Biodegradation- Definition, Microbes, Factors, Steps

Biodegradation is a natural process, whereas Bioremediation is a man-made biotechnological process.

Both these processes are very important for cleaning and recycling environmental resources.

Biodegradation refers to the breaking down of organic matter, and Bioremediation refers to the breakdown of toxic environmental pollutants into simpler molecules. The common factor between both processes is the use of microorganisms to carry out the chemical reaction required in the breakdown of complex matter. The article provides in-depth knowledge of both processes.

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What is Biodegradation?

Biodegradation is the breakdown of organic matter or substances into smaller and simpler substances via a biologically catalyzed reduction in the presence of living microorganisms.

Biodegradation is a general term used for any change or breakdown in a substrate that is biologically mediated.


Biodegradable matter can be metabolically degraded by microbes in the presence of oxygen (aerobically) or in the absence of oxygen (anaerobically). Almost any matter living or non-living, is subjected to biodegradation. The only key element is the ‘duration’ of that matter breakdown. European Union has set a standard biodegradability for materials that 90% of the original substance to be degraded to water, mineral, and carbon dioxide by biological reactions within six months.

The process is brought about by the metabolic and enzymatic actions of microorganisms like bacteria, yeast, and fungi. Microorganisms follow any two modes for biodegradation based on the type of matter and environment. They are Minerilization and Cometabolism. Mineralization is a complete degradation of organic pollutants where organisms use matter as the sole source of carbon to produce energy. Whereas in Cometabolism, it is observed that degradation is done by the addition of a growth substrate as a primary source of carbon and energy to initiate the breakdown of matter. Some naturally occurring microbes show excellent catabolic activity to transform and degrade a wide range of compounds like polychlorinated biphenyls, hydrocarbons (eg. oils), radionuclides, metals, and more. 

Biodegradation is referred to as one of the most favored and sustainable measures of removing any complex organic matter and is often regarded in terms of ecology, the natural environment, and waste management.

Biodegradable Pollutants

Since the time of the industrial revolution and with an increased standard of living, numerous highly toxic organic compounds such as fuels, polycyclic aromatic hydrocarbons (PAHs), dyes, pesticides, and some synthetic chemicals like radionuclides have been synthesized and released for use in the environment for a long period of time for direct or indirect application. These toxic and complex compounds are difficult for the native flora to readily degrade upon release into the environment. Some of the organic pollutants are mentioned below.

Polycyclic Aromatic Hydrocarbons (PAHs)

Hydrocarbons are organic molecules composed of hydrogen and carbon as the primary functional units of a compound. They are either aliphatic in nature (linear and branched compounds) or aromatic (compounds with a benzene ring). Aliphatic compounds include alkanes, alkene, and alkynes, while aromatic compounds include a benzene ring, such as phenols, toluene, etc. 

PAHs have been categorized as an important organic pollutant in the ‘Hydrophobic Organic Contaminants (HOCs)’ class that’s readily found in sediments, soils, and air. 

  • They are present naturally in gasoline, crude oil, and coal.
  • They can be formed by burning coal and wood and also while cooking meat in high heat.
  • PAHs can be easily bound to and form minute particles that can get accumulated in organisms.
  • In the United States, a man-made PAH called the ‘Naphthalene’ are used to make mothballs and other chemicals.
  • Cigarette smoking also releases many PAHs into the environment.
  • They can get accumulated in the fish and other aquatic organisms, which can be transferred to humans when consuming seafood.
  • In the NHANES (National Health and Nutrition Examination Survey) of 2003-2004, CDC Scientists measured the urine sample of 2,504 individuals aged from six years old to above and found ten different PAH metabolites.
  • Higher exposure to Naphthalene and other PAHs present in the air can irritate eyes and nasal passages and can also cause liver problems.

Polychlorinated Biphenyls (PCBs)

PCBs are categorized as man-made chemicals with an oily texture, no taste or smell, and are yellow in color. Found in air, water, sediments, and soil across the world.

