Natural Resources, 2010, 1, 110-125
doi:10.4236/nr.2010.12012 Published Online December 2010 (
Copyright © 2010 SciRes. NR
Use of Bio-Resources for Remediation of Soil
Sharmistha Pal1, Ashok K. Patra2*, Sah Kausar Reza3, Walter Wildi4, John Poté4
1Central Soil and Water conservation Research and Training Institute, Research Centre, Madhya Marg, India; 2Division of Soil
Science and Agricultural Chemistry, Indian Agricultural Research Institute, New Delhi, India; 3National Bureau of Soil Survey and
Land Use Planning, Jorhat, India; 4University of Geneva, Forel Institute, Versoix, Switzerland.
Received October 28th, 2010; revised December 4th, 2010; accepted December 6th, 2010.
In recent years, economic boom in fast developing countries has been witnessed with spectacular progress in industri-
alization and concurrent progress in modern agriculture. Such development is however not without any socio-political
and environmental side effects. A major concern has been the environmental pollution. If the current unabated disposal
of various forms of wastes to agricultural lands is continued, the inherent capacity of soil to support agricultural pro-
duction and sustain other ecosystem services will be in peril. Heavy metals with soil residence times of thousands of
years present numerous health hazards to higher organisms. They are also known to decrease plant growth, ground
cover and have a negative impact on soil biodiversity. Inorganic and organic contaminants typically found in urban
areas are heavy metals and petroleum derived products. The presence of both types of contaminants on the same site
presents technical an d economic challenges for decontamina tion strategies. In this article we have reviewed th e devel-
opments to ameliorate the contaminated soils, with special emphasis on biological approaches, which have shown po-
tential to low-cost remediation of soil pollution. Also the limitations of such approaches and direction of further re-
search have been highlighted.
Keywords: Soil pollution, Bioremediation, Phytoremed iation, Metals, Organic Pollutants, Rhizosphere
1. Introduction
Intense industrial activity in the 20th century, especially
in developing countries, has led to serious environmental
pollution, resulting in a large number and variety of con-
taminated sites which became a threat to the local eco-
systems. In India, the application of industrial and city
effluents to land has become popular in recent years as
an alternative means of treatment and disposal [1-3].
Heavy metals, with soil residence times of thousands of
years, present numerous health dangers to higher organ-
isms [4]. They are also known to decrease plant growth,
ground cover and have a negative impact on soil micro-
flora [5]. There is increasing and widespread interest in
the maintenance of soil quality and remediation strategies
for management of soils contaminated with trace metals,
metalloids or organic pollutants. Heavy metals are de-
posited in soils by atmospheric input and the use of min-
eral fertilizers or compost, and sewage sludge disposal.
Conventional remediation methods usually involve ex-
cavation and removal of contaminated soil layer, physic-
cal stabilization (mixing of soil with cement, lime, apa-
tite etc.), and washing of contaminated soils with strong
acids or HM chelators [6]. However, if no remediation
action is undertaken, the availability of arable land for
cultivation will decrease, because of stricter environ-
mental laws limiting food production on contaminated
lands. Inorganic and organic contaminants typically found
in urban areas are heavy metals and petroleum derived
products. The presence of both types of contaminants on
the same site presents technical and economic challenges
for decontamination strategies.
Bioremediation, i.e. the use of living organisms to
manage or remediate polluted soils, is an emerging tech-
nology. It is defined as the elimination, attenuation or
transformation of polluting or contaminating substances
by the use of biological processes. Initially, bioremedia-
tion employed microorganisms to degrade organic pol-
lutants [7]. Microorganisms have been used since 600
B.C. by the Romans and others to treat the wastewater.
The first commercial use of a bioremediation system was
in 1972 to clean up a Sun Oil pipeline spill in Ambler,
Pennsylvania [8]. Since 1972, bioremediation has be-
Use of Bio-Resources for Remediation of Soil Pollution
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come a well-developed way of cleaning up different
contaminants. But ever since the use of green plants was
proposed for in situ soil remediation phytoremediation
has become an attractive topic of research and develop-
ment [9]. As concluded by Anderson et al. [10], “under-
standing the mechanisms and critical factors influencing
the plant–microbe–toxicant interaction in soils will per-
mit more rapid realisation” of bioremediation of polluted
soils. This review aims to contribute towards this goal by
examining the current concepts and published data on the
biological processes and major controls that may be used
for their management in phytoremediation of inorganic
and organic soil pollutants.
2. Sources of Soil Pollution
Trace metal contamination of soils can occur naturally
from geological sources, for example Cu and Ni con-
tamination of basaltic soils from the basalt parent mate-
rial [11], or as a result of a wide ranges of industrial and
agricultural activities. Therefore, trace metal pollution
may harm human food safety and health, and there is
much interest in the protection of unpolluted sites and the
effective management of contaminated sites. Zinc is an
essential plant nutrient and is one of the most ubiquitous
trace metals in soils and it is often regarded as a poten-
tially toxic element when present in excessive concentra-
tions [12]. As chromium is widely used in many Indus-
tries of which leather industries are the biggest consum-
ers, wastes from tanneries pose a serious threat to the
environment. Metals and metalloids enter soils and wa-
ters due to many processes including atmospheric depo-
sition from industrial activities or power generation; dis-
posal of wastes such as sewage sludge, animal manures,
ash, domestic and industrial wastes or byproducts; irriga-
tion and flood or seepage waters and the utilization of
fertilizers, lime, or agrochemicals. Radionuclides are
building up in some areas due to deliberate or accidental
releases related to their use of energy production or for
military purposes. It has been found that sewage sludge
contents maximum amount of metals among different
3. Microbial Remediation of Soil Pollutants
Microbes can reduced the activity of different types of
metals or it can convert active forms of toxic metals to
inactive forms by the processes as shown in Figure 1.
