ENVIRONMENTAL MICROBIOLOGY

Bioremediation
Anushree Malik
Centre for Rural Development & Technology
Indian Institute of Technology Delhi
New Delhi-110 016
27-Feb-2006 (Revised 21-Aug-2006)
CONTENTS
Introduction
Principles of Bioremediation
Bioremediation
Bioremediation technologies
Intrinsic bioremediation
Biostimulation
Bioventing
Bioaugmentation
Biofilters
Bioreactors
Composting
Land-farming
Is it a new concept?
Mechanism of Bioremediation
Broad categories of contaminants
Mechanism of biodegradation
Contaminant structure Vs biodegradability relation
Bioremediation Microorganisms/Agents
Pure Cultures
Acclimatized Microorganisms & Molecular Breeding
Genetically Engineered Microorganisms (GEMS)
Consortium
Enzymes
Implementing Bioremediation: The Engineering Concepts
In-situ Bioremediation (ISB)
Parameters affecting ISB
Steps in ISB
Advantages of ISB
Limitations to ISB
Microbes in Reclamation of Wastelands including Oil Spills
Steps in bioremediation of oil contaminated site
Petroleum degrading microbes
Case studies
Role of biosurfactants
Keywords
Bioremediation, biodegradation, bio stimulation, bio augmentation, genetically engineered microorganisms

Introduction
As is clear from the word itself bioremediation (bio + remediation) should involve two
components the bio i.e. the live component and remediation i.e. the treatment of the
contaminant. The term denotes the existence of some contaminant in the matrix which is to
be remediated. Therefore, before going into the classical definitions of bioremediation let us
discuss what do we need to remediate and why. The answer we will soon find once we begin
to analyze the present state of the environment.

Present state of our environment

Rapid industrialization and urbanization over the past many decades has resulted in
contamination of all the components of the environment that is the air, the water, the soils and
even our food. The process began with the generation of a plethora of synthetic organic
compounds for use as solvents, pesticides, refrigerants and chemical intermediates etc. The
contamination of the environment has also occurred through a variety of industrial operations
like fugitive emissions, accidental spills and leaks, discharge of effluents or dumping of
waste. Over the years indiscriminate use of the synthetic chemicals has released several such
organic contaminants which are recalcitrant to natural degradation and may also turn
hazardous or toxic. Even if released in the sewers, the compounds come back to soil system
and the food chain through contaminated sludge. Nevertheless, the next question is why we
should be worried about such pollutants.

Potential hazards
The hazards posed by the contaminants depend upon the type of contaminant, chemical
species, spatial distribution, the concentration and the route of exposure etc. Apart from this,
the nature of matrix (for example, hydrogeological characteristics in case of soil) also affect
the potential hazards. Broadly the effect could be summarized in two categories
Short-term hazard: Direct contacts, inhalation of toxic dust/fumes or immediate risk of
fire/explosion.
Long-term hazard: Resulting by movement to other components of the environment or
generation of secondary toxic products. For example, transportation of contaminants through
rain water followed by percolation to ground water and contamination of the drinking water
source. The situation that we face today is thus alarming and calls for urgent action for
ensuring environmental and health safety.

Solutions
As far as the solution to this problem is concerned, there can be two options i.e. prevention or
cure. As the common saying insists that prevention is always better than cure, the former
should always be practiced well. The strategy collectively termed Cleaner Production also
states that prevention of pollution is a better and more effective answer to the current
environmental problems. Thus the challenge today is to develop technologies that consume
fewer resources, incorporate recycling and reuse of components thereby reducing the
production of wastes while maintaining/improving the efficiency. Even if the switching to
cleaner processes is by and large accepted, we still face the toxicity and environmental
persistence of xenobiotic compounds in the transitional phase. Therefore, there is a need to
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develop a wide variety of physico-chemical and biological techniques that can remediate the
hazardous contaminants from the environment without causing further damage. The
conventional techniques of incineration/land-fills etc. basically transfer pollutants from one
medium to another, are expensive and energy demanding. Further, these techniques are often
inefficient for handling voluminous effluents containing complexing organic matter and low
concentration of contaminants. Biotechnological approaches that are designed to cover such
niches have, therefore, received great deal of attention in the recent years.
Bioremediation is an attractive and potential alternative for treatment of contaminated sites.
Let us now examine in detail what exactly the term bioremediation implies and the host of
technologies that this term encompasses.

Principles of Bioremediation
Bioremediation
The word "bioremediation" was coined by scientists in the early 1980s as a term to describe
the use of microorganisms to clean polluted soils and waters. The prefix bio defined the
process as biological that is, carried out by living organisms. The noun remediation defined
the process as one that resulted in the cleaning, or remediation, of the environment, via
complete degradation, sequestration, or removal of the toxic pollutants as the result of
microbial activity. Degradation means that the microorganisms decompose the pollutants to
harmless natural products such as carbon dioxide (CO2), water (H2O), or other nontoxic
naturally occurring compounds. Sequestration means that the pollutant is trapped or changed
in a way that makes it nontoxic or unavailable to biological systems. Removal means that
while the pollutant is not necessarily degraded, the microbes physically remove it from the
soil or water so that it can be collected and disposed of safely.
Thus bioremediation can be defined as the process of using specific microorganisms to
transform hazardous contaminants in soil/water to nonhazardous waste products. However,
some definitions that give a broader outlook define bioremediation as biological treatment
systems to destroy, or reduce the concentration of hazardous waste from contaminated site.
Thus some definitions restrict to the use of microbes only while others seem to incorporate all
the biological entities such as plants (phtoremediation). Whatever barriers we define, in fact
in nature the process of biological remediation involves both plants and microbes and rather
the plant-microbe interaction in root zone has a very important role. Nevertheless, in this
chapter we will focus on microbial remediation only.

Bioremediation technologies
There are different treatment technologies under bioremediation and before we begin
exploring the basics of bioremediation, let us get acquainted with these terms
Intrinsic bioremediation
This is a process whereby the natural microflora and environmental conditions exist for
natural attenuation of a pollutant to safe levels within acceptable time frame. Here natural
subsurface processes such as dilution, volatilization, biodegradation, adsorption, and
chemical reactions with subsurface materials are allowed to reduce contaminant
concentrations to acceptable levels. This requires no intervention but just monitoring of the
natural process of biodegradation. However, it should not be perceived as no action plan as
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long term monitoring must be conducted throughout the process to confirm that degradation
is proceeding at rates consistent with meeting cleanup objectives.
Compared with other remediation technologies, natural attenuation has several advantages
such as less generation or transfer of remediation wastes; less intrusive (as few surface
structures are required) and may be applied to all or part of a given site, depending on site
conditions and cleanup objectives. Further it may be used in conjunction with, or as a followup to, other (active) remedial measures and the overall cost will likely be lower than active
remediation.

Biostimulation
This involves injection of specific nutrients at the site (soil/ground water) to stimulate the
activity of indigenous microorganisms. Fertilizers and growth supplements are common
stimulants. Presence of small amount of pollutant can also act as stimulant by turning on the
operons for bioremediation enzymes. Biostimulation can be done in situ or ex situ.

