Phytoremediation

Phytoremediation describes the treatment of environmental problems (bioremediation) through the use of plants.

The word's etymology comes from the Greek φυτο (phyto) = plant, and Latin « remedium » = restoring balance, or remediating. Phytoremediation consists in depolluting contaminated soils, water or air with plants able to contain, degrade or eliminate metals, pesticides, solvents, explosives, crude oil and its derivatives, and various other contaminants, from the mediums that contain them.

It is clean, efficient, inexpensive and non-environmentally disruptive, as opposed to processes that require excavation of soil. The definitive textbook on phytoremediation was published in 2003 with contributed, peer reviewed articles from all major research groups involved in phytoremediation research (Phytoremediation: Transformation and Control of Contaminants, edited by Steven C. McCutcheon and Jerald L. Schnoor).

Various phytoremediation processes
A range of processes mediated by plants are useful in treating environmental problems:
 * Phytoextraction - uptake and concentration of substances from the environment into the plant biomass.
 * Phytostabilization - reducing the mobility of substances in the environment, for example by limiting the leaching of substances from the soil.
 * Phytotransformation - chemical modification of environmental substances as a direct result of plant metabolism, often resulting in their inactivation, degradation (phytodegradation) or immobilization (phytostabilization).
 * Phytostimulation - 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.
 * Phytovolatilization - 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 - filtering water through a mass of roots to remove toxic substances or excess nutrients. The pollutants remain absorbed in or adsorbed to the roots.

Phytoextraction
Phytoextraction (or phytoaccumulation) uses plants to remove contaminants from soils, sediments or water into harvestable plant biomass. Phytoextraction has been growing rapidly in popularity world-wide for the last twenty years or so. Generally 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. 'Mining with plants', or phytomining, is also being experimented with.

The plants absorb contaminants through the root system and store them in the root biomass and/or transport them up into the stems and/or leaves. A living plant may continue to absorb contaminants until it is harvested. 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.

Two versions of phytoextraction:
 * natural hyper-accumulation, where plants naturally take up the contaminants in soil unassisted, and
 * induced or assisted hyper-accumulation, in which 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 of phytoextraction from soils (see also 'Table of hyperaccumulators'):
 * Arsenic, using the Sunflower (Helianthus annuus), or the Chinese Brake fern ("Pteris spp"], a hyperaccumulator. Chinese Brake fern stores arsenic in its leaves.
 * 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 its 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.
 * Uranium, using sunflowers, as used 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 focuses on long-term stabilization and containment of the pollutant. For example, the plant's presence can reduce wind erosion, or the plant's roots can prevent water erosion, immobilize the pollutants by adsorption or accumulation, and provide a zone around the roots where the pollutant can precipitate and stabilize. Unlike phytoextraction, phytostabilization mainly focuses on sequestering pollutants in soil near the roots but not in plant tissues. Pollutants become less bioavailable and livestock, wildlife, and human exposure is reduced. An example application of this sort is using a vegetative cap to stabilize and contain mine tailings.

Phytotransformation
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, carbondioxide 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 Model" is used to describe phytotransformation, as plants behave similar 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 the human liver increases the polarity of drugs and foreign compounds (Drug Metabolism. While in the human liver, enzymes like Cytochrome P450s are responsible for the initial reactions, in plants enzymes such as 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 wherein glucuronidation (addition of glucose molecules by the UGT (e.g. UGT1A1) class of enzymes) and glutathione addition reactions occur on reactive centers 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 at least in the case of the human liver. 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 get a complex structure which is sequestered in the plant. This ensures that the xenobiotic is safely stored in the plant, 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. The human liver differs from plants in Phase III metabolism, since the liver can transport the xenobiotics into the bile for eventual excretion. Since plants have no excretory mechanisms, they sequester the modified xenobiotics. Hence, the plants reduce toxicity (with exceptions) and sequester the xenobiotics in phytotransformation. Trinitrotoluene phytotransformation has been extensively researched a transformation pathway has been proposed.

The role of genetics
Breeding programs and genetic engineering are powerful methods for enhancing natural phytoremediation capabilities, or for introducing new capabilities into plants. Genes for phytoremediation may originate from a micro-organism or may be transferred from one plant to another variety better adapted to the environmental conditions at the cleanup site. For example, genes encoding a nitroreductase from a bacterium were inserted into tobacco and showed faster removal of TNT and enhanced resistance to the toxic effects of TNT.

