Microbial
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Degradation Potential of
the Environment Rajendran, N. Graduate School of
Environment and Information Sciences, Yokohama National
University, Yokohama, Japan |
Past and current pollution of the environment
is driving an interest, active work, and a need
to understand the environmental problems. An apprehension
of what has been tried and what has failed to
solve environmental problems is now growing. Pollution
monitoring programs have focused on measuring
the parent compounds and their metabolites, and
made general conclusions on the status of pollution
based on chemical transformations in the environment.
These studies are expected to provide information
about the exact level of pollution in the environment,
but they do not make any attempt to explain the
exact degradation processes that are taking place
in the environment. Microorganisms are not only
involved in mineralization processes, but also
they play a quantitatively dominant role in many
applied environmental problems including degradation
of pollutants, sewage treatment, eutrophication
of aquatic systems, emission of green house gases,
ore leaching in mines etc. (Fig. 1). Biodegradation
is one of the biological processes facilitating
the chemical changes of pollutants by microorganisms
present in the polluted environment. Microorganisms
are involved in the removal of toxic wastes, either
in the environment or in controlled treatment
systems. Such microbial transformation processes
have been either conveniently avoided or inadvertently
left out from the environmental assessment programs,
and they are considered as "black boxes"
in many ecological modeling programs. Despite
obvious importance of the microorganisms for efficient
monitoring of the environment, not many studies
have included the examination of microorganisms
(biomass, activity and community structure), possibly
because of the limitations of the available methods.. |
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Microorganisms: |
The small size, ubiquitous distribution, high
specific surface area, potentially high metabolic
activity, rapid growth rate, genetic malleability,
and unrivaled enzymatic and nutritional versatility
of microorganisms cast them in the role of recycling
agents for the biosphere. The small size and simple
structure of bacteria imply a greater degree of
contact with their environment than is the case
for larger organisms. Bacteria have more direct
communication between events in the environment
at cell surface and in the intracellular matrix.
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Biodegradation: |
While a precise definition of biodegradation is
nonexistent, the process generally involves the
breakdown of organic compounds usually by microorganisms
into more cell biomass and less complex compounds
and ultimately to water. Biodegradation of organic
compounds is the partial breakdown or complete
destruction of their molecular structure by physiological
reactions catalyzed by microorganisms. Biodegradability
can be defined as the susceptibility of substances
(organic or inorganic) to alteration by microbial
processes. The alteration has been brought about
by enzymatic (intra- or extra-cellular) attack
that is essential for growth of the microorganisms.
Furthermore, some of the enzymatic reactions are
either beneficial (mobilization of toxic mercury)
or no detectable benefit to the microorganisms.
The extent of biodegradation and the rate at which
it occurs depend on interactions between the environment,
the number and type of microorganisms present
and the chemical nature of the contaminants being
degraded. |
Biodegradation
in the Environment: |
Biodegradation
of most organic pollutants occurs at a faster
rate under aerobic conditions (when oxygen is
present for use as a final electron acceptor).
A common misconception is that oxygen is readily
available in soils. Oxygen availability is very
often the limiting factor because of the low soil
porosity or the locations that are well below
the surface. Biodegradation of many organic compounds
will occur under anaerobic conditions (in the
absence of oxygen), although the rate may not
be as rapid as observed under aerobic conditions.
In the absence of oxygen, certain microorganisms
are able to use nitrate, sulfate, iron, or manganese
as final electron acceptors. However biodegradation
of some compounds such as halogenated hydrocarbons
can be faster at least initially under anaerobic
conditions. Relatively little is known about the
ecology and diversity of microorganisms that degrade
the organic pollutants (Fig. 2). |
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Both the microorganisms and their abiotic environment,
each influencing the properties of the other are
the major functional unit of an ecosystem. Understanding
the detailed microbial mechanisms of the maintenance
of ecosystems provides both practical and intellectual
challenges for inquires into environmental microbiology
in general and biodegradation processes in particular. |
Biodegradation is routinely measured by applying
chemical and physiological assays to laboratory
incubations of flasks containing pure cultures,
mixed cultures or environmental samples. Measurements
of biodegradability include cell growth, substrate
loss, consumption of final electron acceptors,
and production of both intermediary metabolites
and final metabolic end products. These types
of measures have been developed and traditionally
applied microbial physiologists to pure cultures
of microorganisms in laboratory prepared media
containing high concentrations of simple sugars
and other growth substances. Pure culture studies
under highly controlled conditions in rich culture
media will not mimic nature and they do not involve
attempts to duplicate critical features of the
natural environment. Sometimes it is possible
to focus on only a part of a system and make general
conclusions about some particular process taking
place in it. At other times, it may be necessary
to identify many types of organisms in an ecosystem
and ascertain the individual biomass, the biological
components and the viability of the individual
species or populations. Further it may be necessary
to estimate the collective living biomass and
nonliving organic substances in the system. |
Bioremediation:
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Bacteria
are considered as the key components of most natural
ecosystems, principally due to their metabolic
versatility and their physiological adaptability.
