Meaning and Applications

Meaning of Environmental
Biotechnology
 Environmental biotechnology in particular is the application of
processes for the protection and restoration of the quality of the
environment.
 Environmental biotechnology can be used to detect, prevent and
remediate the emission of pollutants into the environment in a
number of ways.
 Solid, liquid and gaseous wastes can be modified, either by recycling
to make new products, or by purifying so that the end product is less
harmful to the environment. Replacing chemical materials and
processes with biological technologies can reduce environmental
damage.
 Thus, environmental biotechnology can make a significant
contribution to sustainable development. Environmental
Biotechnology is one of today‘s fastest growing and most practically
useful scientific fields.
 Objectives of Environmental Biotechnology
(According to Agenda 21):

 The aim of environmental biotechnology is to

prevent, arrest and reverse environmental
degradation through the appropriate use of
biotechnology in combination with other
technologies, while supporting safety procedures as a
primary component of the programme.
 Specific Objectives are

1. To adopt production processes that make optimal

use of natural resources, by recycling biomass,
recovering energy and minimizing waste
generation.
2. To promote the use of biotechnological techniques
with emphasis on bioremediation of land and
water, waste treatment, soil conservation,
reforestation, afforestation and land rehabilitation.
3. To apply biotechnological processes and their
products to protect environmental integrity with a
view to long-term ecological security.
 Use of biotechnology to treat pollution problems is not a new idea.
Communities have depended on complex populations of naturally
occurring microbes for sewage treatment for over a century. Every living
organism—animals, plants, bacteria and so forth—ingests nutrients to live
and produces a waste as a by-product. Different organisms need different
types of nutrients.
 Certain bacteria thrive on the chemical components of waste products.
Some microorganisms feed on materials toxic to others.
 Research related to environmental biotechnology is vital in developing
effective solutions for mitigating, preventing and reversing environmental
damage with the help of these living forms.
 Growing concern about public health and the deteriorating quality of the
environment has prompted the development of a range of new, rapid
analytical devices for the detection of hazardous compounds in air, water
and land.
 Recombinant DNA technology has provided the possibilities for the
prevention of pollution and holds a promise for a further development of
bioremediation.
 Applications of Environmental
Biotechnology

 Environmental protection is an integral component of sustainable

development. The environment is threatened every day by the
activities of man. With the continued increase in the use of
chemicals, energy and non-renewable resources by an expanding
global population, associated environmental problems are also
increasing.
 Despite escalating efforts to prevent waste accumulation and to
promote recycling, the amount of environmental damage caused by
over-consumption, the quantities of waste generated and the degree
of unsustainable land use appear likely to continue growing.
 The remedy can be achieved, to some extent, by the application of
environmental biotechnology techniques, which use living
organisms in hazardous waste treatment and pollution control.
Environmental biotechnology includes a broad range of applications
such as bioremediation, prevention, detection and monitoring,
genetic engineering for sustainable development and better quality
of living.
 Bioremediation

 Bioremediation refers to the productive use of microorganisms to remove

or detoxify pollutants, usually as contaminants of soils, water or sediments
that otherwise intimidate human health. Bio treatment, bio reclamation
and bio restoration are the other terminologies for bioremediation.
Bioremediation is not a new practice. Microorganisms have been used for
many years to remove organic matter and toxic chemicals from domestic
and manufacturing waste discharge.
 However, the focus in environmental biotechnology for fighting different
pollution is on bioremediation. The vast majority of bioremediation
applications use naturally occurring microorganisms to identify and filter
toxic waste before it is introduced into the environment or to clean up
existing pollution problems.
 Some more advanced systems using genetically modified microorganisms
are being tested in waste treatment and pollution control to remove
difficult-to-degrade materials. Bioremediation can be performed in situ or
in specialized reactors (ex situ). Bioremediation by microorganisms need
appropriate environment for the clean up of the polluted site.
 Waste Water and Industrial Effluents

