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1. Details of Module and its Structure
Module Detail
Subject Name < Botany>
Paper Name < Applied ecology>
Module Name/Title <Bioremediation>
Module Id
Pre-requisites Basic knowledge on Bioremediation
Objectives To make students aware of the bioremediation process and
different techniques
Keywords Bioremediation, types, process
Structure of Module/Syllabus of a module (Define Topic / Sub-topic of module )
Bioremediation
2. Development Team
Role Name Affiliation
Subject Coordinator <Prof. Sujata Bhargava> Savitribai Phule Pune
University
Paper Coordinator <Prof. NSR Krishnayya> MS University Baroda
Content Writer/Author (CW) < Dr. Deepa Gavali> Gujarat Ecological
Society, Vadodara
Content Reviewer (CR) <Prof. N S R Krishnayya>
Language Editor (LE) <Dr Latey> Savitribai Phule Pune
University
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TABLE OF CONTENTS (for textual content)
1. Introduction
2.Types of bioremediation
2.1 Phytoremediation
2.2 Mycoremediation
2.3 Biosorption
3. Advantages of Bioremediation
4 Disadvantages of Bioremediation
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BIOREMEDIATION
1. General Introduction
Bioremediation is a waste management technique that involves the use of organisms to remove or
neutralize pollutants from a contaminated site.According to the EPA, bioremediation is a “treatment
that uses naturally occurring organisms to break down hazardous substances into less toxic or non
toxic substances”. Technologies can be generally classified as in situ 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.
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.
However, not all contaminants are easily treated by bioremediation using microorganisms. For
example, heavy metals such as cadmium and lead are not readily absorbed or captured by
microorganisms. The assimilation of metals such as mercury into the food chain may worsen
matters. Phytoremediation 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.
Bioremediation can occur on its own in nature (natural attenuation or intrinsic bioremediation) or
can be spurred via addition of fertilizers for the enhancement of bioavailability within the medium
(biostimulation). Bioventing, bioleaching, bioreactor, bioaugmentation, composting, biostimulation,
land farming, phytoremediation and rhizofiltration are all examples of bioremediation
technologies. On the basis of removal and transportation of wastes, bioremediation technology can
be classified as in-situ and ex-situ. In-situ bioremediation involves treatment of contaminated
material at the same site, while ex-situ involves complete removal of contaminated material form
one site and its transfer to another site, where it has been treated using biological agents. In the
comparison of both methods, it was found that the rate of biodegradation and consistency of process
outcome differs between in- situ and ex-situ methods. With the need for excavation of contaminated
samples for treatment, the cost of ex situ bioremediation is relatively high as compared to in-
situ. In-situ and ex-situ, both the bioremediation methods depends essentially on microbial
metabolism, however, so far in-situ methods are preferred over ex-situ for ecological restoration of
contaminated soil, water and environment.
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2. TYPES OF BIOREMEDIATION
2.1 Phytoremediation
Phytoremediation, the use of plants to remove or degrade contamination from soils and surface
waters, has been proposed as a cheap, sustainable, effective, and environmentally friendly
alternative to conventional remediation technologies. Plants use solar energy (through
photosynthesis) to extract chemicals from the soil and to deposit them in the above-ground part of
their bodies, or to convert them to a less toxic form. These plants can then be harvested and treated,
removing the pollutants.
An ideal phytoremediator would have: high tolerance to the pollutant; the ability to either degrade
or concentrate the contaminant at high levels in the biomass; extensive root systems; the capacity to
absorb large amounts of water from the soil; and fast growth rates and high levels of biomass.
Although several species can tolerate and grow in some contaminated sites, these species typically
grow very slowly, produce very low levels of biomass, and are adapted to very specific
environmental conditions. And trees- which have extensive root systems, high biomass, and low
agricultural inputs requirements- tolerate pollutants poorly, and do not accumulate them.
Conventional plants therefore fail to meet the requirements for successful phytoremediators.