The choice of micro organisms to be used for biore-
mediation depends on availability of energy and carbon
source, environmental conditions like temperatures, oxy-
gen, moisture and the presence of hazardous contamni-
nants. The aerobic bacteria recognized for their degrada-
tive abilities are Pseudomonas, Alcaligenes, Sphingo-
monas, Rhodococcu s, and Mycobacterium (Table 1).
These microbes have often been reported to degrade pes-
ticides and hydrocarbons, both alkanes and polyaromatic
compounds. Many of these bacteria use the contaminant
as the sole source of carbon and energy. The contact be-
tween the bacteria and contaminant is a precondition for
degradation. This is not easily achieved, as neither the
microbes nor contaminants are uniformly spread in the
Intracellular sequestration
Intracellular precipitation
DOC mineralization
Fe oxidation
Methylation Reduction
, CO
Fe(II), sulfide
. li
Metal release
and speciation
e.g. Mn, Fe
e.g. As
e.g. Hg, Se, As, Sn,
Figure 1. Processes involved in microbial mobilization and immobilization of metals and metalloids in soil (modified from
Wengel [9]).
Use of Bio-Resources for Remediation of Soil Pollution
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soil. Some bacteria are mobile and exhibit a chemotactic
response, sensing the contaminant and moving toward it.
Other microbes such as fungi grow in a filamentous form
toward the contaminant. It is possible to enhance the mo-
bilization of the contaminant utilizing some surfactants
such as sodium dodecyl sulphate. Substrates can be used
to facilitate the contact between contaminants and mi-
crobes by enhancing the mobilization of contaminants
There is an increasing interest in anaerobic bacteria
used for bioremediation of polychlorinated biphenyls in
river sediments, dechlorination of the solvent trichloro-
ethylene, and chloroform. Ligninolytic fungi, such as the
white rot fungus Phanaerochaete chrysosporium have
the ability to degrade an extremely diverse range of per-
sistent or toxic environmental pollutants. Common sub-
strates used include straw, saw dust, or corn cobs. Me-
thylotrophs are the aerobic bacteria that grow by utilizing
methane for carbon and energy. The initial enzyme in the
pathway for aerobic degradation, methane monooxy-
genase, has a broad substrate range and is active against a
wide range of compounds, including the chlorinated ali-
phatic trichloroethylene and 1,2-dichloroethane.
4. Bioremediation Strategies
Different bioremediation techniques are employed de-
pending on the degree of saturation and aeration of an
area. In situ techniques are defined as those that are ap-
plied to soil and groundwater at the site with minimal
disturbance, whereas ex situ techniques are applied to at
the site which has been removed via excavation (soil) or
pumping (water) (Table 2).
4.1. In Situ Bioremediation
These techniques are generally the most desirable options
due to lower cost and fewer disturbances since they pro-
vide the treatment in place avoiding excavation and
transport of contaminants ( In
situ treatment is limited by the depth of the soil that can
be effectively treated. In many soils effective oxygen
diffusion for desirable rates of bioremediation extend to a
range of only a few centimeters to about 30 cm into the
soil, although depths of 60 cm and greater have been
effectively treated in some cases. The most important in
situ land treatments are bioventing, in situ biodegrada-
tion, biosparging and bioaugmentation.
Table 1. Miroorganisms capable of degrading heavy metals.
Heavy metal Microorganisms References
Pseudomonas fluorescens
Pseudomonas aeruginosa
Pseudomonas mendocina
Enterobacter cloacae.
Ni Pseudomonas
Methylobacterium, Rhodococcus and Okibacterium [29]
Se Stenotrophomo nas sp [31]
U Glomus intraradices took [35]
Zn, Cd and Mn Arbuscular mycorrhizae [40-47]
Table 2. Summary of bioremediation strategies.
Technology Examples Benefits Limitations
In situ
In situ bioremediation
Most cost efficient
Natural attenuation processes
Treats soil and water
Environmental constraints
Extended treatment time
Monitoring difficulties
Chemical solubility, biodegradability and distribution
of pollutants
Biodegradative ability of indigenous microbes
Ex situ Landfarming
Cost efficient
Can be done on site
Space requirements
Extended treatment time
Need to control abiotic loss
Mass transfer problem
Bioavailability limitations
Bioreactors Slurry reactors
Aqueous reactors
Rapid degradation kinetics
Optimized environmental parameters
Enhances mass transfer
Effective use of inoculants and surfactants
Soil requires excavation
Relatively high operating cost
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Bioventing is the most common in situ treatment and
involves supplying air and nutrients through wells to
contaminated soil to stimulate the indigenous bacteria.
Bioventing employs low air flow rates and provides only
the amount of oxygen necessary for the biodegradation
while minimizing volatilization and release of contami-
nants to the atmosphere. It works for simple hydrocar-
bons and can be used where the contamination is deep
under the surface.
In situ biodegradation involves supplying oxygen and
nutrients by circulating aqueous solutions through con-
taminated soils to stimulate naturally occurring bacteria
to degrade organic contaminants. Generally, this tech-
nique includes conditions such as the infiltration of wa-
ter-containing nutrients and oxygen or other electron
acceptors for groundwater treatment.
