed reductive dehalogenation of bromine and iodine moieties in aromatic pesticides.^[5] Other reactions, such as biologically induced abiotic reduction by soil minerals,^[6] has been shown to deactivate relatively persistent aniline-based herbicides far more rapidly than observed in aerobic environments. Many novel biochemical reactions were discovered enabling the respective metabolic pathways, but progress in the molecular understanding of these bacteria was rather slow, since genetic systems are not readily applicable for most of them. However, with the increasing application of genomics in the field of environmental microbiology, a new and promising perspective is now at hand to obtain molecular insights into these new metabolic properties. Several complete genome sequences were determined during the last few years from bacteria capable of anaerobic organic pollutant degradation. The ~4.7 Mb genome of the facultative denitrifying Aromatoleum aromaticum strain EbN1 was the first to be determined for an anaerobic hydrocarbon degrader (using toluene or ethylbenzene as substrates). The genome sequence revealed about two dozen gene clusters (including several paralogs) coding for a complex catabolic network for anaerobic and aerobic degradation of aromatic compounds. The genome sequence forms the basis for current detailed studies on regulation of pathways and enzyme structures. Further genomes of anaerobic hydrocarbon degrading bacteria were recently completed for the iron-reducing species Geobacter metallireducens(accession nr. NC_007517) and the perchlorate-reducing Dechloromonas aromatica (accession nr. NC_007298), but these are not yet evaluated in formal publications. Complete genomes were also determined for bacteria capable of anaerobic degradation of halogenated hydrocarbons by halorespiration: the ~1.4 Mb genomes of Dehalococcoides ethenogenes strain 195 and Dehalococcoides sp. strain CBDB1 and the ~5.7 Mb genome of Desulfitobacterium hafniense strain Y51. Characteristic for all these bacteria is the presence of multiple paralogous genes for reductive dehalogenases, implicating a wider dehalogenating spectrum of the organisms than previously known. Moreover, genome sequences provided unprecedented insights into the evolution of reductive dehalogenation and differing strategies for niche adaptation.^[7]

Recently, it has become apparent that some organisms, including Desulfitobacterium chlororespirans, originally evaluated for halorespiration on chlorophenols, can also use certain brominated compounds, such as the herbicide bromoxynil and its major metabolite as electron acceptors for growth. Iodinated compounds may be dehalogenated as well, though the process may not satisfy the need for an electron acceptor.^[5]

Bioavailability, chemotaxis, and transport of pollutants[edit]

Bioavailability, or the amount of a substance that is physiochemically accessible to microorganisms is a key factor in the efficient biodegradation of pollutants. O'Loughlin et al.(2000)^[8] showed that, with the exception of kaolinite clay, most soil clays and cation exchange resins attenuated biodegradation of 2-picoline by Arthrobacter sp. strain R1, as a result of adsorption of the substrate to the clays. Chemotaxis, or the directed movement of motile organisms towards or away from chemicals in the environment is an important physiological response that may contribute to effective catabolism of molecules in the environment. In addition, mechanisms for the intracellular accumulation of aromatic molecules via various transport mechanisms are also important.^[9]

Oil biodegradation[edit]

General overview of microbial biodegradation of petroleum oil by microbial communities. Some microorganisms, such as A. borkumensis, are able to use hydrocarbons as their source for carbon in metabolism. They are able to oxidize the environmentally harmful hydrocarbons while producing harmless products, following the general equation C_nH_n + O₂ → H₂O + CO₂. In the figure, carbon is represented as yellow circles, oxygen as pink circles, and hydrogen as blue circles. This type of special metabolism allows these microbes to thrive in areas affected by oil spills and are important in the elimination of environmental pollutants.