Bioventing
Similar to biostimulation but it involves venting of oxygen through soil to stimulate growth
of natural or introduced microorganisms. Thus bioventing may complement biostimulation as
well as bioaugmentation. It is a promising technology that stimulates the natural in situ
biodegradation of any aerobically degradable compounds in soil by providing oxygen to
existing soil microorganisms. Bioventing typically uses low air flow rates to provide only
enough oxygen to sustain microbial activity. Oxygen is most commonly supplied through
direct air injection into residual contamination in soil. In addition to degradation of adsorbed
fuel residuals, volatile compounds are biodegraded as vapors move slowly through
biologically active soil. Bioventing techniques have been successfully used to remediate soils
contaminated by petroleum hydrocarbons, nonchlorinated solvents, some pesticides, wood
preservatives, and other organic chemicals. This technique shows considerable promise of
stabilizing or removing inorganics from soil as it can induce changes in the valence state of
inorganics and cause adsorption, uptake, accumulation, and concentration of inorganics in
micro or macroorganisms. However, several factors may limit the applicability and
effectiveness of the process for example highly saturated soils, extremely low moisture
content or low permeability soils negatively affect the bioventing performance. Build up of
vapours needs to be avoided by extracting the air followed by monitoring of off-gases at the
soil surface. The biggest limitation is that aerobic biodegradation of many chlorinated
compounds may not be effective unless a co-metabolite or anaerobic cycle is present.

Bioaugmentation
Addition of pollutant-degrading microorganisms (natural/exotic/acclimatized/genetically
engineered) to augment the biodegradative capacity of indigenous microbial populations is
termed as bioaugmentation. Sometimes microorganisms from the remediation site are
collected, separately cultured, and returned to the site as a means of rapidly increasing the
microorganism population at the site. Usually an attempt is made to isolate and accelerate the
growth of the population of natural microorganisms that preferentially feed on the
contaminants at the site. In some situations different microorganisms may be added at
different stages of the remediation process because the contaminants change in abundance as
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the degradation proceeds. However there is no evidence to suggest that the use of non-native
microorganisms is beneficial in the situations tested.

Biofilters
Use of microbial stripping columns (containing microorganism enriched compost/soil) is to
treat organic gases (volatile organic compounds).

Bioreactors
Biodegradation of contaminants in a large tank or reactor. Bioreactors can be used to treat
liquid effluents/slurries or contaminated solid waste/soil.

Composting
Composting is aerobic, thermophilic treatment process in which contaminated material is
mixed with a bulking agent (compost rich in bioremediation microorganisms). This is a
controlled biological process by which organic contaminants (e.g., PAHs) are converted by
microorganisms to safe, stabilized byproducts. Typically, thermophilic conditions (54 to
65C) must be maintained to properly compost soil contaminated with hazardous organic
contaminants and in most cases, this is achieved by the use of indigenous microorganisms.
Soils are excavated and mixed with bulking agents and organic amendments, such as wood
chips, animal, and vegetative wastes etc. to enhance the porosity of the mixture to be
decomposed. Maximum degradation efficiency is achieved through maintaining aeration and
moisture as necessary, and closely monitoring moisture content, and temperature.
Basically three different process designs are used in composting:
Aerated static pile composting where compost is formed into piles and aerated with
blowers or vacuum pumps
Mechanically agitated in-vessel composting where compost is placed in a reactor vessel,
mixed and aerated
Windrow composting where compost is placed in long piles known as windrows and
periodically mixed with mobile equipment
Windrow composting is usually considered to be the most cost-effective composting
alternative but it may also have the highest fugitive emissions. Pilot and full-scale projects
have demonstrated that aerobic, thermophilic composting is able to reduce the concentration
of explosives (TNT, RDX, and HMX), ammonium picrate (or yellow-D), and associated
toxicity to acceptable levels and is also applicable to PAH-contaminated soil. The substantial
requirement of space and aeration coupled with the need for excavation of contaminated soil
limit the application of composting. If VOC (volatile organic compounds) or SVOC (semivolatile organic compounds) contaminants are present in soils, off-gas control may be
required. Lastly, this method cannot treat metals and due to addition of amendments
ultimately leads to volumetric increase in the amount.

Landfarming
It is a solid phase treatment system for contaminated soil where tilling and soil amendment
techniques are used to encourage the growth of beneficial microorganisms in contaminated
area. Different conditions that are controlled during land farming are:
Moisture content (usually by irrigation or spraying).
Aeration (by tilling the soil with a predetermined frequency)
pH (buffered near neutral pH by adding crushed limestone or agricultural lime).
Other amendments (e.g., Soil bulking agents, nutrients, etc.).
It may be done in situ or in a treatment cell and has been successfully used to remove large
petroleum spills, wood-preserving wastes (PCP and creosote), coke wastes, and certain
pesticides in the soil. The large requirement of space, proper management of leachates and
prevention of volatile gases are some of the limitations associated with landfarming. Table 1
summarizes the advantages and disadvantages of different types of bioremediation strategies.
Table 1: Advantages and disadvantages of different types of bioremediation strategies
Techniques

Examples

Advantages

Limitations

In situ

In situ
bioremediation
Bioventing
Biostimulation
Bioaugmentation

Environmental constraints
Extended treatment times
Monitoring difficulties

Ex situ

Land farming
Composting
Biopiles/Biocells

Most cost efficient

Noninvasive
Relatively passive
Natural attenuation
Treats soil and water
Cost-efficient
Can be done on site

Bioreactors

Slurry/aqueous
reactors

Extended treatment time

Need to control abiotic
loss
Mass transfer problem
Bioavailability limitation
Rapid degradation kinetics Requires excavation
Optimized environmental Relatively high capital
cost & operating cost
parameters
Enhances mass transfer
Effective use of inoculants
and surfactants

(Source: M. Vidali Bioremediation. An overview Pure Appl. Chem., 73, 11631172, 2001)

Is it a new concept?
Around the world bioremediation technologies are categorized as the innovative
technologies. However, this does not mean that it is a novel phenomenon. Actually
bioremediation has been going on since the life began on this planet. It is a relatively slow
process, but eventually nature has healed itself of all the disturbances. As a contaminant is
introduced into the environment, the microbes of the surrounding area get gradually adapted
to this changed environment. They begin to elaborate the process of degrading the
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contaminant by evolving the ability to use it as a carbon or energy source. During this natural
process, the nature caters to the nutritional and physiological needs of the bacteria and the
overall process is thus quite slow (Fig. 1). With our fast development we have introduced the
contaminants at a staggering high rate and now we need instant cleanup solution that is not
within the scope of the natural processes. The natural process can however be speeded up by
man-assisted interventions (Fig. 1) as discussed in the earlier section i.e. either by providing
favourable conditions or by increasing the number of efficient microorganisms at the
contaminated site. However, the things are not as simple as they appear in Fig. 1. After taking
a bird eye view of the different bioremediation technologies let us take an insight into what
kind of contaminants can be degraded and how does microbe metabolism handle them.