 Water pollution is a serious problem in many countries of the world. Rapid

industrialisation and urbanization have generated large quantities of waste water
that resulted in deterioration of surface water resources and ground water reserves.
Biological, organic and inorganic pollutants contaminate the water bodies.
 In many cases, these sources have been rendered unsafe for human consumption as
well as for other activities such as irrigation and industrial needs. This illustrates
that degraded water quality can, in effect, contribute to water scarcity as it limits its
availability for both human use and the ecosystem. Treatment of the waste water
before disposal is of urgent concern worldwide.
 In sewage treatment plants microorganisms are used to remove the more common
pollutants from waste water before it is discharged into rivers or the sea. Increasing
industrial and agricultural pollution has led to a greater need for processes that
remove specific pollutants such as nitrogen and phosphorus compounds, heavy
metals and chlorinated compounds.
 Methods include aerobic, anaerobic and physico-chemical processes in fixed-bed
filters and in bioreactors in which the materials and microbes are held in
suspension. Sewage and other waste waters would, if left untreated, undergo self-
purification but the process requires long exposure periods. To speed up this
process bioremediation measures are used.
 Aerobic Biological Treatment

 Trickling filters, rotating biological contactors or

contact beds, usually consist of an inert material
(rocks/ash/ wood/ metal) on which the
microorganisms grow in the form of a complex
biofilm. These have been used for more than 70
years for sewage and waste water treatment. In these
processes the degradable organic matter is oxidized
by the microorganisms to CO2 that can be vented to
the atmosphere.
 Activated Sludge Process

 This process is used for treatment and removal of dissolved

and biodegradable wastes, such as organic chemicals,
petroleum refining wastes textile wastes and municipal
sewage. The microorganisms in activated sludge generally are
composed of 70-90% organic and 10-30% inorganic matters.
 The microorganisms found in this sludge are usually bacteria,
fungi, protozoa and rotifers. Petroleum hydrocarbons are
degraded by species of bacteria (Acinetobacter, Mycobacteria,
Pseudomonas etc.), yeasts, Cladosporium and
Scolecobasidium. Pesticides (aldrin, dieldrin, parathion,
malathion) are detoxified by fungus Xylaria xylestrix.
Pseudomonas (a predominant soil microrganism) can detoxify
organic compounds like hydrocarbons, phenols,
organophosphates, polychlorinated biphenyls and polycyclic
aromatics.
 Utilisation of immobilized cyanobacterium Phormidium laminosum in
batch and continuous flow bioreactors for the removal of nitrate, nitrite
and phosphate from water has been reported by Garbisu et al. (2003).
Blanco et al. (2003) showed the biosorption of heavy metal by Phormidium
laminosum immobilised in micro-porous polymeric matrices. Photo-
bioreactors are currently used to grow algae and cyanobacteria under
closely controlled environmental conditions, with a view to making high-
value products (such as beta-carotene and gamma-linoleic acid), designing
efficient effluent treatment processes, and providing new energy sources.
 The costs of wastewater treatment can be reduced by the conversion of
wastes into useful products. Sulphur metabolizing bacteria can remove
heavy metals and sulphur compounds from waste streams of the
galvanization industry and reused. Most anaerobic wastewater treatment
systems produce useful biogas.
 In some cases, the by-products of the pollution-fighting microorganisms
are themselves useful. Methane, for example, can be derived from a form of
bacteria that degrades sulphur liquor, a waste product of paper
manufacturing.
 Soil and Land Treatment