Petroleum oil contains aromatic compounds that are toxic to most life forms. Episodic and chronic pollution of the environment by oil causes major disruption to the local ecological environment. Marine environments in particular are especially vulnerable, as oil spills near coastal regions and in the open sea are difficult to contain and make mitigation efforts more complicated. In addition to pollution through human activities, approximately 250 million litres of petroleum enter the marine environment every year from natural seepages.^[10] Despite its toxicity, a considerable fraction of petroleum oil entering marine systems is eliminated by the hydrocarbon-degrading activities of microbial communities, in particular by a recently discovered group of specialists, the hydrocarbonoclastic bacteria (HCB).^[11] Alcanivorax borkumensiswas the first HCB to have its genome sequenced.^[12] In addition to hydrocarbons, crude oil often contains various heterocyclic compounds, such as pyridine, which appear to be degraded by similar mechanisms to hydrocarbons.^[13]

Cholesterol biodegradation[edit]

Many synthetic steroidic compounds like some sexual hormones frequently appear in municipal and industrial wastewaters, acting as environmental pollutants with strong metabolic activities negatively affecting the ecosystems. Since these compounds are common carbon sources for many different microorganisms their aerobic and anaerobic mineralization has been extensively studied. The interest of these studies lies on the biotechnological applications of sterol transforming enzymes for the industrial synthesis of sexual hormones and corticoids. Very recently, the catabolism of cholesterol has acquired a high relevance because it is involved in the infectivity of the pathogen Mycobacterium tuberculosis (Mtb).^[1][14] Mtb causes tuberculosis disease, and it has been demonstrated that novel enzyme architectures have evolved to bind and modify steroid compounds like cholesterol in this organism and other steroid-utilizing bacteria as well.^[15][16] These new enzymes might be of interest for their potential in the chemical modification of steroid substrates.

Analysis of waste biotreatment[edit]

Sustainable development requires the promotion of environmental management and a constant search for new technologies to treat vast quantities of wastes generated by increasing anthropogenic activities. Biotreatment, the processing of wastes using living organisms, is an environmentally friendly, relatively simple and cost-effective alternative to physico-chemical clean-up options. Confined environments, such as bioreactors, have been engineered to overcome the physical, chemical and biological limiting factors of biotreatment processes in highly controlled systems. The great versatility in the design of confined environments allows the treatment of a wide range of wastes under optimized conditions. To perform a correct assessment, it is necessary to consider various microorganisms having a variety of genomes and expressed transcripts and proteins. A great number of analyses are often required. Using traditional genomic techniques, such assessments are limited and time-consuming. However, several high-throughput techniques originally developed for medical studies can be applied to assess biotreatment in confined environments.^[17]

Metabolic engineering and biocatalytic applications[edit]

The study of the fate of persistent organic chemicals in the environment has revealed a large reservoir of enzymatic reactions with a large potential in preparative organic synthesis, which has already been exploited for a number of oxygenases on pilot and even on industrial scale. Novel catalysts can be obtained from metagenomic libraries and DNA sequencebased approaches. Our increasing capabilities in adapting the catalysts to specific reactions and process requirements by rational and random mutagenesis broadens the scope for application in the fine chemical industry, but also in the field of biodegradation. In many cases, these catalysts need to be exploited in whole cell bioconversions or in fermentations, calling for system-wide approaches to understanding strain physiology and metabolism and rational approaches to the engineering of whole cells as they are increasingly put forward in the area of systems biotechnology and synthetic biology.^[18]

Fungal biodegradation[edit]

In the ecosystem, different substrates are attacked at different rates by consortia of organisms from different kingdoms. Aspergillus and other moulds play an important role in these consortia because they are adept at recycling starches, hemicelluloses, celluloses, pectins and other sugar polymers. Some aspergilli are capable of degrading more refractory compounds such as fats, oils, chitin, and keratin. Maximum decomposition occurs when there is sufficient nitrogen, phosphorus and other essential inorganic nutrients. Fungi also provide food for many soil organisms.^[19]

For Aspergillus the process of degradation is the means of obtaining nutrients. When these moulds degrade human-made substrates, the process usually is called biodeterioration. Both paper and textiles (cotton, jute, and linen) are particularly vulnerable to Aspergillus degradation. Our artistic heritage is also subject to Aspergillus assault. To give but one example, after Florence in Italy flooded in 1969, 74% of the isolates from a damaged Ghirlandaio fresco in the Ognissanti church were Aspergillus versicolor.^[20]

The Invisible Workforce

Bioremediation uses micro-organisms to reduce pollution through the biological degradation of pollutants into non-toxic substances. This can involve either aerobic or anaerobic micro-organisms that often use this breakdown as an energy source. There are three categories of bioremediation techniques: in situ land treatment for soil and groundwater; biofiltration of the air; and bioreactors, predominantly involved in water treatment.