Biostimulation

Bioventing

Landfarming

Bioaugmentation

Composting

Bioreactor
T=Weeks/Months

T=Years

Fig. 1: (a) Natural and (b) Man-Assisted bioremediation

Mechanism of Bioremediation
Broad categories of contaminants
As noticed above, if favourable nutritional and environmental conditions occur, the bacteria
are able to readily incorporate the simple organic substances into their cells and oxidize them.
However, degradation of complex organic compounds with longer molecular structures is
slower. Some compounds are so complex that they cannot be degraded at all, which are
termed as recalcitrant or refractory compounds. Still other may be toxic and thus inhibit the
growth of microorganisms and their metabolic activity. Such compounds need special
techniques or integration of physico-chemical and biological techniques for effective
remediation (Fig. 2).

Contaminant

Degradable &
Non-toxic

Bioremediation
effective

Degradable &
Toxic

Non-degradable
& Toxic

No
Bioremediation

Dilution

No
Bioremediation

Bioremediation
effective

Non-degradable
& Non toxic

GEMS

No
Bioremediation

Bioremediation
effective

Not Much
Concern

Prevent
Entry

Fig. 2: Bioremediation: Influence of contaminant type

Mechanism of biodegradation
Microbes are the key players in bioremediation as they generate the enzymes that catalyze the
degradative reactions. Why the microbes carry out degradative reactions? It is because the
microbes use organic substances as a source of carbon and energy. Thus while transforming
the contaminant microbes gain energy and raw material for their multiplication and
maintenance. Based on the mechanism by which microbes gain energy, they are broadly
categorized into three categories (Table 2). However, several xenobiotic contaminants might
not be amenable to one of the above described categories and other mechanisms are
employed by the microorganisms for degradation of such compounds.
Table 2: Mechanisms of energy generation by the microbes
Mechanism

Electron donor

Aerobic respiration Organic

compound
Anaerobic
Organic
respiration
compound
Fermentation
Organic
compound

Electron acceptor

Product

Oxygen

CO2, H2O

NO3, SO4, Fe3+, Mn4+, N2,

H2S,
CH4,
CO2
Reduced metals
Organic compound
Organic
acids,
alcohols, H2 & CO2

Reductive dehalogenation: It plays very important role in the detoxification of halogenated

organic contaminants. Microorganisms catalyze a reaction in which halogen atom of
contaminant is replaced by hydrogen atom. Thus the reaction adds 2 electrons to contaminant
and reduces it. It yields no energy but seems to be detoxification mechanism as
dehalogenated derivatives are less toxic and susceptible to further microbial decay.
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Cometabolism: In this case also the conversion reaction yields no benefit to the cell. This
non-beneficial transformation is often termed as secondary utilization, cometabolism or
gratuitous metabolism. Co-metabolism is one form of secondary substrate transformation in
which enzymes produced for primary substrate oxidation are capable of degrading the
secondary substrate fortuitously, even though the secondary substrates do not afford
sufficient energy to sustain the microbial population. It is thus defined as degradation of a
compound only in presence of other organic compound that serves as a primary energy
source. Several contaminants such as Polynuclear Aromatic Hydrocarbons (PAHs) and
pesticides are degraded by this mechanism. An emerging application involves the injection of
water containing dissolved primary substrate (e.g. methane, toluene) and oxygen into ground
water to support the co-metabolic breakdown of targeted organic contaminants. The addition
of methane or methanol supports methanotrophic activity, which has been demonstrated
effective to degrade chlorinated solvents, such as vinyl chloride and Trichloroethane (TCE),
by co-metabolism (Fig. 3).

Fig. 3: Schematic diagram of the In-situ ground water remediation via cometabolic
activity
(Source: EPA, 1993. In Situ Bioremediation: Biodegradation of Trichloroethylene and Tetrachloroethylene by
Injection of Air and Methane, Innovative Remedial Technology Information Request Guide)

Contaminant structure Vs biodegradability relation

Biodegradability is essential for bioremediation of organic pollutants. Chemical structure of
pollutant governs the ability of microorganisms to metabolize them, especially the rate and
extent of biodegradation. As we discussed above, some compounds are readily biodegradable
whereas others are not. Let us look at the general rules that determine this.

Low to mid molecular weight hydrocarbons and alcohols represent readily

biodegradable chemicals.
Branched and polynuclear compounds are more difficult to degrade that the straightchain and simple non-aromatic compounds.
Halocarbons are resistant to biodegradation and are often termed as xenobiotic
compounds. Dioxns are very difficult to degrade. Increasing degree of halogenation
decreases the rate of biodegradation. For example Dichloromethane as well as
Monochloro biphenyls are degraded fast as these are used as carbon and energy
source by the microbes. On the other hand Trichloroethane or TCE (widely used
solvent) and Polychlorinated biphenyls (widely used in transformers/pesticides) are
not used as carbon/energy source and are degraded slowly through cometabolic route.

Such rules have been more clearly defined for broad structural categories of the pollutants as
below:
(A) Petroleum hydrocarbons

Short chain alkanes are more toxic and relatively difficult to biodegrade
N-alkanes of intermediate chain length (C10-C24) degraded most rapidly
Very long chain alkanes are increasingly resistant to degradation
When molecular weight is greater than 500, such long chain alkanes are no longer
feasible as carbon source
Aromatic hydrocarbons (especially condensed polynuclear aromatic compounds)
degrade more slowly than alkanes
Some aromatic compounds (benzene, toluene) metabolized under anaerobic
conditions but the rates are slower than aerobic reactions
Alicyclic compounds cannot serve as carbon source unless they have long aliphatic
side chains, hence often degraded by cometabolism

(B) Halocarbons

Most common mechanism is stepwise reductive dehalogenation under anerobic

conditions e.g.
TCE

Stepwise dechlorination

Vinyl Chloride

Ethane

Cometabolic degradation by methanogenic consortium also reported

Aerobic degradation of TCE by methane utilizing consortium is also possible
Microcosm studies report both aerobic/anaerobic transformations
In case of haloaromatics such as chlorobenzenes, aerobic biodegradability decreases
with number of halosubstituents
Extensively chlorinated haloaromatics degraded by stepwise anaerobic dechlorination.
The consecutive dechlorination steps are more difficult, slow and often incomplete
but the mono and dichloro substitutes can be aerobically degraded for example

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Hexachlorobenzene
Anaerobic, fast

Reductive dechlorination

1, 3, 5 Trichloro benzene
Anaerobic, Slow

Dichloro or Monchlorobenzene
Fast

Aerobic biodegradation
(Pseudomonas, Alcaligens)

Chlorocatechols

(C) Nitroaromatics

Nitrosubstitution makes the compounds less biodegradable

Excessively nitrosubstituted aromatics transformed under anaerobic conditions by
stepwise conversion of nitro groups to amino groups

