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A range of processes mediated by plants or algae are useful in treating environmental problems:

Phytoextraction
See also: Phytoextraction process

Phytoextraction (or phytoaccumulation or phytosequestration) uses plants or algae to remove contaminants from soil or water into harvestable plant biomass. The roots take up substances from the soil or water and concentrate it above ground in the plant biomass Organisms that can uptake extremely high amounts of contaminants from the soil are called hyperaccumulators. Phytoextraction can also be performed by plants (e.g.Populus and Salix) that take up lower levels of pollutants, but due to their high growth rate and biomass production, may remove a considerable amount of contaminants from the soil. Phytoextraction has been growing rapidly in popularity worldwide for the last twenty years or so. In general, this process has been tried more often for extracting heavy metals than for organics. At the time of disposal, contaminants are typically concentrated in the much smaller volume of the plant matter than in the initially contaminated soil or sediment. After harvest, a lower level of the contaminant will remain in the soil, so the growth/harvest cycle must usually be repeated through several crops to achieve a significant cleanup. After the process, the cleaned soil can support other vegetation. Mining of these extracted metals through phytomining, is also being experimented with as a way of recovering the material.

Two versions

 * natural hyper-accumulation, where plants naturally take up the contaminants in soil unassisted. In many cases natural hyperaccumulators are metallophyte plants that can tolerate and incorporate high levels of toxic metals.
 * induced or assisted hyper-accumulation, where a conditioning fluid containing a chelator or another agent is added to soil to increase metal solubility or mobilization so that the plants can absorb them more easily.

Examples
See also: 'Table of hyperaccumulators'

Examples of plants that are known to accumulate the following contaminants:
 * Arsenic, using the sunflower (Helianthus annuus), or the Chinese Brake fern (Pteris vittata).
 * Cadmium, using willow (Salix viminalis): In 1999, one research experiment performed by Maria Greger and Tommy Landberg suggested willow has a significant potential as a phytoextractor of cadmium (Cd), zinc (Zn), and copper (Cu), as willow has some specific characteristics like high transport capacity of heavy metals from root to shoot and huge amount of biomass production; can be used also for production of bio energy in the biomass energy power plant.
 * Cadmium and zinc, using alpine pennycress (Thlaspi caerulescens), a hyperaccumulator of these metals at levels that would be toxic to many plants. On the other hand, the presence of copper seems to impair its growth (see table for reference).
 * Lead, using Indian mustard (Brassica juncea), ragweed (Ambrosia artemisiifolia), hemp dogbane (Apocynum cannabinum), or poplar trees, which sequester lead in their biomass.
 * Salt-tolerant (moderately halophytic) barley and/or sugar beets are commonly used for the extraction of sodium chloride (common salt) to reclaim fields that were previously flooded by sea water.
 * Caesium-137 and strontium-90 were removed from a pond using sunflowers after the Chernobyl accident.
 * Mercury, selenium and organic pollutants such as polychlorinated biphenyls (PCBs) have been removed from soils by transgenic plants containing genes for bacterial enzymes.

Phytostabilization
Phytostabilization reduces the mobility of substances in the environment, for example, by limiting the leaching of substances from the soil. It focuses on the long term stabilization and containment of the pollutant. The plant immobilizes the pollutants by binding them to soil particles making them less available for plant or human uptake. Unlike phytoextraction, phytostabilization focuses mainly on sequestering pollutants in soil near the roots but not in plant tissues. Pollutants become less bioavailable, resulting in reduced exposure. The plants can also excrete a substance that produces a chemical reaction, converting the heavy metal pollutant into a less toxic form. An example application of phytostabilization is using a vegetative cap to stabilize and contain mine tailings.

Phytodegradation
Phytodegradation (also called phytotransformation) uses plants or microorganisms to degrade organic pollutants in the soil or within the body of the plant. The organic compounds are broken down by enzymes that the plant roots secrete and these molecules are then taken up by the plant and released through transpiration.

Phytotransformation
Phytotransformation results in the chemical modification of environmental substances as a direct result of plant metabolism, often resulting in their inactivation, degradation (phytodegradation), or immobilization (phytostabilization). In the case of organic pollutants, such as pesticides, explosives, solvents, industrial chemicals, and other xenobiotic substances, certain plants, such as Cannas, render these substances non-toxic by their metabolism. In other cases, microorganisms living in association with plant roots may metabolize these substances in soil or water. These complex and recalcitrant compounds cannot be broken down to basic molecules (water, carbon-dioxide, etc.) by plant molecules, and, hence, the term phytotransformation represents a change in chemical structure without complete breakdown of the compound. The term "Green Liver" is used to describe phytotransformation, as plants behave analogously to the human liver when dealing with these xenobiotic compounds (foreign compound/pollutant). After uptake of the xenobiotics, plant enzymes increase the polarity of the xenobiotics by adding functional groups such as hydroxyl groups (-OH).

This is known as Phase I metabolism, similar to the way that the human liver increases the polarity of drugs and foreign compounds (drug metabolism). Whereas in the human liver enzymes such as cytochrome P450s are responsible for the initial reactions, in plants enzymes such as peroxidases, phenoloxidases, esterases and nitroreductases carry out the same role.

In the second stage of phytotransformation, known as Phase II metabolism, plant biomolecules such as glucose and amino acids are added to the polarized xenobiotic to further increase the polarity (known as conjugation). This is again similar to the processes occurring in the human liver where glucuronidation (addition of glucose molecules by the UGT class of enzymes, e.g. UGT1A1) and glutathione addition reactions occur on reactive centres of the xenobiotic.

Phase I and II reactions serve to increase the polarity and reduce the toxicity of the compounds, although many exceptions to the rule are seen. The increased polarity also allows for easy transport of the xenobiotic along aqueous channels.

In the final stage of phytotransformation (Phase III metabolism), a sequestration of the xenobiotic occurs within the plant. The xenobiotics polymerize in a lignin-like manner and develop a complex structure that is sequestered in the plant. This ensures that the xenobiotic is safely stored, and does not affect the functioning of the plant. However, preliminary studies have shown that these plants can be toxic to small animals (such as snails), and, hence, plants involved in phytotransformation may need to be maintained in a closed enclosure.

Hence, the plants reduce toxicity (with exceptions) and sequester the xenobiotics in phytotransformation. Trinitrotoluene phytotransformation has been extensively researched and a transformation pathway has been proposed.

Phytostimulation
Phytostimulation is the enhancement of soil microbial activity for the degradation of contaminants, typically by organisms that associate with roots. This process is also known as rhizosphere degradation. Phytostimulation can also involve aquatic plants supporting active populations of microbial degraders, as in the stimulation of atrazine degradation by hornwort.

Phytovolatilization
Phytovolatilization is the removal of substances from soil or water with release into the air, sometimes as a result of phytotransformation to more volatile and/or less polluting substances.

Rhizofiltration
Rhizofiltration is a process that filters water through a mass of roots to remove toxic substances or excess nutrients. The pollutants remain absorbed in or adsorbed to the roots.

Biological hydraulic containment
Biological hydraulic containment occurs when some plants, like poplars, draw water upwards through the soil into the roots and out through the plant, which decreases the movement of soluble contaminants downwards, deeper into the site and into the groundwater.

Phytodesalination
Phytodesalination uses halophytes (plants adapted to saline soil) to extract salt from the soil to improve its fertility