Bioremediation
Overview
 
Bioremediation is the use of microorganism
Microorganism
A microorganism or microbe is a microscopic organism that comprises either a single cell , cell clusters, or no cell at all...

 metabolism to remove pollutants. Technologies can be generally classified as in situ
In situ
In situ is a Latin phrase which translated literally as 'In position'. It is used in many different contexts.-Aerospace:In the aerospace industry, equipment on board aircraft must be tested in situ, or in place, to confirm everything functions properly as a system. Individually, each piece may...

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 phytoremediation
Phytoremediation
Phytoremediation Phytoremediation Phytoremediation (from the Ancient Greek , and Latin (restoring balance or remediation) describes the treatment of environmental problems (bioremediation) through the use of plants that mitigate the environmental problem without the need to excavate the...

, bioventing, bioleaching
Bioleaching
Bioleaching is the extraction of specific metals from their ores through the use of living organisms. This is much cleaner than the traditional heap leaching using cyanide...

, landfarming
Landfarming
Land Farming is a bioremediation treatment process that is performed in the upper soil zone or in biotreatment cells. Contaminated soils, sediments, or sludges are incorporated into the soil surface and periodically turned over to aerate the mixture....

, bioreactor
Bioreactor
A bioreactor may refer to any manufactured or engineered device or system that supports a biologically active environment. In one case, a bioreactor is a vessel in which a chemical process is carried out which involves organisms or biochemically active substances derived from such organisms. This...

, composting, bioaugmentation
Bioaugmentation
Bioaugmentation is the introduction of a group of natural microbial strains or a genetically engineered variant to treat contaminated soil or water....

, rhizofiltration
Rhizofiltration
Rhizofiltration is a form of bioremediation that involves filtering water through a mass of roots to remove toxic substances or excess nutrients.-Overview:...

, and biostimulation
Biostimulation
Biostimulation involves the modification of the environment to stimulate existing bacteria capable of bioremediation. This can be done by addition of various forms of rate limiting nutrients and electron acceptors, such as phosphorus, nitrogen, oxygen, or carbon...

.

Bioremediation can occur on its own (natural attenuation or intrinsic bioremediation) or can be spurred on via the addition of fertilizers to increase the bioavailability within the medium (biostimulation).
Encyclopedia
Bioremediation is the use of microorganism
Microorganism
A microorganism or microbe is a microscopic organism that comprises either a single cell , cell clusters, or no cell at all...

 metabolism to remove pollutants. Technologies can be generally classified as in situ
In situ
In situ is a Latin phrase which translated literally as 'In position'. It is used in many different contexts.-Aerospace:In the aerospace industry, equipment on board aircraft must be tested in situ, or in place, to confirm everything functions properly as a system. Individually, each piece may...

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 phytoremediation
Phytoremediation
Phytoremediation Phytoremediation Phytoremediation (from the Ancient Greek , and Latin (restoring balance or remediation) describes the treatment of environmental problems (bioremediation) through the use of plants that mitigate the environmental problem without the need to excavate the...

, bioventing, bioleaching
Bioleaching
Bioleaching is the extraction of specific metals from their ores through the use of living organisms. This is much cleaner than the traditional heap leaching using cyanide...

, landfarming
Landfarming
Land Farming is a bioremediation treatment process that is performed in the upper soil zone or in biotreatment cells. Contaminated soils, sediments, or sludges are incorporated into the soil surface and periodically turned over to aerate the mixture....

, bioreactor
Bioreactor
A bioreactor may refer to any manufactured or engineered device or system that supports a biologically active environment. In one case, a bioreactor is a vessel in which a chemical process is carried out which involves organisms or biochemically active substances derived from such organisms. This...

, composting, bioaugmentation
Bioaugmentation
Bioaugmentation is the introduction of a group of natural microbial strains or a genetically engineered variant to treat contaminated soil or water....

, rhizofiltration
Rhizofiltration
Rhizofiltration is a form of bioremediation that involves filtering water through a mass of roots to remove toxic substances or excess nutrients.-Overview:...

, and biostimulation
Biostimulation
Biostimulation involves the modification of the environment to stimulate existing bacteria capable of bioremediation. This can be done by addition of various forms of rate limiting nutrients and electron acceptors, such as phosphorus, nitrogen, oxygen, or carbon...

.