Advantages and limitations

 * Advantages:
 * the cost of the phytoremediation is lower than that of traditional processes both in situ and ex situ
 * the plants can be easily monitored
 * the possibility of the recovery and re-use of valuable metals (by companies specializing in “phytomining”)
 * it is the least harmful method because it uses naturally occurring organisms and preserves the natural state of the environment.


 * Limitations:
 * phytoremediation is limited to the surface area and depth occupied by the roots.
 * slow growth and low biomass require a long-term commitment
 * with plant-based systems of remediation, it is not possible to completely to prevent the leaching of contaminants into the groundwater (without the complete removal of the contaminated ground which in itself does not resolve the problem of contamination)
 * the survival of the plants is affected by the toxicity of the contaminated land and the general condition of the soil.
 * possible bio-accumulation of contaminants which then pass into the food chain, from primary level consumers upwards.

Hyperaccumulators and biotic interactions
This section is for the first four points (Protection, Interferences, Mutualism, and Commensalism) mainly inspired from the article: The significance of metal hyperaccumulation for biotic interactions, by R.S. Boyd and S.N. Martens.

A plant is said to be a hyperaccumulator if it can concentrate the pollutants in a minimum percentage which varies according to the pollutant involved (for example: more than 1000 mg/kg of dry weight for nickel, copper, cobalt, chromium or lead; or more than 10,000 mg/kg for zinc or manganese. Most of the 215 metal-hyperaccumulating species included in their review hyperaccumulate nickel. They listed 145 hyperaccumulators of nickel (around 300 Ni accumulators are known; see Hyperaccumulators table – 2 : Nickel and its notes), 26 of cobalt, 24 of copper, 14 of zinc, four of Lead, and two of Chromium. This capacity for accumulation is due to hypertolerance, or phytotolerance: the result of adaptative evolution from the plants to hostile environments along multiple generations. Boyd and Martens list 4 biotic interactions that may be affected by metal hyperaccumulation, to which can be added the biofilm as a particular aspect of micorrhizae:
 * 1) protection
 * 2) Interferences with neighbour plants of different species
 * 3) Mutualism (Mycorrhizal associations or micorrhizae, and Pollen and seed dispersal)
 * 4) Commensalism
 * 5) The biofilm

Protection
More and more evidence show that the metals in hyperaccumulating plants give them some protection from various bacteria, fungi and / or insects. For instance, with foliar Ni concentrations as low as 93 mg/kg, the larval weight of Spodoptera exigua (Lepidoptera: Noctuidae) (beet army worm) is reduced and time to pupation extended (Boyd & Moar, subm.).

The defense against viruses is not always supported. Davis et al. (2001) have compared two close species S. polygaloides Gray (Ni hyperaccumulator) and S. insignis Jepson (non-accumulator), inoculating them with Turnip mosaic virus. They showed that the presence of nickel weakens the plant's response to the virus.

Circumvention of plants' elemental defences by their predators may occur in three ways : (1) selective feeding on low-metal tissues, (2) use of a varied diet to dilute metal-containing food (likely more efficient in large-sized herbivores), and (3) tolerance of high dietary metal content.

Mishra & Kar (1974) reported nickel to be transported through the xylem of crop plants. Similarly, Kramer et al. (1996) showed that Ni is transported as a complex with the amino-acid histidine in the xylem. This implies that phloem fluid may contain little nickel; thus phloem fluid may be used by able organisms as a rich source of carbohydrates.
 * 1)  - Avoidance of an elemental defence via selective feeding:

Pea aphids (Acyrthosiphon pisum [Harris]; Homoptera: Aphididae) feeding on Streptanthus polygaloides Gray (Brassicaceae) have equal survival and reproduction rates for plants containing ca. 5000 mg/kg nickel amended with NiCl2, and those containing 40 mg/kg nickel. This means that either the phloem fluid is poor in nickel even for nickel hyperaccumulators, or that the aphids tolerate nickel. Moreover the aphids feeding on high nickel-content plants only show a small increase of nickel content in their bodies, relatively to the nickel content of aphids feeding on low-nickel plants. On the other hand, aphids (Brachycaudus lychnidis L.) fed on the zinc-tolerant plant Silene vulgaris (Moench) Garcke (Caryophyllaceae) - which can contain up to 1400 mg/kg zinc in its leaves – were reported showing elevated (9000 mg/kg) zinc in their bodies.

