During the past 70 years, a wide variety of synthetic organic compounds have been produced. While some of these compounds were similar to naturally occurring compounds and were slowly degraded by microorganisms, others had molecular structures microorganisms were never exposed to before and were not recognized by then. These synthetic organic chemicals called xeno-biotics (foreign to biological systems) are also resistant to degradation and accumulate in the environment.

Chemical structure of a compound can give certain clues as to its biodegradability, but similar compound can still be biodegraded at different rates and to variable extents. For example, many of organophosphorus pesticides have very similar structures, but show very different biodegradation rates. Aerobic biodegradation is faster than anaerobic biodegradation, but some chlorinated compounds are only degraded anaerobically. Some generalization about chemical structure of a synthetic compound and its persistence in the environment can be made and are described here.

Unusual substitutions. Unusual substitutions can alter the synthetic organic compound in a way that it either becomes partially or wholly resistant to degradation. For example, addition of a single Cl, NO2, SO3H, Br, CN, or CF 3 to a readily degradable substrate may increase their resistance to biodegradation. Similarly, addition of two identical or different substitutions may make organic chemicals even more resistant to degradation. The position of substitution greatly influences biodegradation of a compound. For example, if Cl is substituted in phenol at meta-position in soil, degradation is slow; but if substitution is not at meta-position then degradation is faster.

Unusual bonds or bond sequences, for example, tertiary and quaternary carbon atoms. In this regard much has been learned from the detergent industry. When alkyl benzyl sulfonates (ABS) detergents were first manufactured and used by consumers worldwide, it was not realized until much later that these compounds persisted in the environment. Their persistence in the lakes and rivers led to foaming of water and causing damage to the environment. Later on public concern forced detergent industry to investigate the cause of such persistence. Researchers quickly found that extensive methyl branching interfered with biodegradation process. Thus, switching to linear ABS detergents that were more easily biodegraded alleviated this problem (Table 1). Methyl branching is also associated with persistence of aliphatic hydrocarbons. The nonbranched alkanes are easily biodegraded in the environment than alkanes having multiple methyl branching.

Excessive molecular size. Biodegradation of long chain n-alkanes declines with increasing molecular weight. Synthetic polymers, for example, polyethylene, polyvinyl chloride, and polystyrene, have high molecular weight and are virtually nonbiodegradable. Many naturally occurring microorganisms have the ability to aerobically degrade polycyclic aromatic hydrocarbons (PAHs), but the process of biodegradation is inversely proportional to ring size of PAH molecule (Figure 1). Lower-molecular-weight PAHs are degraded much more rapidly in soil than higher-molecular-weight PAHs when oxygen is present.

Chlorinated aromatic hydrocarbons are degraded aerobically by a variety of mechanisms. Chlorine can be removed by ring cleavage in one- or two-chlorine-substituted compounds. In highly chlorinated compounds, chlorine can be removed by hydrolytic and oxidative reactions. In anaerobic environments, removal of chlorine is by reductive dechlorination reactions. The initial step in anaerobic biodegradation of these compounds is often reductive removal of chlorine atom from aromatic ring.

Pesticides. Most pesticides have simple hydrocarbon backbone bearing a variety of substituents such as halogens, amino, nitro, hydroxyl, and others. Aliphatic carbon chains are initially degraded by the B-oxidation and then by tricarboxylic acid cycle. Substituents on aromatic ring structures are first removed and then the ring is metabolized by dihydroxylation and ring cleavage mechanisms. Pesticides with substitutions such as halogens, nitro-, and sulfonates that are not common in nature are resistant to biodegradation. Often just a single additional chlorine substitution can make a pesticide quite recalcitrant. For example, 2,4-dichloro-phenoxya-cetic acid (2,4-D) is biodegraded within a few days, but 2,4,5-tricholorophnyoxyacetic acid (2,4,5-T), on the other hand, is highly resistant to biodegradation and will persist in the environment. The difference is one additional Cl substitution at meta-position in 2,4,5-T (Figure 2).

Table 1 Chemical structures of nonlinear and linear alkyl benyl sulfonates (ABS) detergents Nonlinear ABS detergent resistant to biodegradation

Biodegradable linear ABS detergent

- S03Na

Figure 1 Chemical structure of some biodegradable polycyclic aromatic hydrocarbons.

Anthracene Phenanthrene 1 -Methylphenanthrene

Figure 1 Chemical structure of some biodegradable polycyclic aromatic hydrocarbons.