Biosparging involves the injection of air under pres-
sure below the water table to increase groundwater oxy-
gen concentrations and enhance the rate of biological
degradation of contaminants by naturally occurring bac-
teria. Biosparging increases the mixing in the saturated
zone and thereby increases the contact between soil and
Bioaugmentation involves the addition of microorgan-
isms indigenous or exogenous to the contaminated sites
to enhance the degradation of the contaminants.
4.2. Ex Situ Bioremediation
These techniques involve the excavation or removal of
contaminated soil from ground. The most important ex-
situ treatments are landfarming, composting, biopiles and
Landfarming is a simple technique in which contami-
nated soil is excavated and spread over a prepared bed
and periodically tilled until pollutants are degraded. The
goal is to stimulate indigenous biodegradative microor-
ganisms and facilitate the aerobic degradation of con-
taminants. The practice is limited to the treatment of su-
perficial 10–35 cm of soil. Since landfarming has the
potential to reduce monitoring and maintenance costs, as
well as clean-up abilities, it has received much attention
as a disposal alternative.
Is a technique that involves combining contaminated
soil with nonhazardous organic amendments such as
manure or agricultural wastes. The presence of these or-
ganic materials supports the development of a rich mi-
crobial population and elevated temperature characteris-
tics of composting.
Biopiles are a hybrid of landfarming and composting,
typically used for treatment of surface contamination
with petroleum hydrocarbons [13]. They are a refined
version of landfarming that tend to control physical losses
of the contaminants by leaching and volatilization. Bio-
piles provide a favorable environment for indigenous
aerobic and anaerobic microorganisms.
Bioreactors. Slurry reactors or aqueous reactors are
used for ex situ treatment of contaminated soil and water
pumped up from a contaminated plume. Bioremediation
in reactors involves the processing of contaminated solid
material (soil, sediment, sludge) or water through an en-
gineered containment system. A slurry bioreactor is a
containment vessel and apparatus used to create a three-
phase (solid, liquid, and gas) mixing condition to in-
crease the bioremediation rate of soilbound and water-
soluble pollutants as a water slurry of the contaminated
soil and biomass (usually indigenous microorganisms)
capable of degrading target contaminants. In general, the
rate and extent of biodegradation are greater in a biore-
actor system than in situ or in solid-phase systems be-
cause the contained environment is more manageable and
hence more controllable and predictable.
5. Role of Bacteria in Bioremediation
5.1. Rhizosphere Bacteria Affect Plant Growth
and Metal Uptake
There is increasing evidence that rhizosphere bacteria
contribute to the metal extraction process (Table 3), but
the mechanisms of this plant–microbe interaction are yet
to be fully understood. The rhizosphere of heavy metal
accumulating plants provides a niche for adapted metal
resistant microorganisms [14,15] and the mobility of
heavy metals is higher in the rhizosphere of metal accu-
mulators than in bulk soil, due to active mobilization by
roots and microorganisms [16]. Bacterial IAA, ACC
deaminase, siderophores, organic acids or specific ligands
have been associated with enhanced growth and accu-
mulation and mobilization of heavy metals under heavy
metal exposure [17-19].
The rhizosphere bacteria of Salix caprea were reported
to influence metal mobilization and uptake. Experimental
results indicated that plant growth promotion might be an
important parameter besides the enhancement of metal
uptake. Zinc resistances of the Salix caprea rhizosphere
bacteria ranged between 2 and 11 mM and were much
higher than those of bacteria associated with Zn hyper-
accumulating Thlaspi. This suggests a high bioavailabil-
ity of Zn in the rhizosphere of Salix caprea and a specific
adaptation of the associated bacteria. Salix caprea trees
growing at the contaminated site in Arnoldstein were
found to accumulate higher amount of Zn and Cd, but
less Pb which indicates the relatively low Pb tolerance of
the bacteria [15]. The possible mechanisms of microbial
uptake and detoxification of toxic metals in soil matrix is
presented in Figure 2.
Use of Bio-Resources for Remediation of Soil Pollution
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Table 3. Overview of phytoremediation applications.
Technique Plant mechanism Surface reacting medium
Phytoextraction Concentration of metal into the plant tissue via direct uptake
with subsequent removal of the plant Soils
Phytotransformation Plant uptake and degradation of organic compounds Surface water, ground water
Phytostabilization Root exudates cause metals to precipitate and become less
available Soils, ground water, mine tailing
Phytodegradation Enhances microbial degradation in rhizosphere Soils, groundwater within rhizosphere
Rhizo filtration Uptake of metals into plant roots Soils, Surface water
Phytovolatilization Plants evaporate selenium, mercury and volatile hydrocar-
bons Soils, ground water
Cell wall
Adssorption/ion exchange and
Covalent binding
Entrapment of particles
Redox reactions
Cell-associtaed materials
(polysaccharides, mucilage, capsules etc)
Particulate entrapment
on-specific binding
Cell membrane/ periplasmic space
Adsorption/ion exchange
Redox reactions/transformations
Diffusion and transport (influx and efflux)
etal Y-glutamyl peptides
on-specific binding/sequestration
Organellar compartmentation
edox reactions/ transformations
Ex t racellu lar reacti ons
Precipitation with excreted products
e.g. oxalate, sulphide
Complexation and chelation
Figure 2. The microbial uptake and detoxification of toxic metals.