Bioremediation Microorganisms/Agents
Different microorganisms are able to degrade different contaminants depending upon the
nature and coencentration of contaminant and the metabolic needs of the microorganisms.
Scientists around the world are continuously working to find out novel and more efficient
biodegraders. Let us discuss the important bioremediation microorganisms under the
following heads
Pure Cultures
Since the conventional techniques of microbiology are designed for pure culture studies and
also it is easy to work out the efficiency of microbes in such systems, most of the laboratory
studies focus on biodegradative capacity of pure cultures. Table 3 shows the famous
bioremediation microorganisms. Pseudomonas species are most widely detected microbes in
the contaminated site due to their extensive biodegradation capacities (Table 4). Among the
fugal groups, phanerochaete has been proposed for the biodegradation of various pollutants
such as DDT, TNT, high molecular weight polynuclear aromatics like benzo (a) pyrene and
plastics such as polyethylene.
Acclimatized Microorganisms & Molecular Breeding
The metabolic range of naturally occurring microbiota may not be capable of degrading
certain compounds or certain classes of compounds. There it may be necessary to supplement
with the specialized microbes. One way of developing such specialized microbes is by
repeatedly exposing them to higher concentration of contaminants. Often the microorganisms
with specialized degradation ability can also be enriched from the contaminated site
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Table 3: Microorganisms (Pure cultures) helpful in bioremediation

Pollutant

Microorganism(s)

Reference

Atrazine

Acinetobacter species
Pseudomonas sp. strain
ADP

Singh et al., 2004

Shapir and R.T. Mandelbaum,
1997

Chlorpyrifos

Aspergillus niger
Trichoderma viride
Bacterium strain B-14
Alcaligenes eutrophus
TCP
Ralstonia eutropha (pJP4)
Ralstonia eutropha
JMP134
Pseudomonas stutzeri KC
Hydrogenophaga flava
ENV735
-proteobacterium strain
PM1
B. sp. Strain JS150
B. Cepacia G4
R. Pickettii PKO1
S. yanoikuyae B1

Mukherjee and Gopal, 1996

2,4,6-Trichlorophenol
2,4-Dichlorophenoxyacetic
acid
Carbon tetrachloride
Methyl tert-butyl ether

BTEX

Orange 3, 4-(4nitrophenylazo) aniline

Pleurotus ostreatus

Singh et al., 2004

Andreoni et al., 2003
Daane and Hggblom, 1999
Roane et al., 2001
Dybas et al., 2002
Streger et al., 2002
Smith et al., 2005
Kahng et al.,( 2001)
Shields et al.,( 1995)
Byrne et al., (1995)
Kim and Zylstra, (1999)
Xueheng Zhao et.al.,(2006)

Table 4: Pseudomonas strains with proven ability for bioremediation of BTEX

P. putida MT15

Keil et al., (1985)

P. putida F1

Zylstra and Gibson, (1989)

P. putida mt-2 (PaW1)

Burlage et al., (1989)

P. aeruginosa JI104

Kitayama et al., (1996)

P. stutzeri OX1

Bertoni et al., (1998)

P. putida MT53

Kok et al., (1999)

Pseudomonas putida, P. fluorescens Hojae Shim (2002)

To achieve a complete catabolic pathway for a xenobiotic compound is the ultimate objective
for its biodegradative clean up. Biochemical pathways are under constant evolution and this
process can be accelerated by plasmid mediated genetic exchange, recombination. A
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specially constructed Pseudomonas strain in this way (as shown in Fig. 4) has been found to
be very effective for degradation of chlorobenzoate and chlorophenols. It has been introduced
into the waste streams of chemical manufacturing plant where it could bring about the
removal of haloaromatic hydrocarbons.

Higher
concentration of
related but utilizable
substrate

Small concentration
of xenobiotics

Enrichment

Xenobiotic
concentration
increased

T=Weeks/Months

UV light

Substrate
concentration
decreased

Chemical
mutagens

Spontaneous mutant with increased ability to utilize

xenobiotics (e.g. specially constructed Pseudomonas strain
for degradation of chlorobenzoate & chlorophenols

Fig. 4: Molecular Breeding

Genetically Engineered Microorganisms (GEMS)
The microorganisms can be genetically engineered to enhance its enzymatic capability to
degrade wide range of compounds. GEMS have the advantage of possessing high growth
affinity, rapid growth rate and resistance to toxicity. With such solutions several
shortcomings of the bioremediation can be overcome. However, practically the potential
results of release of such GEMS into the environment cannot be predicted because
suboptimal conditions exist in the field and the GEMS might also face tough competition
from the native communities. The artificially introduced genes can persist in environment for
example phenol-degrading plasmid has been found in soil 6 years after addition of GEM. A
lot of debate exists concerning safety, persistence, containment, and potential ecological
damage associated with the release of GEMS in the environment. Due to these constraints it
is unlikely that GEMS could be utilized for large-scale bioaugmentation in the coming days.
To overcome the problem of persistence and long-term ecological damage suicidal
microorganisms have been designed. These cells have suicide mechanisms (e.g. hok/sok
system) so that the cells or the recipients of plasmid die in absence of pollutant.
Adhesion deficient microorganisms: Natural adhesive properties of native bacteria limit their
penetration through soil and rock matrix. A specialized adhesion deficient TCE-degrading
strain B. cepacia has been developed (which could rapidly disperse 25 feet depth) and used
successfully for in-situ bioremediation of TCE-contaminated aquifer.

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Consortium
In nature there is a diversity of types of microorganisms and energy sources. This diversity
makes it possible to break-down a large number of different organic chemicals. Even in the
most commonly applied activated sludge processes uncharacterized consortia of
microorganisms accomplish the task of waste water treatment. Actually microorganisms
individually cannot mineralize most hazardous substances. At times the target pollutant is a
complex molecule or a mixture of compounds that can only be broken down by a very
specific combination of microorganisms (a consortium) and pathways (Table 5). Typical
pollutants of this type include polyaromatic hydrocarbons, halogenated organics (both
aliphatic and aromatic), polychlorinated biphenyls, multi-nitrated arenes (such as the
explosive 2, 4, 6-trinitrotoluene [TNT]), organophosphorous or triazinic pesticides and
herbicides. In such cases, the solution for successful bioremediation might be inoculation of
the polluted biotope with specific populations of microorganisms bioaugmentation.
Complete mineralization can be accomplished through a sequential degradation by a
consortium of microorganisms and involves synergism and cometabolic actions (Fig. 5).
Table 5: Consortium for degradation of recalcitrant compounds
Compound
Polychlorinated
biphenyl (soil)
BTEX
Chloroethenes

Chlorobenzenes
1,1,1-Trichloroethane
Atrazine
Toluene

Tolune

Organism
Arthrobacter sp. B1B and Ralstonia
eutrophus H850
Methanogenic consortia