 As the human population grows, its demand for food from crops increases, making
soil conservation crucial. Deforestation, over-development, and pollution from
man-made chemicals are just a few of the consequences of human activity and
carelessness. The increasing amounts of fertilizers and other agricultural chemicals
applied to soils and industrial and domestic waste-disposal practices, led to the
increasing concern of soil pollution. Pollution in soil is caused by persistent toxic
compounds, chemicals, salts, radioactive materials, or disease-causing agents,
which have adverse effects on plant growth and animal health.
 Many species of fungi can be used for soil bioremediation. Lipomyces sp. can
degrade herbicide paraquat. Rhodotorula sp. can convert benzaldehyde to benzyl
alcohol. Candida sp. degrades formaldehyde in the soil. Aspergillus niger and
Chaetomium cupreum are used to degrade tannins (found in tannery effluents) in
the soil thereby helping in plant growth.
 Phanerochaete chrysosporium has been used in bioremediation of soils polluted
with different chemical compounds, usually recalcitrant and regarded as
environmental pollutants. Decrease of PCP (Pentachlorophenol) between 88-91%
within six weeks was observed in presence of Phanerochaete chrysosporium.
 Bioremediation of contaminated soil has been used as a safe, reliable, cost-
effective and environment friendly method for degradation of various
pollutants. This can be effected in a number of ways, either in situ or by
mechanically removing the soil for treatment elsewhere.
 In situ treatments include adding nutrient solutions, introducing
microorganisms and ventilation. Ex situ treatment involves excavating the
soil and treating it above ground, either as compost, in soil banks, or in
specialised slurry bioreactors. Bioremediation of land is often cheaper than
physical methods and its products are largely harmless.
 During biological treatment soil microorganisms convert organic pollutants
to CO2, water and biomass. Degradation can take place under aerobic as
well as under anaerobic conditions. Soil bioremediation can also be
accomplished with the help of bioreactors. Degradation can take place
under aerobic as well as under anaerobic conditions. Soil bioremediation
can also be accomplished with the help of bioreactors. Liquids, vapours, or
solids in a slurry phase are treated in a reactor. Microbes can be of natural
origin, cultivated or even genetically engineered.
 Research in the field of environmental biotechnology has made it
possible to treat soil contaminated with mineral oils. Solid-phase
technologies are used for petroleum-contaminated soils that are
excavated, placed in a containment system through which water and
nutrients percolate. Biological degradation of oils has proved
commercially viable both on large and small scales, in situ and ex
situ.
 In situ soil bioremediation involve the stimulation of indigenous
microbial populations (e.g. by adding nutrients or aeration). In this
process the environmental conditions for the biological degradation
of organic pollutants are optimized as far as possible. Oxygen has to
be supplied by artificial aeration or by adding electron acceptors
such as nitrates or oxygen releasing compounds. Ozone dissolved in
water and H2O2 are sometimes used which degrade the organic
contaminants.
 Air and Waste Gases

 With the onset of human civilization, the air is one of the first and
most polluted components of the atmosphere. Most air pollution
comes from one human activity: burning fossil fuels—natural gas,
coal, and oil—to power industrial processes and motor vehicles.
When fuels are incompletely burned, various chemicals called
volatile organic chemicals (VOCs) also enter the air. Pollutants also
come from other sources.
 For instance, decomposing garbage in landfills and solid waste
disposal sites emits methane gas, and many household products
give off VOCs. Expanding industrial activities have added more
contaminants in the air.
 The concept of biological air treatment at first seemed impossible.
With the development of biological waste gas purification
technology using bioreactors—which includes bio filters, bio
trickling filters, bio scrubbers and membrane bioreactors—this
problem is taken care of. The mode of operation of all these reactors
is similar.
 Air containing volatile compounds is passed through the
bioreactors, where the volatile compounds are transferred
from the gas phase into the liquid phase. Microbial
community (mixture of different bacteria, fungi and protozoa)
grow in this liquid phase and remove the compounds acquired
from the air.
 In the bio filters, the air is passed through a bed packed with
organic materials that supplies the necessary nutrients for the
growth of the microorganisms. This medium is kept damp by
maintaining the humidity of the incoming air. Biological off-
gas treatment is generally based on the absorption of the VOC
in the waste gases into the aqueous phase followed by direct
oxidation by a wide range of voracious bacteria, which include
Nocardia sp. and Xanthomonas sp.
 Next class on 25th Non 20
 Prevention