5.2. Chromium in the Environment: Factors
Affecting Biological Remediation
The detoxification of chromium in soil is based on the
fact that Cr(VI) is readily reduced to Cr(III) and immobi-
lized in organic matter rich soils. The use of Cr(VI)-
contaminated groundwater to irrigate organic matter rich
soil based on the mechanism of reduction and precipita-
tion of Cr in the soil as Cr(III) [20,21]. In a study to ex-
amine the processes responsible for Cr(VI) reduction in
soil, it was reported that organic matter content, bioactiv-
ity, and oxygen status were among the important factors
[21]. Under aerobic, field-moist conditions, organic mat-
ter rich soil (amended with 50 tons ha1 organic matter)
was reported to reduce 96% of added Cr(VI), whereas
sterile soils receiving similar amendments reduced only
75% of the original Cr(VI), demonstrating the impor-
tance of the presence of soil microorganisms in conjunc-
tion with a readily available carbon source. These studies
assert that soil organic matters play a key role in reduc-
tion of Cr(VI) to Cr(III). Organic matter enhances the
reduction of chromate in soil by increasing microbial
activities, acting as electron donors, and by lowering the
O2 level of the soil, thus creating reducing conditions.
Realizing the potential importance of soil microorgan-
isms in reducing Cr(VI) in contaminated soils, several
groups attempted to identify and isolate microorganisms
that can mediate the reduction of Cr(VI) to Cr(III) in
soils [22,23]). These microorganisms thought to be Cr
resistant as well since the reduction rate is slower than
the uptake rate [24]. Some of the bacterial strains found
to be resistant to high levels of Cr(VI) include Pseudo-
monas fluorescens [25], P. aeruginosa [26], and Pseu-
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domonas mendocina [27]. Bacterial populations resistant
to as much as 500 mg L1 Cr(VI) and fungal populations
resistant to 1000 mg L1 Cr(VI) were directly isolated
from soils [28].
5.3. Nickel Tolerance and Accumulation by
Bacteria from Rhizosphere of Nickel
The bacteria in the rhizosphere of Ni-hyperaccumulators
are capable of tolerating high concentration of Ni and
also possess nickel uptake potential. The Ni-hyperac-
cumulators in combination with these Ni-resistant bacte-
ria could be an ideal tool for nickel bioremediation. This
high concentration of bioaccessible nickel in the rhizo-
sphere of Ni-hyperaccumulators in turn provides a niche
for nickel-resistant microflora.
The predominant Ni-resistant bacteria belonged to
Pseudomonas in the rhizosphere of Ni-hyperaccumulator,
Alyssum bertolonii [29], while the same under Thlaspi
goesingense were identified as Methylobacterium, Rho -
dococcus and Okibacterium [14]. The rhizosphere of
Rinorea bengalensis and Dichapetalum gelonioides ssp.
andamanicum, the endemic Ni-hyperaccumulators from
serpentines of Andaman harbor Ni-resistant bacteria,
which are capable of accumulating nickel and could tol-
erate >8 mM Ni and viable cells were capable of accu-
mulating Ni from aqueous solution. This may be attrib-
uted to the presence of Ni-binding sites on the cell sur-
face of metallophiles [30].
5.4. Improvement of Selenite and Selenate
Abatement in Selenium Contaminated
Soils through Rhizospheric Bacterial
Brass ica juncea cultivation on the soil has been found to
result in a higher volatilisation rate when compared with
non-vegetated soil. However, the presence of B. juncea
in soil amended with selenium as selenite or selenate has
revealed to promote a significant Se precipitation by elic-
iting rhizobacteria (Stenotrophomonas sp) capable of
reducing the metalloid oxyanions to SeO. In fact, the
capacity of certain rhizobacteria to precipitate Se oxyan-
ions, reducing their toxicity in contaminated matrices,
could be seen as an alternative option to Se phytoextrac-
tion or phytovolatilisation, so far emphasized for the re-
moval of the toxic metalloid from soil. B. juncea effi-
ciently accumulates as well as volatilizes selenium [31]).
Thus, the rhizosphere of B. juncea resulted to be an ef-
fective source and carrier of microorganisms capable to
in vitro reduction and precipitation of toxic Se(IV) and
Se(VI) to non toxic elemental Selenium volatilisation by
B. juncea has been confirmed as a relevant mechanism of
Se detoxification in contaminated soil.
6. Role of Arbuscular Mycorrhiza in
6.1. Effects of the Mycorrhizal Fungus
Glomus intraradices on Uranium
Uptake and Accumulation in
Uranium-Contaminated Soil
Arbuscular mycorrhizae (AM) are ubiquitous symbiotic
associations between higher plants and soil fungi [32]
and their extraradical mycelium form bridges between
plant roots and soil, and mediate the transfer of various
elements into plants. There is also a growing body of
evidence that arbuscular mycorrhizal fungi can exert
protective effects on host plants under conditions of soil
metal contamination. Binding of metals in mycorrhizal
structures and immobilization of metals in the my-
corrhizosphere may contribute to the direct effects. Indi-
rect effects may include the mycorrhizal contribution to
balanced plant mineral nutrition, especially P nutrition,
leading to increased plant growth and enhanced metal
tolerance. It has been widely reported that ectomycorrhi-
zal and ericoid mycorrhizal fungi can increase the toler-
ance of their host plants to heavy metals when the metals
are present at toxic levels. The underlying mechanism is
thought to be the binding capacity of fungal hyphae to
metals in the roots or in the rhizosphere which immobi-
lizes the metals in or near the roots and thus depresses
their translocation to the shoots [22,33]. Being strongly
adsorbed and bound by mycorrhizal structures, metals in
soils may be retained within a certain volume of soil,
with minimization of leaching processes and restriction
of the zone of contamination, and plants may be pro-
tected from metal toxicity and environmental stress.