Metabolic versatility of microbes can be modified
to serve a key function in bioremediation. Bioremediation
is the intentional use of biodegradation processes
to eliminate environmental pollutants from sites
where they have been intentionally or inadvertently
released. Bioremediation technologies use the
physiological potential of microorganisms to eliminate
environmental pollutants at field sites. Intrinsic
bioremediation is the biodegradation of a target
pollutants without intervention and it is passive
and relies on the innate capacity of microorganisms
present in the field to respond to and metabolize
the pollutants. Enhanced bioremediation involves
increasing the rate of biodegradation which can
be accomplished in two ways, 1. to supply required
nutrients to the indigenous microbial populations
(biostimulation) and 2. inoculating microorganisms
capable of degrading the target pollutants, either
with or without nutrients into the contaminated
environment, thus augmenting the indigenous microbial
populations (bioaugmentation). As there are some
problems to monitor the in situ microbial processes,
questions have been asked about the validity of
the bioremediation processes. |
Assessment of Biodegrdation
Potential: |
The assessment of biodegradation potential is
warranted simply because 1. the measures are often
applied field sites or field derived samples.
2. the substrates of interest are environmental
pollutants that show little structural resemblance
to substrates traditionally used in laboratory,
3. degradation of the pollutants is usually studied
at low environmentally relevant concentrations,
4. when naturally occurring microbial communities
are the object of study, the populations of organisms
responsible for the metabolic reactions are almost
always unknown, 5. microorganisms are isolated
and selected from field habitats on the basis
of biodegradation capabilities of the culture. |
Determination of
Microbial Biomass and its Activity:
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Work on heavy metal detoxification and biosorption
was initially started by employing the bacterium
Bacillus sp. YW, which was found to be
effective in reducing hexavalent Cr to its non
toxic trivalent form and the chromate resistance
and reduction was found to be plasmid mediated
process. Further work was carried out to remove
the less toxic trivalent Cr through biosorption
using the EPS of Azotobacter sp. as the
biomatrix. The Cr bound EPS-Azotransformant was
flocculated from the tannery effluent using copper,
which flocculates the culture of Azotobacter
sp; Leuconostoc sp., an EPS producer
(Plate 1) has been characterized and cloned for
its EPS production for biosorption of many heavy
metals like Cadmium, Zinc, Arsenate, Chromium
etc. from polluted samples. EPS is also used as
matrix to entrap bacteria for column reactor.
EPS also induces rapid and more root nodulations
of symbiotic nitrogen fixers. |
Degradation of hydrocarbons: |
The urgent need is the development of quantitative
models that will not only describe the rate of
growth and activity of biodegrading microorganisms
but which will also describe these processes under
a wide range of environmental conditions. One
will have to assess the environmental conditions
in the habitat of interest, at the microenvironmental
level. There are a number of potential methods
to estimate microbial biomass in environmental
samples. However a few have withstood the tests
of time and peer-review. In developing rationale
for the application of methods, the conceptual
justification suggesting each method and limitations
are given below. |
Culture methods: |
Selected groups of bacteria can be cultured using
selected media and a set of growth conditions.