  • They are chemically very stable mixtures, highly resistant to high temperatures, non-flammable, and with electrical insulation properties. 
  • Due to these features, they are widely used in hydraulic and electrical equipment, as plasticizers in rubber products, and as pigments in dyes. 
  • Once released in the environment, they are easily spread across long distances via air and soil, making them persistent in the atmosphere.
  • Humans are generally exposed to PCBs by consuming contaminated meat, fish, dairy products, fruits, and vegetables.
  • They are absorbed and stored in the fatty tissue, which can cause cancer and act as an endocrine disruptor.
  • PCBs were sold commercially by the name of Aroclor by the company named Monsanto Inc. in the United States. The levels of PCBs have been declining in the food chain and environment since its ban in 1977 due to its exposure which led to ill health effects.


The concept of a pesticide is a combination of poisonous compounds that target pathogens and is safe for non-pathogens like humans and animals. They belong to a class of chemicals that includes herbicides, fungicides, rodenticides, molluscicides, plant growth regulators, insecticides, and nematicides, used to regulate the growth of weeds, killing of pests, and prevention of diseases. 

  • Pesticides use enhances the productivity of crops and the prevention of vector-borne diseases. 
  • The United States is one of the world’s largest traders, producers, and consumers.
  • Pesticides cause a serious health hazard to non-target organisms because they are readily fat solubility and bioaccumulation.
  • The introduction of pesticides leads to a decline in the population of zooplankton and phytoplankton
  • They can be neurotoxic and carcinogenic and decrease fertility in fishes, invertebrates, insects, mammals, and amphibians.
  • Regular use of their presence develops resistance to pests, reducing their toxicity.
  • The biodegradation of pesticides is mostly done by soil microorganisms using it as a food source, whereas persistent xenobiotics become incorporated into the environment leading to biomagnification.


They have applications in a wide range of industries, such as cosmetics, textiles, pharmaceuticals, rubber products, and more.

  • The most dye used are Azo dyes that contain diazotized amine coupled with phenol or an amine group and single or more azo (–N=N–) groups.
  • Microorganisms have potential oxidoreductive enzymes and a dynamic metabolism ability that allows them to use dyes with complex xenobiotic compounds as a substrate, helping in the decolorization of polluted sites.

Radionuclides and Heavy metals

An atom has a highly unstable nucleus with the ability to impart excess energy during the radiation process in which they undergo radioactive decay to produce subatomic alpha or beta particles or emission of gamma rays. Microbial degradation of radionuclides results in the formation of less toxic and more stable compounds.

Heavy metals, such as arsenic, cadmium, chromium, etc, cannot be destroyed like organic compounds but can be converted into stable forms. The mechanism applied by microbes includes:

  • Bioleaching – mobilization of heavy metal through methylation reactions or excretion of organic acids
  • Biosorption – metal absorption in the cell surface.
  • Enzyme-catalyzed redox reactions.
  • And Intracellular accumulation of heavy metals.
  • Extraction of heavy metals can be achieved by recovering the precipitate of metals from microbial samples.

Microorganism in Biodegradation and their Impact

In nature, biodegradation is a natural process that is carried out to recycle wastes and break down complex and toxic organic compounds into a much simpler form that can be reused as a food source by other organisms. Microorganisms, such as bacteria, fungi, and yeast, are the most common species that help in the biodegradation process.

Bacterial Strain

Bacteria constitute a key organism in the biodegradation process, which can be easily isolated from any place. 

