What is Biodegradation?

• Biodegradation refers to the process of breaking down organic matter or substances into smaller and simpler substances through the action of living microorganisms. It is a natural process that occurs with the help of microorganisms like bacteria, fungi, and yeast. These microorganisms play a crucial role in catalyzing the biodegradation process.
• The process of biodegradation can be categorized into three stages. The first stage is biodeterioration, where the structure of the object undergoes mechanical weakening. This can be observed, for example, in the decay of wood or the corrosion of metals. The second stage is biofragmentation, which involves the breakdown of materials by microorganisms. During this stage, the organic matter is broken down into smaller components. Finally, in the third stage called assimilation, the old material is incorporated into new cells.
• Almost any matter, whether living or non-living, can undergo biodegradation. However, the key factor that influences biodegradation is time. Some materials, like vegetables, can degrade within a matter of days, while others such as glass and certain types of plastics may take thousands of years to decompose. To determine the biodegradability of materials, the European Union has set a standard stating that more than 90% of the original material must be converted into carbon dioxide, water, and minerals through biological processes within six months.
• Microorganisms are responsible for carrying out biodegradation through their metabolic and enzymatic actions. They can degrade a wide range of compounds, including organic pollutants like polychlorinated biphenyls, hydrocarbons, radionuclides, and metals. Microbes follow different modes of biodegradation depending on the type of matter and the environment. In mineralization, microorganisms use the organic matter as the sole source of carbon to produce energy and completely degrade the pollutants. On the other hand, cometabolism involves the addition of a growth substrate as a primary source of carbon and energy to initiate the breakdown of matter.
• Biodegradation is highly regarded as a sustainable and environmentally friendly approach for removing complex organic matter. It plays a significant role in ecology, the natural environment, and waste management. By harnessing the natural abilities of microorganisms, biodegradation offers an effective means of reducing the environmental impact of organic substances and promoting a cleaner and healthier planet.

Definition of Biodegradation

Biodegradation is the natural process by which microorganisms break down organic matter into simpler substances, such as carbon dioxide, water, and minerals.

Examples of Some biodegradable pollutants

Biodegradable pollutants encompass a range of highly toxic synthetic compounds that have been introduced into the environment over time. Some examples of biodegradable pollutants include:

1. Hydrocarbons: Hydrocarbons are organic compounds composed of hydrogen and carbon. They can be found in various forms, such as linear, branched, cyclic, aromatic, or aliphatic hydrocarbons. These pollutants are commonly associated with fuels and can have detrimental effects on the environment.
2. Polycyclic Aromatic Hydrocarbons (PAHs): PAHs are hydrophobic organic contaminants that are widespread in air, soil, and sediments. They are primarily generated through industrial processes and have been studied extensively due to their toxicity and persistence in the environment. PAHs can accumulate in organisms and pose risks to human health through the consumption of contaminated seafood. Biodegradation of PAHs plays a crucial role in mitigating their environmental impact, and the use of microorganisms for bioremediation is a promising approach.
3. Polychlorinated Biphenyls (PCBs): PCBs are mixtures of synthetic organic chemicals that were commonly used in various industrial applications. They possess properties such as non-flammability and chemical stability, but their persistence in the environment and toxicity make them significant pollutants of concern. PCBs can act as endocrine disruptors and are associated with cancer risks. Consequently, the environmental pollution caused by PCBs is a growing issue.
4. Pesticides: Pesticides are substances intended for controlling pests. They can be categorized as either nonpersistent or persistent based on their degradation rates. Microorganisms, particularly fungi and bacteria, play a vital role in degrading pesticides in the soil. However, some persistent pesticides pose challenges due to their resistance to degradation.
5. Dyes: Dyes are widely used in various industries, including textiles, rubber, paper, and cosmetics. Azo dyes, which contain (-N=N-) groups, are the largest class of synthetic dyes used commercially. These dyes are often difficult to biodegrade, necessitating the use of physical or chemical treatment methods for wastewater containing dyes.
6. Radionuclides: Radionuclides are atoms with unstable nuclei that undergo radioactive decay, emitting gamma rays or subatomic particles. They pose unique challenges as pollutants due to their radioactive nature. Bioremediation of radionuclides involves processes such as biosorption, bioleaching, biomineralization, intracellular accumulation, and enzyme-catalyzed transformations.
7. Heavy Metals: Heavy metals are inorganic contaminants that cannot be destroyed but can undergo biotransformation or removal. Microorganisms play a crucial role in bioremediation processes by utilizing mechanisms such as biosorption, bioleaching, biomineralization, intracellular accumulation, and enzyme-catalyzed transformations.

These examples demonstrate the diversity of biodegradable pollutants and highlight the importance of bioremediation strategies in addressing their environmental impact.