Reference
Singer et al., 2000

Da Silva and
Alvarez, 2004
Consortium that contains Dehalococcoides Lendvay et al.,
2003
Consortium that contains Dehalococcoides Adamson et al.,
2003
Consortium that contains Dehalococcoides Major et al., 2002
P. putida GJ31, P. aeruginosa RHO1 and P. Wenderoth et al.,
putida F1CC
2003
Butane-utilizing enrichment culture
Jitnuyanont et al.,
2001
Consortia degrading atrazine
Goux et al., 2003
Harwood, C.S
nitrate-reducing genera Azoarcus and
et.al.,(1997)
Thauera, iron-reducing Geobacter
metallireducens
Meckenstock et al.,
Pseudomonas putida strain mt-2
(1999)
Thauera aromatica strain K172,
Geobacter metallireducens

Microbial mats are laminated, cohesive microbial communities, composed of a consortium of

bacteria dominated by photoautotrophic cyanobacteria (also referred to bluegreen algae).
Mats generally include anoxygenic photoautotrophs (purple bacteria) and sulfur-reducing
bacteria. They are embedded in a negatively charged polymeric matrix of gel. Ecological
success of microbial mats and their broad array of microbial activities suggest that these
microbial ecosystems might be useful to bioremediation of environmental pollutants and
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biogeneration of useful products. Microbial mats sequester heavy metals, metalloids,

radionuclides and oxyanions. Although these contaminants have complex and contrasting
chemistries, mats display a wide variety of mechanisms for removal which occur at the
cellular level of the constituent microorganisms and at the community level of the entire
consortium. Microbial mats are capable of degrading various organic compounds also and
often these compounds are completely mineralized. These include petroleum distillates,
trichloroethylene (TCE), tetrachloroethylene (PCE), 2,2-4,4-5,5-hexachlorobiphenyl (PCB),
octachlorocyclopentadine (chlordane), 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT),
the pesticides (carbofuran, paraquat and prophos) and absorbable organochlorine compounds
(AOX) as effluents from the pulp and paper kraft mill industries.

Contaminant

1st intermediate

2nd intermediate

3rd intermediate

Mineralized form
CO2

H2O

Fig. 5: Mineralization of contaminant by microbial consortia

Enzymes
An appealing alternative to the bioremediation of polluted sites could be that of utilizing cellfree enzymes isolated from their originating cells. Extra cellular enzymes include a large
range of oxidoreductases and hydrolases which may explicate a degradative function and
transform polymeric substances into partially degraded or oxidized products that can be
easily up-taken by cells. For instance, partial oxidation of recalcitrant pollutants such as
PAHs by extra cellular oxidative enzymes give rise to products of increased polarity and
water solubility and thus with a higher biodegradability. Pesticides of different chemical
nature, very recalcitrant compounds like asphaltenes and PCBs, polychlorophenols, PAHs
and others toxic pollutants were successfully transformed (in lab-scale studies) by
oxidoreductases and hydrolases isolated by fungal, bacterial and plant cells.
Cell-free enzymes can offer several advantages over the use of microbial cells. The most
significant features of cell-free enzymes are their unique substrate-specificity and catalytic
power; their capability to act in the presence of many toxic, even recalcitrant, substances,
and/or under a wide range of environmental conditions, often unfavourable to active
15

microbial cells (i.e. relatively wide temperature, pH and salinity ranges, high and low
concentrations of contaminants); and their low sensitivity or susceptibility to the presence of
predators, inhibitors of microbial metabolism, and drastic changes in contaminant
concentrations. However, in a natural environment such as soil, several drawbacks or
disadvantages may hinder or diminish the catalytic potential of these enzymatic catalysts. The
disadvantages of in situ application of either extra cellular, cell-associated or cell-free
enzymes, may depend on both the pollutants and the enzymes. For instance, the simultaneous
presence of several polluting substances in a contaminated site with synergistic, often
negative, effects on the enzyme efficiency, the high costs associated with the isolation and
purification of free enzymes, the low stability of enzymes to the harsh conditions of soil all
concur to restrict the wide use of enzymes as remediating agents of polluted soils. However,
exploration of extreme environments, exploitation of genome using advanced technologies,
and protein engineering might open new frontiers for the production and application of
enzymes.

Implementing Bioremediation: The Engineering Concepts

Till now we have discussed the fundamentals on which the technology of bioremediation
stands. It is very essential to realize and understand these principles before we think of the
practical implementation where the main objectives are:
To enhance the rate and extent of biodegradation of the pollutant
To utilize or develop microorganisms that can survive the toxic effect of pollutants
To utilize microorganisms in such a way that no toxic products are produced
As the following discussion on engineering aspects of bioremediation proceeds, we will
realize that translating these fundamentals into field applications is not an easy task. It
requires a judicious exchange of skills among professionals from various disciplines as
shown in Fig. 6.

Microbiologist

Environmental
Scientist

Engineer

Bioremediation

Chemical
Analyst

Geologist

Genetic
Engineer

Fig. 6: Bioremediation: An Interdisciplinary Activity

16

Bioremediation can be performed in-situ or off-site. The decision often depends upon the
nature of contaminant, objective of the remedial action, availability of funds/time and
viewpoints of the local people and authorities. Whenever the pollution effects shallow soil
layers, excavation and subsequent treatment at other sites (off-site bioremediation) is
recommended either in a biopile (contaminant material is piled on the ground surface) or
biocell (contaminant material is deposited and treated underground at a clean site) both of
which must be lined to confine the contaminant and leachates.

In-situ Bioremediation (ISB)

Fig. 7 shows the design of the in-situ bioremediation (ISB) system. At first the physically
removable fraction of the unaltered phase of contaminant (e.g. oil) is removed. It is called as
Free Product Recovery. The remaining fraction that cannot be easily removed in this way is
then subjected to bioremediation. Free product recovery prevents the microorganisms from
the toxicity effects of high concentration of contaminant and makes the bioremediation more
feasible. After free product recovery, water is pumped from the recovery well and passed
through a filter and then above ground treatment system such as bioreactor/air-stripper. The
water is then supplemented with nutrients/electron acceptors and returned to the aquifer close
to the source of contamination through injection wells. Oxygen is supplied by sparging air,
pure oxygen and sometimes by addition of hydrogen peroxide. First inorganic nutrients are
added which is followed by oxygen addition because simultaneous additions may cause plug
formation. Gravity and pumping actions pull nutrient/microbe rich water into saturated zone
where it comes in contact with the contaminant and eventually treats it.
Nutrients

BIOREACTOR
FILTER
Infiltration
gallery

Nutrients
and air
injection

Free
product
extraction

Groundwater
pumping

Air
extraction

Contaminated zone

Water
table

Bioventing

Groundwater flow

Fig. 7: In-situ Bioremediation technique

(Redrawn from S. Saval, Bioremediation: clean-up Biotechnologies for soils and aquifers in Environmental
Biotechnology and cleaner bioprocesses (Eds EJ Olguin, G. Sanchez and E Hernandez, 2000. pp 155166)