Bioremediation can occur on its own (natural attenuation or intrinsic bioremediation) or can be spurred on via the addition of fertilizers to increase the bioavailability within the medium (biostimulation). 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.

Not all contaminants, however, are easily treated by bioremediation using microorganisms. For example, heavy metals
Heavy metals
A heavy metal is a member of a loosely-defined subset of elements that exhibit metallic properties. It mainly includes the transition metals, some metalloids, lanthanides, and actinides. Many different definitions have been proposed—some based on density, some on atomic number or atomic weight,...

 such as cadmium
Cadmium
Cadmium is a chemical element with the symbol Cd and atomic number 48. This soft, bluish-white metal is chemically similar to the two other stable metals in group 12, zinc and mercury. Similar to zinc, it prefers oxidation state +2 in most of its compounds and similar to mercury it shows a low...

 and lead
Lead
Lead is a main-group element in the carbon group with the symbol Pb and atomic number 82. Lead is a soft, malleable poor metal. It is also counted as one of the heavy metals. Metallic lead has a bluish-white color after being freshly cut, but it soon tarnishes to a dull grayish color when exposed...

 are not readily absorbed or captured by microorganisms. The assimilation of metals such as mercury
Mercury (element)
Mercury is a chemical element with the symbol Hg and atomic number 80. It is also known as quicksilver or hydrargyrum...

 into the food chain
Food chain
A food web depicts feeding connections in an ecological community. Ecologists can broadly lump all life forms into one of two categories called trophic levels: 1) the autotrophs, and 2) the heterotrophs...

 may worsen matters. Phytoremediation
Phytoremediation
Phytoremediation Phytoremediation Phytoremediation (from the Ancient Greek , and Latin (restoring balance or remediation) describes the treatment of environmental problems (bioremediation) through the use of plants that mitigate the environmental problem without the need to excavate the...

 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. The heavy metals in the harvested biomass may be further concentrated by incineration or even recycled for industrial use.

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
Biotransformation
Biotransformation is the chemical modification made by an organism on a chemical compound. If this modification ends in mineral compounds like CO2, NH4+, or H2O, the biotransformation is called mineralisation....

 processes.

Genetic engineering approaches

The use of genetic engineering
Genetic engineering
Genetic engineering, also called genetic modification, is the direct human manipulation of an organism's genome using modern DNA technology. It involves the introduction of foreign DNA or synthetic genes into the organism of interest...

 to create organisms specifically designed for bioremediation has great potential. The bacterium
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...

 Deinococcus radiodurans
Deinococcus radiodurans
Deinococcus radiodurans is an extremophilic bacterium, one of the most radioresistant organisms known. It can survive cold, dehydration, vacuum, and acid, and is therefore known as a polyextremophile and has been listed as the world's toughest bacterium in The Guinness Book Of World Records.-Name...

(the most radioresistant
Radioresistance
Radioresistance is the property of organisms that are capable of living in environments with very high levels of ionizing radiation.Radioresistance is surprisingly high in many organisms, in contrast to previously held views...

 organism known) has been modified to consume and digest toluene
Toluene
Toluene, formerly known as toluol, is a clear, water-insoluble liquid with the typical smell of paint thinners. It is a mono-substituted benzene derivative, i.e., one in which a single hydrogen atom from the benzene molecule has been replaced by a univalent group, in this case CH3.It is an aromatic...

 and ion
Ion
An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge. The name was given by physicist Michael Faraday for the substances that allow a current to pass between electrodes in a...

ic mercury
Mercury (element)
Mercury is a chemical element with the symbol Hg and atomic number 80. It is also known as quicksilver or hydrargyrum...

 from highly radioactive nuclear waste.

Most commonly, the process is misunderstood. The microbes are ever-present in any given context and are generally referred to as "normal microbial flora". During bioremediation (biodegradation) processes, fertilizer/nutrient supplementation is introduced to the environments in efforts to maximize growth and production potential. Common misbelief is that microbes are transported and dispersed into an unadulterated environment.

Mycoremediation

Mycoremediation is a form of bioremediation in which fungi are used to decontaminate the area. The term mycoremediation
Mycoremediation
Mycoremediation, a phrase coined by Paul Stamets, is a form of bioremediation, the process of using fungi to degrade or sequester contaminants in the environment. Stimulating microbial and enzyme activity, mycelium reduces toxins in-situ...

refers specifically to the use of fungal mycelia
Mycelium
thumb|right|Fungal myceliaMycelium is the vegetative part of a fungus, consisting of a mass of branching, thread-like hyphae. The mass of hyphae is sometimes called shiro, especially within the fairy ring fungi. Fungal colonies composed of mycelia are found in soil and on or within many other...

 in bioremediation.