Microorganism in Biodegradation

1. Bacterial degradation

• Bacterial degradation plays a crucial role in the bioremediation of various pollutants. Bacteria have been found to degrade a wide range of environmental pollutants, including hydrocarbons, aromatic hydrocarbons, polychlorinated biphenyls (PCBs), pesticides, dyes, radionuclides, and heavy metals.
• Hydrocarbon-degrading bacteria have been extensively studied and are known to feed exclusively on hydrocarbons. They can degrade hydrocarbons under both aerobic and anaerobic conditions. Some bacterial strains, such as Pseudomonas sp. and Brevibacillus sp., have been isolated from petroleum-contaminated soil and have shown the ability to degrade hydrocarbons even under anaerobic conditions.
• Aromatic hydrocarbons, including those found in pollutants such as PCBs, are commonly degraded by gram-negative bacteria, particularly from the Pseudomonas genus. Other bacteria from genera like Mycobacterium, Corynebacterium, Aeromonas, Rhodococcus, and Bacillus have also been reported to degrade aromatic hydrocarbons.
• Bacterial degradation of pollutants is often more effective when conducted by mixed microbial communities rather than individual bacterial strains. Mixed cultures have a greater biodegradative potential as they possess genetic information from multiple organisms, enabling the breakdown of complex mixtures of organic compounds present in contaminated areas.
• For pollutants like PCBs, aerobic bacteria have been extensively studied, with gram-negative strains from genera such as Pseudomonas, Burkholderia, Ralstonia, Achromobacter, Sphingomonas, and Comamonas showing PCB-degrading activity. However, some gram-positive strains from genera like Rhodococcus, Janibacter, Bacillus, Paenibacillus, and Microbacterium have also demonstrated the ability to degrade PCBs. The aerobic catabolic pathway for PCB degradation typically involves enzymes like biphenyl dioxygenase, dihydrodiol dehydrogenase, 2,3-dihydroxybiphenyl dioxygenase, and hydrolase.
• Pesticide-degrading bacteria have been isolated for various compounds, including atrazine and chlorpyrifos. Bacterial strains from genera like Providencia, Bacillus, Staphylococcus, and Stenotrophomonas have shown efficacy in degrading specific pesticides.
• Dye degradation by bacteria has been extensively researched, with both aerobic and anaerobic bacteria capable of decolorizing azo dyes. Anaerobic conditions have been found to be more effective for azo dye decolorization, but subsequent aerobic stages are often required to degrade the resulting aromatic amines, which can be mutagenic and toxic. Bacterial consortia, such as Proteus sp., Pseudomonas sp., and Enterococcus sp., have been used for biodegradation and decolorization of dyes. Some single bacterial strains, like Shewanella decolorans, have also shown high efficacy in azo dye removal.
• Bacteria play a significant role in heavy metal bioremediation, as they possess various mechanisms to protect themselves from heavy metal toxicity. Microorganisms can reduce metals through dissimilatory metal reduction or reduction mechanisms that impart metal resistance. They can also facilitate metal leaching, biosorption, and methylation. Mixed bacterial consortia have been used successfully for heavy metal removal, including Cd, Cr, Cu, Ni, Pb, and more.
• In summary, bacterial degradation is a vital process in the bioremediation of pollutants. Bacteria have the capability to degrade a wide range of environmental pollutants, and their activity can be enhanced through the use of mixed microbial cultures. Their ability to break down complex organic compounds and transform heavy metals offers promising avenues for environmental remediation.

2. Plant Growth Promoting Bacteria (PDPB and PGBR) degradation

• Plant-associated bacteria, including endophytic and rhizospheric bacteria, play a significant role in the degradation of toxic organic compounds in contaminated soil. These bacteria have the potential to enhance phytoremediation, which is the use of plants to remediate polluted environments.
• Plant growth promoting rhizobacteria (PGPR) are naturally occurring soil bacteria that colonize plant roots and provide growth promotion benefits to plants. Some plants release phenols, which are structural analogs of polycyclic aromatic hydrocarbons (PAHs), to stimulate the growth of hydrocarbon-degrading microbes and enhance PAH degradation. Pseudomonas spp. are important PGPR bacteria that possess both PGPR activity and the capacity to degrade hydrocarbons. The rhizosphere of vegetation in contaminated fields harbors a diverse population of PAH-degrading bacteria, including strains of Lysini bacillus.
• Rhizosphere-associated bacteria also play a role in the degradation of polychlorinated biphenyls (PCBs). Mature trees growing naturally in contaminated sites have been found to harbor culturable PCB-degrading bacteria in both the rhizosphere and root zone. These bacteria belong to the genera Rhodococcus, Luteibacter, and Williamsia, indicating the potential of rhizoremediation, which involves the stimulation of PCB degradation through plant-microbe interactions.
• In addition to hydrocarbon and PCB degradation, plant growth promoting rhizobacteria have shown potential for heavy metal remediation. Soil bacteria, particularly plant growth promoting bacteria (PGPB), can be used as adjuncts in metal phytoremediation to facilitate plant growth in the presence of high levels of metals that would otherwise inhibit plant growth. The application of plants in combination with microorganisms, known as rhizoremediation, has been shown to increase the efficiency of contaminant extraction.
• Overall, the utilization of plant-associated bacteria, such as PGPR and PGPB, offers promising strategies for enhancing the degradation of toxic organic compounds and the remediation of contaminated soils. These bacteria contribute to the growth and health of plants, leading to improved phytoremediation outcomes and the potential for more effective and sustainable environmental cleanup.

3. Degradation by Microfungi and mycorrhiza

Microfungi, including yeasts and molds, are eukaryotic aerobic microbes that play a crucial role in the degradation of organic matter. They have the ability to metabolize dissolved organic matter and are key organisms responsible for the decomposition of carbon in the biosphere.

Fungi possess unique characteristics that enable them to thrive in low moisture environments and low pH solutions, making them effective in breaking down organic matter. Equipped with extracellular multienzyme complexes, fungi excel at breaking down natural polymeric compounds. Their hyphal systems allow them to rapidly colonize and penetrate substrates, facilitating nutrient transport and redistribution within their mycelium.

Mycorrhiza, a symbiotic association between fungi and the roots of vascular plants, is an important aspect of fungal degradation. There are two types of mycorrhizal associations: arbuscular mycorrhizal fungi (AMF), which colonize plant roots intracellularly, and ectomycorrhizal fungi, which colonize plant roots extracellularly. Mycorrhizal associations are crucial for soil life and soil chemistry. The utilization of mycorrhizal fungi in bioremediation is referred to as mycorrhizoremediation.

Fungi possess significant degradative capabilities that have implications for the recycling of recalcitrant polymers like lignin and the elimination of hazardous wastes from the environment. Unicellular and filamentous fungi have been studied for their ability to degrade various pollutants. Below are some aspects of microfungal degradation of specific pollutants:

1. Lignin: Fungi are known for their ability to degrade lignin, a complex polymer found in plant cell walls. Certain fungi, such as white-rot fungi, produce enzymes capable of breaking down lignin, thus playing a vital role in lignin degradation and carbon recycling in ecosystems.
2. Hazardous wastes: Fungi have the capability to degrade hazardous wastes, contributing to environmental cleanup. Their enzymatic activities and ability to colonize substrates make them effective in breaking down various toxic compounds.
3. Organic pollutants: Unicellular and filamentous fungi have been studied for their ability to degrade organic pollutants, including pesticides, polycyclic aromatic hydrocarbons (PAHs), and petroleum hydrocarbons. These fungi utilize enzymatic systems to break down and metabolize these pollutants, contributing to their remediation in the environment.

The degradation abilities of fungi, including microfungi and mycorrhizal fungi, have significant implications for the recycling of organic matter and the remediation of contaminated environments. Their unique characteristics and enzymatic capabilities make them valuable tools in bioremediation efforts, offering sustainable and eco-friendly approaches to address pollution challenges.