 Sustainable development and quality living depends

upon the rational, eco-friendly use of natural resources
with economic growth. To comply with this trend,
industrial development has to change to sustainable style
from degradative type and for such a purpose cleaner
technologies have to be adopted.
 According to United Nations Environment Programme
(1996) ‗the continuous application of an integrated
preventive environmental strategy to processes, products
and services to increase eco-efficiency and reduce risks to
humans and the environment‘ defines the eco-friendly
concept. The application of preventive and clean concept
can only be achieved by the 5R policies (Olguin et al,
2003).
 5R Vs 3R
Five Environmental Buzzwords are the 5Rs for Efficient
Use of Energy and Better Control of Waste, Which Might
Help in Sustainable Development and Quality Living:
1. Reduce (Reduction of waste)
2. Reuse (Efficient use of water, energy)
3. Recycle (Recycling of wastes)
4. Replace (Replacement of toxic/hazardous raw materials for more
environment- friendly inputs)
5. Recover (useful non-toxic fractions from wastes)

Innovation and adoption of clean technologies is the target of

research and development worldwide. Industrial companies are
developing processes with reduced environmental impact
responding to the international call for the development of a
sustainable society. There is a pervading trend towards less harmful
products and processes; away from ―end-of-pipe‖ treatment of waste
streams. Environmental biotechnology, with its appropriate
technologies, is suitable to contribute to this trend.
 Use of Enzymes

 Enzymes are widely employed in industries for many years.

Enzymes, non-toxic and biodegradable, are biological
catalysts that are highly competent and have numerous
advantages over non-biological catalysts. The use of enzyme
by man, both directly and indirectly, have been for thousands
of years.
 In the recent years enzymes have played important roles in
the production of drugs, fine chemicals, amino acids,
antibiotics and steroids. Industrial processes can be made
eco-friendly by the use of enzymes. Enzyme application in the
textile, leather, food, pulp and paper industries help in
significant reduction or complete elimination of severe
chemicals and are also more economic in energy and resource
consumption.
 Biotechnological methods can produce food materials with
improved nutritional value, functional characteristics, shelf
stability. Plant cells grown in fermenters can produce flavours
such as vanilla, reducing the need for extracting the
compounds from vanilla beans. Food processing has benefited
from biotechnologically produced chymosin which is used in
cheese manufacture; alpha-amylase, which is used in
production of high-fructose corn syrup and dry beer; and
lactase, which is added to milk to reduce the lactose content
for persons with lactose intolerance.
 Genetically engineered enzymes are easier to produce than
enzymes isolated from original sources and are favoured over
chemically synthesized substances because they do not create
by-products or off-flavours in foods.
 Environmental Detection and Monitoring

 A wide range of biological methods are in use to detect pollution and for the
continuous monitoring of pollutants. The techniques of biotechnology have
novel methods for diagnosing environmental problems and assessing
normal environmental conditions so that human beings can be better-
informed of the surroundings. Applications of these methods are cheaper,
faster and also portable.
 Rather than gathering soil samples and sending them to a laboratory for
analysis, scientists can measure the level of contamination on site and
know the results immediately. Biological detection methods using
biosensors and immunoassays have been developed and are now in the
market. Microbes are used in biosensors contamination of metals or
pollutants. Saccharomyces cerevisiae (yeast) is used to detect cyanide in
river water while Selenastrum capricornatum (green alga) is used for heavy
metal detection. Immunoassays use labelled antibodies (complex proteins
produced in biological response to specific agents) and enzymes to measure
pollutant levels. If a pollutant is present, the antibody attaches itself to it
making it detectable either through colour change, fluorescence or
radioactivity.
 Biosensor

 A biosensor is an analytical device that converts a biological response into an physical,

