BiCnews

A quarterly publication by the Malaysian Biotechnology Information Centre (MABIC)

*Issue 9* PP 12739/12/2004 Published on 1st April 2005 www.bic.org.my

Bioremediation:
Nature's Way to A Cleaner Environment

Soils and waters contaminated with toxic metals pose a major environmental and human health
problem that needs an effective and affordable technological solution. Many areas remain
contaminated with no remediation in sight because it is too expensive to clean them up with the
available technologies. Bioremediation may provide an economically viable solution for remediating
some of these sites.

Bioremediation is the application of biological treatment to the cleanup of hazardous chemicals. This
process involves detoxification, where the waste is made less toxic, and mineralization, where the
waste material is converted into inorganic compounds such as carbon dioxide, water and methane
(Martello, 1991). Bioremediation is an example of environmental biotechnology. This is not a
new concept. Microorganisms have been used to remove organic matter and toxic chemicals from
domestic and manufacturing waste effluents for many years. However, recent developments in
biotechnology have greatly improved the range of treatments available. Bioremediation is becoming
the technology of choice for the remediation of many contaminated environments, particularly sites
contaminated with petroleum hydrocarbons. In recent decades, serious attempts have been made to
harness nature’s biodegradative capabilities with the goal of large-scale technological applications
for effective and affordable environmental restoration.

In this issue of BiCnews, we have attempted to uncover the principles of bioremediation, its
advantages, applications, and obstacles in practicing this technology.
Photo courtesy of Dr. Ram Nayar

Bacteria are natural biodegraders

1
 CONTENTS

What is bioremediation 1

A Brief History of Bioremediation 3

Bioremediation Treatment Approaches 3

Q&A with Dr. Ting Yen Peng, Associate Professor, Dept. of Chemical & 4
Biomolecular Engineering, National University of Singapore

Laboratory Scale Composting 8

Microbes as Biodegraders 9

Plants as Biodegraders: Phytoremediation 9

The Reality of Bioremediation 12

Potential Benefits of Bioremediation 13

Limitations of Bioremediation 14

The Malaysian Experience 15

Challenges Ahead 17

The Road Ahead 18

References 19

Glossary 20

2
A Brief History of Bioremediation
Commercialization of bioremediation began in
Bioremediation has developed from the laboratory earnest at the end of the 1980s and in the 1990s,
to a fully commercialized technology over the particularly for the treatment of contaminated
last 30 years in many industrialized countries soils and more recently groundwater. A powerful
and has been the subject of active concern. promotion of the technology occurred after its
The use and manipulation of microorganisms high profile use on contaminated shorelines after
for treatment of municipal waste-water have the Exxon Valdez spill in 1989 and the term
been applied since ancient times. The Romans bioremediation began to get more widespread
and others built intricate networks of sewers as use.
early as 600 B.C. for collecting wastewater which
underwent subsequent biological treatment. Though bioremediation has been used to treat oil
The Roman architects planned, designed, and contaminated shorelines, most of the applications
constructed sewage systems that served their have been field scale research and development.
To date there have been relatively few examples
intended purpose for centuries. of the commercial use of the technology in
response to oil spills.
The initial interest in bioremediation in modern
days appears to be routed in treating oil sludges
Bioremediation Treatment
arising from refineries (CONCAWE, 1980), a
process that has been probably used for at least Approaches
40 years. This technique exploited the ability of
naturally occurring microorganisms in soil to A variety of bioremediation technologies have
degrade hydrocarbons, a phenomenon that had been developed to treat toxic waste. Several
been first recognized over 100 years ago. Later factors, such as site conditions, indigenous
research showed that microorganisms indigenous microorganism population, and the type,
to soil, groundwater and marine ecosystems could quantity, and toxicity of contaminant chemicals
degrade a wide range of compounds released into present determine the bioremediation technology
natural environment. These included aromatic most suitable for a specific site. Some treatment
and aliphatic compounds, hydrocarbons, technologies involve the addition of nutrients to
chlorinated solvents and pesticides. stimulate or accelerate the activity of indigenous

3
 Q & A with Dr. Ting Yen Peng, Associate Professor, Dept of Chemical &
Biomolecular Engineering, National University of Singapore
Q: How long have you been involved in
bioremediation research?
My first project in bioremediation was in 1983
when, as an engineer in petroleum refinery, I
implemented a programme in sludge farming as
a treatment for oily sludge (i.e. using natural oil-
degrading microorganisms). My research since
the mid 1980’s was in the area of biosorption,
bioremediation and bioleaching. (Bioleaching
since 2000)
Q: Could you define biosorption, bioremediation
and bioleaching?
Biosorption refers to the removal of trace levels
of heavy metals using sorbents of biological
origin. These sorbents are dead or inactive
organisms. Bioremediation refers to the use of
organisms to remediate the environment (using
biological principles to treat the pollutants).
Bioleaching refers to the use of microorganisms
to transform heavy metals from solid state into
aqueous phase, i.e. dissolution of heavy metals
from solid wastes.
Q: Is biosorption and bioleaching part of
bioremediation?
The broad definition of bioremediation would
include biosorption, although most work in the
field of bioremediation refers to the remediation
of organic pollutants, where microorganisms are
used to breakdown the organics. Bioleaching
is generally not seen as part of bioremediation,
since the leaching of metals from the solid phase
(i.e. comparatively stable, and not released into
the environment) to the aqueous phase actually
brings about more pollution problem, and
the metals are subsequently released into the
environment.
Q: Could you explain the different methods used Singapore? Could you give examples?
in bioremediation?
In general, in-situ and ex-situ treatment. The
former refers to treatment of the pollutants on
site, i.e. without removing the pollutants to be
treated at another facility, while the latter refers
to the removal of the pollutants to be treated in
another facility.
Q: What are the common pollutants that can be
treated through bioremediation technology?
This could include halogenated aliphatic
compounds, and aromatic compounds
Q: Could you name a few microorganisms that
could absorb or metabolize heavy metals?
Microorganisms can absorb heavy metals, but
they cannot metabolize heavy metals, since
heavy metals are not biodegradable (unlike
hydrocarbons). Many microorganisms are
known to be capable of absorbing heavy metals.
This includes bacteria, fungi, yeast, algae, etc.
These organisms in general have different degree
of affinity and specificity for different metals.
Q: Are these microorganisms found naturally in
the ecosystem or are they modified?
These organisms are naturally occurring
organisms, and there is in general no need to
modify these organisms. However, treatment
of these organisms (e.g. using chemical
modification) can often result in enhanced
performance of these microorganisms.
Q: What are the common hydrocarbon
degraders?
Numerous bacteria and fungi. E.g. Common
bacteria in soil includes Pseudomonas,
Arthrobacter, Achromobacter, Micrococcus,
Vibrio, Acinetobacter, Brevibacterium,
Corynebacterium, and Flavobacterium. A well
known fungi: Phanerochaete chrysosporium
(white rot fungi) is capable of treating hazardous
compounds via the production of extracellular
enzymes known as peroxidases).
Q: Is bioremediation practiced widely in
No, it is not widely practiced.
4
Q: What are the benefits in bioremediation
technology?
Benefits: (i) generally cheaper than the use of
conventional technologies; (ii) bioremediation
biodegrades and detoxifies the hazardous
contaminants; other conventional treatment (e.g.
venting, sorption, solidification/stabilization, soil
washing, disposal in landfills etc) merely transfer
the pollutants from one medium to another.