Hopkin (1989) and Klerks (1990) demonstrated it for animal species; Brown & Hall (1990) for fungal species; and Schlegel & al. (1992) and Stoppel & Schlegel (1995) for bacterial species.
 * 3 - Metal tolerance

Plants of Streptanthus polygaloides (Brassicaceae, Ni hyperaccumulator) can be parasited by Cuscuta californica var. breviflora Engelm. (Cuscutaceae). Metal contents of Cuscuta ranged from 540–1220 mg/kg Ni, 73-fold higher than the metal contents of Cuscuta parasitizing a co-occurring non-hyperaccumulator plant species. Cuscuta plants are therefore very Ni-tolerant - 10 mg Ni/kg is sufficient for growth to start decreasing in unadapted plants. According to Boyd & Martens (subm.) this is "the first well-documented instance of the transfer of elemental defences from a hyperaccumulating host to a seed plant parasite".

Interferences with neighbour plants of different species
Its likelihood between hyperaccumulators and neighbouring plants was suggested but no mechanism was proposed. Gabrielli et al. (1991), and Wilson & Agnew (1992) , suggested a decrease in competition experienced by the hyperaccumulators for the litterfall from hyperaccumulators' canopy.

This mechanism mimics allelopathy in its effects, although technically due to redistribution of an element in the soil rather than to the plant manufacturing an organic compound. Boyd et Martens call it ‘‘elemental allelopathy’’ - without the autoxicity problem met in other types of allelopathy (Newman 1978).

Mutualism
Two types of mutualism are considered here, mycorrhizal associations or mycorrhizae, and animal-mediated pollen or seed dispersal.

1 - Mycorrhizal associations or mycorrhizae

There are two types of mycorrhizal fungi: ectomycorrhizae and endomycorrhizae. Ectomycorrhizae form sheaths around plant roots, endomycorrhizae enter cortex cells in the roots.

Mycorrhizae are the symbiotic relationship between a soil-borne fungus and the roots of a plant. Some hyperaccumulators may form mycorrhizae and, in some cases, the latter may have a role in metal treatment. . In soils with low metal levels, vesicular arbuscular mycorrhizae enhance metal uptake of non-hyperaccumulating species. On the other hand, some mycorrhizae increase metal tolerance by decreasing metal uptake in some low-accumulating species. Mycorrhizae thus assists Calluna in avoiding Cu and Zn toxicity. Most roots need about 100 times the amount of carbon than do the hyphae of its associated ectomycorrhizae in order to develop across the same amount of soil. It is therefore easier for hyphae to acquire elements that have a low mobility than it is for plant roots. Caesium-137 and strontium-90 both have low mobilities.

Mycorrhizal fungi depend on host plants for carbon, while enabling host plants to absorb the soil's nutrients and water with more efficiency. In mycorrhizae, nutrient uptake is enhanced for the plants while they provide energy-rich organic compounds to the fungus. Although certain plant species that are normally symbiotic with mycorrhizal fungi can exist without the fungal association, the fungus greatly enhances the plant’s growth. Hosting mycorrhizae is much more energy effective to the plant than producing plant roots.

The Brassicaceae family reportedly forms few mycorrhizal associations. But Hopkins (1987) notes mycorrhizae associated with Streptanthus glandulosus Hook. (Brassicaceae), a non-accumulator. Some fungi tolerate easily the generally elevated metal contents of serpentine soils. Some of these fungal species are mycorrhizal. High levels of phosphate in the soil inhibit mycorrhizal growth.

The uptake of radionuclides by fungi depends on its nutritional mechanism (mycorrhizal or saprotrophic). Pleurotus eryngii absorbs Cs best over Sr and Co, while Hebeloma cylindrosporum favours Co. But increasing the amount of K increases the uptake of Sr (chemical analogue to Ca) but not that of Cs (chemical analogue to K). Moreover, the uptake of Cs decreases with  Pleurotus eryngii (mycorrhizal) and Hebeloma cylindrosporum (saprotrophic) if the Cs content is increased, but that of Sr increases if its content is increased – this would indicate that the uptake is independent from the nutritional mechanism.