chemical or electrical signal. The development of biosensors involves integration of a
specific and sensitive biologically derived sensing elements (immobilized cells, enzymes
or antibodies) are integrated with physico-chemical transducers (either electrochemical
or optical). Immobilised on a substrate, their properties change in response to some
environmental effect in a way that is electronically or optically detectable.
 It is then possible to make quantitative measurements of pollutants with extreme
precision or to very high sensitivities. The biological response of the biosensor is
determined by the bio catalytic membrane, which accomplishes the conversion of
reactant to product. Immobilised enzymes possess a number of advantageous features
which makes them particularly applicable for use in such systems.
 They may be re-used, which ensures that the same catalytic activity is present for a series
of analyses. Biosensors are powerful tools, which rely on biochemical reactions to detect
specific substances, which have brought benefits to a wide range of sectors, including the
manufacturing, engineering, chemical, water, food and beverage industries. They are able
to detect even small amounts of their particular target chemicals, quickly, easily and
accurately.
 For this character of biosensors they have been ardently
adopted for a variety of process monitoring applications,
principally in respect to pollution assessment and control.
Biosensors for detection of carbohydrates, organic acids,
glucosinolates, aromatic hydrocarbons, pesticides, pathogenic
bacteria and others have already been developed.
 The biosensors can be designed to be very selective, or
sensitive to a broad range of compounds. For example, a wide
range of herbicides can be detected in river water using algal-
based biosensors; the stresses inflicted on the organisms
being measured as changes in the optical properties of the
plant‘s chlorophyll. Biosensors are of different types such as
calorimetric biosensors, immunosensors, optical biosensors,
BOD biosensors, gas biosensors.
 The remarkable ability of microbes to break down chemicals is
proving useful, not only in pollution remediation but also in
pollutant detection. A group of scientists at Los Alamos
National Laboratory work with bacteria that degrade a class of
organic chemicals called phenols. When the bacteria ingest
phenolic compounds, the phenols attach to a receptor.
 The phenol-receptor complex then binds to DNA, activating
the genes involved in degrading phenol. The Los Alamos
scientists added a reporter gene that, when triggered by a
phenol-receptor complex, produces an easily detectable
protein, thus indicating the presence of phenolic compounds
in the environment. Biosensors employing acetylcholine
esterase can be used for the detection of organophosphorus
compounds in water.
 Use of Genetic Engineering