Q: What are the shortcomings in this

technology?
Disadvantages: (i) Time consuming. Not as rapid
as conventional physical/chemical technologies.
(ii) Often difficult in predicting field performance,
and difficult to scale up from lab to the field.
(iii) Microorganisms are sensitive to the
environment, i.e. temperature, pH, contaminant
level and toxicity, moisture content, need
to provide nutrients, etc. (iv) Sometimes
cleanup goals cannot be attained because some
contaminants are only partially biodegradable.
Q: Can bioremediation be an economically
feasible method to treat waste?
Yes, but bear in mind the benefits and
disadvantages discussed above.
Dr. Ting Yen Peng is an Associate Professor
with the Department of Chemical and
Biomolecular Engineering, National
University of Singapore. Dr. Ting obtained
his Bachelor and Master degrees in Chemical
Engineering from University of Manchester
Institute of Science and Technology. He later
earned his PhD from Monash University. Dr.
Ting has numerous publications in his areas
of research in biosorption of heavy metals,
bioremediation and contamination, and
bioleaching of metals from solid wastes.

Q: Is bioremediation practiced widely elsewhere

in the world? Could you give examples?
The most famous case is the Exxon Valdez in
Prince Williams Sounds, Alaska.

5
microbes. Optimizing environmental conditions
will enhance the growth of microorganisms
and increase microbial population resulting in
improved degradation of hazardous substances.
However, if the biological activity needed to
degrade a particular contaminant is not present
at the site, suitable microbes from other locations,
called exogenous microorganisms, can be
introduced into the system and nurtured.
Bioremediation techniques can be easily
combined to make the clean up process
more efficient. Dr. Ting Yen Peng, Associate
Professor from the Department of Chemical and
Biomolecular Engineering, National University
of Singapore, describes bioremediation as the use
of microorganisms to mediate the transformation
of hazardous chemicals to less toxic and
environmentally acceptable compounds.
According to Dr. Ting, bioremediation processes
may be classified into two main categories: in-
situ and ex-situ which are discussed below.
In-situ Bioremediation
In-situ method involves the remediation of
contaminated material within the confines of
the area in which it was originally contaminated.
In-situ techniques do not require excavation of
the contaminated soils so may be less expensive,
create less dust, and cause less release of
contaminants than ex-situ techniques. However,
it may be slower than ex-situ techniques, difficult
to manage, and are most effective at sites with
permeable (sandy or uncompacted) soil.
A common procedure for in-situ bioremediation
starts with the introduction of nutrients
and oxygen and relying on the indigenous
microflora to destroy the unwanted molecules.
This process is sometimes called biorestoration.
Oxygen can be provided by pumping air into
the soil above the water table (bioventing) or by
delivering the oxygen in liquid form as hydrogen
peroxide. In-situ bioremediation may not work
well in clays or in highly layered subsurface
environments because oxygen cannot be evenly
distributed throughout the treatment area. In-situ
remediation often requires years to reach cleanup
goals, depending mainly on how biodegradable
specific contaminants are. Less time may be
required with easily degraded contaminants.
Source: Prof. Dr. P. Agamuthu, University of Malaya
6
Ex-situ Bioremediation Examples of solid-phase soil treatments include
composting and landfarming which are discussed
Ex-situ techniques can be faster, easier to control, below.
and used to treat a wider range of contaminants
and soil types compared to in-situ techniques. Composting. This form of bioremediation has
However, they require excavation and treatment been practiced for a long time and is a fairly
of the contaminated soil before and, sometimes, common household practice in some countries.
after the actual bioremediation step. Ex-situ Biodegradable waste is mixed with bulking agent
treatment is usually more expensive than in- such as straw, hay, or corn cobs to make it easier
situ approach, but it is used because properties to deliver the optimum levels of air and water
of the waste or the site make in-situ treatment to the microorganisms. Bioremediation through
impractical. The higher costs of an ex-situ composting has proven effective in degrading and
treatment come from the expenses of moving altering many types of contaminants, including
the contaminated material, the capital required chlorinated and nonchlorinated hydrocarbons,
for constructing the needed equipment for the wood preserving chemicals, solvents, heavy
particular cleanup, additional labour, the need for metals, pesticides, petroleum products and
power, or a combination of these factors. explosives. Compost also has been shown to
bind various heavy metals, making them less
Ex-situ techniques include slurry- bioavailable to plants and animals.
phase bioremediation and solid-phase
bioremediation. There are three methods of composting
– windrow composting, aerated static pile, and
Slurry-Phase Bioremediation. This technique of in-vessel composting. Windrow composting,
bioremediation involves the combination of soil, as its name suggests, consists of placing the
water and other additives in a large tank called mixture of raw materials in a long narrow piles
a "bioreactor". The content of this tank is then which are agitated or turned on a regular basis.
mixed to keep microorganisms in contact with the In aerated static pile, a blower is used to supply
contaminants in the soil. Nutrients and oxygen air to the composting materials and no turning or
are added, and conditions in the bioreactor are agitation of the materials occurs once the pile is
controlled to create the optimum environment for formed, while in-vessel composting is confined
the microorganisms to degrade the contaminants. within a building, container, or vessel. This
Upon completion of the treatment, water is method requires a variety of forced aeration and
removed from the solids, which are disposed mechanical turning techniques to speed up the
or treated further if they still contain pollutants. process. Some examples of in-vessel composting
include bin composting, rectangular agitated
Slurry-phase biological treatment can be a
Photo courtesy of New York State Department