Arbuscular mycorrhizae may play an important role in
plant adaptation to U contaminated soils by not only im-
proving plant P acquisition ability, but also enhancing U
immobilization by roots, thus reducing U partitioning
into plant shoots and environmental risks. As U behav-
iour in soil is similar to heavy metals such as Pb, it can
be deduced that mycorrhizal fungi, may have significant
effects on U mobilization and uptake [34,35]. It has been
found that extraradical AM fungal mycelium of Glomus
intraradices took up and translocated U towards root in
in vitro culture system [35], and hyphae were more effi-
cient in U translocation compared with roots [36]. Solu-
ble uranyl cations or uranyl-sulphate species that are sta-
ble under acidic conditions were translocated to a higher
extent to roots through fungal tissues, while phosphate
and hydroxyl species dominating under acidic to near
neutral conditions or carbonate species dominating under
alkaline conditions were rather immobilized by hyphal
structures. It is documented that plant uptake of U is af-
fected by various factors, such as soil properties [37] and
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uranium–phosphorus interactions [38,39].
6.2. Arbuscular Mycorrhiza can Depress
Translocation of Zinc to Shoots of
Host Plants in Soils Moderately
Polluted with Zinc
It has been demonstrated that at high soil heavy metal
concentrations, arbuscular mycorrhizal infection reduced
the concentrations of Zn, Cd and Mn in plant leaves [40,
41]. Field investigations have indicated that mycorrhizal
fungi can colonize plant roots extensively even in metal
contaminated sites [42-44], and Zn- and Cd-tolerant fun-
gal strains have been isolated from contaminated sites by
several research groups [45,46]. Numerous experimental
studies have indicated that under conditions of moderate
Zn contamination, arbuscular mycorrhizal plants may
exhibit much lower shoot concentrations of Zn and
higher plant yields than non-mycorrhizal controls, indi-
cating a protective effect of mycorrhizas on the host
plants against potential Zn toxicity [47].
7. Advantages and Disadvantages of
7.1. Advantages
1) Bioremediation is a natural process and is therefore
perceived by the public as an acceptable waste treatment
process for the complete destruction of a wide variety of
2) The residues for the treatment are usually harmless
products and include carbon dioxide, water, and cell
biomass. Many compounds that are legally considered to
be hazardous can be transformed to harmless products.
This eliminates the chance of future liability associated
with treatment and disposal of contaminated material.
3) Bioremediation can often be carried out on site, of-
ten without causing a major disruption of normal active-
ties. This also eliminates the need to transport quantities
of waste off site and the potential threats to human health
and the environment that can arise during transportation.
4) Bioremediation can prove less expensive than other
technologies that are used for clean-up of hazardous
7.2. Disadvantages
1) Bioremediation is limited to those compounds that are
biodegradable. Not all compounds are susceptible to rapid
and complete degradation.
2) Biological processes are often highly specific.
Therefore, the success of the technique requires several
site factors like the presence of metabolically capable
microbial populations, suitable environmental growth
conditions, and appropriate levels of nutrients and con-
3) Research is needed to develop and engineer biore-
mediation technologies that are appropriate for sites with
complex mixtures of contaminants that are not evenly
dispersed in the environment.
4) Bioremediation often takes longer than other treat-
ment options, such as excavation and removal of soil or
5) Regulatory uncertainty remains regarding accept-
able performance criteria for bioremediation and there
are no acceptable endpoints for bioremediation treat-
6) There are some concerns that the products of bio-
degradation may be more persistent or toxic than the
parent compound.
8. Plant Assisted Bioremediation
Phyto rem edia tion may be defined as use of vegetation to
contain, sequester, remove, or degrade organic and inor-
ganic contaminants in soils, sediments, surface water and
groundwater. Phytoremediation is an emerging technol-
ogy that uses plants to remove contaminants from soil
and water [48]. The basic idea that plant can be used for
environmental remediation is very old and cannot be
traced to any particular source. However, a series of fas-
cinating scientific discoveries combined with an interdis-
ciplinary research approach have allowed the develop-
ment of this idea into a promising, cost-effective, and
environmental friendly technology.
Although the application of microbial biotechnology
has been successful with petroleum-based constituents,
microbial digestion has met limited success for wide-
spread residual organic and metals pollutants. Vegeta-
tion- based remediation shows potential for accumulating,
immobilizing, and transforming a low level of persistent
contaminants. We can find five types of phytoremedia-
tion techniques, classified based on the contaminant fate:
phytoextraction, phytotransformation, phytostabilization,
phytodegradation, rhizofiltration, even if a combination
of these can be found in nature (Table 3).
Phytoextraction or phytoaccumulation: This is a proc-
ess used by the plants to accumulate contaminants into
the roots and aboveground shoots or leaves. This tech-
nique saves tremendous remediation cost by accumulat-
ing low levels of contaminants from a widespread area.
Unlike the degradation mechanisms, this process pro-
duces a mass of plants and contaminants (usually metals)
that can be then harvested, incinerated, and the ash re-
lated to a confined area or the heavy metals are extracted
from it (Figure 3, [49]).
Phytostabilization is a technique in which plants re-
duce the mobility and migration of contaminated soil.
Leachable constituents are adsorbed and bound into the
plant structure so that they form a stable mass of plant
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Figure 3. Phytoextraction of metals from soil and their utilization [49].
from which the contaminants will not reenter the envi-
Phytodegradation or rhizodegradation is the break-
down of contaminants through the activity existing in the
rhizosphere due to the presence of proteins and enzymes
produced by the plants or by soil organisms such as bac-
teria, yeast, and fungi. Rhizodegradation is a symbiotic
relationship where the plants provide nutrients necessary
for the microbes to thrive, while microbes provide a
healthier soil environment.