Soil

Industrial soils can be polluted by a variety of sources, such as chemical spillages, or the accumulation of heavy metals from industrial emissions. Agricultural soils can become contaminated due to pesticide use or via the heavy metals contained within agricultural products.

A visible example of where bioremediation has been used to good effect can be found in London’s Olympic Park. The grounds that held the 2012 Olympics had previously been heavily polluted, after hundreds of years of industrial activity. Bioremediation cleaned 1.7 million cubic metres of heavily polluted soil to turn this brownfield site into one containing sports facilities surrounded by 45 hectares of wildlife habitats. Groundwater polluted with ammonia was cleaned using a new bioremediation technique that saw archaeal microbes breaking down the ammonia into harmless nitrogen gas. The converted park marked the London 2012 Olympic and Paralympic Games as the “greenest” and most sustainable games ever held, only possible with bioremediation techniques.

While some soil cleaning techniques require the introduction of new microbes, ‘biostimulation’ techniques increase natural degradation processes by stimulating the growth of microbes already present. Natural biodegradation processes can be limited by many factors, including nutrient availability, temperature, or moisture content in the soil. Biostimulation techniques overcome these limitations, providing microbes with the resources they need, which increases their proliferation and leads to an increased rate of degradation.

Cleaning up oil-polluted soil is an example of where stimulating microbial growth can be used to good effect. Research has shown that poultry droppings can be used as a biostimulating agent, providing nitrogen and phosphorous to the system, which stimulates the natural growth rate of oil-degrading bacteria. Systems like these may prove cheaper and more environmentally friendly than current chemical treatment options.

Air

Air is polluted by a variety of volatile organic compounds created by a range of industrial processes. While chemical scrubbing has been used to clean gases emitted from chimneys, the newer technique of ‘biofiltration’ is helping to clean industrial gases. This method involves passing polluted air over a replaceable culture medium containing micro-organisms that degrade contaminates into products such as carbon dioxide, water or salts. Biofiltration is the only biological technique currently available to remediate airborne pollutants.

Water

In the UK, access to clean, potable water and modern sanitation is something we take for granted. However, there are billions of people on Earth for which this is a luxury. The WHO estimate that each year 842,000 people die as a result of diarrhoeal diseases, many of which could be prevented if they had access to clean water and proper sanitation. Around 2.6 billion people lack any sanitation, with over 200 million tons of human waste untreated every year.

Sewage treatment plants are the largest and most important bioremediation enterprise in the world. In the UK, 11 billion litres of wastewater are collected and treated everyday. Major components of raw sewage are suspended solids, organic matter, nitrogen and phosphorus.

Wastewater entering a treatment plant is aerated to provide oxygen to bacteria that degrade organic material and pollutants. Microbes consume the organic contaminants and bind the less soluble fractions, which can then be filtered off. Toxic ammonia is reduced to nitrogen gas and released into the atmosphere.

The Future

Bioremediation is not a new technique, but as our knowledge of the underlying microbial reactions grow, our ability to use them to our advantage increases. Frequently, bioremediation requires fewer resources and less energy than conventional technology, and doesn’t accumulate hazardous by-products as waste. Bioremediation has technical and cost advantages, although it can often take more time to carry out than traditional methods.

Bioremediation can be tailored to the needs of the polluted site in question and the specific microbes needed to break down the pollutant are encouraged by selecting the limiting factor needed to promote their growth. This tailoring may be further improved by using synthetic biology tools to pre-adapt microbes to the pollution in the environment to which they are to be added.

Pollution is a threat to our health and damages the environment, affecting wildlife and the sustainability of our planet. Damage to our soils affects our ability to grow food, summarised in our policy briefing on Food Security. Bioremediation can help to reduce and remove the pollution we produce, to provide clean water, air and healthy soils for future generations.