One of the primary roles of fungi in the ecosystem
Ecosystem
An ecosystem is a biological environment consisting of all the organisms living in a particular area, as well as all the nonliving , physical components of the environment with which the organisms interact, such as air, soil, water and sunlight....

 is decomposition
Decomposition
Decomposition is the process by which organic material is broken down into simpler forms of matter. The process is essential for recycling the finite matter that occupies physical space in the biome. Bodies of living organisms begin to decompose shortly after death...

, which is performed by the mycelium. The mycelium secretes extracellular enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...

s and acid
Acid
An acid is a substance which reacts with a base. Commonly, acids can be identified as tasting sour, reacting with metals such as calcium, and bases like sodium carbonate. Aqueous acids have a pH of less than 7, where an acid of lower pH is typically stronger, and turn blue litmus paper red...

s that break down lignin
Lignin
Lignin or lignen is a complex chemical compound most commonly derived from wood, and an integral part of the secondary cell walls of plants and some algae. The term was introduced in 1819 by de Candolle and is derived from the Latin word lignum, meaning wood...

 and cellulose
Cellulose
Cellulose is an organic compound with the formula , a polysaccharide consisting of a linear chain of several hundred to over ten thousand β linked D-glucose units....

, the two main building blocks of plant fiber. These are organic compounds composed of long chains of carbon
Carbon
Carbon is the chemical element with symbol C and atomic number 6. As a member of group 14 on the periodic table, it is nonmetallic and tetravalent—making four electrons available to form covalent chemical bonds...

 and hydrogen
Hydrogen
Hydrogen is the chemical element with atomic number 1. It is represented by the symbol H. With an average atomic weight of , hydrogen is the lightest and most abundant chemical element, constituting roughly 75% of the Universe's chemical elemental mass. Stars in the main sequence are mainly...

, 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
VX (nerve agent)
VX, IUPAC name O-ethyl S-[2-ethyl] methylphosphonothioate, is an extremely toxic substance whose only application is in chemical warfare as a nerve agent. As a chemical weapon, it is classified as a weapon of mass destruction by the United Nations in UN Resolution 687...

 and sarin
Sarin
Sarin, or GB, is an organophosphorus compound with the formula [2CHO]CH3PF. It is a colorless, odorless liquid, which is used as a chemical weapon. It has been classified as a weapon of mass destruction in UN Resolution 687...

.

In one conducted experiment, a plot of soil contaminated with diesel oil was inoculated with mycelia of oyster mushroom
Oyster mushroom
Pleurotus ostreatus, the oyster mushroom, is a common edible mushroom. It was first cultivated in Germany as a subsistence measure during World War I and is now grown commercially around the world for food. However, the first documented cultivation was by Kaufert There is some question about the...

s; traditional bioremediation techniques (bacteria) were used on control plots. After four weeks, more than 95% of many of the PAH (polycyclic aromatic hydrocarbon
Polycyclic aromatic hydrocarbon
Polycyclic aromatic hydrocarbons , also known as poly-aromatic hydrocarbons or polynuclear aromatic hydrocarbons, are potent atmospheric pollutants that consist of fused aromatic rings and do not contain heteroatoms or carry substituents. Naphthalene is the simplest example of a PAH...

s) 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
Petroleum
Petroleum or crude oil is a naturally occurring, flammable liquid consisting of a complex mixture of hydrocarbons of various molecular weights and other liquid organic compounds, that are found in geologic formations beneath the Earth's surface. Petroleum is recovered mostly through oil drilling...

), as well as chlorinated compounds (certain persistent pesticides; Battelle, 2000).

Mycofiltration
Mycofiltration
Mycofiltration is the process of using mushroom mycelium mats as biological filters. The term was coined by mycologist Paul Stamets.Stamets originally came up with the technique to control E. coli in the water outflow from his property. After planting a mushroom bed in the gulch where the water was...

is a similar process, using fungal mycelia to filter toxic waste and microorganism
Microorganism
A microorganism or microbe is a microscopic organism that comprises either a single cell , cell clusters, or no cell at all...

s from water in soil.