2 - Pollen and seed dispersal

Some animals obtain food from the plant (nectar, pollen, or fruit pulp - Howe & Westley 1988). Animals feeding from hyperaccumulors high in metal content must either be metal-tolerant or dilute it with a mixed diet. Alternatively hyperaccumulators may rely on abiotic vectors or non-mutualistic animal vectors for pollen or seed transport, but we lack information on seed and pollen dispersal mechanisms for hyperaccumulating plants.

Jaffré & Schmid 1974; Jaffré et al. 1976; Reeves et al. 1981; have studied metal contents of entire flowers and/or fruits. They have recorded elevated metal levels in these. We find an exception with Walsura monophylla Elm. (Meliaceae), originating from the Philippines and showing 7000 mg/kg Ni in leaves but only 54 mg/kg in fruits. Some plants may thus have a mechanism by which metal or other contaminants is excluded from their reproductive structures.

Commensalism
This is an interaction benefiting one organism while being of neutral value to another. The most likely one with hyperaccumulators would be epiphytism. But this is most  noticeable in  humid habitats, whereas only a few detailed field studies of hyperaccumulators have been conducted in such habitats, and those studies (mostly to do with humid tropical forests on serpentine soils) pay little or no attention to that point (e.g., Proctor et al. 1989; Baker et al. 1992). Proctor et al. (1988) studied the tree Shorea tenuiramulosa, which can accumulate up to 1000 mg Ni/kg dry weight in leaf material. They estimated covers of epiphytes on the boles of trees in Malaysia, but did not report values for individual species. Boyd et al. (1999) studied the occurrence of epiphytes on leaves of the Ni hyperaccumulating tropical shrub Psychotria douarrei (Beauvis.). Epiphyte load increased significantly with increasing leaf age, up to 62% for the oldest leaves. An epiphyte sample of leafy liverworts removed from P. douarrei, was found to contain 400 mg Ni /kg dry weight (far less than the host plant, whose oldest and most heavily epiphytized leaves contained a mean value of 32,000 mg Ni/kg dry weight). High doses of Ni therefore do not prevent colonization of Psychotria douarrei by epiphytes.

Chemicals that mediate host-epiphyte interactions are most likely to be located in the outermost tissues of the host (Gustafsson & Eriksson 1995). Also, most of the metal accumulates in epidermal or subepidermal cell walls or vacuoles (Ernst & Weinert 1972; Vazquez et al. 1994; Mesjasz- Rzybylowicz et al. 1996; Gabrielli et al. 1997). These findings suggest that epiphytes would experience higher metal levels when growing on hyperaccumulator leaves. But Severne (1974) measured the release of metal via leaching of leaves from the Ni hyperaccumulator Hybanthus floribundus (Lindl.) F. Muell. (Violaceae) from western Australia; he concluded that its leaves do not easily leach Ni.

In theory another commensal interaction could exist, if the high metal content of the soil under hyperaccumulator plants was needed for another plant species to establish itself. No evidence is known showing such effect.

The biofilm
This section needs be developed. See relevant articles on biofilm and Pseudomonas aeruginosa. A biofilm is a layer of organic matter and microorganism formed by the attachment and proliferation of bacteria on the surface of the object. Biofilms are characterised by the presence of bacterial extracellular polymers glyocalyx that create a thin visible slimy layer on solid surface.

Table of hyperaccumulators
A comprehensive literature survey of hyperaccumulating plants and their uses was started by Stevie Famulari for her students at the University of New Mexico. It is now considerably increased in size and has had to be split into 3 sections:


 * Hyperaccumulators table – 1 : Al, Ag, As, Be, Cr, Cu, Mn, Hg, Mo, Naphtalene, Pb, Pd, Pt, Se, Zn
 * Hyperaccumulators table – 2 : Nickel
 * Hyperaccumulators table – 3 : Radionuclides (Cd, Cs, Co, Pu, Ra, Sr, U), Hydrocarbures, Organic Solvents.