relatively rapid process compared to other

biological treatment processes, particularly for
of Environmental Conservation

contaminated clays.

Solid-Phase Bioremediation. Solid-phase

bioremediation is a process that treats soils in
above-ground treatment areas equipped with
collection systems to prevent any contaminant
from escaping the treatment. Moisture, heat,
nutrients, or oxygen are controlled to enhance
biodegradation for the application of this
treatment. Solid-phase systems are relatively
simple to operate and maintain, but require a A pile of compost. Materials resulting from
large amount of space, and cleanups require more compsting can be used as soil conditioner or
partial fertilizer.
time to complete than the slurry-phase processes.
7
beds, silos, and rotating drums. for a long time, more research is needed to
perfect the technique to make it commercially
Landfarming. Landfarming, also known as land feasible. Much research work is being carried
treatment or land application, is an above-ground out locally and one such work is by Associate
remediation technology for soils that reduces Prof. Dr. Mohd. Nasir Hassan from the Faculty
concentrations of petroleum constituents through of Environmental Studies, Universiti Putra
biodegradation. Landfarming is the lowest cost Malaysia.
approach to the bioremediation of contaminated
soil. In landfarming, soil is removed and taken Dr. Nasir’s research is on treating domestic waste
to another area where it is spread out in thin in a semi-aerobic condition. The operation of a
layers. Again, factors like moisture is controlled, semi-aerobic bioreactor is favoured because
nutrients are provided, and there is some tilling it generates less landfill gases and leachate
to support aeration of the soil to optimize the compared to anaerobic conditions. Landfill
process. Microbes can also be added to enhance gases such as methane, ammonia, hydrogen
microbial activity. sulfide and carbon dioxide have to be reduced
to minimize the greenhouse effect. The leachate
Laboratory Scale Composting generated from anaerobic composting, if not
treated, contaminates river, sea and underground
The management of waste materials is a global water. It also creates a very offensive odour and
problem. In the developing countries, waste has extremely high Chemical Oxygen Demand
management is becoming an acute problem as (COD) and Biological Oxygen Demand (BOD).
urbanization and economic development increase The COD and BOD of this leachate are 30,000
leading to larger quantities of waste materials. ppm and 10,000 – 15,000 ppm respectively. Dr.
This is especially true in Malaysia, which has Nasir’s research has shown very promising effect
been categorized as an emerging industrialized in eliminating these problems.
country. Malaysia is facing an increase in the
amount of waste generated. Overall, the local Dr. Nasir uses a bioreactor or a compost bin that is
communities generate 16,000 tons of domestic made from bamboos which has a capacity of 500
waste per day and the amount per capita vary kg. The waste that goes into Dr. Nasir’s bioreactor
from 0.45 to 1.44 kg per day depending on the is domestic waste with very high nitrogen
economic status of the areas concerned (GAIA content. No additional nutrients are needed to
Global Meeting, 2003). enhance the growth of microbes. Microbes that
are naturally occurring in the waste take charge
The rapid increase in domestic waste is beginning in the biodegradation process. Some wood chips
to produce social, economic and environmental are added to the bioreactor to improve aeration.
problems of The landfill gases
significant that are generated
proportion. An such as carbon
Photo courtesy of Dr. Mohd. Nasir

answer to this dioxide, methane,

problem might and ammonia are
be composting. analyzed using an
Composting in situ multigas
is the natural analyzer. The gases
decomposing of are analyzed at
organic waste different positions
materials. While of the bioreactor
this technique has – exhaust, inlet,
been employed and upper,

