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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..
     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. .
     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).
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.
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:
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.


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.
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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