Phytoremediation of heavy metals from the environment serves as an excellent example of the
process of plant-facilitated bioremediation and its role in removing environmental stress. The ideal
type of phytoremediator is a species that creates a large biomass, grows quickly, has an extensive
root system, and must be easily cultivated and harvested (Clemens et al., 2002). The only problem
with this criterion is that natural phytoremediators often lack these qualities. Lead is one of the non-
essential compounds hyperaccumulated by several species of plants including
Thalaspirotundifolium and Brassica juncea.
The entry of heavy metals into the plant system is a complex process and involves both apoplastic
and symplastic pathways. The three main steps in inorganic ion transport in the symplastic
pathways are (i) active transport of metals across root membranes (ii) entry of metals into symplast
during translocation from root to shoot (iii) and chelation and sequestration of metals into specific
compartments in the leaves (Maestriet al.2010).
Chelation of metals within the plant allows for xylem loading and transport, as well as for
sequestration. These mechanisms involve many metal-specific chelators - i.e. ligands and organic
acids—many of which have only begun to be studied or have not yet been characterized.The role of
chelators in hyper-accumulation is to form complexes with heavy ions. This can serve the
functionof aiding intransport, orit can be the terminus of the ion, leading to sequestration in the
shoot of the plant. Metallothioneins and phytochelatins are two classes of chelators involved in
metal accumulation.
Different organic acids and ligands have been found to be associated with various metals in distinct
parts of different plants; for example, in Thalaspicaerulescens, most Zn in roots was associated with
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histidine, while in shoots it was associated with organic acids (Verbruggenet al.2009). Also in
Thalaspicaerulescens, Cd in the leaves was found to be bound with sulfur ligands (Verbruggenet al.
2009). In Arabidopsis halleri, Zn was mostly stored in the vacuoles of mesophyll, while in
Thalaspicaerulescens it was in the vacuoles of the epidermal cells (Verbruggenet al. 2009). In both
cases, vacuolar sequestration of Zn in the leaves was thought to be the main mechanism of
detoxification and this is a distinguishing trait between hyperaccumulators and non-
hyperaccumulators.
There are several advantages of phytoextraction. The cost of phytoextraction is fairly low, when
compared to conventional methods. Another benefit is that the contaminant is permanently removed
from the soil. In addition, the amount of waste material that must be disposed of is substantially
decreased (up to 95%) and in some cases, the contaminant can be recycled from the contaminated
plant biomass. The use of hyperaccumulator species is limited by slow growth, shallow root system,
and small biomass production. In addition, the plant biomass must also be harvested and disposed
of properly. There are several factors limiting the extent of metal phytoextraction including:
• Metal bioavailability within the rhizosphere
• Rate of metal uptake by roots
• Proportion of metal “fixed” within the roots
• Rate of xylem loading/translocation to shoots
• Cellular tolerance to toxic metals
Some drawbacks associated with phytoremediation are dependency on the growing conditions
required by the plant (i.e., climate, geology, altitude, temperature); tolerance of the plant to the
pollutant affect the success for remediation; contaminants collected in senescing tissues may be
released back into the environment in certain seasons; time taken to remediate sites far exceeds that
of other technologies and contaminant solubility may be increased leading to greater environmental
damage and the possibility of leaching.
2.2 Mycoremediation
Remediation through fungi is also called as mycoremediation. Mycoremediation tool refers to
mushrooms and their enzymes due to having ability to degrade a wide variety of environmentally
persistent pollutants, transform industrial and agro-industrial wastes into products.
In 1992, this theory was put into practice by U.S. Geological Survey scientists. During the cleaning
of San Francisco Bay oil spillin 2007 mycoremediationwas used usingPleurotusostreatus,
Ganoderma lucidum.