Degradation by Yeasts

• Yeasts are capable of degrading various aromatic and aliphatic hydrocarbons, making them important contributors to biodegradation processes. While some yeasts can utilize aromatic compounds as growth substrates, their cometabolic ability to convert aromatic substances is particularly significant. Certain yeasts, such as Trichosporon cutaneum, possess specific energy-dependent uptake systems for aromatic substrates like phenol.
• When it comes to the biodegradation of aliphatic hydrocarbons found in crude oil and petroleum products, yeasts have been extensively studied. They are particularly efficient in utilizing n-alkanes, with chain lengths between C10 and C20 being the most suitable substrates.
• However, yeasts have also demonstrated the ability to degrade n-alkanes with chain lengths up to n-C24. Candida lipolytica, C. tropicalis, Rhodotorula rubra, and Aureobasidium (Trichosporon) pullulans are among the typical yeasts known for their ability to utilize alkanes. Some yeasts, such as Rhodotorula aurantiaca and C. ernobii, have been found capable of degrading diesel oil. Yeasts also play a role in the biodegradation of aniline, which is a potential degradation product of azo dyes.
• In addition to hydrocarbons, yeasts can transform a wide range of other aromatic organopollutants, including polycyclic aromatic hydrocarbons (PAHs), biphenyls, dibenzofurans, nitro aromatics, various pesticides, and plasticizers. Yeasts such as Candida boidinii, C. lipolytica, and Saccharomyces cerevisiae have been studied for their metabolism of polychlorinated biphenyls (PCBs). Saccharomyces cerevisiae is also known to adsorb insecticides and fungicides during aerobic fermentation.
• Yeasts are actively involved in the removal of toxic heavy metals through a process called biosorption. They have been found to accumulate heavy metals such as Cu(II), Ni(II), Co(II), Cd(II), and Mg(II), often surpassing the metal accumulation capabilities of certain bacteria.
• Yeasts like Pichia anomala have been shown to remove hexavalent chromium (Cr(VI)), and studies have explored the biosorption of Cr(VI) by live and dead cells of yeasts such as Cyberlindnera fabianii, Wickerhamomyces anomalus, and C. tropicalis. Some yeast strains, including S. cerevisiae, Pichia guilliermondii, Rhodotorula pilimanae, Yarrowia lipolytica, and Hansenula polymorpha, are capable of reducing Cr(VI) to the less toxic Cr(III).
• The tolerance of P. guilliermondii to chromate depends on its capacity for extracellular reduction of Cr(VI) and chelation of Cr(III). Immobilized cells of yeasts, like Schizosaccharomyces pombe, have also been utilized for the efficient removal of metals, such as copper.
• Overall, yeasts play a crucial role in the degradation of hydrocarbons, aromatic organopollutants, and heavy metals, making them valuable contributors to biodegradation and bioremediation processes.

Degradation by Filamentous fungi

• Filamentous fungi possess several attributes that make them effective biodegraders. Their mycelial growth habit allows them to efficiently colonize insoluble substrates and penetrate them through the secretion of a variety of extracellular degradative enzymes.
• The high surface-to-cell ratio of filaments maximizes both mechanical and enzymatic contact with the environment. Additionally, the extracellular nature of their degradative enzymes enables fungi to tolerate higher concentrations of toxic chemicals. This characteristic also allows them to attack insoluble compounds that cannot cross cell membranes.
• Filamentous fungi participate in various bioremediation strategies, including using the target compound as a carbon source, enzymatically attacking the compound without using it as a carbon source (cometabolism), and taking up and concentrating the compound without metabolizing it (bioaccumulation).
• While fungi can participate in all three strategies, they are particularly proficient in cometabolism and bioaccumulation, rather than using xenobiotics as sole carbon sources. Some filamentous fungi, such as Cladophialophora, Exophiala, Leptodontium, and Pseudeurotium zonatum, have been identified as toluene-degrading fungi, utilizing toluene as their sole carbon and energy source.
• Although filamentous fungi are unable to completely mineralize aromatic hydrocarbons, they can transform them into indirect products that are less toxic and more susceptible to decomposition by bacteria. Cladosporium and Aspergillus are examples of filamentous fungi that participate in the biodegradation of aliphatic hydrocarbons, while Cunninghamella, Penicillium, Fusarium, and additional Aspergillus species can contribute to the decomposition of aromatic hydrocarbons.
• Fungal genera such as Amorphoteca, Neosartorya, and Talaromyces have shown potential for hydrocarbon degradation in petroleum-contaminated soil. In the case of polychlorinated biphenyls (PCBs), ligninolytic fungi have been specifically investigated due to their extracellular, non-specific oxido-reductive enzymes, which have been successfully utilized in the degradation of various aromatic pollutants. Ectomycorrhizal fungi and other fungi like Aspergillus niger have also been studied for their ability to metabolize PCBs.
• Filamentous fungi are known for their ability to degrade standing timber, finished wood products, non-cellulosic products (such as plastics, fuels, paints, glues, and drugs), and a wide range of pollutants, including metals. They can tolerate and detoxify metals through mechanisms such as valence transformation, extra and intracellular precipitation, and active uptake.
• Fungi can adsorb heavy metals like cadmium, copper, lead, mercury, and zinc into their mycelium and spores. Some fungi, like Rhizopus arrhizus, have been used for the treatment of uranium and thorium. The cell surface functional groups of fungi, as well as the proteins in the cell walls of arbuscular mycorrhizal fungi (AMF), play a role in the sorption and sequestration of potentially toxic elements, aiding in phytostabilization and the survival of mycorrhizal plants in polluted soils.
• Ligninolytic fungi are widely researched for their ability to degrade dyes. Various strains of filamentous fungi, including Aspergillus, Penicillium, Cladosporium, Alternaria, Mucor, Phoma, and Trichoderma, have demonstrated the ability to biodegrade gelatin emulsion.
• Filamentous fungi can also degrade pesticides using intracellular enzymatic systems like cytochromes P450 and exocellular systems, predominantly consisting of peroxidases and lactases. These enzymatic systems can be induced or inhibited by pesticides, thus modulating their metabolism.
• Overall, filamentous fungi possess unique characteristics and enzymatic capabilities that make them effective in the degradation of a wide range of pollutants, including hydrocarbons, dyes, pesticides, and heavy metals. Their mycelial growth habit, extracellular enzyme secretion, and ability to tolerate and transform toxic compounds contribute to their importance in biodegradation and bioremediation processes.