Dr. Mohd. Nasir Hassan giving a presentation

8
middle and bottom parts of the compost. The
temperature could go up to 70 degrees Celsius
in the bioreactor.
According to Dr. Nasir, with his method of
composting, he has reduced the time required
to completely degrade the domestic waste from
three months to three weeks. He also manages
to collect 50kg of humus at the end of the
biodegradation. Although this only amount to
10% of the waste treated and more research is
needed to make it economically feasible, the
volume of landfill could be reduced by 90%,
which is a substantial amount.
Microbes as Biodegraders
Microbes found in natural waters and soils
have a very broad ability to utilize virtually all
naturally occurring compounds as their source of
carbon and energy. The breadth of this catabolic
ability of microbes far exceeds the hugely more
limited abilities of higher organisms which can
only use a relatively small range of compounds
"The breadth of this catabolic ability of microbes far exceeds the
hugely more limited abilities of higher organisms which can only
use a relatively small range of compounds as foodstuffs."
as foodstuffs. This ability of bacteria and fungi
to utilize a wide range of compounds makes
microorganisms ideal candidates for use in the
bioremediation of pollutants. They are genetically
extremely adaptable and, in addition to their rapid
growth rates, these organisms have a range of
mechanisms which enable them to adapt to
new environments. The goal in bioremediation
is to stimulate microorganisms with nutrients
and other chemicals that will enable them to
destroy the contaminants. Undergoing complex
chemical reactions, the waste is metabolized
into final metabolic waste products, water and
carbon dioxide.
The bacteria involved in the process of
bioremediation are simply gluttonous microbes.
These microbes either naturally occur in the
contaminated sites or newly introduced to the
site. However, most of the time the naturally
occurring microbes are not sufficient to degrade
Photo courtesy of NASA
Mixed culture of bacteria like this one are natural
degraders
the contaminants due to the nature of these
compounds. Thus, researchers are currently
investigating ways to augment contaminated sites
with non-native microbes suited to degrading the
contaminants of concern at particular sites. This
process is known as bioaugmentation. Optimum
environmental conditions must be created to
enable microbes to detoxify the maximum
amount of contaminants. To stimulate the growth
of these microbes, the proper soil temperature,
oxygen, and nutrient content may need to be
provided. The process of adding nutrients to help
microbes grow and reproduce faster is known as
biostimulation.
Plants as Biodegraders:
Phytoremediation
Besides microorganisms, plants too play a
great role in the cleansing of our environment.
The word ‘phyto’, pronounced as ‘fie-toh’,
originated from Greek which also means plant.
Phytoremediation is a process whereby plants are
used for the cleanup of heavy metal contamination
in soil and water. This approach to environmental
restoration allows the treatment of many sites
that cannot be addressed with currently available
methods, and phytoremediation preserves the
topsoil and reduced the amount of hazardous
9
materials generated during cleanup. Rhizodegradation

There are many types of phytoremediation and Rhizodegradation is a specific kind of

they are explained below: phytodegradation that occurs in the root zone. It is
the break down of organic contaminants through
Phytoextraction microbial biodegradation that is enhanced by the
presence of plants. The rhizosphere is the area
An idea of what phytoextraction is can be of soil around plant roots that contains higher
developed just by understanding the word populations of microbes and more microbial
itself. One would be able to deduce that it activity than soil where no vegetation exists.
involves the usage of plants for extraction. Plant roots release exudates such as short chain
More correctly, phytoextraction is the use of organic acids, phenolics, enzymes, and proteins
metal-accumulating plants that can transport that affect the enzyme systems of the bacteria
and concentrate metals from the soil to the roots already living in the soil. Plants also make the
and aboveground shoots. The contaminants are soil in the rhizosphere a habitat for mycorrhizae
generally removed by harvesting the plants. In fungi that metabolize organic pollutants. The
developing phytoextraction, researchers have mechanisms for rhizodegradation metabolism
focused on plant species that have such desirable are the same as those of microbial degradation.
characteristics as high biomass production, The difference is that rizodegradation involves
handling ease, genetic characterization, and enhancement of the microbial processes by plants
established cultivation practices. Phytoextraction and their root systems.
may potentially be used in large-scale, cost-
effective, on-site treatment because of its Another form of rhizodegradation is
relatively low cost. Topsoil would be preserved rhizofiltration. Rhizofiltration is the use of plant
and the amount of hazardous materials generated roots to absorb, concentrate as well as precipitate
reduced significantly. heavy metals from water. The ability to absorb
different metal ions is a common property of all
plant roots but varies between plant species. The
Photo courtesy of USDA

Bacteria around the roots of a plant helps in phytoremediation

10
roots of sunflowers have been used to treat water
containing lead, uranium, strontium, cesium,
cobalt, and zinc to concentrations below the
accepted water standards (Dushenkov et. al.,
1995). The other potential plants are eastern
cottonwood and water hyacinth.
Phytostabilization
Phytostabilization is a process in which plants
are used to immobilize metals and radionuclides
in the soil (and thus minimize their mobility in
water or dust). Plants are capable of immobilizing
contaminants in soil through absorption and
accumulation by roots, or precipitation within
the root zone. Phytostabilization also involves
the use of plants and plant roots to prevent
contaminant migration via wind and water
erosion, leaching, and soil dispersion (USEPA,
Introduction to Phytoremediation).
This method also refers to establishing a plant
cover on the surface of the contaminated soil or
sediment to wind, water, and direct contact with
humans or animals. In short, plants can be used as
shields to protect the environment. Specifically,
the contaminants to other substances and/or
transpires them, or volatilizes them, into the
atmosphere.
Phytodegradation
Lastly, phytodegradation is the uptake and break
down of organic contaminants through metabolic
processes within the plants. This process of
phytoremediation does not apply to inorganic
contaminants such as metals because metals are
already in their elemental form, and thus cannot
be degraded. The extent to which degradation
is a successful method of phytoremediation
depends on how well the plant can uptake the
contaminants. Once the organic contaminants
have been taken up by the plant, they are degraded
via metabolic pathways and incorporated into the
plant tissues and used as nutrients (EPA, 1998).
Studies have shown that enzymes produced by
the plant are responsible for the degradation of
many contaminants, particularly chlorinated
solvents (EPA, 2000).
Photo courtesy of Department of Agriculture, Western Australia

metal immobilizing plant species that are

tolerant of higher levels of contaminants are
used to decrease toxicity and enable the growth
of vegetation over areas where contaminant
concentrations are toxic to plants.

Phytovolatilization

This particular form of phytoremediation

involves the uptake and transpiration of a
contaminant by a plant. Either the contaminant
or a modified form of the contaminant is released
into the atmosphere (EPA, 1998). It has been
mainly applied to groundwater, but it can also
be applied to sludges, soil and sediments. Mostly
used to remove chlorinated solvents, it has also
shown promise in removing selenium, mercury
and arsenic (EPA, 2000).