Advantages

There are a number of cost/efficiency advantages to bioremediation, which can be employed in areas that are inaccessible without excavation
Earthworks (engineering)
Earthworks are engineering works created through the moving or processing of quantities of soil or unformed rock.- Civil engineering use :Typical earthworks include roads, railway beds, causeways, dams, levees, canals, and berms...

. For example, hydrocarbon
Hydrocarbon
In organic chemistry, a hydrocarbon is an organic compound consisting entirely of hydrogen and carbon. Hydrocarbons from which one hydrogen atom has been removed are functional groups, called hydrocarbyls....

 spills (specifically, petrol spills) or certain chlorinated solvents may contaminate groundwater
Groundwater
Groundwater is water located beneath the ground surface in soil pore spaces and in the fractures of rock formations. A unit of rock or an unconsolidated deposit is called an aquifer when it can yield a usable quantity of water. The depth at which soil pore spaces or fractures and voids in rock...

, and introducing the appropriate electron acceptor or electron donor amendment, as appropriate, may significantly reduce contaminant concentration
Concentration
In chemistry, concentration is defined as the abundance of a constituent divided by the total volume of a mixture. Four types can be distinguished: mass concentration, molar concentration, number concentration, and volume concentration...

s after a long time allowing for acclimation. This is typically much less expensive than excavation followed by disposal elsewhere, incineration
Incineration
Incineration is a waste treatment process that involves the combustion of organic substances contained in waste materials. Incineration and other high temperature waste treatment systems are described as "thermal treatment". Incineration of waste materials converts the waste into ash, flue gas, and...

 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.

Monitoring bioremediation

The process of bioremediation can be monitored indirectly by measuring the Oxidation Reduction Potential or redox
Redox
Redox reactions describe all chemical reactions in which atoms have their oxidation state changed....

 in soil
Soil
Soil is a natural body consisting of layers of mineral constituents of variable thicknesses, which differ from the parent materials in their morphological, physical, chemical, and mineralogical characteristics...

 and groundwater, together with pH
PH
In chemistry, pH is a measure of the acidity or basicity of an aqueous solution. Pure water is said to be neutral, with a pH close to 7.0 at . Solutions with a pH less than 7 are said to be acidic and solutions with a pH greater than 7 are basic or alkaline...

, temperature, oxygen
Oxygen
Oxygen is the element with atomic number 8 and represented by the symbol O. Its name derives from the Greek roots ὀξύς and -γενής , because at the time of naming, it was mistakenly thought that all acids required oxygen in their composition...

 content, electron acceptor/donor concentrations, and concentration of breakdown products (e.g. carbon dioxide
Carbon dioxide
Carbon dioxide is a naturally occurring chemical compound composed of two oxygen atoms covalently bonded to a single carbon atom...

). This table shows the (decreasing) biological breakdown rate as function of the redox potential.
Process Reaction  Redox potential (Eh in mV
Volt
The volt is the SI derived unit for electric potential, electric potential difference, and electromotive force. The volt is named in honor of the Italian physicist Alessandro Volta , who invented the voltaic pile, possibly the first chemical battery.- Definition :A single volt is defined as the...

aerobic
Aerobic organism
An aerobic organism or aerobe is an organism that can survive and grow in an oxygenated environment.Faculitative anaerobes grow and survive in an oxygenated environment and so do aerotolerant anaerobes.-Glucose:...

:
O2 + 4e + 4H+ → 2H2O 600 ~ 400
anaerobic
Hypoxia (environmental)
Hypoxia, or oxygen depletion, is a phenomenon that occurs in aquatic environments as dissolved oxygen becomes reduced in concentration to a point where it becomes detrimental to aquatic organisms living in the system...

:
 
 
denitrification
Denitrification
Denitrification is a microbially facilitated process of nitrate reduction that may ultimately produce molecular nitrogen through a series of intermediate gaseous nitrogen oxide products....

2NO3 + 10e + 12H+ → N2 + 6H2O 500 ~ 200
  manganese
Manganese
Manganese is a chemical element, designated by the symbol Mn. It has the atomic number 25. It is found as a free element in nature , and in many minerals...

 IV reduction
  MnO2 + 2e + 4H+ → Mn2+ + 2H2O     400 ~ 200
iron
Iron
Iron is a chemical element with the symbol Fe and atomic number 26. It is a metal in the first transition series. It is the most common element forming the planet Earth as a whole, forming much of Earth's outer and inner core. It is the fourth most common element in the Earth's crust...