Biodegradable Recalcitrant

Figure 2 Structures of 2,4-dichloro-phenoxyacetic acid (2,4-D) and 2,4,5-tricholorophnyoxyacetic acid (2,4,5-T).

Recalcitrant Compounds

Many organic compounds persist for long periods in the environment. A persistent or recalcitrant toxic chemical may travel to thousands of miles from the application site. The distances it may travel depend on particle size, solubility, and, in some cases, on atmospheric forces. In traveling long distances, the toxic chemical may become diluted. However, even at very low concentrations toxic chemicals may cause harm because of increased concentration of the compound due to its accumulation over time in the food chain. This process is called biomagnification. Therefore, it is not surprising that the concentration of DDT in aquatic environment is roughly around 0.3 ppb in water, but in plankton and fish due to the biomagnification process DDT levels have been found to exceed 30 and 300 ppb, respectively. Unfortunately, under such circumstances DDT levels are expected to continue to rise in higher trophic levels in the food chain. The toxic compounds that increase in concentration in food chain are both persistent and lipo-philic. Because the compound is lipophilic, small dissolved amounts are partitioned from water into the lipids of the microorganisms. Grazing of these microorganisms by protozoa leads to further concentration of these toxic chemicals in protozoa in amounts much higher compared to microorganisms and so on. In higher trophic levels (predator fish, carnivores) the concentration of the pollutant may exceed by a factor of 104-106. Another example of persistent compound is polychlori-nated biphenyls (PCBs) with one to ten chlorine atoms per molecule. They were once used, for example, as plasticizers in polyvinyl polymers and as insulators in transformers. By law their production and use is now banned worldwide. However, even now these compounds are found in the environment; PCBs have also been found in US population with no exposure history. Though highly toxic and recalcitrant, DDT has been the most effective pesticide in controlling mosquitoes that carried malaria-causing larvae, and with re-emergence of malaria epidemic in some African countries, UN is now considering allowing the production and use of DDT once again.


Some microorganisms can degrade an organic compound without using the substrate as carbon or energy source. This is called cometabolism. The microorganisms obtain no nutritional benefit from the substrate they cometabo-lize. In this case, the microorganism may be growing on a second substrate. However, presence of that substrate is necessary for cometabolism to occur. A large number of chemicals, for example, PCBs, chlorophenols, and pesticides, may undergo cometabolism in culture. Some of the species of bacteria that can cometabolize organic compounds include Pseudomonas, Acinobacter, Bacillus, and Arthrobacter. Penicillium and Rhizoctonia are some of the fungi that also cometabolize organic compounds.

Threshold Concentration

In aquatic environments, chemicals that are accumulated through biomagnification may eventually become toxic to higher organisms as well. The lowest substrate concentration that is required to sustain growth of a species is generally referred to as 'threshold' concentration. In biodegradation, it is the lowest toxic substrate concentration below which a microorganism cannot degrade the toxic substrate any further. Definitive proof of existence of threshold substrate concentration was obtained from biodegradation studies where one bacterium isolated from environmental samples was capable of degrading a toxic substrate at certain concentration, but failed to degrade the same substrate in quantities below their threshold concentration. However, the other bacterium isolated from same environment degraded the same chemical at considerably lower concentrations, indicating that different bacteria have different threshold values.

Acclimation Period

In biodegradation studies there is an initial period when little or no biodegradation takes place; this period is called acclimation period. During this time the concentration of the toxic substrate remains unchanged. This acclimation period may be short for readily degradable compounds and long for others, but the ultimate rate and extent of degradation depends on the chemical in question and the environment itself. The length of acclimation period is critically important for risk assessment purposes. Longer the acclimation phase, longer the period of exposure in humans, animals, and plants. From an environment perspective, if a chemical is introduced into a river or groundwater, the impact will be considerable as the chemical may potentially move long distances unchanged and risk exposure to population on a much wider scale. In anaerobic environments, the acclimation phase is especially long for some compounds.

Biodegradable Recalcitrant

Figure 2 Structures of 2,4-dichloro-phenoxyacetic acid (2,4-D) and 2,4,5-tricholorophnyoxyacetic acid (2,4,5-T).

End of acclimation period is indicated by start of detectable biodegradation. This period can be shortened if higher inoculums of bacteria are used. This may indicate that acclimation period is the period required for bacteria to grow in sufficient numbers to start degradation of the chemical. Interestingly, once degraded, if the same toxic chemical is added a second time, little or no acclimation period is observed. The acclimation of the microbial community to one substrate may also result in acclimation to some related compounds and is retained for some time.

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