Cells often found in clumps or attached to particulate
matter. Numbers based on plate counts typically
a small percentage (1%) of that estimated by direct
microscopy. This method can not be used for reliable
quantitative biomass determination, but does have
other specialized applications for enumeration
of certain target organisms. |
Microscopic methods: |
Cell
size and number can be determined by direct microscopy
following the addition of a nucleic acid stain,
but small cells are difficult to see and impossible
to size accurately. Not all stained particles
are viable cells, and also overlapping problems
will occur due to high biomass, but most widely
used for biomass estimation despite uncertain
accuracy. |
ATP: |
Most reliable method of total microbial biomass
because of the fact that all living organisms
contain ATP and constant C:ATP ratio. Nonspecific
measure of microbial biomass and cell quota of
ATP varies with nutrient limitation, especially
P are some of the limitations. |
Phospholipid and
phosholipid fatty acides: |
All
living microorganisms contain membrane phospholipids
and rapid turnover rate of PL following cell death.
This method is reliable for estimation of viable
microbial biomass and also for the description
of different microbial populations in a sample,
but specialized instrumentation is required and
overlapping of PLFA profiles among the different
microbial populations will pose problems to quantify
those microbial populations accurately. |
Ergosterol, Lipopolysaccharide,
muramic acid: |
These biomarker
analyses have been used for the biomass estimation,
but they are all indicators of specific groups
of microorganisms. |
DNA: |
Since DNA is
present in all living organisms and is not present
in organic detritus and a constant C: DNA ratio,
DNA estimation can be used to measure microbial
biomass, but dissolved and nonliving particulate
DNA may limit the accurate estimation of microbial
biomass. The DNA analysis can be used for phylogenetic
studies with appropriate oligonucleotide probes. |
Although the
above methods have certain limitations to quantify
the entire microbial biomass, they are being used
to quantify the microbial biomass in a sample.
Since all the microorganisms present in the environment
are not involved in the degradation processes,
it is difficult to quantify only the biomass of
microorganisms that are responsible for the degradation
of pollutants. Better methods are becoming available
to measure the pollutants, their metabolic products,
and their metabolism in natural environments,
which means that there are many new opportunities
to analyze the biodegradation processes or microbial
degradation processes in totality in a given environment.
There have been many developments in molecular
methodologies to establish, enumerate and identify
the microorganisms that grow and persist in various
ecosystems. Application of molecular techniques
that will allow us to detect, discriminate and
quantify the microorganisms that are responsible
for the degradation of pollutants has been suggested. |
Molecular methods
have application in biodegradation largely because
they provide a direct means to detect, discriminate
and quantify species in a sample. As DNA sequences
of genes that code for metabolic pathways become
increasingly available, molecular procedures will
continue to gain predominance in biodegradation
protocols. mRNA based methods will allow us to
compare environmental expression of individual
members of gene families and they may be useful
in determining relationships between environmental
conditions prevailing in microhabitats and particularly
in situ activities of native microorganisms.
The molecular techniques can provide a means for
assessing overall community diversity and a species
of particular interest (DNA) and in situ
microbial activity (RNA) or any particular activity
(mRNA). In order to assess the biodegradation
potential of an environment, it is necessary to
monitor the genetic potential of the environment. |
I wish to mention
the following quote "We live on an
island of knowledge surrounded by a sea of ignorance.
As our island of knowledge grows, so does the
shore of ignorance" - John Archibald
Wheeler. It should be noted that one microorganism
is capable of degrading a wide range of compounds
and also one pollutant can be degraded by a number
of microorganisms. Since most genes encode enzymes
that catalyze reactions, we desperately need to
know whether or not we are knowledgeable about
most of the reactions catalyzed by microbes. It
may be easy to assess the biodegradation capabilities
of a microorganism but, not as easy as it is to
monitor the biodegradation potential of a environment.
Since the entire microbial communities are not
involved in biodegradation processes, molecular
approaches are useful to accurately monitor specific
biodegradation processes and also to assess the
biodegradation potential of an environment. |
About the Author: |
Prof.N.Rajendran
has obtained his Ph.D degree in the Centre of
Advanced Study in Marine Biology, Annamalai University,
India and D.Sc.(Ag.)degree in the Hiroshima University,
Japan. Subsequently he worked as a postdoctoral
research fellow in a National Research Institute,
Senior Scientist in a private Environmental Research
Institute, Full Professor in a National University
and Visiting Professor in a few Universities for
the past 15 years. He has been working in the
emerging areas of modern sciences such as Environmental
Pollution, Microbial Ecology, Molecular Biology
and Bioinformatics. |
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