4. Degradative capacities of algae and protozoa

• The involvement of algae and protozoa in hydrocarbon biodegradation is not well-documented, but there are some instances where their degradative capacities have been observed. Prototheca zopfi, an alga, has been found to utilize crude oil and various hydrocarbon substrates, leading to the degradation of n-alkanes, isoalkanes, and aromatic hydrocarbons. However, the ecological significance of algae and protozoa in hydrocarbon degradation remains unclear, as evidence is limited and their presence may not always be beneficial for hydrocarbon removal.
• Algae have shown the ability to bioaccumulate and biotransform pesticides. They can accumulate and degrade certain environmental pollutants, demonstrating their potential involvement in the degradation of specific compounds. Some algae species, such as Chlorella vulgaris, Scenedesmus platydiscus, S. quadricauda, and S. capricornutum, have been found to uptake and degrade polycyclic aromatic hydrocarbons (PAHs).
• Regarding dye degradation, Chlorella vulgaris and C. pyrenoidosa have been studied for their ability to degrade azo dyes, using the dyes as carbon and nitrogen sources. The degradation process is inducible and dependent on the chemical structure of the dyes. Other algae species, including Lyngbyala gerlerimi, Nostoc lincki, Oscillatoria rubescens, Elkatothrix viridis, and Volvox aureus, have been reported to decolorize and remove various dyes.
• Certain species of algae, such as Chlorella, Anabaena inacqualis, Westiellopsis prolifica, Stigeoclonium lenue, and Synechoccus sp., exhibit tolerance to heavy metals and have been used for the removal of these contaminants. Algae can adsorb metals through surface adsorption and chelation mechanisms. Brown algae are known for their ability to sorb heavy metals, utilizing cell wall constituents such as alginate and fucoidan. However, the practical application of algae in heavy metal bioremediation is limited due to operational constraints.
• Protozoa play a crucial role as grazers of degrading bacteria in the degradation of organic contaminants. The interaction between protozoa and degrading bacteria directly affects the degradation process. Protozoa can enhance the biodegradation of organic compounds, such as polycyclic aromatic hydrocarbons (PAHs) and benzene derivatives, by grazing on bacteria. Their presence can improve the degradation rates by stimulating bacteria activity, reducing competition for resources, and providing additional energy and carbon resources through sym-metabolism. The mechanisms behind protozoa’s acceleration of biodegradation include nutrient mineralization, bacteria activation, selective grazing, physical disturbance, direct degradation through enzyme secretion, and sym-metabolism.
• In conclusion, while algae and protozoa’s involvement in hydrocarbon biodegradation is not extensively studied, there are indications that they can contribute to the degradation of specific compounds. Algae have been observed to accumulate and transform pesticides, degrade dyes, and tolerate heavy metals. Protozoa, on the other hand, enhance the biodegradation of organic contaminants through their interactions with degrading bacteria. Further research is needed to explore and understand the full potential of algae and protozoa in biodegradation processes.

Degradation by genetically engineered microorganisms

Genetically engineered microorganisms (GEMs) have emerged as potential tools for bioremediation, offering enhanced degrading capabilities for a wide range of chemical contaminants. Through recombinant DNA technology, the genetic material of microorganisms can be modified to optimize their biodegradative capacities, accelerate the evolution of new activities, and construct novel metabolic pathways.

There are four principal approaches to the development of GEMs for bioremediation: modification of enzyme specificity and affinity, pathway construction and regulation, bioprocess development, monitoring, and control, and bioaffinity bioreporter sensor applications for chemical sensing, toxicity reduction, and end point analysis.

Genes responsible for the degradation of environmental pollutants, such as toluene, chlorobenzene acids, and halogenated pesticides, have been identified and used for the modification of microorganisms. Different plasmids, grouped into categories based on the compounds they degrade, have been developed. For example, the OCT plasmid degrades octane, hexane, and decane, while the XYL plasmid degrades xylene and toluenes. Genetically engineered Pseudomonas putida strains containing multiple plasmids have been created, demonstrating the ability to degrade aliphatic, aromatic, terpenic, and polyaromatic hydrocarbons.

One of the challenges in using GEMs for bioremediation is the issue of safety and risk assessment. Biosafety measures and risk assessment protocols need to be developed and implemented to ensure the safe release of genetically modified microorganisms into the environment.

In addition to hydrocarbons, genetically engineered microorganisms have also shown potential for heavy metal removal. For example, Alcaligenes eutrophus AE104 (pEBZ141) and recombinant photosynthetic bacterium Rhodopseudomonas palustris have been engineered for chromium and mercury removal from industrial wastewater, respectively.

The application of genetic engineering techniques in the development of endophytic and rhizospheric bacteria for plant-associated degradation of toxic compounds in soil is considered a promising technology for environmental remediation. The selection of suitable strains for gene recombination and inoculation into the rhizosphere is based on criteria such as stability after cloning, high expression of target genes, tolerance to contaminants, and compatibility with specific plant rhizospheres.

However, there are obstacles associated with the use of GEMs in bioremediation applications. The strains and bacterial species commonly used in enrichment procedures may not be the most effective biodegraders in natural environments. The use of fast-growers as agents for biodegradation can lead to the accumulation of biomass, which may have undesirable effects. Strategies such as uncoupling biodegradation genes from growth and developing “suicidal genetically engineered microorganisms” (S-GEMS) have been explored to address these issues.

The release of genetically engineered bacteria into the environment raises concerns about their ecological impact. Field testing and risk assessment are necessary before the widespread use of these organisms in bioremediation. Encapsulation of the inoculum or protection in tubing can be used to mitigate potential risks associated with the release of GEMs.

In conclusion, genetic engineering offers the potential to optimize the biodegradative capacities of microorganisms for bioremediation applications. However, challenges related to safety, ecological impact, and field conditions need to be addressed before the widespread adoption of genetically engineered microorganisms in environmental bioremediation.