Rhizofiltration is a water remediation technique that
involves the uptake of contaminants by plant roots.
Rhizofiltration is used to reduce contamination in natural
wetlands and estuary areas. In Table we can see an over-
view of phytoremediation applications.
8.1. Phytoextraction
Phytoextraction employs metal hyperaccumulator plant
species to transport high quantities of metals from soils
into the harvestable parts of roots and aboveground
shoots [50,51]. Phytoextraction is an innovative, novel
and potentially inexpensive technology (Table 4) using
higher plants for in situ decontamination of metal-pol-
luted soils, sludges and sediments [52-55]. Large biomass
production and high rates of metal uptake and transloca-
tion into shoots are critical to achieve reasonable metal
extraction rates. Effective phytoextraction requires both
plant genetic ability and the development of optimal ag-
ronomic management practices [1,56]. Hyper accumu-
lators are defined as plants that contain in their tissue
more than 1,000 mg kg-1 dry weight of Ni, Co, Cu, Cr,
Pb, or more than 10,000 mg kg-1 dry weight of Zn, or Mn
[6]. Apart from metal tolerance, hyper accumulation is
thought to benefit the plant by means of allelopathy, de-
fense against herbivores, or general pathogen resistance
In-situ phytoextraction of Ni by a native population of
Alyssum murale on an ultramafic site (Albania) have
been reported by Bani et al., [60]. In the case of phyto-
mining, the use of native flora (including local popula-
tions of hyperaccumulators) with limited agronomic pra-
ctices (extensive phytoextraction) could be an alternative
to intensively managed crops. Ebbs et al. [61] showed
that T. caerulescens (UK) could achieve approximately
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Table 4. Phytoremediation of heavy metals.
Heavy metal Plant species References
Zn and Cd Salix caprea [15]
Alyssum bertolonii
Thlaspi goesingense
Rinorea bengalensis and Dichapetalum gelonioides ssp. andamanicum
Se Brassica juncea [31]
Alyssum murale
T.caerulescens, Brassica spp.
Red root pigweed, Indian mustard , tepary bean
10 times higher shoot Cd concentration as compared to
Brassica spp. Lasat et al. [62] conducted a field study to
investigate the potential of three plant species for phy-
toremediation of a 137Cs-contaminated site. Approximately
40-fold more 137Cs was removed from the contaminated
soil in shoots of red root pigweed than in those Indian
mustard and tepary bean. The greater potential for 137Cs
removal from the soil by red root pigweed was associated
with both high concentration of 137Cs in shoot and high
shoot-biomass production. Among the plants, Urtica
dioica found to be very effective due to its higher uptake
capacity for chromium. Zea mays showed high tolerance
towards Cr with negligible concentration in leaves. Due
to its higher Cr uptake and low biomass production Ur-
tica dioica, commonly known as ‘stinging nettle’, in
German ‘Brennnessel’, can be considered as the right
plant for remediation of Cr contaminated sites. As nettle
grows both in tropical and cold climates, therefore its
value as ‘nature cleaner’ is universal.
The lack of success of phytoremediation is largely re-
lated to the small biomass of most true hyperaccumulator
plants or to metal accumulation by high-biomass (crop)
plants being too low. For example while contaminant
mixtures appear to be the rule rather than the exception at
polluted sites, metal tolerance, as well as efficient metal
accumulation by a given plant species is typically re-
stricted to one or few elements. Moreover, high metal/
metalloid uptake rates in plants as required for phytoex-
traction can only be achieved if the metal/metalloid ac-
tivity in the rhizosphere soil solution is sustained by
rapid re-supply from the solid phase [63,64]. The most
studied approach is chelant-assisted phytoextraction us-
ing EDTA and other artificial chelants. Other researchers
have employed acidifying amendments such as elemental
sulphur [65,66] and ammonium fertilization along with
nitrification inhibitors [67,68] to enhance metal mobility
in the rhizosphere of phytoextraction crops. Co-cropping
of different plant species has been proposed as a strategy
to increase metal bioavailability [69] and to better ex-
plore the soil volume and address the heterogeneous dis-
tribution of pollutants in field soils [70], for instance by
combining deep rooting metal accumulating willows with
small hyperaccumulator species that can efficiently ex-
plore the uppermost soil horizons. Co-cropping of metal
accumulators with alder trees (Alnus sp.) may offer an
interesting alternative to chemical mobilisation of metals
in phytoextraction crops [71]. Alder species are associ-
ated with N2-fixing actinorhizal symbionts (Frankiae).
Nitrogen fixation has been shown to result in substantial
acidification in alder rhizospheres [72] because nitrogen
uptake relying on N2-fixation rather than anionic nitrate
results in enhanced proton exudation to maintain the
cation–anion balance [73]. These indigenous processes
could be used to increase metal bioavailability to co-
cropped metal accumulators and to improve nitrogen
nutrition. Another interesting approach to enhance pol-
lutant tolerance, plant performance and accumulation of
metals at root surfaces using recombinant rhizobacterium
Pseudomonas putida expressing a metal-binding peptide
(E20) was recently demonstrated in hydroponic culture
by Wu et al. [74].