As a plant grows, it takes up water through its Water hyacinth has the ability to absorb heavy metals
root. After the plant has absorbed and captured
the contaminants, the plant’s metabolic processes
begin to take over. The plant then converts
11
The Reality of Bioremediation Nitrogen and phosphorus-rich nutrients were
applied to the shorelines to stimulate the growth
Exxon Valdez Oil Spill of these naturally occurring oil-degrading
microorganisms. The results were encouraging.
On March 24, 1989, the tanker Exxon Valdez, Laboratory studies and visual observation
en route from Valdez, Alaska, to Los Angeles, confirmed that added nutrients enhanced the
California, grounded on Bligh Reef in Prince extent and rate of oil degradation, and oil samples
William Sound, Alaska. Eleven tanks were torn showed changes in hydrocarbon composition
open in the grounding, spilling an estimated 11 that indicated that extensive biodegradation had
million gallons of crude oil. The oil contaminated occurred.
some 350 miles of shoreline in Prince William
Sound, Alaska. Initial cleaning operations Overall, the clean up was regarded as a successful
involved physical methods such as flooding example of the possibilities of bioremediation.
with water, vacuum extraction, skimming, It was estimated that conventional cleaning
tilling, and high-pressure hot-water washing. methods would take five to ten years before
But some oil still coated rocks and other surfaces natural conditions were achieved, but with
and remained trapped in and below the matrix bioremediation this was possible in two to five
of gravel. A panel investigated the feasibility of years.
using bioremediation to deal with the difficult
task of cleaning the shore.
Hanahan, South Carolina leakage
Large community of microorganisms were
found at the contaminated site, which were able The problem in Hanahan, South Carolina, a
to produce enzymes that work to breakdown quiet suburb of Charleston, was not particularly
the hydrocarbons in the oil into carbon dioxide, unusual. In 1975, a massive leak from a military
water and other simpler, non toxic compounds. fuel storage facility released about 8,000 gallons of
Photo courtesy of National Ocean Service

Exxon Valdez oil spill: In Northwest Bay of Knight Island, tides have deposited oil on this rocky beach

12
kerosene-based jet fuel. Immediate and extensive
recovery measures managed to contain the spill, In 1992, this theory was put into practice by
but could not prevent some fuel from soaking USGS scientists. Nutrients were delivered to
into the permeable sandy soil and reaching the contaminated soils, contaminated ground water
underlying water table. Soon, the ground water was removed by a series of extraction wells, and
was leaching such toxic chemicals as benzene the arduous tasks of monitoring contamination
from the fuel-saturated soils and carrying them levels began. By the end of 1993, contamination
toward a nearby residential area. in the residential area had been reduced by 75
percent. The results were even better nearer to
In 1985, contamination had reached the residential the site where nutrients were pumped in. Ground
area, and there was a serious environmental water that once had contained more than 5,000
problem. Removing the contaminated soil parts per billion toluene now contained no
was technically impractical, and removing detectable contamination.
contaminated ground water did not address
the source of the contaminants. How could Potential Benefits of Bioremediation
contaminated ground water be kept from seeping
toward the residential area in the future? Several aspects of bioremediation make it an
appealing choice. Bioremediation has several
One possible solution was bioremediation. advantages over other approaches, and is often
Studies by the U.S. Geological Survey (USGS) used in combination with other solutions. Some
had shown that microorganisms naturally of the advantages of bioremediation are briefly
present in the soils were actively consuming discussed here:
fuel-derived toxic compounds and transforming
them into harmless carbon dioxide. Furthermore, Cost Effective. The costs of bioremediation
these studies had shown that the rate of these as compared to other remedial alternatives
biotransformations could be greatly increased are comparably much lower. For instance,
by the addition of nutrients. By stimulating the bioremediation techniques are typically more
natural microbial community through nutrient economical than traditional methods. It is
addition, it was theoretically possible to increase estimated that bioremediation costs 1/3 to 1/2
rates of biodegradation and thereby shield the that of incineration, and for complex mixtures
residential area from further contamination. of waste, bioremediation typically offers
Photo courtesy of European Union Gas

A biogas plant in Denmark. Landafill gases can be used as fuel

13
savings of 60-90% over landfill-disposal costs. liability associated with treatment and disposal
Conventional treatments usually involve high- of contaminated material.
end engineering methods and structures that
require more revenue. Another example of Exposure risks are at minimal. Conventional
conventional method is chemical treatment methods often include personnel to come in
which is equally costly. Also, companies needclose contact with contaminants while executing
to adhere to regulatory acts posed by government
clean up procedures like excavation. Apart from
when treating wastes and in most cases, the that, these methods also include the transfer of
cost is higher when conventional methods are contaminants to a secondary site which would run
employed. Thus, many companies are opting forthe risk of a more widespread exposure should
bioremediation technology. accidents happen. Bioremediation keeps these
risks at a minimal as the process of degradation
Natural treatment and environmentally safe is left for it to take its natural turn.
process. Bioremediation is a natural process
Photo courtesy of Boulder Area Sustainability
Information Network