Examples of genetically-engineered microorganisms (GEM) include:

1. GMM Pseudomonas putida: This genetically modified microorganism, also known as Superbug or Oil Eating Bug, contains multiple plasmids for the degradation of different compounds. It carries plasmids such as pKF 349 for salicylate toluene degradation, pAC 25 for 3-cne chlorobenxoate degradation, as well as XYL, NAH, OCT, and CAM plasmids. Pseudomonas putida has been engineered to efficiently metabolize various hydrocarbons and is widely used in bioremediation processes.
2. Alcaligenes eutrophus AE104 (pEBZ141): This genetically modified microorganism is used for the removal of chromium from industrial wastewater. By introducing the specific gene responsible for chromium removal, Alcaligenes eutrophus AE104 can efficiently reduce and remove chromium contaminants, contributing to the remediation of polluted water sources.
3. Rhodopseudomonas palustris: This recombinant photosynthetic bacterium has been genetically engineered for mercury removal from wastewater. By expressing genes encoding mercury transport systems and metallothionein, Rhodopseudomonas palustris can effectively uptake and accumulate mercury ions, aiding in the detoxification of heavy metal-contaminated water.
4. GEM Achromobacter sp. LBS1C1 and A. denitrificans JB1: These genetically modified microorganisms are used for the degradation of polychlorinated biphenyls (PCBs). By transferring the chromosomally located PCB catabolic genes of Achromobacter sp. LBS1C1 and A. denitrificans JB1 to other microbial strains, such as Pseudomonas putida CH34, the engineered microorganisms gain the ability to degrade PCBs, contributing to the remediation of PCB-contaminated environments.

These examples highlight the application of genetic engineering techniques to develop microorganisms with enhanced capabilities for bioremediation, allowing them to efficiently degrade specific pollutants and contribute to environmental cleanup efforts.

Advantages using Genetically-Modified Microorganisms (GMM)

Biodegradation by genetically-modified microorganisms (GMM) offers several advantages over natural microorganisms for environmental remediation purposes. Here are some of the advantages:

1. Enhanced degradation capabilities: GMM can be engineered to possess enhanced degradation capabilities for specific pollutants. By introducing genes encoding catabolic enzymes or pathways responsible for the degradation of target compounds, GMM can efficiently break down and metabolize pollutants that are otherwise recalcitrant or slow to degrade. This enables GMM to accelerate the remediation process and enhance the overall degradation efficiency.
2. Targeted degradation: GMM can be designed to specifically target and degrade particular contaminants. Through genetic engineering, specific pathways or enzymes can be introduced into the microorganism’s genome, allowing it to selectively degrade the target pollutants. This targeted approach ensures that GMM focus their degradation activities on the pollutants of concern, reducing the potential for non-specific or incomplete degradation.
3. Increased environmental stability: GMM can be engineered to exhibit increased environmental stability compared to their natural counterparts. This stability can include tolerance to harsh environmental conditions, such as high temperatures, pH extremes, or the presence of toxic substances. GMM’s ability to withstand these conditions allows them to maintain their degradation capabilities over a longer period, even in challenging environments.
4. Faster degradation rates: GMM can exhibit faster degradation rates compared to natural microorganisms. By introducing genetic modifications, GMM can express enzymes or metabolic pathways at higher levels, leading to accelerated degradation of pollutants. This increased degradation rate can significantly reduce the time required for environmental cleanup, making GMM a valuable tool for remediation efforts.
5. Versatility and adaptability: GMM can be engineered to degrade a wide range of pollutants, including various organic compounds and heavy metals. This versatility allows GMM to be tailored for specific remediation applications, targeting different classes of contaminants. Additionally, GMM can be designed to adapt to different environmental conditions, further enhancing their applicability in diverse remediation scenarios.
6. Controllable and predictable behavior: GMM can be designed to exhibit controlled and predictable behavior in the environment. Through precise genetic modifications, researchers can manipulate the expression and regulation of genes involved in degradation processes, ensuring the desired metabolic activities of GMM. This control enables better management and monitoring of GMM’s behavior during biodegradation processes.

While the use of GMM for biodegradation offers significant advantages, it is crucial to carefully assess the potential risks and ensure appropriate safety measures are in place to prevent unintended environmental consequences. Strict regulation and risk assessment protocols should be followed to ensure the safe and responsible use of GMM in environmental remediation applications.

Disadvantages of Genetically-Modified Microorganisms (GMM)

Biodegradation by genetically-modified microorganisms (GMM) for environmental remediation purposes also comes with certain disadvantages and challenges. Here are some of the key disadvantages:

1. Uncertainty of long-term effects: The long-term effects of releasing GMM into the environment are not yet fully understood. The potential ecological impacts and unintended consequences of GMM, such as gene transfer to other organisms or disruption of natural microbial communities, need to be thoroughly evaluated before widespread use. There is a need for comprehensive risk assessments to ensure the safety and minimize the potential risks associated with GMM release.
2. Genetic drift and persistence: GMM may undergo genetic drift over time, which refers to the accumulation of genetic changes or mutations. These changes can alter the behavior or characteristics of the GMM, potentially affecting their degradation capabilities or environmental interactions. Additionally, GMM may persist in the environment beyond the intended timeframe, raising concerns about the long-term consequences of their presence.
3. Regulatory challenges: The use of GMM in environmental applications is subject to strict regulations and oversight due to concerns about their potential ecological and health risks. Obtaining regulatory approvals for the field release of GMM can be time-consuming and expensive. The regulatory framework surrounding GMM can vary between countries, posing challenges for international collaborations and standardized guidelines.
4. Public perception and acceptance: The use of GMM in environmental biodegradation can raise public concerns and ethical debates. There may be resistance or skepticism from certain stakeholders, including communities living near remediation sites or environmental advocacy groups. Public acceptance of GMM applications may require transparent communication, robust risk assessments, and addressing ethical and social considerations.
5. Limited knowledge and unpredictable outcomes: Despite advancements in genetic engineering techniques, our understanding of complex microbial interactions and ecosystems is still incomplete. The behavior and interactions of GMM in real-world environmental settings can be difficult to predict accurately. There is a need for further research to enhance our understanding of GMM behavior, potential ecological impacts, and the long-term consequences of their release.
6. Potential for unintended ecological impacts: GMM, with their enhanced degradation capabilities, may inadvertently affect non-target organisms or disrupt natural ecological processes. The introduction of GMM into ecosystems could alter microbial community dynamics, impact nutrient cycling, or disrupt the balance of ecological interactions. Assessing and minimizing these unintended ecological impacts is crucial for responsible use of GMM.
7. Cost and scalability: The development and implementation of GMM for biodegradation can be costly and resource-intensive. The production, monitoring, and maintenance of GMM strains require specialized facilities and expertise. Scaling up GMM applications from laboratory-scale to field-scale can present logistical and economic challenges.