17

Parameters affecting ISB

The important parameters that affect ISB are discussed below:
Oxygen level
The rate of bioremediation of organic contaminants by microbes is enhanced by increasing
the concentration of electron acceptors and nutrients in ground water, surface water, and
leachate. Oxygen is the main electron acceptor for aerobic bioremediation. Nitrate serves as
an alternative electron acceptor under anoxic conditions. Oxygen level in the soil is increased
by avoiding saturation of the soil with water, the presence of sandy and loamy soil as
opposed to clay soil, avoiding compaction, avoiding high redox potential, and low
concentrations of degradable materials. To ensure that oxygen is supplied at a rate sufficient
to maintain aerobic conditions, forced air/oxygen or hydrogen peroxide injection can be used.
The use of hydrogen peroxide is limited because at high concentrations it is toxic to
microorganisms. Also, hydrogen peroxide tends to decompose into water and oxygen rapidly
in the presence of some soil constituents. Anaerobic conditions may be used to degrade
highly chlorinated contaminants, although at a very slow rate. This can be followed by
aerobic treatment to complete biodegradation of the partially dechlorinated compounds as
well as the other contaminants.
Water Content
Water serves as the transport medium through which nutrients and organic constituents pass
into the microbial cell and metabolic waste products pass out of the cell. However, too much
water can be detrimental, however, because it may inhibit the passage of oxygen through the
soil (unless anaerobic conditions are desired).
Nutrients
Nutrients required for cell growth are nitrogen, phosphorous, potassium, sulfur, magnesium,
calcium, manganese, iron, zinc, copper, and trace elements. If nutrients are not available in
sufficient amounts, microbial activity will become limited. Nitrogen and phosphorous are the
nutrients most likely to be deficient in the contaminated environment. These are usually
added to the bioremediation system in a useable form (e.g., as ammonium for nitrogen and as
phosphate for phosphorous). Phosphates can cause soil plugging as a result of their reaction
with minerals, such as iron and calcium, to form stable precipitates that fill the pores in the
soil and aquifer.
pH
pH affects the solubility, and consequently the availability, of many constituents of soil,
which can affect biological activity. Many metals that are potentially toxic to microorganisms
are insoluble at elevated pH; therefore, elevating the pH of the treatment system can reduce
the risk of poisoning the microorganisms.
Temperature
Temperature affects microbial activity in the environment. The biodegradation rate will slow
with decreasing temperature; thus, in cold climates bioremediation may be ineffective during
part of the year unless it is carried out in a climate-controlled facility. The microorganisms
remain viable at temperatures below freezing but will resume activity when the temperature
rises. Heating the bioremediation site, such as by use of warm air injection, may speed up the
remediation process. At Eielson AFB, Alaska, passive solar warming by incubation tanks (ex
18

situ) or the application of heated water below the ground surface to the contaminated vadose
zone is being investigated. On the other hand, too high a temperature can also be detrimental
to some microorganisms, essentially sterilizing the soil.
Temperature also affects nonbiological losses of contaminants mainly through the increased
volatilization of contaminants at high temperatures. The solubility of contaminants typically
increases with increasing temperature; however, some hydrocarbons are more soluble at low
temperatures than at high temperatures. Additionally, oxygen solubility decreases with
increasing temperature.
It is important to take precautions and prevent the following during ISB
Flow of pumped water into unwanted area
Excessive use of nutrients
Enhancement of micrrorganisms in the unwanted area
Unwanted interaction of soil/ground water matrix with added nutrients for e.g.
reduced Fe and Mn can get precipitated upon oxidation to cause plug formation
Therefore, it is quite clear that a lot of investigations and meticulous planning is required
prior to the full-scale ISB. To begin with it is very essential to know whether the site is
suitable for bioremediation or not.

Steps in ISB
Information about the site characteristics should be examined beforehand to evaluate the
viability of bioremediation technology, which should be followed by confirmation of the
biodegradative activity at microcosm level and then at larger scale.
Site characterization
Site characterizations must be done in a logical sequence to be able to respond to the
following major questions:
What chemical compounds are present as contaminants and whether the contamination is
superficial or has reached the subsoil?
What is the depth and extension of contaminant plume and the water table?
Is the contaminant biodegradable and whether the microorganisms present at the site can
degrade it? Are the environmental conditions conducive to biodegradation?
Is it possible to build bioreactor at the site?
The answers to these questions are obtained by the following characterizations:
(a) Pollutant and geohydrochemical characterization
Pollutant characterization involves determination of composition, concentration, toxicity,
bioavailability, solubility, sorption and volatilization of all the pollutants. The examination of
hydrological characteristics of the site is essential to understand the mobility of the
contaminant. The following geotechnical tests should be conducted to determine:
Hydraulic conductivity and/or permeability of soil to determine how rapidly water and
nutrients can move through the saturated/vadose zone
Specific yield and storage coefficient of the aquifer
Zone of influence of recovery and injection wells and the ground water flow direction
Cation exchange capacity of soils to estimate the nutrient sorption on the soil particles
Anionic/cationic composition of the soils and ground water.
19

The favourable and unfavourable conditions have been identified (Table 6) for
implementation of the bioremediation. Apart from this location of underground objects like
electricity cables, water pipes, sewers and above ground topographical evaluations including
the buildings, roads and parking lots etc. should also be conducted.
Table 6: Favorable and unfavorable conditions for implementation of the
Bioremediation
S.No. Favorable

Unfavorable
Chemical Characteristics

1.

Few organic contaminants

2.
3.
4.
4.

Non-toxic concentration
Diverse microbial groups
Suitable electron acceptors
Ph 6-8

Numerous contaminants; complex mixture

of inorganic and organic contaminants
Toxic concentrations
Sparse microbial activity
Absence of suitable electron acceptors
pH extremes

Hydrogeological characteristics
1.
2.
3.
4.

Granular porous media

High permeability
Uniform mineralogy
Homogenous saturated medium

Fractured rock
Low permeability
Complex mineralogy
Heterogeneous
medium,
saturated conditions

unsaturated-

(Source: Trejo M and Quintero R (2000) Bioremediation of contaminated soils. In Olguin EJ, Sanchez G and
Hernandez E (eds) Environmental Biotechnology and Cleaner Bioprocesses. Taylor and Francis, pp 179-188)

(b) Microbiological characterization

The three important prerequisites for successful ISB are:
Appropriate microorganism should be present on the subsurface
These should be adapted to the contaminants
All necessary nutrients should be present or must be added
Interestingly even till mid 1970s the general belief was that there are extremely low number
of microorganisms in deep soil layers/ground water as all of them shall be retained by natural
filtration through the upper soil columns. However, later on it was shown that naturally
occurring species of Pseudomonas and Arthrobacter were involved in the disappearance of
subsurface gasoline. Since then several hydrocarbon degrading microorganisms have been
reported. It is desirable to analyze the native microbial flora with respect to its degradative
capacity and size of the population with degradative potential.
Biotreatability studies
These tests are normally performed at a mesocosm level and efforts are made to
simulate/reproduce the environmental conditions that prevail in the field. For example if a
20

shallow stratum is to be remediated, large trays or jars filled with soil layers can be used. On
the other hand if contamination is present at the ground water table, column packed with
contaminated soil can be used as for biotreatability studies. The main purpose of
biotreatability studies is to determine the nutritional requirement of microorganisms to
perform biodegradation for which following parameters are monitored
Oxygen consumption
Carbon dioxide generation
Exhaustion of added nutrients (Nitrogen and phosphorus sources)
Contaminant removal
Biotic and abiotic controls should be included to ensure that the contaminant is being
removed by microbial activity. When the tests are properly conducted, it is possible to predict
the behaviour of bioremediation and the time for large scale applications.

