Biodegradation Processes

      Biodegradation (transformation of a chemical by microorganisms) is the decay or breakdown of chemicals that occurs when microorganisms use an organic substance as a source of carbon and energy. For example, sewage flows to the wastewater treatment plant where many of the organic compounds are broken down; some compounds are simply biotransformed (changed), others are completely mineralized. These biodegradation processes are essential to recycle wastes so that the elements in them can be used again. Recalcitrant materials, which are hard to break down, may enter the environment as contaminants.

      Biodegradation is a microbial process that occurs when all of the nutrients and physical conditions involved are suitable for growth. Temperature is an important variable; keeping a substance frozen can prevent biodegradation. Most biodegradation occurs at temperatures between 10 and 35°C (50 and 95°F), and water is essential for the biodegradation process. Bacteria and fungi, including yeasts and molds, are the microorganisms responsible for biodegradation. The biodegradation of organic matter in the aquatic and terrestrial environments is a crucial environmental process. Some organic pollutants are biocidal; for example, effective fungicides must be antimicrobial in action. Therefore, in addition to killing harmful fungi, fungicides frequently harm beneficial saprophytic fungi (fungi that decompose dead organic matter) and bacteria. Herbicides are designed for plant control, and insecticides are used to control insects.

      The biodegradation process can be divided into three stages: (i) biodeterioration, (ii) biofragmentation, and (iii) assimilation. The first stage (biodeterioration) is often described as a surface-level degradation that modifies the chemical, physical, and mechanical properties of the contaminant and occurs when the material is exposed to abiotic factors in the environment and allows for further degradation by weakening the structure of the contaminant. Some abiotic factors that influence these initial changes are compression (mechanical), light, temperature and chemicals in the environment. While biodeterioration typically occurs as the first stage of biodegradation, it can in some cases occur in be parallel (simultaneously) to biofragmentation which is the conversion of the spilled chemical to lower molecular weight fragment that are more amenable to removal from the environment (or ecosystem). Assimilation occurs when the fragment (or fragments) are assimilated into the environment (or ecosystem) without any deleterious effect to the system.

On the other hand, the resulting products from biofragmentation can be assimilated into microbial cells this is the assimilation stage. Some of the products from fragmentation are easily transported within the cell by membrane carriers. However, other products of the biofragmentation stage still have to undergo biotransformation reactions to yield products that can then be transported inside the cell. Once inside the cell, the products enter catabolic pathways that either lead to the production of adenosine triphosphate (ATP) or elements of the structure of the cell.

      By way of explanation, the catabolic pathways are those metabolic pathways that break down molecules into smaller units that are either oxidized to release energy or used in other reactions. Catabolism breaks down larger molecules into smaller units and is, in fact, the molecular breaking-down aspect of metabolism, whereas anabolic pathways are the building-up aspect.

      The biodegradation of the chemicals that occur in crude oil and crude oil products is essential to the elimination of the harmful effects of these spills. This oil is degraded by both marine bacteria and filamentous fungi. The physical form of crude oil makes a large difference in its potential for degradation. Degradation in water occurs at the water-oil interface. Therefore, thick layers of crude oil prevent contact with bacterial enzymes and oxygen. Apparently, bacteria synthesize an emulsifier that keeps the oil dispersed in the water as a fine colloid and is therefore accessible to the bacterial cells.

      The biodegradation process is, in general, an important process for the removal of chemical compounds (especially organic chemicals) from the environment. The versatility and activity of microbial enzymes as catalysts mean that biodegradation is much more significant than purely chemical reactions such as hydrolyses and redox reactions. Enzymatically catalyzed transformation also occurs in higher organisms, but this process is quantitatively less important than the contribution from microorganisms. Some of the most important microorganism-mediated chemical reactions in aquatic and soil environments are those involving nitrogen compounds and the cycle of such compounds throughout the Earth system. Among the biochemical transformations in the nitrogen cycle are (i) nitrogen fixation, whereby molecular nitrogen is fixed as organic nitrogen, (ii) nitrification, the process of oxidizing ammonia to nitrate, (iii) nitrate reduction in which nitrogen in nitrate ions is reduced to nitrogen in a lower oxidation state, and (iv) denitrification, the reduction of nitrate and nitrite to ammonia.

      Biodegradation of phosphorus compounds is important in the environment for two reasons. The first of these is that it provides a source of algal nutrient orthophosphate from the hydrolysis of polyphosphates. Secondly, biodegradation deactivates highly toxic organophosphate compounds, such as the organophosphate insecticides. The organophosphorus compounds of greatest environmental concern tend to be sulfur-containing phosphorothionate and phosphorodithioate ester insecticides. These are used because they exhibit higher ratios of insect: mammal toxicity than do their non-sulfur analogs. The biodegradation of these compounds is an important environmental chemical process. Fortunately, unlike the organic halogen insecticides that they largely displaced, the organophosphates readily undergo biodegradation and do not accumulate.

      Sulfur compounds are common in water. Sulfate ions (SO/) are found in varying concentration in practically all natural waters. Organic sulfur compounds, both those of natural origin and pollutant species, are common in natural aquatic systems, and the degradation of these compounds is an important microbial process. Sometimes, the degradation products, such as the odorous and toxic hydrogen sulfide, cause serious problems with water quality.

      One consequence of bacterial action on metal compounds is the occurrence of drainage of acidic aqueous solutions from mines (Hall, 2006). Acid mine drainage is a common and damaging problem in the waters flowing from coal mines, and draining from the spoil piles (mine tippage, gob piles) left over from coal processing and washing is highly acidic and has the ability to sterilize the surrounding land and water systems with the ensuing serious (often fatal) effects on the flora and fauna.

      Acidic mine water results from the presence of sulfuric acid produced by the oxidation of pyrite (FeS2). Microorganisms are involved in the overall process. The prevention and cure of acid mine water is a major challenge facing the environmental chemist.