Microorganisms involved in the biodegradation of pesticides

• Microorganisms play a crucial role in the biodegradation of pesticides, as they have the ability to break down these toxic compounds into simpler and less harmful substances. The presence of pesticides in the environment can provide a suitable carbon source and electron donors for certain soil microorganisms, enabling them to develop the ability to degrade these chemicals. This natural process offers a potential solution for the treatment of pesticide-contaminated sites.
• Microorganisms with the capability to degrade pesticides can be isolated and utilized for bioremediation purposes. They have the potential to be effective in the degradation of other chemical compounds as well. However, the successful transformation of these compounds depends on various environmental factors. Factors such as physiological, ecological, biochemical, and molecular aspects also influence the microbial transformation of pollutants.
• Microorganisms with pesticide-degrading abilities can be sourced from different environments. Soil is a common medium that receives pesticides due to agricultural practices. Other sources include pesticide industry effluents, sewage sludge, activated sludge, wastewater, natural waters, sediments, areas surrounding pesticide manufacturing, and even certain live organisms. Microorganisms capable of pesticide degradation have been isolated from various contaminated sites, and collections of these microorganisms have been established in laboratories worldwide. The isolation and characterization of these microorganisms provide valuable tools for the restoration of polluted environments and the treatment of waste prior to final disposal.
• In the field of biodegradation, the advancement of knowledge and techniques relies on the characterization of microorganisms. Pure-culture isolates, laboratory enrichment cultures, and studies conducted in contaminated field sites have contributed to the understanding of biodegradation mechanisms, the identification of active players, and the occurrence of biodegradation of organic environmental pollutants.
• Several examples of microbial pesticide degradation have been reported in the literature. Pseudomonas species, known for their efficiency in the degradation of toxic compounds, have shown great potential in the biodegradation of herbicides such as aroclor 1242. Fungi species like Aspergillus, Absidia, Rhizopus, and Botrytis have demonstrated the ability to degrade various herbicides. Trichoderma viridae, a fungus, has been found to degrade endosulfan and methyl parathion pesticides. Bacteria of the Rhodococcus genus have been effective in the degradation of triazines to nitrate. These examples highlight the diverse microbial capabilities in the biodegradation of pesticides.
• Bacterial genera adapted to pesticide-contaminated soils possess enzymes involved in the hydrolysis of bonds found in a wide variety of organophosphorus pesticides. Some bacteria isolated from soil have exhibited the ability to degrade specific pesticides such as ethyl-parathion and methyl-parathion.
• Overall, microorganisms play a vital role in the biodegradation of pesticides and offer potential solutions for the treatment of pesticide-contaminated sites. The identification and characterization of these microorganisms provide valuable insights for the development of bioremediation strategies.

Steps of Biodegradation (Process of Biodegradation)

The steps of biodegradation can be categorized into three processes: biodeterioration, bio-fragmentation, and assimilation.

1. Biodeterioration: Biodeterioration involves the mechanical, physical, and chemical weakening of the compound’s structure. Abiotic factors such as light, temperature, and chemicals in the environment can initiate these changes. For example, exposure to sunlight, heat, or moisture can cause physical degradation of materials like plastics, while chemical reactions can break down complex organic compounds. Biodeterioration is the initial step in the biodegradation process, preparing the compound for further breakdown.
2. Bio-fragmentation: Once the compound’s structure has been weakened, microorganisms come into action to break down the complex and toxic compounds. Bio-fragmentation involves the cleavage of polymeric bonds, resulting in the transformation of larger molecules into smaller oligomers and monomers. This process can occur under aerobic (oxygen-rich) or anaerobic (oxygen-depleted) conditions. In aerobic conditions, microorganisms digest the compounds, converting them into simpler molecules such as water, carbon dioxide, and small organic molecules. These products can serve as a source of nutrients for the microorganisms. In anaerobic conditions, complex materials can undergo anaerobic digestion, leading to the production of natural gases like methane. Anaerobic reactions are widely utilized in waste management facilities to generate renewable energy.
3. Assimilation: In the final step of biodegradation, microorganisms assimilate the newly formed molecules. The microorganisms take up the transformed molecules through membrane carriers. These molecules can be used as an energy source, typically in the form of ATP (Adenosine Triphosphate), to fuel the microorganisms’ metabolic activities. Additionally, the assimilated molecules can also serve as building blocks for the microorganisms’ cellular components, contributing to cell growth and reproduction.

Overall, the steps of biodegradation involve the progressive breakdown of complex compounds through biodeterioration, bio-fragmentation, and subsequent assimilation of the transformed molecules by microorganisms. This process plays a crucial role in the recycling and turnover of organic matter in the environment.

Pesticides Biodegradation mechanisms of

Factors Affecting Biodegradation

Factors affecting biodegradation can be broadly categorized into biological factors related to microorganisms and their metabolic abilities, and environmental factors related to the physical and chemical characteristics of the environment.

1. Biological factors

• Metabolic ability of microorganisms: The metabolic capacity of microorganisms plays a crucial role in the degradation of organic compounds. Different microorganisms possess specific enzymes and metabolic pathways that enable them to degrade certain pollutants. The efficiency of biodegradation depends on the presence and activity of these specific enzymes.
• Competition and inhibition: Microbial degradation can be influenced by competition between microorganisms for limited carbon sources, as well as antagonistic interactions among microorganisms. Inhibition of enzymatic activities can occur due to the presence of inhibitory substances or the predation of microorganisms by protozoa and bacteriophages.
• Enzyme activity and catalysis: The rate of contaminant degradation is influenced by the concentration of degrading microorganisms and the enzymes they produce. The extent of contaminant metabolism depends on the specific enzymes involved and their affinity for the contaminant, as well as the availability of the contaminant and sufficient nutrients and oxygen for microbial growth.
• Temperature, pH, and moisture: Biodegradation rates are affected by temperature, pH, and moisture levels. Enzymes involved in degradation have optimum temperature ranges, and the rate of biodegradation decreases with decreasing temperature. pH influences enzyme activity, and a pH range of 6.5 to 8.5 is generally optimal for biodegradation. Moisture content affects the availability of soluble materials, osmotic pressure, and pH, influencing the microbial activity and degradation rates.

