Role of Microorganisms in bioremediation and biodegradation

Bioremediation is the use of living organisms, primarily microorganisms, for the degradation of
hazardous chemicals in soil sediments, water, or other contaminated materials into less toxic
forms. Bioremediation is any process that uses organisms (microorganism, algae and plant) or
their enzymes to return the polluted environment to its original condition. Other names used for
bioremediation are biotreatment, bioreclamation and biorestoration.

The removal of organic wastes by microbes for environmental clean-up is the essence of
bioremediation

 Bioremediation-by microorganisms (soil, groundwater-organic contaminants)

 Phytoremediation-by plants (mostly soil and surface water)

How bioremediation works

Microorganisms obtain energy for growth by degrading organic contaminants in an enzyme-

mediated process referred as direct metabolism for instance aerobic biodegradation of BTEX in
the presence of an oxygenase (by Pseudomonas). Some enzymes are not very specific and in
addition to the growth substrate transform other compounds referred as cometabolism for
example oxygenases are not very substrate-specific and can also degrade TCE (however TCE
cannot be used as a growth substrate).

Use of microorganisms in bioremediation

Microorganisms metabolize the pollutants or toxic chemicals to produce carbon dioxide or

methane, water and biomass. Microorganisms enzymatically transform the toxic chemicals
and/or pollutants to metabolites that are less toxic or innocuous. In some instances, the
metabolites formed are more toxic than the parent compound. For example, perchloroethylene
and trichloroethylene may degrade to vinyl chloride.

Genus pseudomonas is the most predominant microorganisms that degrade xenobiotics (e.g.
hydrocarbons, phenols, organophosphates, polycyclic aromatics and naphthalein). Other
microorganisms are Mycrobacterium, Mycococcus, Nitrosomonas, Nocardia, Penicillium,
Phanerochaete etc.

Mechanisms of Bioremediation

Metabolism modes are broadly classified as aerobic and anaerobic. Aerobic transformations
occur in the presence of molecular oxygen, with molecular oxygen serving as the electron
acceptor. This form of metabolism is known as aerobic respiration. Anaerobic reactions occur
only in the absence of molecular oxygen and the reactions are subdivided into Anaerobic
respiration, Fermentation or Methane fermentation. In fermentation organic compounds serve as
both electron donors and electron acceptors. It can proceed only under strictly anaerobic
conditions. The end products depend on the type of microorganisms but usually include a
number of acids, alcohols, ketones and gases such as CO2 and CH4.

Aerobic or anaerobic metabolism involve oxidation and reduction (Redox) reactions for
detoxification. Oxygen could be reduced to water and oxidized organic compounds. While,
anaerobic reaction can use nitrate. In return, biomass is gained for bacterial or fungal growth. In
many cases, combined efforts are needed; indigenous microbes found naturally in polluted sites
are useful.

Different modes of Microbial transformations of organic compounds

 Degradation ----- Initial substrate no longer exists

 Mineralization ------- complete conversion of the organic structure to inorganic forms

such as CO2, H2O, and Cl–

 Detoxification ------ transformation of the compound to some intermediate form that is

nontoxic or less toxic.

 Activation ----The process of forming toxic end products or intermediate products

Microorganisms are capable of catalyzing a variety of reactions including

 Hydrolysis—frequently conducted outside the microbial cell by exoenzymes. Hydrolysis

is simply a cleavage of an organic molecule with the addition of water.

 Cleavage—cleaving of a carbon–carbon bond ------- An organic compound is split or a

terminal carbon is cleaved off from an organic chain.

 Oxidation—breakdown of organic compounds using an electrophilic form of oxygen.

 Reduction—breakdown of organic compounds by a nucleophilic form of hydrogen or by

direct electron delivery.

 Dechlorination—the chlorinated compound becomes an electron acceptor; in this

process, a chlorine atom is removed and is replaced with a hydrogen atom.

 Dehydrogenation—an oxidation–reduction reaction that results in the loss of two

electrons and two protons, resulting in the loss of two hydrogen atoms.

 Dehydrohalogenation—results in the loss of a hydrogen and chlorine atom from the

organic compound.

 Substitution—these reactions involve replacing one atom with another.

Methods of bioremediation

On the basis of removal and transportation of the wastes for the treatment, basically there are two
methods:

In-situ (without excavation) bioremediation involves a direct approach for the microbial
degradation of pollution (soil, ground water).

Addition of adequate quantities of nutrients at the site promote indigenous microbial growth
is referred as Biostimulation. When microorganisms are imported to a contaminated site to
enhance degradation, the process is called as Bio-augmentation.

There are two types of in situ bioremediation

 Intrinsic bioremediation is the conversion of environmental pollutants into the harmless

forms through the innate capabilities of naturally occurring microbial population. The
intrinsic (that is inherent) capacity of microorganisms to metabolize the contaminants
should be tested at the laboratory and field levels before use for intrinsic bioremediation.
Through site monitoring programs progress of intrinsic bioremediation should be
recorded time to time. The conditions of site that favor intrinsic bioremediation are
ground water flow throughout the year, carbonate minerals to buffer acidity produced
during biodegradation, supply of electron acceptors and nutrients for microbial growth
and absence of toxic compounds.