 Biotechnology, which is expected to make a great contribution to

the welfare of mankind, is an important technology that should be
steadily developed. The application of DNA technology, among the
different kinds of biotechnology, has the possibility to create new
gene combinations that have not previously existed in nature.
 Since its beginning, genetic engineering has claimed to be able to
construct tailor-made microorganisms with improved degrading
capabilities for toxic substances. With the development of GEM
(genetically engineered microorganism) and their possible
utilization in the treatment of contaminated soil and water, stability
of plasmids is extremely desirable. Plasmids are circular strands of
DNA that replicates as separate entities independent of the host
chromosome. Plasmids can range in size from those that carry only
a couple of genes to ones carrying much greater numbers. Small
plasmids may be present as multiple copies. Exchange of genetic
information via plasmids is achieved by the process of conjugation.
 The use of restriction enzymes has enabled the isolation of particular DNA
fragments that can be transferred to another organism lacking the same.
Genes which code for metabolism of environmental pollutants such as
PCB‘s and other xenobiotic compounds are frequently, although not
always, located on plasmids.
 The possibility of genetic transfer in non-biodegradative microbes has
opened a new outlook of bio treatment of wastes. The recombinant DNA
has the ability to multiply and may also confer the specific derivative
capacity to detoxify environmental contaminants.
 Gene transfer among microbial communities has improved the derivative
capacity in vitro. The first patent for a genetically modified organism
(GMO) or GEM, filed in the USA by Professor A. M. Chakrabarty was for a
bacterium Pseudomonas putida with hydrocarbon degrading abilities.
Subsequent reports have noted the role of plasmids in degradation of
alkanes, naphthalene, toluene, m— and p— xylenes
 Given the overwhelming diversity of species, biomolecules and
metabolic pathways on this planet, genetic engineering can, in
principle, be a very powerful tool in creating environmentally
friendlier alternatives for products and processes that presently
pollute the environment or exhaust its non-renewable resources.
 Nowadays organisms can be supplemented with additional genetic
properties for the biodegradation of specific pollutants if naturally
occurring organisms are not able to do that job properly or not
quickly enough. By combining different metabolic abilities in the
same microorganism blockage in environmental cleanup may be
circumvented.
 In the USA some genetically modified bacteria have been approved
for bioremediation purposes but large scale applications have not
yet been reported. In Europe only controlled field tests have been
authorized. Just as light, heat, and moisture can degrade many
materials, biotechnology relies on naturally occurring, living
bacteria to perform a similar function but the action is faster.
 Some bacteria naturally feed on chemicals and other wastes, including some
hazardous materials. They consume those materials, digest them, and excrete
harmless substances in their place. Bioremediation uses natural as well as
recombinant microorganisms to break down toxic and hazardous substances
already present in the environment. Bio treatment can be used to detoxify waste
streams at the source before they contaminate the environment – rather than at the
point of disposal. This approach involves carefully selecting organisms, known as
biocatalysts, which are enzymes that degrade specific compounds and accelerate the
degradation process.
 However, the application of GMOs/GEMs, in the environment for bioremediation
may create problems in the ecosystem. These exclusively designed organisms do not
get a chance to experience the various fluctuating environmental conditions which is
faced by naturally occurring organisms during the evolutionary processes spaning
millions of years.
 As a result, the latter are well adapted to the changing environmental conditions
such as changes in temperature, substrate or waste concentrations. But when
exposed to the contaminated site, GMOs show a higher viability than naturally
occurring bacteria, due to their tailored enzymatic equipment.
 There are concerns about the negative effect of these GMOs on
the complex and delicate microbial ecosystems by competition
or the exchange of genetic material in the soils to which they are
applied. Even more worrisome is their potential effect outside
the treatment area. While recombinant strains may appear
harmless in the laboratory, it is virtually impossible to assess
their impact in the field.
 Biotechnical methods are now used to produce many proteins
for pharmaceutical and other specialized purposes. Human
insulin, the first genetically engineered product to be produced
commercially (1982) is made by nonvirulent strain of
Escherichia coli bacteria, by introduction of a copy of the gene
for human insulin.
 When the gene is ―amplified‖ the bacterial cells produce large
quantities of human insulin that are purified and used to treat
diabetes in human beings. A number of other genetically
engineered products have been approved since then, including
human growth hormone, alpha interferon, recombinant
erythropoietin and tissue plasminogen activator.
 Biotechnology techniques are being applied to plants to produce plant
materials with improved composition, functional characteristics. Among
the first commercially available whole food products was the slow-ripening
tomato, the gene for polygalacturonase, the enzyme responsible for
softening, is turned off in this tomato. Plants that are resistant to disease,
pests, environmental conditions, or selected herbicides or pesticides are
also being developed.
 In 1995, the Environmental Protection Agency (EPA) gave clearance for
development of transgenic corn seed, cotton seed, and seed potatoes that
contain the genetic material to resist certain insects. The advantage of such
products is that they allow the use of less toxic and more environmentally
friendly herbicides and pesticides.
 The first approved application of biotechnology to animal production was
the use of recombinant bovine somatotropin (BST) in dairy cows. Bovine
somatotropin, a protein hormone found naturally in cows, is necessary for
milk production. When the recombinant BST is administered to dairy cows
under ideal management conditions, milk production has been shown to
increase by 10% to 25%.
 Other uses of biotechnology in animal production include development of vaccines
to protect animals from disease, production of several calves from one embryo
(cloning), artificial insemination, improvement of growth rate and/or feed
efficiency, and rapid disease detection.
 Natural bio-pesticides are another development of biotechnology that help farmers
reduce chemical use. They degrade rapidly, leave no residues, and are toxic only to
target insects. Bacillus thuringiensis (B.t.), produces a protein that is naturally toxic
to certain insects. Scientists have extracted the B.t. gene that expresses the
insecticide and inserted it into common bacteria that can be grown in large
quantities by the same fermentation techniques used to produce such everyday
products as beer and antibiotics. Spread on cotton and other crops, these harmless
bacteria control insects naturally.
 Moreover, a wide range of crop plants have been genetically engineered to express
the cry genes (found in B. t.) in their tissues, so the insects get killed as they feed on
these crops. Pollution control by genetic engineering is likely to work best when
pollutants are a known mixture of relatively concentrated organic compounds that
are related to each other in structure, where conventional alternative organic
nutrients are absent, and when there is no competition from indigenous
microorganisms.
 The spectacular metabolic versatility of bacteria and fungi is exploited in
the area environmental bioremediation as in sewage and waste water
treatment, degradation of xenobiotics and metal abatement. Genetic
manipulation offers a way of engineering microorganisms to deal with a
pollutant, or a family of closely related pollutants, that may be present in
the waste stream from an industrial process.
 The simplest approach is to extend the degradative capabilities of existing
metabolic pathways within an organism either by introducing additional
enzymes from other organisms or by modifying the specificity or catalytic
mechanisms of enzymes already present.
 A treatment plant at the Homestake Mine in Lead, South Dakota, purifies 4
million gallons of cyanide-containing wastewater a day by completely
converting cyanide to nitrate. Pseudomonas sp. convert cyanide and
thiocyanate to ammonia and bicarbonate and the nitrifying bacteria
Nitrosomonas and Nitrobacter cooperate in converting ammonia to nitrate.
Recombinant DNA technology has had amazing repercussion in the last
few years in environmental protection and also in other fields for better
quality of living.
 Environmental Biotechnology is Divided
into Different Areas