 III reduction
Fe(OH)3 + e + 3H+ → Fe2+ + 3H2O 300 ~ 100
sulfate
Sulfate
In inorganic chemistry, a sulfate is a salt of sulfuric acid.-Chemical properties:...

 reduction
SO42− + 8e +10 H+ → H2S + 4H2O 0 ~ −150
fermentation
Fermentation (biochemistry)
Fermentation is the process of extracting energy from the oxidation of organic compounds, such as carbohydrates, using an endogenous electron acceptor, which is usually an organic compound. In contrast, respiration is where electrons are donated to an exogenous electron acceptor, such as oxygen,...

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
    Sample (statistics)
    In statistics, a sample is a subset of a population. Typically, the population is very large, making a census or a complete enumeration of all the values in the population impractical or impossible. The sample represents a subset of manageable size...

     enough points on and around the contaminated site to be able to determine contours
    Contour line
    A contour line of a function of two variables is a curve along which the function has a constant value. In cartography, a contour line joins points of equal elevation above a given level, such as mean sea level...

     of equal redox potential. Contouring is usually done using specialised software, e.g. using Kriging
    Kriging
    Kriging is a group of geostatistical techniques to interpolate the value of a random field at an unobserved location from observations of its value at nearby locations....

     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.

See also

  • Biodegradation
    Biodegradation
    Biodegradation or biotic degradation or biotic decomposition is the chemical dissolution of materials by bacteria or other biological means...

  • Bioleaching
    Bioleaching
    Bioleaching is the extraction of specific metals from their ores through the use of living organisms. This is much cleaner than the traditional heap leaching using cyanide...

  • Biosurfactant
  • Dutch standards
    Dutch standards
    Dutch Standards are environmental pollutant reference values used in environmental remediation, investigation and cleanup....

  • Folkewall
    Folkewall
    The Folkewall is a construction with the dual functions of growing plants and purifying waste water. It was designed by Folke Günther in Sweden. Inspired by the "Sanitas wall" at Dr Gösta Nilsson's Sanitas farm project in Botswana, this technique makes an efficient use of space by fulfilling two...

  • List of environment topics
  • Living machines
    Living machines
    Living Machine is a trademark and brand name for a patented form of ecological wastewater treatment designed to mimic the cleansing functions of wetlands. The latest generation of the technology is based on fixed-film ecology and the ecological processes of a natural tidal wetland, one of nature’s...

  • Living wall
    Living wall
    A green wall is a wall, either free-standing or part of a building, that is partially or completely covered with vegetation and, in some cases, soil or an inorganic growing medium. The concept of the green wall dates back to 600 BC with the Hanging Gardens of Babylon...

  • Microbial biodegradation
    Microbial biodegradation
    Interest in the microbial biodegradation of pollutants has intensified in recent years as humanity strives to find sustainable ways to clean up contaminated environments...

  • Mycoremediation
    Mycoremediation
    Mycoremediation, a phrase coined by Paul Stamets, is a form of bioremediation, the process of using fungi to degrade or sequester contaminants in the environment. Stimulating microbial and enzyme activity, mycelium reduces toxins in-situ...

  • Phytoremediation
    Phytoremediation
    Phytoremediation Phytoremediation Phytoremediation (from the Ancient Greek , and Latin (restoring balance or remediation) describes the treatment of environmental problems (bioremediation) through the use of plants that mitigate the environmental problem without the need to excavate the...

  • Pseudomonas putida
    Pseudomonas putida
    Pseudomonas putida is a gram-negative rod-shaped saprotrophic soil bacterium. Based on 16S rRNA analysis, P. putida has been placed in the P. putida group, to which it lends its name....

    (used for degrading oil)
  • US Microbics
    US Microbics
    U.S. Microbics is a biotech holding company. Nicknamed "Bugs", it owns several subsidiaries that utilize its patented microbe technology. Bugs is notable because it is the first US Corporation to build a business around the various commercial uses for microorganisms.Bugs, engages through its...

  • Xenocatabolism
    Xenocatabolism
    Xenocatabolism is a concept in bioremediation that was introduced by Dr. Aubrey de Grey on May 29, 2007, at the Googleplex Google TechTalks. Dr. de Grey posited that there are microbes that feed on substances such as amyloid, cholesterol and other related substances in places that are full of human...



External links

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