Environmental & Soil Microbiology


Written by MicroDok

The phrase “bioremediation” is derived from two words viz: Biowhich means “life” and remediatewhich means “to solve a problem”. Thus, bioremediation is defined as the use of biological organisms including microorganisms to solve environmental problems such as contamination of the soil, land, air and water. It is a waste management technique that makes use of microorganisms to remove or neutralize pollutants from the environment or from a contaminated site. Bioremediation can also be defined as a microbial treatment that uses naturally occurring-microorganisms to breakdown hazardous substances into less-toxic substances. It is a microbe-based (biotechnological) clean-up of pollutants in the environment (aqueous or terrestrial). One of the most significance of bioremediation is that it helps to return already contaminated soil or environment to its original state.

Bioremediation is the primary mechanism to reduce biodegradable contaminants by employing organisms like bacteria, fungi, algae or plants. Typical examples of microbes involved in bioremediation include aerobic bacteria (Pseudomonas, Alcaligenes, Sphingomonas, Rhodococcus and Mycobacterium), anaerobic bacteria, fungi, and methanotrophic bacteria (that metabolize methane as their only source of carbon and energy). The types of pollutants can be remedied using bioremediation include but not limited to atmospheric pollution (pollution of the air); water pollution (pollution of the hydrosphere or water); industrial effluents pollution (pollution due to disposal of waste water from domestic homes and industries); domestic effluent pollution (pollution due to indiscriminate dispersal of domestic sewage); pesticides, hydrocarbons, alkanes and soil pollution (pollution of the lithosphere or land).

Bioremediation helps to restore polluted/contaminated soil to its unpolluted state; and thus remove all toxic wastes and chemicals that rendered the soil polluted. Bioremediation is unique and different from other environmental clean-up protocols because it allows polluted environments (including water, soil and air) to be cleaned-up at the site of contamination without having to move the contaminated area to somewhere else for clean-up. And bioremediation utilizes natural processes including microbes and plants to clean-up contaminated/polluted environments. Bioremediation is not labour intensive and it is also cost efficient since it does not require much equipments or labour as other environmental clean-up methods in restoring contaminated environments to their former clean/natural states. Since the microbes involved in bioremediation activities feed on the contaminants of the environment by transforming toxic or harmful chemicals and substances into less-toxic gases and water, there is usually no release of harmful gases or chemicals into the surrounding atmosphere where bioremediation is taking place. When microbes come into contact with contaminants (e.g. oil spill) in the environment, these organisms feed on the contaminants, digest them and thus change them into water and other harmless gases such as carbondioxide (Figure 1).

Apart from microorganisms, plants have also been used to support the process of bioremediation. And bioremediation can also be achieved through bioaugmentation, biostimulation, bioattenuation and by the use of extracellular enzymes secreted by microbes. The extracellular enzymes secreted by microbes such as the white rot fungi are significant in bioremediation activities because they are able to cleave to and breakdown the carbon-carbon bonds that are associated or found in most of the contaminants such as polyaromatic hydrocarbons or polycyclic aromatic hydrocarbons (PAHs) found in polluted environments. These enzymes also possess lignolytic peroxidase activity and manganese peroxidase activity – which gives them the ability to act on a wide range of pollutants. Typical example of extracellular enzymes secreted by the white rot fungi and which are applied in bioremediation processes include manganese peroxidase (MnP), laccase and lignin peroxidase (LiP).

The use of plants in situ (i.e. at the site of contamination), their enzymes or enzymatic systems, their roots and other associated microbes to degrade pollutants present in the environment (soil, water and air) is known as phytoremediation. The involvement of plants in the bioremediation of pollutants (phytoremediation) is an emerging green technology that facilitates the removal or degradation of the toxic chemicals in soils, sediments, groundwater, surface water and air and other contaminated environments.

Figure 1: Illustration of how microbes eat contaminants in the environment.

Several factors including but not limited to nutrient availability, oxygen, pH, temperature and water are known to affect the rate or process of bioremediation. And in order for microorganisms including bacteria and fungi to clean up harmful chemicals and other toxic materials and contaminants in a polluted area, the right temperature, pH, nutrients, suitable choice of microbes, and amount of oxygen must be present in the soil, groundwater, sediment or contaminated site because these microbes require these critical conditions and/or growth factors to grow and multiply (Table 1). When these growth conditions are made available in the contaminated site, microbial growth will occur at an exponential rate; and it is then that these microbes will grow and multiply and feed on the contaminants. However, when these materials or growth factors are limiting, microbial growth will be slowed or the microbes will die off; and this will slow down the bioremediation process. Bioremediation can occur either naturally; or by the use of bioaugmentation (in which whole cells of microbes are introduced); or through biostimulation approaches (in which microbial growth is stimulated through the addition of growth nutrients) as aforementioned.

Bioaugmentation is defined as the practice of adding actively growing, specialized microbial strains or cultures into a microbial community in an effort to enhance the ability of the microbial community to degrade certain compounds in a given environment. It is the applications of indigenous (allochthonous) wide-type microbes or genetically modified microorganisms (GMMs) to polluted hazardous waste sites in order to accelerate the removal of undesired or harmful compounds present in them.

Table 1: Factors that influence bioremediation

Bioaugmentation is an important aspect of bioremediation; and it is a technique used for the improvement of the degradative capacity of contaminated areas through the introduction of specific competent strains or consortia of microorganisms that are genetically engineered to speed up microbial degradation of pollutants. One of the in situ (on site or in place) bioremediation strategies is bioaugmentation, which improves the biodegradative capacities of contaminated sites by introduction of single strains or consortia of microorganisms with desired catalytic capabilities. In bioaugmentation, specifically selected strains of bacteria (microbes) are applied to remedy environmental hazards or to enhance the performance of a certain type of production or processes that is microbially-driven.

Biostimulation is the addition of nutrients to a polluted site in order to encourage the growth of naturally-occurring chemical-degrading microbes that feed on the pollutants. It is the modification of the environment to stimulate existing microorganisms (bacteria) capable of carrying out bioremediation through the addition of various forms of nutrients such as phosphorus, nitrogen, oxygen, or carbon that stimulate microbial growth. Bioattenuation is the method that relies on natural processes to dissipate contaminants through biological transformation. In enzymatic bioremediation, extracellular enzymes secreted by microbes may also be used to transform contaminants/pollutants in contaminated sites or environment into less-toxic or non-toxic compounds that are not harmful to the environment as aforementioned.


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