8.2. Phytoremediation of Heavy
Metal–Contaminated Soils:
Natural Hyperaccumulation
versus Chemically Enhanced
Recent research has shown that chemical amendments,
such as synthetic organic chelates, can enhance phytoex-
traction by increasing HMs bioavailability in soil thus
enhancing plant uptake, and translocation of HMs from
the roots to the green parts of tested plants [42,75,76]. Of
the chelates tested, ethylene diamine tetraacetic acid
(EDTA) was often found to be the most effective [77,78].
Huang et al. [76] found that among different chelating
agent EDTA is more effective in accumulation Pb in corn
and pea and also found that on increasing the concentra-
tion of EDTA accumulation efficiency of Pb in shoot of
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corn and pea was increased Therefore, the potential risks
of use of EDTA or other chelators for phytoextraction
should be thoroughly evaluated before steps towards
further development and commercialization of this reme-
diation technology are attempted. Research (reference)
indicated up to 104.6, 2.3 and 3.2-fold increase of Pb, Cd
and Zn concentration, respectively, in leaves of Chinese
cabbage grown on EDTA (10 mmol kg1) treated soil.
EDTA effectively prevents cell wall retention of HM and
influenced not only HM uptake but also enhanced HM
translocation in the plant [77]. The use of chelates as soil
amendments to increase the bioavailability of HM has
raised some concern over the potential increased mobility
of the metalchelate complex in the soil. Several authors
have emphasized the possibility of HM groundwater
contamination or other off site migrations [79]. The ad-
verse effects of HMs on the occurrence of arbuscular
mycorrhizal fungi, HM tolerance in these micro-organ-
isms, and their effects on metal uptake and transfer to
plants are well documented [80]. There is, however, very
little information on the direct effects of EDTA on ar-
buscular mycorrhiza [81]. The toxicity of EDTA on soil
bacteria, actinomycetes and fungi was studied with PLFA
and DGFA methods. PLFA and DGFA are relatively new
tools in environmental microbiology and enable the in-
sight into the structure of microbial populations in com-
plex substrates, and give an indication of environmental
stress inflicted on microbial populations [82]. The results
are in accord with phytotoxicity and arbuscular my-
corrhize tests. Increasing doses of EDTA increased the
cultural stress (DGFA analysis, trans/cis ratio of PLFA
methyl esters) of soil microflora. The PLFA results indi-
cated that soil fungi are more sensitive to EDTA or to
EDTA mediated increase of HMs bioavailability than are
soil bacteria and actinomycetes. This can be partly ex-
plained by a very diverse bacterial metabolism which
enables bacterial species to adjust to different environ-
mental conditions. Therefore, emphasize the importance
of EDTA risk assessment for each specific soil and phy-
toextraction conditions. New non-toxic chelates, and
methods to prevent the leaching of the HMs-chelate com-
plex down the soil profile need to be evaluated.
8.3. Rhizovolatilisation
Rhizovolatilisation of inorganic contaminants differs
significantly from other remediation techniques as it re-
leases the contaminants in the atmosphere. In the case of
selenium, volatile methylated species are less toxic than
inorganic forms [83]. The concern related to volatilisa-
tion of contaminants is significant especially for elements
such as mercury and arsenic, which are not essential and
can form extremely toxic volatile compounds [84]. Ele-
mental mercury is far less toxic than methylmercury and
its half-life in the atmosphere is in the order of years
which should enable a substantial dilution into the large
atmospheric pool [85]. For this reason an approach based
on the accumulation of Hg2+ in the plant shoot rather than
volatilisation of elemental mercury has been pro- posed
as an alternative strategy [86]. Studies on arsenic uptake
and distribution in higher plants indicate that ar- senic
predominantly accumulated in root and only small quan-
tities are transported to shoots. However, plant may en-
hance the biotransformation of arsenic by rhizospheric
bacteria, thus increasing rates of volatilization.
8.4. Rhizodegradation
Field-contaminated soils that have undergone prolonged
periods of ageing [87-91] generally appear to be much
less responsive to rhizodegradation than fresh soil [92-
98]. Characterising root exudation in terms of chemical
composition and quantity and investigation of utilization
pattern by microbial strains competent to degrade organic
pollutants is a prerequisite for this purpose. In long-term
field contaminated soil, enhancement of bioavailability
appears to be the key of successful biodegradation. Se-
lection and engineering of plants and microbial strains
that can modify solubility and transport of organic pol-
lutants through exudation of biosurfactants holds promise
[99]. Recent attempts to genetically engineer plant– mi-
crobial systems to enhance rhizodegradation include
gene cloning of plants containing bacterial enzymes for
the degradation of organic pollutants such as PCBs and
of recombinant, root-colonising bacteria (e.g. Pseudo-
monas fluorescens) expressing degradative enzymes (e.g.
ortho-monooxygenase for toluene degradation) [100].
Soils and sediments polluted with crude oil hydrocar-
bons are of major environmental concern on various
contaminated sites. Hydrocarbon-degrading microorgan-
isms are ubiquitously distributed in soils and constitute
less than 1% of the total microbial communities but may
increase to 10% in the presence of crude oil [101]. Deg-
radation of HC further requires a balanced nutrient sup-
ply in soil which can be achieved by fertilisation (bio-
stimulation). Mainly nitrogen and, to a lesser extent,
phosphorus are reported to be limiting factors of HC
degradation processes in oxic soil environments [102-
104]. Microorganisms are able to use HC as a carbon and
energy source [103] preferentially in the absence of a
readily available carbon source like labile natural organic
matter. Read et al. [105] observed increased phosphorus
mobilisation due to exudation of biosurfactants by lupine
(Lupinus angustifolius L. cv. Merrit). The identified
biosurfactants consisted of phospholipids which could
provide an additional phosphorus source to microorgan-
isms. Polycyclic aromatic hydrocarbons (PAHs) are con-
taminants generated from many sources such as the
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combustion of coal and fossil fuels for energy production
and are potential carcinogens that can induce mutations.