Advantages of ISB
1. Bioremediation is a natural process and is therefore perceived by the public 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.
2. Bioremediation is useful for the complete destruction of a wide variety of
contaminants. Many hazardous compounds can be transformed to harmless products.
This eliminates the chance of future liability associated with treatment and disposal of
contaminated material.
3. 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.
4. 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.
5. ISB is almost always faster than baseline pump-and-treat remediation.
6. ISB may be used in both short and long term timeframes, either by itself or following
a more aggressive source zone treatment technology.
7. Bioremediation can prove less expensive than other technologies that are used for
clean-up of hazardous waste.

Limitations to ISB
Factors that may limit the applicability and effectiveness of the process include:
Bioremediation is limited to those compounds that are biodegradable. There are some
concerns that in some cases 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.
Cleanup goals may not be attained if the soil matrix prohibits contaminant-microorganism
21

contact. A surface treatment system, such as air stripping or carbon adsorption, may be
required to treat extracted groundwater prior to re-injection or disposal.
It is difficult to extrapolate from bench and pilot-scale studies to full-scale field
operations.
The circulation of water-based solutions through the soil may increase contaminant
mobility and necessitate treatment of underlying ground water. Preferential colonization
by microbes may occur causing clogging of nutrient and water injection wells.
Bioremediation often takes longer than other treatment options, such as excavation and
removal of soil or incineration. Bioremediation slows at low temperatures.
High concentrations of heavy metals, highly chlorinated organics, long chain
hydrocarbons, or inorganic salts are likely to be toxic to micro organisms. Concentrations
of hydrogen peroxide greater than 100 to 200 ppm in groundwater inhibit the activity of
micro organisms.
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.

Many of the above factors can be controlled with proper attention to good engineering
practice. The length of time required for treatment can range from 6 months to 5 years and is
dependent on many site-specific factors.

Microbes in Reclamation of Wastelands including Oil Spills

Petroleum hydrocarbons, although not xenobiotics, are one of the main potential sources of
environmental contamination due to their large-scale use. Soil and groundwater are often
contaminated with gasoline or diesel fuel from leaking underground storage tanks and
because of accidental spills and leakage from pipelines. Due to their mobility, these
compounds may cause considerable damage not only in soils but also in water intakes or
groundwater reservoirs. As a consequence, cost-effective bioremediation techniques have
been developed during this period, especially to clean up oil- and gas-polluted sites.
Petroleum contaminated soils and aquifers constitute about 60% of the sites where
bioremediation is being used in filed demonstrations or full-scale operations.

Steps in Bioremediation of oil contaminated site

The basic steps involved in the development of such bioremediation strategies are (Fig. 8).
(A) Microbe Isolation and identification
(B) Selection of petroleum degrading bacteria
(C) Generation of biomass
(D) Application of biomass to the contaminated site
(E) Maintenance of the selected bacterial population at the site
(A) Microbe Isolation and identification
Microbe is usually isolated by inoculating trypticase soya broth with the contaminated soil.
To enrich the petroleum degrading bacteria a two layered medium comprising lower layer of
22

minimal nitrogen medium (nitrogen source) covered with petroleum layer (carbon source)
can be used. After 48 hours of incubation, the petroleum degrading bacteria can be streaked
on trypticase soy agar plate and incubated for 2-3 days. The developed colonies are picked
and again inoculated on two layered medium till the pure bacterial cultures are obtained. The
bacterial identification can be done by standard biochemical tests, fatty acid analysis or by 16
S rDNA analysis. Care should be taken that the selected organisms are non-pathogenic. It is
better to conduct the screening and isolation at around 200C temperatures as most of the
pathogens best survive around 370C. However, further confirmation must be done to ensure
the non-pathogenic nature before proceeding with the bioremediation experiments.
Soil
Petroleum

Petroleum
Nitrogen medium

Soil+media

(A) Microbe Isolation and identification

(B) Selection of petroleum degrading bacteria

Cell Concentrate

(C) Generation of biomass

(D) Application of biomass at site

Fig. 8: Steps in bioremediation of petroleum contaminated site

(B) Selection of petroleum degrading bacteria
As shown in Fig. 9, further confirmation of the petroleum biodegradation ability of the
selected strains should be done by inoculating petroleum laden sterile soil with the selected
culture and incubating it for about 15 days. Total bacterial count and total petroleum
hydrocarbon (TPH) of the samples can be monitored to select the most efficient strains.

(C) Generation of biomass

After the microorganism has been identified and its ability to degrade petroleum oil has been
tested in the laboratory, the next step is to increase the number of microorganisms for field
application. Biomass production is done in large fermentors (Fig. 8) and the subsequent
culture is concentrated (by high speed centrifugation) to produce mud like precipitated cells.
The concentrated biomass is packed in plastic, tight sealing bags and transported to the
contaminated site on ice.

23

Degradation (%)

90
80
70
60
50
40
30
20
10
0
Control

NA

BS1

BS2

BA

Bioremediation strategy

Non-biological degradation

Biological degradation

Total degradation

NA: Natural attenuation (No amendment)

BS1: Biostimulation with inorganic N & P source
BS2: Biostimulation with sterilized sewage sludge
BA: Bioaugmentation with live/active sewage sludge

Fig. 9: Diesel biodegradation after 45 days

(Source: Gallego JLR, Loredo J, Llamas JF, Vazquez F & Sanchez J (2001) Biodegradation 12: 325335)

(D) Application of biomass to the contaminated site

Biomass should be applied to the contaminated soil as soon as possible but before 48 hours of
production. The amount of biomass to be applied depends on the total area of the
contaminated site as well as the degree of contamination. The biomass is appropriately
diluted and applied to the contaminated soil by injection or spray technique. If the
contamination is in the upper layers (2-3 feet of surface soil), spraying of the diluted biomass
after agitation of the soil (Fig. 8) may suffice but if the contamination has reached lower
layers, injection of the biomass to the deeper soil layers is required. Since the untraviolet rays
from sun are lethal to the microorganisms, the application of biomass to soil should be best
made in the early morning hours before sunrise.
(E) Maintenance of the selected bacterial population at the site
Since the soil has been augmented with more than natural microbial load of that particular
soil, special attention needs to be paid to monitor and maintain the oxygen levels, nutrients,
water content and pH so that the selected population can effectively degrade the
contaminants.