 Engineered bioremediation

Intrinsic bioremediation is satisfactory at some places, but it is slow process due to the
poorly adapted microorganisms, limited ability of electron acceptor and nutrients, cold
temperature and high concentration of contaminants. When site conditions are not
suitable, bioremediation requires construction of engineered system to supply materials
that stimulate microorganisms. Engineered in situ bioremediation accelerates the desired
biodegradation reactions by encouraging growth of more microorganisms via
optimizing physico-chemical conditions.

Ex-situ bioremediation involves removal of waste materials and their collection at the place to
facilitate microbial degradation.

In-situ bioremediation Techniques

Bioventing

It is a technology that stimulates the natural in-situ biodegradation of any aerobically degradable
compounds in soil by providing oxygen to existing soil microorganisms. It 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. Bioventing
techniques have been successfully used to remediate soils contaminated by petroleum
hydrocarbons, no chlorinated solvents, some pesticides, wood preservatives, and other organic
chemicals.

Biosparging

It involves the injection of a gas (usually air or oxygen) and occasionally gas-phase nutrients,
under pressure, into the saturated zone to promote aerobic biodegradation. In air sparging,
volatile contaminants also can be removed from the saturated zone by desorption and
volatilization into the air stream. Typically, biosparging is achieved by injecting air into a
contaminated subsurface formation through a specially designed series of injection wells.
Phytoremediation

Phytoremediation is use of plants for accumulation, removal or conversion of pollutants.

Phytoremediation can be achieved by Phytostabilization, Rhizofilration, Phytovolatilization,
Phytoextraction and Phytostimulation.

Ex-situ bioremediation Techniques

On the basis of phases of contaminated materials ex situ bioremediation is classified in to two:

Solid phase system and Slurry phase system.

Solid phase system

Solid waste system includes organic wastes (e. g leaves, animal manure and agriculture wastes)
and problematic wastes (e.g. domestic and industrial wastes, sewage sludge and municipal solid
wastes.

Bioremediation techniques applied are

▶ Composting

▶ Land farming
Composting is aerobic, thermophilic treatment process in which contaminated material is mixed
with bioremediation microorganisms. This is a controlled biological process by which organic
contaminants (e.g. PAHs) are converted by microorganisms to safe, stabilized by-products.
Typically, thermophilic conditions (54 to 65°C) and pH 6-9 are maintained. In composting, soils
are excavated and mixed with bulking agents and organic amendments, such as wood chips and
vegetative wastes, to enhance the porosity of the mixture to be decomposed. Degradation of the
bulking agent heats up the compost, creating thermophilic conditions. Oxygen content usually is
maintained by frequent mixing, such as daily or weekly turning of windrows. Surface irrigation
often is used to maintain moisture content. Temperatures are controlled, to a degree, by mixing,
irrigation, and air flow, but are also dependent on the degradability of the bulk material and
ambient conditions.

Vermicomposting is a process in which the earthworms convert the organic waste into manure
rich in high nutritional content. The compost produced in this green process is traditionally and
popularly used as a natural fertilizer for enhancing plant growth.

Land farming also called Land treatment is performed in upper soil zone or biotreatment cells.
Contaminants are transported to the landfarming site, mixed into the soil and periodically turned
over or tilled to aerate the mixture. Moisture is added when needed. In some cases, amendments
may be added to improve the tilth of the soil (is defined as physical condition of soil as related to
its ease of tillage, fitness as a seedbed, and its promotion of seedling emergence and root
penetration), supply nutrients, moderate pH, or facilitate bioremediation. This method is useful in
treating aerobically degradable contaminants. This process is suitable for non-volatile
contaminants at sites where large areas for treatment cells are available.
Slurry phase treatment

The contaminated solid materials (soil, degraded sediments etc.), microorganisms and water
formulated into slurry are brought within a bioreactor. A triphasic system involving three major
components: water, suspended particulate matter and air. Water serves as suspending medium
where nutrients, trace elements, pH adjustment chemicals and desorbed contaminants are
dissolved. Suspended particulate matter includes a biologically inert substratum consisting of
contaminants (soil particles) and biomass attached to soil matrix or free in suspended medium.
And air provides oxygen for bacterial growth. Biologically there are two types of slurry phase
reactors (a) Aerated lagoons and (b) Low shear air lift reactors.

Water and gas bioremediation

Biofiltration is a process, in which, microorganisms supported on inert materials are used to

degrade organic pollutants. It is used for air, gas and water bioremediation. Types of biofilters:

 Bioscrubbers
 Biotrickling filters
 Slow sand or carbon filters

Bioscrubber filters
Slow sand or carbon filters

Slow sand or carbon filters work through the formation of a gelatinous layer (or biofilm layer) on
the top few millimetres of the fine sand or carbon layer. This layer contains bacteria, fungi,
protozoa, rotifera and a range of aquatic insect larvae (i.e. rotifers).