Not all types of waste can be treated with bioremediation techniques

and is therefore accepted as a safe process. Limitations of Bioremediation

Microbes are able to degrade contaminants to
harmless substances that are not detrimental to Though bioremediation shows promise in
the environmental such as carbon dioxide, water remediating contaminated sites, there are
and cell biomass. Heavy metals are absorbed other concerns that makes this technology less
from soil and accumulated in the plants with thefavorable. There are a number of disadvantages
technology of phytoremediation resulting with that are associated to bioremediation and more
soil that is more fertile and less toxic. research in this area is needed to perfect the
technology. The main limitations are discussed
Holistic approach. Bioremediation transforms below:
pollutants instead of simply moving them from
one media to another. For example, in the past Incomplete transformation. There are
some polluted soils were buried in landfills in possibilities that contaminants are not completely
which case the pollutant was not destroyed transformed into innocuous substances.
but only transferred and the problem was only There are some concerns that the products of
delayed. This eliminates the chance of future biodegradation may be more persistent or toxic
14
than the parent compound. There is no guarantee Technology still at its infancy. Bioremediation
that all contaminants are transformed into safe technology is still fairly new and a lot needs to be
compounds. ironed out before the technology can be widely
and successfully practiced. It is also difficult to
Biological processes are highly specific. In order extrapolate from bench and pilot-scale studies to
for organisms to successfully reduce pollutant full-scale field operations.
levels, their growth conditions must be determined
and maintained at the contaminated site. The Not all contaminants are biodegradable. The
presence of metabolically capable microbial extent of remediation is highly dependent on the
populations, suitable environmental growth toxicity and the initial levels of contaminants,
conditions, and appropriate levels of nutrients their ability to be biodegraded and the properties
and contaminants need to be closely monitored. of the soil in which the contaminants lie. Sites
Controlling these conditions may prove difficult, that are unable to be cleaned with microbes
particularly as conditions may vary from site to include those with high metal concentrations
site. Even in an ideal environment, an organism (i.e. mercury), highly chlorinated organics
may prefer to metabolize other more readily (compounds with many chlorine elements
available nutrients within a contaminated area attached), and inorganic salts. These types of
instead of the contaminant, or the contaminant compounds are toxic to the microbes.
may be partially or completely inaccessible to
the degrading organism. Moreover, the addition The Malaysian Experience
of nutrients and oxygen might affect the growth
of other organisms found in the area. Solid waste management is one of the major
problems for local governments in Malaysia.
Introduction of non-native organisms. The Solid wastes are by-products of human and
introduction of non-native organisms may have animal activities that come from domestic,
long-term effects that are incomprehensible to commercial, and industrial entities. The rates of
us. This act may or may not be harmful to the waste generation are expected to grow steadily
environment. Generally, when knowledge of how as Malaysian economy grows. Malaysian solid
these treatments will affect the environment is wastes contain very high organic matters and
not at hand, it could pose as a hindrance to the consequently high moisture content and bulk
use of the technology. density of above 200kg/m3. A recent study
conducted in Kuala Lumpur has revealed that
62 to 72% of residential wastes are organic (CAP
Photo courtesy of US Department of Energy

More research is needed to tackle various kind of waste effectively

15
report, 2001).
Under the Seventh Malaysia Plan (1995-2000),
the Federal Government had spent RM20.9
million to build nine sanitary landfills and upgrade
27 existing landfills in 34 local authorities. The
Malaysian Government has recognized integrated
waste management as a new option in solid waste
management. This includes waste minimization,
reuse, material recycling, energy recovery and
landfill. According to the Economic Planning
Unit, generating energy from waste is one of
the new technologies that will be emphasized in
the near future.
Prof. Agamuthu; a Professor of Solid and
Hazardous Waste Management from University
of Malaya who has vast experience in waste
management believes bioremediation can help
solve many environmental problems plaguing
waste management in Malaysia. According to
Prof. Agamuthu, waste generated in Malaysia
can be categorized to solid and hazardous
wastes. Examples of solid wastes are municipal
waste which comes from residential areas and
some industries which generate non-hazardous
waste that is high in organic matter. Waste from
breweries, food producers, and some agricultural
based industries are considered as municipal
waste since they are non-hazardous and could be
released to the main waterways after treatment.
Hazardous wastes are highly flammable, and are
high in heavy metals and inorganic substances.
The main producers of this category are
industries, hospitals and universities.
Though, bioremediation is not the main option
for most industries and local government in
Malaysia, there has been some significant
success when this method is employed. Several
companies in Malaysia have embarked on
bioremediation and minimization of waste.
Most companies shy away from this technology
due to the cost of operation and the time needed
to achieve the desired results. Prof. Agamuthu
says specific microbes are needed to remedy
the contaminants and the cost of identification,
isolation, cultivation, and storage is high. He
also added that government policies and low
enforcement of regulations does not motivate or
encourage industries to be more environmental
Photo courtesy of Prof. Agamuthu
Prof. Agamuthu; Professor of Solid and Hazardous
Waste Management in University of Malaya
friendly.
However, it is not a doom and gloom situation.
There are already some successes in biological
treatment of domestic waste. A sanitary landfill
located at the Air Hitam Forest Reserve is one
such example. This landfill is managed by
Worldwide Sita Environmental Management
Sdn Bhd, a consortium which has built similar
landfills in Japan, Thailand and Hong Kong.
The landfill measures 10million cubic metres
and accepts waste from seven local authorities.
The wastes treated here are either domestic or
industrial wastes that are non-toxic and non-
radioactive. The landfill has a capacity of 2
MegaWatt power generation. This project is
being implemented by Jana Landfill Sdn Bhd,
a wholly-owned subsidiary of Tenaga Nasional
Berhad. The landfill gases are generated through
the natural decomposition process of municipal
waste at the landfill site. The main components of
landfill gases are methane (50 – 60%) and carbon
dioxide (30 – 40%). However, this landfill has
served its life-span and a similar landfill will
soon commence operation in Bukit Tagar, Kuala
Selangor.
In order for bioremediation techniques to be used
widely, Malaysia needs a paradigm shift, says
Prof. Agamuthu. He also believes a change in
government’s approach towards the management
of waste will set a new horizon in this area.
Proper planning and strict regulations will go
a long way. Lack of consumer awareness and
16
 "Government policies and low enforcement of regulations does
not motivate or encourage industries to be more environmental
friendly"....... Prof. Agamuthu