 (i) Direct studies of the environment,

 (ii) Research with a focus on applications to the
environment and
 (iii) Research that applies information from the
environment to other venues.
 In addition to DNA inside living organisms, there is much free DNA in the environment that
might also be a source of new genes. The field of environmental biotechnology has
revolutionized the study of the life-forms which have not been studied earlier and DNA.
 This approach is direct analyses of the environment and the natural biochemical processes that
are present. A significant study in this aspect is metagenomics. Metagenomics is the study of
the genomes of whole communities of microscopic life forms and it deals with a mixture of DNA
from multiple organisms, viruses, viroids, plasmids and free DNA.
 In other words, metagenomics, the genomic analysis of a population of microorganisms, is the
method to gain access to the physiology and genetics of uncultured organisms.
 Using metagenomics, researchers investigate, catalogue the current microbial diversity. New
proteins, enzymes and biochemical pathways are identified. The knowledge garnered from
metagenomics has the potential to affect the ways we use the environment. Metagenomic
analyses involves isolating DNA from an environmental sample, cloning the DNA into a suitable
vector, transforming the clones into a host bacterium and screening the resultant
transformants.
 The clones can be screened for phylogenetic markers such as 16S rRNA and rec A or for other
conserved genes by hybridization or multiplex PCR or for expression of specific traits such as
enzyme activity or antibiotic production or they can be sequenced randomly.
 One very important method for metagenomic study is stable isotope
probing (SIP). An environmental sample of water or soil is first mixed with
a precursor such as methanol, phenol, carbonate or ammonia that has been
labeled with a stable isotope such as 15N, 13C or 18O. If the organisms in the
sample metabolize the precursor substrate, the stable isotope is
incorporated into their genome.
 When the DNA from the sample is isolated and separated by centrifugation,
the genomes that incorporated the labeled substrate will be heavier and can
be separated from the other DNA in the sample. The heavier DNA will
migrate further in a cesium chloride gradient during centrifugation. The
DNA can be used directly or cloned into vectors to make a metagenomic
library. This technique is useful to find new organisms that can degrade
contaminants such as phenol.
 Microorganisms are crucial participants in cleaning up a large variety of
hazardous substances/chemicals by transforming them into forms that are
harmless to people and environment. One very important example is given
here. Gasoline is leaked into soil in every gas station in United States.
 There is every possibility that gasoline will be mixed with ground
water which is the prime source of drinking water. However, the
dormant members of the soil microbial community are triggered to
become active and degrade the harmful chemicals in gasoline.
 Since gasoline is composed of hundreds of chemicals it takes a
variety of microbes working together to degrade them all. When
some bacteria cause a depletion of O2 in ground water near a
gasoline spill, other types of bacteria that can use nitrate for energy
begin biodegrading the gasoline. Bacteria that use iron, manganese
and sulfate follow.
 All these microbial communities work together in a pattern to
transform leaking gasoline into CO2 and water. Metagenomic
analysis may help us identify the particular community member and
function needed to achieve the full chemical transformation that
will keep our planet livable