2. Environmental factors

• Soil type and organic matter content: The type of soil and its organic matter content affect the adsorption and absorption of organic compounds. Adsorption and absorption processes can reduce the availability of contaminants to microorganisms, thereby decreasing the rate of degradation.
• Porosity and permeability: Variations in porosity and permeability of soils and aquifer matrices impact fluid movement and contaminant migration. The ability of the matrix to transmit gases such as oxygen, methane, and carbon dioxide can influence the type and rate of biodegradation.
• Oxidation-reduction potential (redox potential): The redox potential of a soil indicates the electron density of the system. It determines the availability of electron acceptors for microbial energy production. Low redox potential indicates aerobic conditions, while high redox potential indicates anaerobic conditions. The availability of suitable electron acceptors affects the type and extent of biodegradation processes.

These biological and environmental factors collectively influence the rate and efficiency of biodegradation processes by microorganisms. Understanding and optimizing these factors are important for effective bioremediation strategies and the successful application of biodegradation in environmental cleanup efforts.

Bioremediation and biodegradation

Bioremediation, as a biotechnological process, utilizes microorganisms to degrade pollutants through biodegradation, offering a low-cost and effective approach to remediate contaminated sites. It is based on principles such as natural attenuation, bioaugmentation, and biostimulation.

1. Natural Attenuation: Natural attenuation refers to the reduction of contaminant concentrations in the environment through biological, physical, and chemical processes. Microorganisms play a crucial role in biodegradation, transforming contaminants into less harmful forms. Monitoring natural attenuation ensures that the pollutant transformation is actively occurring.
2. Biostimulation: Biostimulation involves enhancing the biotransformation of soil contaminants by providing additional nutrients, trace minerals, electron acceptors, or electron donors. This stimulation promotes the activity of indigenous microorganisms, accelerating the degradation process. Examples include the addition of lactate to enhance the conversion of trichloroethene and perchloroethene, and the use of electron shuttles like humic substances to facilitate the transformation of organic pollutants.
3. Bioaugmentation: Bioaugmentation is the technique of introducing specific competent strains or consortia of microorganisms to enhance the capacity of a contaminated matrix to remove pollution. It increases the metabolic capacities of the indigenous microbial community by introducing exogenous genetic diversity. Genetically engineered microorganisms (GEMs) can also be used for soil bioaugmentation, as they possess enhanced degradative capabilities for aromatic hydrocarbons.

Factors affecting the effectiveness of bioremediation include abiotic factors such as temperature, moisture, pH, and organic matter content, as well as aeration, nutrient content, and soil type. Biotic factors, including competition between indigenous and exogenous microorganisms for carbon sources, and interactions with predators like protozoa and bacteriophages, also influence the outcome of bioaugmentation.

The combination of bioaugmentation and biostimulation can be a promising strategy to accelerate bioremediation processes. Indigenous and exogenous microorganisms can benefit from biostimulation, while bioaugmentation-assisted phytoextraction using plant growth-promoting rhizobacteria (PGPR) or arbuscular mycorrhizal fungi (AMF) shows potential for cleaning up metal-contaminated soils.

Overall, bioremediation utilizing biodegradation processes offers a cost-effective and environmentally friendly approach to address pollution challenges, with the potential to restore contaminated sites and protect human health and the environment.

Applications of Bioremediation

Bioremediation, the use of biological processes to remove or neutralize pollutants, has a wide range of applications for environmental cleanup. Here are some key applications of bioremediation:

1. Soil Remediation: Bioremediation is commonly used to treat soil contaminated with organic pollutants such as petroleum hydrocarbons, pesticides, solvents, and industrial chemicals. Microorganisms are introduced or stimulated in the soil to degrade these pollutants into harmless byproducts.
2. Groundwater Remediation: Bioremediation can be applied to clean up groundwater contaminated with various pollutants, including petroleum products, chlorinated solvents, and heavy metals. Microorganisms are used to degrade or transform these contaminants, either in situ or in constructed wetlands or bioreactors.
3. Oil Spill Cleanup: Bioremediation has been used successfully to clean up oil spills in marine and coastal environments. Oil-degrading microorganisms are employed to break down the hydrocarbons in the oil, accelerating the natural biodegradation process.
4. Wastewater Treatment: Bioremediation is widely used in wastewater treatment plants to remove organic pollutants. Microorganisms are utilized in aerobic or anaerobic processes to break down and remove contaminants, converting them into harmless substances such as water, carbon dioxide, and biomass.
5. Industrial Waste Treatment: Bioremediation is applied to treat various types of industrial waste, including chemical and pharmaceutical manufacturing waste, mining waste, and landfill leachate. Microorganisms are employed to degrade or transform the hazardous components in these wastes, reducing their environmental impact.
6. Agricultural Remediation: Bioremediation can be used in agriculture to address soil and water contamination caused by pesticide use, fertilizers, and animal waste. Microorganisms are harnessed to degrade these pollutants and restore the environmental quality of agricultural lands.
7. Bioremediation of Contaminated Sites: Bioremediation is employed to clean up contaminated sites, such as former industrial sites and landfills. It offers an eco-friendly and cost-effective approach to remediate these areas, reducing the risks posed by pollutants to human health and ecosystems.
8. Phytoremediation Support: Bioremediation techniques can be combined with phytoremediation, where plants are used to uptake and accumulate contaminants. Microorganisms are applied to enhance the effectiveness of phytoremediation by facilitating the degradation or transformation of pollutants in the plant rhizosphere.

Bioremediation offers a sustainable and environmentally friendly approach to address various types of pollution. It can be applied to diverse environments, including terrestrial, aquatic, and marine systems. However, the specific application and success of bioremediation depend on the nature of the contaminants, site conditions, and the selection and optimization of appropriate microbial species or consortia for the remediation process.