The mushrooms and other fungi possess enzymatic machinery for the degradation of
waste/pollutants and can be applied for a wide variety of pollutants (Purnomoet al. 2013;
Kulshreshthaet al. 2013). However, mushrooms, basidiomycetous fungus, are becoming more
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popular nowadays for remediation purposes because it is not only a bioremediation tool but also
provide mycelium or fruiting bodies as a source of protein. Fungi break down most contaminants
into non-toxic by-products but just act like dynamic accumulators with heavy metals. Oyster
mushrooms are also powerful absorbers of mercury and cadmium. Their mycelium channels
mercury from the ground up into the mushroom itself. Enzymes from the fungal mycelia are able to
cleave certain atoms like chloride (Cl-) off of larger molecules, and then break the bond between
hydrogen and carbon.Bacteria can help to further degrade these compounds into final products
including carbon dioxide (CO2), water, and potentially methane (CH4).Fungi have also proven
useful in remediation of heavy metals, such as lead (Pb) and cadmium (Cd)(Table 1).These metals
are already at their simplest state and are not degraded further; fungi can extract them from soil or
water and accumulate them in their tissues.Mushroom fruit bodies attracted innumerable flies and
insects and the previously contaminated soil became its own life sustaining habitat.
Table 1: Plant species and fungal spores used in the bioremediation process of the heavy
metals
Heavy Plant species Fungus
metal
Cd Trifoliumrepens Glomus mosseae
Hordeum vulgare
Ni BErkheyacoddii Gigaspora sp.
Glomus tenue
Zn Viola calaminaria Glomus sp.
Pb Zea mays Glomus intraradices
Cd, Cu Zea mays Glomus caledonium
Zn, Pb Lygeumspartum Glomus mosseae,
Glomus macrocarpum
Cd, Zn Glycine max Glomus mosseae
Zn, Cd, Cu, Ni, Pb Sorghum bicolour Glomus caledonium
Recently, it isreported that mushroom species are able to degradepolymers such as plastics (da Luz
et al. 2013) (Table 2).The biodegradation mechanism is very complex. Thereason is the influence of
other biochemical systems andinteractions of ligninolytic enzymes with cytochromeP450
monooxygenase system, hydroxyl radicals and thelevel of H2O2 which are produced by the
mushroom.
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2.3 Biosorption
The removal of metals/pollutants from the environment by bacteria is - biosorption. Biosorption is
considered as an alternative to the remediation of industrial effluents as well as the recovery of
metals present in effluent. Biosorption is a process based on the sorption of metallic
ions/pollutants/xenobiotics from effluent by live or dried biomass which often exhibits a marked
tolerance towards metals and other adverse impact. Biosorption can be defined as the ability of
biological materials to accumulate heavy metals from wastewater through metabolically mediated
or physico-chemical pathways of uptake.
The idea of using biomass as a tool in environmental cleanup has been around since the early 1900s
when Arden and Lockett discovered certain types of living bacteria cultures were capable of
recovering nitrogen and phosphorus from raw sewage when it was mixed in an aeration tank. This
discovery became known as the activated sludge process which is structured around the concept of
bioaccumulation and is still widely used in wastewater treatment plants today. It wasn't until the late
1970s when scientists noticed the sequestering characteristic in dead biomass which resulted in a
shift in research from bioaccumulation to biosorption.
Table 3: Microorganisms used for biosorption of heavy metals
Microorganism Elements References
References
Bacillus spp. Cu, Zn Philip et al., 2000; Gunasekaran et al., 2003
Pseudomonas U, Cu, Ni Sar et al., 1999; Sar and D’Souza,2001
aeruginosa
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Zooglea spp. Co, Ni, Cd Gunasekaran et al., 2003; Yan and
Viraraghavan, 2001;
Citrobacter spp. Cd, U, Pb Gunasekaran et al., 2003; Pearson, 1969;
Chlorella vulgaris Au, Cu, Ni, U, Pb,Hg, Gunasekaran et al.,2003
Zn
Aspergilusniger Cd, Zn Zn, Ag, Th,U Guibalet al., 1995;
Pleurotusostreatus Cd, Cu, Zn, Ag, Hg, P Gunasekaran etal., 2003
Kulshreshthaet al., (2010)
Essential Factors For Microbial Bioremediation
Factor Desired conditions
microbial population suitable kinds of organisms that can biodegrade all of the contaminants
enough to support aerobic biodegradation (about 2% oxygen in the gas
oxygen
phase or 0.4 mg/liter in the soil water)
soil moisture should be from 50–70% of the water holding capacity of the
water
soil
nitrogen, phosphorus, sulfur, and other nutrients to support good microbial
nutrients
growth
temperature appropriate temperatures for microbial growth (0–40˚c)
ph best range is from 6.5 to 7.5
Microbes degrade contaminants because in the process they gain energy that allows them to grow
and reproduce. Microbes get energy from the contaminants by breaking chemical bonds and
transferring electrons from the contaminants to an electron acceptor, such as oxygen. They "invest"
the energy, along with some electrons and carbon from the contaminant, to produce more cells.