attitude towards a number of waste management genomics, geo-chemistry, along with hydrology
issues also hinder the implementation of effective and transport processes. To date, little is known
waste management options. on how introduced microorganisms interact with
different hydrological environment. Apart from
that, the pathways of biodegradation and bio-
Challenges Ahead
transformation remains unclear. Research in
each of the variety of fields is needed to further
Bioremediation is a fairly new technology and
researchers’ comprehension on the actual
holds the promise of becoming the solution to our
activity or rather, the chemistry that is involved
polluted environment. This new technology gives
and interactions between contaminants, native
us alternative routes to cleaning up contaminated
organisms on site and remedial organisms. There
sites was thought to be not possible previously.
is still much to learn and gain from research as
Even so, the technology of bioremediation still
contaminated sites are complex systems- each
has a long way more to go. There are limitations
composed of different types of contaminants,
that hinders the progress of this technology as
diverse organisms, and dissimilar environment.
well as from fulfilling its full capacity.
Only with knowledge can the advancement of
bioremediation take place.
Bioremediation faces several challenges and
some of the most common ones are discussed
Lack of integrated research. Bioremediation
briefly below:
is a multidisciplinary field and researchers from
various fields need to integrate their knowledge.
Deficit of knowledge. A deficit of knowledge on
The success and efficiency of bioremediation
the different fundamental branches of sciences
requires the involvement of microbiologists,
that are involved in the process of bioremediation
biochemists, engineers, geologists, and soil
hinders the progress of bioremediation. Examples
scientists among others. Knowledge on the
of the different disciplines of sciences are such as
combined factors is not enough and mostly,
structural and molecular biology, microbiology,
Photo courtesy of Canberra Connect

Biological treatment can partially solve problems in municipal waste management

17
these are the rate limiting factors of the process
of bioremediation. Interdisciplinary research of
at the least two fields is unavoidable to advance
this technology. Assimilation of scientific ideas
across disciplines is most needed to optimize the
potential of bioremediation.
Lack of revenue. There is no doubt that
governmental and private sectors are investing
on biotechnology companies but not much
of the revenue goes to the improvement of
bioremediation. Lack of revenue is an obstruction
to advancement in bioremediation as it prevents
further research and discoveries from taking
place. Thereupon, progress of bioremediation is
delayed as a result of material deficiency.
Inadequate tools and infrastructure.
Infrastructure and materials are needed to
carry out research. Accuracy in experimental
procedures is crucial to ensure successful
treatment when introduced to contaminated site.
However, there is inadequacy of infrastructure to
analyze the conditions of contaminated sites as
well as monitor the process of degradation that
has been introduced to the site. Insufficiency
of advanced tools specifically designed to aid
research on bioremediation would also hold
back development of research methodology
and prevent discoveries from happening.
The Road Ahead
Humankind has always liked what is familiar economic analysis has not been conducted to
to them, and feared all that is foreign or rather, date.
new to them. Bioremediation is still a fairly new
technology to the public as well as the industries.
Much research and development have to be done
before the technology can really take off, as
there are plenty of challenges, and drawbacks
that pose as a hindrance. Moreover, with each
new development on the technology, education
for the public is needed to help gain acceptance
of the technology. There is no doubt that
bioremediation definitely holds potential but the
technology have yet to come a long way before
it can be realized. In addition, the realization of
the technology will also depend on the public,
as they must be comfortable and in the know of
what is being done to their surroundings.
Previously, bioremediation techniques in
applying to contaminated sites have proven to
be successful. This has shown a positive light
onto the technology as it shows that it is possible
to clean the environment of pollutants through
a ‘natural’ way and in a shorter time span than
expected. Further development on the technology
to remediate all kinds of contaminants in different
conditions will definitely help it to grow and go a
long way in helping us attain a healthier, safer and
undeniably cleaner environment. Turning back
to nature to find the solution to the problems we
created will not only be a new step but one that
is logical. Exploitation of nature’s best through
biotechnology, to our benefit will also in turn
benefit the environment. And, nature has many
secrets that are ignorant to all of humankind.
Therefore, bioremediation is here to stay, as the
possibilities it holds are endless.
The extensive environmental regulations over
the past twenty years that limit the disposal of
toxic compounds have made bioremediation an
attractive solution. Although bioremediation
holds a great promise for dealing with intractable
environmental problems, it is important to
recognize that much of this promise has yet to be
realized. Presently bioremediation is a growing
field. Research is continuing to further the cost-
effectiveness and expand the possibilities. If done
properly, it is believed that bioremediation can
be very cost-effective, although an in-depth
Photo courtesy of Fisheries and Oceans
Canada
Bioremediation is still in its infancy. More research
is needed to perfect the technology
18
References:

1. Alexander, M. 1999. Biodegradation and bioremediation. Second Edition. Academic Press,

USA.
2. CONCAWE. 1980. Sludge farming: A Technique for the Disposal of Oily Refinery Wastes.
Rep. 3/80. CONCAWE, The Hague, Netherlands.
3. Crawford, R.L. and Crawford, D.L. 1998. Bioremediation. Principles and Application.
Cambridge University Press.
4. Dagley, S. 1971. Catabolism of aromatic micro-organisms by micro-organisms. Adv.
Microbial Physiol. 6: 1-46.
5. Dushenkov, S. et al., 1995. Rhizofiltration: The use of plants to remove heavy metals from
aqueous streams. Environ. Sci. Technol. 29: 1239-1245.
6. GAIA Global Meeting 2003. Malaysia. 17-21 March 2003.
7. Gale, E.F. 1952. The Chemical Activities of Bacteria. Academic Press, New York, USA.
8. Introduction to Phytoremediation, USEPA, Office of Research and Development, EPA/600/
R99/107, February 2000.
9. MacRae, I.C. 1989. Microbial metabolism of pesticides and structurally-related compounds.
Rev. Environ. Contam. Toxicol. 109: 1-87.
10. Malaysia Country Report, 2001. Consumers’ Association of Penang.
11. Martello, Angela. “Bioremediation: Cleaning up with Biology and Technology.” Vol. 5,
Issue 1, 7 Jan, 1991.
12. Morgan, P., and Watkinson, R. 1989a. Hydrocarbon degradation in soils and methods for
soil biotreatment. CRC Crit. Rev. Biotechnol. 8: 305-333.
13. Morgan, P., and Watkinson, R. 1989b. Microbiological methods for cleanup of soil and
groundwater contaminated with halogenated organic compounds FEMS Microbiol. Rev. 5:
277-299.
14. Personal communication. Dr. Mohd. Nasir Hassan, Faculty of Environmental Studies,
Universiti Putra Malaysia.
15. Personal communication. Dr. Ting Yen Peng, Department of Chemical and Biomolecular
Engineering, National University of Singapore.
16. Personal communication. Prof. P. Agamuthu, Institute of Biological Sciences, Faculty of
Science, University Malaya.
17. Prince, R.C. 1993. Petroleum spill bioremediation in marine environments. Crit. Rev.
Microbiol. 19: 217-242.
18. Raskin, I and Ensley, B.D. 2000. Phytoremediation of Toxic Metals. Using Plants to Clean
Up the Environment. John Wiley & Sons, Inc.
19. Smith, M.R. 1990. The biodegradation of aromatic hydrocarbons by bacteria. Biodeg. 1:
191-206.
20. The concise Columbia Encyclopedia, 1983, Columbia University Press, New York, p.
907.
21. United States Environmental Protection Agency. 1998. A Citizen’s Guide to Phytoremediation.
Retrieved November 30, 2002, from http://www.clu-in.org/ptoducts/citguide/phyto2.html
22. United States Environmental Protection Agency. 2000. Introduction to Phytoremediation.
Cincinnati: National Risk Management Research Laboratory (EPA Publication No. EPA/
600/R-99/107).
23. Zobell, C.E. 1946. Action of microorganisms on hydrocarbons. Bact Rev. 10: 1-49.
24. Zobell, C.E. 1950. Assimilation of hydrocarbons by microorganisms. Adv. Enzymol. 10:
443-486.

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Glossary

Aerobic An environment that has a partial pressure of oxygen similar to normal

atmospheric conditions.

Bioaugmentation The process of amending contaminated sites with microorganisms that can
metabolize and grow on specific organic compounds.

Biodegradation The breakdown of organic substances effected by microorganisms.

BOD The requirement for molecular oxygen by microbes during oxidation

of biological substances in sewage. The BOD test measures the oxygen
consumed (in mg/ml) over 5 days at 20 degrees C.

Bioremediation The process by which living organisms act to degrade or transform hazardous
organic contaminants.

Biostimulation A process that modify environmental conditions to increase the activity

of microorganisms that degrade contaminants. For example, addition of
nutrients, oxygen, or other electron donors and acceptors.

Bioventing The process of supplying molecular oxygen in-situ to oxygen-limited

soil microbes by forcing air through unsaturated contaminated soil at low
rates.

COD The amount of oxygen in mg/ml to oxidize both organic and oxidizable
inorganic compounds.

Detoxification Change in a molecule that renders it less harmful to one or more susceptible
species.

Ex-situ Out of the original position, such as a stockpile of excavated soil.

In-situ In place, the natural or original position.

Leachate A contaminated liquid that results from water collecting contaminants as it

trickles through a substance containing contaminants, agricultural pesticides,
fertilizers or waste.

Microflora The microorganisms associated with a given environment.

Microorganisms Includes bacteria, algae, fungi, and viruses.

Mineralization The breakdown of organic matter to inorganic minerals (such as carbon

dioxide and water) by bacteria and fungi.

Mycorrhizae A mutually beneficial association between a fungus and the root of a plant.
These occur in a wide range of plants including trees, shrubs, and herbaceous
plants.

20
Phtyodegradation Process by which plants degrade organic pollutants through metabolic
processes.

Phytoextraction Use of plants to extract contaminants such as metals from environmental

media, especially soil. When plants becomes saturated with contaminants,
they are harvested and the remains disposed as waste.

Phytoremediation Use of plants to remediate contaminated soil or groundwater.

Phytostabilization Use of soil amendments and plants to reduce bioavailability and offsite
migration of contaminants.

Phytovolatilization Use of plants to volatilize contaminants from soil and water.

Rhizodegradation The breakdown of contaminants through the activity existing in the

rhizosphere. This activity is due to the presence of proteins and enzymes
produced by the plants or by soil microbes. Rhizodegradation is a symbiotic
relationship that has evolved between plants and microbes.

Rhizofiltration Uptake of contaminants by plant roots and the roots are harvested once they
become saturated with contaminants.

Rhizosphere Soil near the plant roots that is influenced by those roots. Typically includes

ACKNOWLEDGEMENT

On behalf of MABIC, the editorial team would like to send our thanks to the following
individuals for their invaluable contributions to this issue of BICnews. They have kindly
volunteered their time and energy to provide valuable insights and feedback which was of
great assistance to us.

1. Prof. Dr. P. Agamuthu, University of Malaya

2. Dr. Mohd. Nasir Hassan, Universiti Putra Malaysia
3. Dr. Ting Yen Peng, National University of Singapore

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Written by: Mahaletchumy Arujanan & Tan Jung Yee
Edited by: Kelvin Keh

Malaysian Biotechnology Information Centre

c/o Monash University Malaysia, Jalan
Kolej, Bandar Sunway, 46150 Petaling Jaya,
Selangor, MALAYSIA
Tel/Fax: +603-5580-4384
Email:info@bic.org.my

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