Advantages of Bioremediation

Bioremediation offers several advantages as a remediation approach for environmental cleanup. Here are some key advantages of bioremediation:

• Environmentally Friendly: Bioremediation is a natural and environmentally friendly approach to pollution cleanup. It utilizes naturally occurring microorganisms or introduces specific strains that have the ability to degrade or transform contaminants into harmless byproducts. It avoids the use of harsh chemicals and minimizes the generation of secondary pollutants.
• Cost-Effective: Bioremediation is often a cost-effective solution compared to traditional remediation methods. It can be less expensive than technologies such as excavation and off-site disposal of contaminated materials or the installation and maintenance of complex treatment systems. Bioremediation typically requires less equipment and infrastructure, reducing overall project costs.
• Versatility: Bioremediation can be applied to a wide range of contaminants and environmental settings. It is effective for treating both organic pollutants, such as petroleum hydrocarbons, solvents, and pesticides, as well as certain inorganic contaminants, including heavy metals and metalloids. Bioremediation can be implemented in soils, sediments, groundwater, and even marine environments.
• Sustainability: Bioremediation promotes sustainability by utilizing natural processes to restore contaminated environments. It supports the natural self-cleaning capacity of ecosystems by enhancing the activity of indigenous microorganisms or introducing specialized microorganisms. It allows for the restoration and preservation of natural habitats while addressing pollution issues.
• In Situ Treatment: Bioremediation can be performed in situ, directly at the contaminated site, minimizing disturbance and reducing the need for extensive excavation and transportation of contaminated materials. In situ bioremediation is less disruptive to the surrounding environment, preserves the site’s natural characteristics, and reduces the potential risks associated with transporting hazardous materials.
• Long-Term Effectiveness: Bioremediation can provide long-term effectiveness in treating contamination. Once established, microorganisms can continue to degrade contaminants over an extended period, adapting to changing conditions and maintaining their activity. This allows for sustained remediation even in complex and challenging environments.
• Synergy with Other Methods: Bioremediation can be synergistic with other remediation methods. It can complement physical or chemical methods by enhancing their efficiency or treating residual contaminants. For example, bioremediation can be combined with soil vapor extraction or pump-and-treat systems to address the remaining contaminants and improve overall remediation outcomes.
• Potential for On-Site Treatment and Reuse: Bioremediation can offer the potential for on-site treatment and reuse of contaminated materials. It allows for the transformation of pollutants into non-toxic byproducts or the immobilization of contaminants, reducing the need for off-site disposal. In certain cases, treated materials can be reused for beneficial purposes, such as land reclamation or soil amendment.

Overall, bioremediation provides a sustainable, cost-effective, and environmentally friendly approach to address pollution issues. It offers versatility in treating various contaminants and can be implemented in different environmental settings, making it a valuable tool in environmental remediation efforts.

Disadvantages of Bioremediation

While bioremediation offers several advantages, there are also some potential disadvantages and limitations associated with this approach. Here are a few of the key disadvantages of bioremediation:

• Time-Intensive Process: Bioremediation can be a relatively slow process compared to some other remediation methods. It may require an extended period of time for microorganisms to break down and degrade contaminants, especially in complex or highly contaminated sites. The rate of biodegradation can be influenced by factors such as environmental conditions, availability of nutrients, and the specific type of contaminant.
• Site-Specific Factors: The effectiveness of bioremediation can vary depending on site-specific factors. Certain environmental conditions, such as extreme temperatures, low oxygen levels, high salinity, or acidic pH, can limit the activity and growth of microorganisms. In some cases, the presence of certain contaminants or co-contaminants may inhibit microbial activity or degrade the effectiveness of bioremediation.
• Lack of Control: Bioremediation relies on the natural processes and activities of microorganisms, which can be difficult to control and predict. Factors such as changes in environmental conditions, competition among microorganisms, or shifts in microbial populations can impact the overall effectiveness of bioremediation. Achieving consistent and predictable results may be challenging in dynamic and complex environments.
• Site Access and Implementation: Bioremediation may require sufficient access to the contaminated site for the application of microbial cultures, nutrients, or amendments. In some cases, site characteristics or restrictions may limit the feasibility of implementing bioremediation techniques. Additionally, certain sites may pose challenges for the distribution and maintenance of appropriate environmental conditions necessary for microbial activity.
• Contaminant Specificity: Bioremediation techniques may be effective for specific types of contaminants but less suitable for others. Certain compounds or contaminants may be resistant to biodegradation or require specialized microbial strains with specific metabolic capabilities. It is important to consider the specific properties and characteristics of the contaminants present in order to determine the feasibility and suitability of bioremediation as a treatment option.
• Regulatory Considerations: The use of genetically modified microorganisms (GMOs) for bioremediation purposes may involve regulatory considerations and approval processes. Depending on the jurisdiction and specific regulations, the use of GMOs may require permits or undergo rigorous risk assessments to ensure the safety and potential impacts on the environment and human health.
• Monitoring and Verification: Monitoring and verifying the effectiveness of bioremediation can be challenging. It may require the implementation of sampling and analysis techniques to assess the reduction of contaminants over time. The monitoring process can be time-consuming and costly, adding to the overall project expenses.

FAQ

References

1. Laura, Ma., Snchez-Salinas, E., Dantn Gonzlez, E., & Luisa, M. (2013). Pesticide Biodegradation: Mechanisms, Genetics and Strategies to Enhance the Process. InTech. doi: 10.5772/56098
2. Tahri, N., Bahafid, W., Sayel, H., & El Ghachtouli, N. (2013). Biodegradation: Involved Microorganisms and Genetically Engineered Microorganisms. InTech. doi: 10.5772/56194
3. Meckenstock, R. U., Elsner, M., Griebler, C., Lueders, T., Stumpp, C., Aamand, J., … van Breukelen, B. M. (2015). Biodegradation: Updating the Concepts of Control for Microbial Cleanup in Contaminated Aquifers. Environmental Science & Technology, 49(12), 7073–7081. doi:10.1021/acs.est.5b00715 
4. http://www.idph.state.il.us/envhealth/factsheets/polychlorinatedbiphenyls.htm
5. https://www.stahl.com/beyond-chemistry-from-a-to-z/what-is-biodegradation
6. https://www.greendotbioplastics.com/biodegradation-explained/