Petroleum degrading microbes

Several petroleum degrading microbes have been identified till date. Austin et al. 1977
identified 99 strains of petroleum-degrading bacteria isolated from Chesapeake Bay water
and sediment. These groups were identified as actinomycetes (mycelial forms, four clusters),
24

coryneforms, Enterobacteriaceae, Klebsiella aerogenes, Micrococcus spp. (two clusters),

Nocardia species (two clusters), Pseudomonas spp. (two clusters), and Sphaerotilus natans
which indicated that degradation of petroleum is accomplished by a diverse range of bacterial
taxa. A survey of petroleum-degrading bacteria was carried out in the Indian part of deltaic
Sunderbans to evaluate the distribution of the naturally occurring petroleum-degrading
aerobic bacteria. Depending on the location, 0.082.0% of the heterotrophic bacteria
culturable in marine agar medium could degrade crude petroleum hydrocarbons as the sole
source of carbon. There was a maximum number of petroleum-degrading bacteria in the
waters of Haldia Port and its surrounding areas, where the water is highly polluted by
hydrocarbon discharges from a nearby oil refinery and from the ships docking at the port.
Pseudomonas, Mycobacterium, Klebsiella, Acinetobacter, Micrococcus, and Nocardia were
the most common petroleum degraders. Selected strains belonging to Pseudomonas (two
strains), Mycobacterium (two strains), and Nocardia (one strain) degraded 4778% of ArabMix crude oil over a period of 20 days.
The Energy Research Institute (TERI), India has developed the Oilzapper which is crude oil
and oily sludge degrading bacterial consortium. This microbial consortium, developed from
five bacterial isolates (obtained from hydrocarbon-contaminated sites), was immobilized with
a suitable carrier material (powdered corncob). The immobilized culture (oilzapper), which
has the survivability of three months at ambient temperature, can be sealed aseptically into
sterile polythene bags and transported to the contaminated site. It has been successfully used
for clean up of crude oil spills and treatment of oily sludge. More than 40,000 tonnes of oily
sludge/oil contaminated soil and drill cuttings have been treated at various locations. More
than 30,000 tonnes of oily sludge/oil contaminated soil is under treatment at different
locations in India and the Middle East countries.
Further research targets more effective translation of lab results into the real field situations.
Poor performance of in situ treatments involving the addition of bacteria have been due to the
unknown effects of site conditions on the ability of bacteria to degrade contaminants.
Specialized indicator strains of bacteria that produce light in response to the presence of
bioavailable polycyclic aromatic hydrocarbons (PAH) are being developed. The indicator
strains would enable us to predetermine, whether or not the appropriate nutrient and
environmental conditions exist at a site. Microencapsulated bacteria for low-cost
bioremediation of petroleum products that are poorly degraded by naturally-occurring
bacteria are also being examined.
Case studies
A recent case study demonstrated bioremediation of diesel contaminated soil in laboratory
conditions as well as the in-situ bioremediation of a natural diesel spill (400,000 l). Diesel
fuel is a complex mixture of normal, branched and cyclic alkanes, and aromatic compounds
obtained from the middle-distillate, gas-oil fraction during petroleum separation. In this
article the different approaches of bioremediation were tested under laboratory conditions.
The experimental set comprised of Control experiment (Heat-sterilised soil), Natural
attenuation (No amendement), Biostimulation (with a. inorganic N & P source, b. Sterilized
sewage sludge), Bioaugmentation (live/active sewage sludge). The authors found best diesel
biodegradation when biostimulation with inorganic nutrients was done (Fig. 9). In both lab.
and field scale studies the hydrocarbon degraders (Acientobacter & Pesudomonas species)
were found abundant. Therefore, based on the lab results, for the real oil spill an integrated
approach of physical removal of diesel (free product recovery) followed by tilling and
fertilizing biostimulation treatment was recommended.
25

Oil contaminated soil in Kuwait could be successfully bioremediated by land-farming within

12 months. Land-farming could be enhanced by adjusting the C:N ratio to 50:1, inoculating
soil with HUB (hydrocarbon utilizing bacteria), and adding vegetation (alfa-alfa inoculated
with rhizobium cultures) after partial TPH (total petroleum hydrocarbon) reduction. Such
enhanced land-farming resulted in degradation of 90% of TPH from light contaminated soil.
McBean (1995) suggested an ex-situ two-stage process for remediation of semi-volatile
organic compounds. The first stage comprised of excavation, heap piling and washing of
contaminated soil in presence of surfactants, while in the second stage the collected leachate
was biologically treated with removal efficiency of 90% or more. Such a process with
decoupled stages has dual advantage that is quick leaching and soil replacement as well as
differential optimization of each step.
Role of biosurfactants
Biosurfactants are surfactants which are biologically produced by yeast or bacteria from
various substrates including sugars, oils, alkanes and wastes. Examples include rhamnolipids
(produced by Pseudomonas aeruginosa), sophorolipids (produced by Candida bombicola)
and surfactin (produced by Bacillus subtilis). Biosurfactants have shown their potential for
remediation of contaminated soil and water. Both organic and inorganic contaminants can be
treated through desorption or biodegradation processes.
Addition of rhamnolipid produced by Pseudomonas sp. DS10-129 along with poultry litter
and coir pith has been found to enhance ex situ bioremediation of a gasoline-contaminated
soil. Rhamnolipids from P. aeruginosa UG2 were also able to effectively remove a
hydrocarbon mixture from a sandy loam soil and that the degree of removal (from 23 to 59%)
was dependent on the type of hydrocarbon removed and the concentration of the surfactant
used. Surfactant produced by a strain of Bacillus subtilis at was able to remove 62% of the oil
in a sand pack saturated with kerosene and thus could be used for in situ oil removal and
cleaning sludge from sludge tanks. The use of the biosurfactants in cleaning oil from coastal
sand, and from the feathers and furs of marine birds and animals has also been examined. The
biourfactant (PS-17) produced by strain Pseudomonas PS-17 could efficiently remove oil
from sand (95% removal) as well as from feathers (85%) and furs (82%) of marine birds and
animals contaminated by oil as opposed to 1-2% oil removal in the absence of PS-17
biosurfactant. The biosurfactants seem to enhance biodegradation by influencing the
bioavailability of the contaminant. Due to their biodegradability and low toxicity they are
very promising for use in remediation technologies. However, further research regarding
prediction of their behaviour in the fate and transport of contaminants, decreasing production
costs, in situ production, among other issues will be required.

Conclusions
Bioremediation, which is the natures way of dealing with the environmental pollution, is
gaining significant attention these days. Different approaches to accelerate the intrinsic
bioremediation have been developed and used at a number of sites worldwide with varying
degrees of success. Techniques are improving as greater knowledge and experience are
gained, and bioremediation has gained triumph for dealing with certain types of site
contamination. Unfortunately, the principles, techniques, advantages, and disadvantages of
bioremediation are not widely known or understood, especially among those who will have to
deal directly with bioremediation proposals, such as site owners and regulators. Therefore,
apart from the sound fundamental knowledge about these techniques there is a need for
26

providing a straightforward, pragmatic view of the processes involved in bioremediation, the

pros and cons of the technique, and the issues to be considered when dealing with a proposal
for bioremediation.

Suggested Reading
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20.

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