As lipophilic compounds, they present a significant health
risk if they enter the food chain [106]. These compounds
can be used by soil microorganisms as an energy and
carbon source, although four-, five-, and six-ring PAHs
are more resistant to biodegradation. Bacteria initiate
PAH degradation via dioxygenase attack, increasing
PAH chemical reactivity and solubility [107].
8.5. Phytostabilisation/Phytoimmobilisation
Inoculation with metal-resistant PGPR can support the
establishment and improve vitality of the phytostabilisa-
tion crops, and detoxification mechanisms in the rhizo-
sphere may be enhanced by inoculation with microbial
associates. Some plants and microorganisms are able to
precipitate metal compounds in the rhizosphere. This was
shown for lead pyromorphite [108,109], and may provide
an effective means to reduce metal toxicity as well as
metal mobility (phytoimmobilisation) [110]. The design
of phytostabilisation systems relates to combining dif-
ferent approaches to ameliorate multiple constraints (i.e.,
nutrient and water deficiency, toxicity due to mixed con-
tamination) and to control their efficiency in field condi-
tions. The combined use of alders, frankiae and my-
corrhizae for the remediation of contaminated ecosys-
tems is thought to improve plant nutrition through both
the actinorhizal symbiosis (Frankiae) and the mycorrhi-
zal symbioses, and to protect the plant from toxicity
through the mechanisms discussed above for metals and
organic pollutants [71].
8.6. Advantages and Disadvantages of
Phytoremediation is well suited for use at very large field
sites where other methods of remediation are not cost
effective or practicable; at sites with a low concentration
of contaminants where only polish treatment is required
over long periods of time and in conjunction with other
technologies where vegetation is used as a final cap and
closure of the site. There are some limitations to the
technology which include long duration of time for
remediation, potential contamination of the vegetation
and food chain and difficulty in establishing and main-
taining vegetation at some sites with high toxic levels.
8.7. Integrated Approaches
The complexity and heterogeneity of sites often polluted
with multiple metals, metalloids and organic compounds
requires the design of integrated phytoremediation sys-
tems that combine different processes and approaches.
Co-cropping different species may enhance the overall
capabilities of a phytoremediation system to explore the
contaminated soil volume, address different pollutants,
and support differential microbial consortia in their
rhizospheres. Shared rhizospheres may be designed to
optimise the nutritional status, e.g. by combining plants
that support N2-fixing and P-solubilising microorganisms.
Co-cropping could be also used to modify the bioavail-
ability of pollutants, e.g. by combining Alnus sp. with
metal-accumulating willows [71] or to combine metal
phytoextraction crops (e.g. willows) with plants that
support rhizodegradation of organic pollutants (e.g.
grasses). Engineering rhizobacteria capable of heavy
metal accumulation and enhanced degradation of organic
pollutants such as trichloroethylene offers further oppor-
tunities to address multiple contaminated sites [111].
While some phyto-/rhizoremediation technologies are
being used commercially, it is obvious that the complex-
ity of interactions in the plant–microbe–soil pollutant
system requires substantial further research efforts to
improve our understanding of the rhizosphere processes
9. Conclusion and Future Research Needs
It can be concluded that bioremediation is indeed an en-
vironmentally friendly, gentle management option for
polluted soil as it uses solar-driven biological processes
to treat the pollutant. The success of a phytoextraction
technique is largely dependent on the continuous avail-
ability of the metal of interest to the phytoextracting
plants. It appears attractive because in contrast to most
other remediation technologies, it is not invasive and, in
principle, delivers intact, biologically active soil. There is
a need to enhance research efforts on this emerging and
environmentally friendly “green” technology. Research
should focus on identifying remediating plants that are
adapted to the local climate and soil conditions.
As phytoremediation is a slow process, biotechnology-
cal as well as classical hybridization techniques should
be used to develop more efficient metal hyperaccumula-
tor plant species having increasing pollutant tolerance,
root and shoot biomass, root architecture and morphol-
ogy, pollutant uptake properties, and degradation capa-
bilities for organic pollutants etc. [9].
Other approaches to be the management of microbial
consortia: the selection and engineering of microorgan-
isms with capabilities for pollutant degradation, benefi-
cial effects on the phytoremediation crops, or modifying
effects on pollutant bioavailability. Selection and engi-
neering of plants and microbial strains that can modify
solubility and transport of organic pollutants through
exudation of biosurfactants holds a great promise [99].
Additional strategies should include proper manage-
ment of the soil, e.g. via fertilisation or chelant addition
to increase pollutant bioavailability, and of the phytore-
Use of Bio-Resources for Remediation of Soil Pollution
Copyright © 2010 SciRes. NR
mediation crops, e.g. via optimisation of coppicing, har-
vest cycles, development of mixed cropping systems etc.
In long-term field contaminated soil, enhancement of
bioavailability appears to be the key of successful bio-
degradation. Phytoremediation is still a new field which
holds great potential and in order to develop this poten-
tial requires a multidisciplinary approach, spanning field
as diverse as plant biology, agricultural engineering,
agronomy, soil science, microbiology and genetic engi-
neering. Finally, the applicability of these bio-approaches
for rehabilitation of contaminated soils needs to be fully
demonstrated in the fields for wider acceptability.
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