Microorganisms can produce reduced or oxidized species that cause metals to precipitate.
Examples are oxidation of Fe2+ to Fe3+, which precipitates as ferric hydroxide (FeOH3(s));
reduction of SO42- to sulfide (S2-), which precipitates with Fe2+ as pyrite (FeS(s)) or with
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mercury (Hg2+) as mercuric sulfide (HgS(s)); reduction of hexavalent chromium (Cr6+) to
trivalent chromium (Cr3+), which can precipitate as chromium oxides, sulfides, or
phosphates; and, as mentioned previously, reduction of soluble uranium to insoluble U4+,
which precipitates as uraninite (UO2).
Microorganisms can biodegrade organic compounds that bind with metals and keep the
metals in solution. Unbound metals often precipitate and are immobilized.
3 Advantages of Bioremediation
• Bioremediation is a natural process and is therefore perceived as an acceptable waste
treatment process for contaminated material such as soil. Microbes able to degrade the contaminant
increase in numbers when the contaminant is present; when the contaminant is degraded, the
biodegradative population declines. The residues for the treatment are usually harmless products
and include carbon dioxide, water, and cell biomass.
• Bioremediation is useful for the complete destruction of a wide variety of contaminants that
are considered hazardous and can be transformed to harmless products. This eliminates the chance
of future liability associated with treatment and disposal of contaminated material.
• Instead of transferring contaminants from one environmental medium to another, for example,
from land to water or air, the complete destruction of target pollutants is possible.
• Bioremediation can often be carried out on site, often without causing a major disruption of
normal activities. 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.
• Bioremediation can prove less expensive than other technologies that are used for clean-up of
hazardous waste.
4 Disadvantages of Bioremediation
• Bioremediation is limited to those compounds that are biodegradable. Not all compounds are
susceptible to rapid and complete degradation.
• There are some concerns that the products of biodegradation may be more persistent or toxic
than the parent compound.
• Biological processes are often highly specific. Important site factors required for success
include the presence of metabolically capable microbial populations, suitable environmental growth
conditions, and appropriate levels of nutrients and contaminants.
• Research is needed to develop and engineer bioremediation technologies that are appropriate
for sites with complex mixtures of contaminants that are not evenly dispersed in the environment.
• Regulatory uncertainty remains regarding acceptable performance criteria for bioremediation.
There is no accepted definition of “clean”, evaluating performance of bioremediation is difficult,
and there are no acceptable endpoints for bioremediation treatments.
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References
Clemens S, Palmgren MG, Kraemer U. 2002. A long way ahead: understanding and engineering
plant metal accumulation. Trends in Plant Science 7: 309–315.
Kulshreshtha S, Mathur N, Bhatnagar P, Jain BL (2010) Bioremediation of industrial wastes
through mushroom cultivation. J Environ Biol 31:441–444
Kulshreshtha Shweta, Nupur Mathur and Pradeep Bhatnagar (2013). Mushroom as a product and
their role in mycoremediation. AMB Express 2014, 4:29
Maestri E, Marmiroli M, Visioli G &Marmiroli N. 2010. Metal tolerance and hyperaccumulation:
Costs and trade-offs between traits and environment. Environmental and Experimental
Botany 68: 1-13.
Purnomo AS, Mori T, Putra SR, Kondo R (2013) Biotransformation of heptachlor and heptachlor
epoxide by white-rot fungus Pleurotusostreatus. IntBiodeteriorBiodegrad 82:40–44,
doi:10.1016/j.ibiod.2013.02.013
Verbruggen N, Hermans C, Schat H. 2009. Molecular mechanisms of metal hyperaccumulation in
plants.New Phytol. 181(4):759-76.
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