  • Bacterial strains from genus Klebsiella, Enterobacter, Bacillus, Staphylococcus, Acinetobacter, and more belong to the hydrocarbon degradation category. Brevibacillus and Pseudomonas species, anaerobically reduced nitrate-containing compounds, have been isolated from the petroleum-contaminated soil.
  • The genera of gram-negative strains like Pseudomonas, Aeromonas, etc, carry out biodegradation of aromatic hydrocarbons.
  • A mixed population of bacterial strains is better suited to degrade pollutants as they can easily share genetic information related to degradative enzymes and pathways.
  • PCB degradation is carried out aerobically and anaerobically by redox and dehalogenation reactions. PCB degrading activity is shown by both Gram-positive (eg. Rhodococcus, Bacillus, Microbacterium, and more) and Gram-negative strains (genera Pseudomonas, Sphingomonas, Ralstonia, etc.).
  • PCB degradation incorporates these four enzymes biphenyl dehydrogenase, dihydro diol dehydrogenase, 2,3-dihydroxy biphenyl dehydrogenase, and hydrolase.
  • Pesticides such as DDT (Dichlorodiphenyltrichloroethane) are degraded by the strains Staphylococcus and Stenotrophomonas bacteria, and ‘Chlorpyrifos’ pesticide degrading bacteria is Providencia stuartii.
  • Shewanella decolorations are identified as a single bacterium species that can efficiently remove azo dyes. 
  • Heavy metals are transformed via a dissimilatory metal reduction process where bacterial species use metals as a terminal electron acceptors during respiratory reactions. Acidithiobacillus ferrooxidans, an acidophilic iron bacteria, and sulfur-oxidizing bacteria are found to have high concentrations of Arsenic, Cadmium, Zinc, Cobalt, and Copper from contaminated soils.

Plant Growth Promoting Bacteria (PDPB and PGBR)

These bacteria can be generally found in the plants naturally, in roots, or near them. They are non-pathogenic to plants and help in the growth and development of plants. Plants and plant growth-promoting bacteria live in mutualistic relationships, wherein plants give shelter, and food sources, and bacteria, in return, help in metabolizing toxic substances that can be used by plants. 

  • Pseudomonas species and Lysini bacillus show PAH hydrocarbon degrading activity that’s released from plants.
  • Strains of the genus Luteibacter, Williamsia, and Rhodobacter have shown a promising PCB degradation activity present in the contaminated soil.
  • Azospirillum lipoferum, isolated from the rhizoplane of crop plants, is observed to degrade Malathion, an organophosphorus insecticide.

Fungal Species

They are considered the principal microorganism important for the carbon decomposition in the atmosphere. They can easily survive in the low pH and moisture areas. They are highly equipped with special extracellular multienzyme complexes helping in the degradation of natural polymeric compounds. 

  • With the aid of their hyphal structures, they are able to colonize and easily penetrate substances, helping them to redistribute nutrients across the mycelium. 
  • Recycling of recalcitrants like lignin is implicated by the degradative mechanisms of fungi.
  • Toluene-degrading fungi include deuteromycetes species belonging to the genera Exophiala, Leptodontium, and Cladophialophora, and an ascomycete strain Pseudeurotium zonatum, that utilize toluene for carbon and energy sources.
  • Filamentous fungi Cladosporium and Aspergillus show the degrading activity of aliphatic hydrocarbon, whereas fungi that belong to Penicillinum, Fusarium, and Cunninghamella degrade aromatic hydrocarbons.
  • Aspergillus niger has shown biodegrading activity towards PCBs.
  • Fungi detoxify metals via mechanisms like active uptake, transformation, and extra or intracellular precipitation. Examples include Rhiloprzs arrhizus and Aspergillus niger.


Yeast species have been heavily studied to degrade Poly Aromatic Hydrocarbons (PAHs) and use them for energy-dependent uptake systems. Trichosporum cutaneum, a soil yeast, has been seen to degrade phenols.

  • Alkanes of 10 to 20 carbons are degraded by species like Candida lipolytica, Rhodotorula aurantiaca, Candida ernobii, and more.
  • Candida methanosorbosa BP-6 species have been reported to potentially break down azo dye like aniline.
  • Saccharomyces cerevisiae, Candida biodinii, and several others can transform plasticizers, insecticides, fungicides, and polychlorinated biphenyls (PCBs) into simpler forms.
  • Yeast strains such as Hansenula polymorpha, Cyberlindnera fabianii, Rhodotorula pilimanae, etc, accumulate heavy metals like Cr, Co, Ni, Mg, and other heavy metals and reduce metals via redox reactions.

Genetically-Modified Microorganisms (GMM)

Genetically-modified microorganisms have altered genetic material inspired by the microorganisms’ gene transfer methods using genetic engineering like DNA Recombinant Technology. GMMs have shown great potential with enhanced biodegradation capabilities for various chemical contaminants. 

The main aspects to be kept in mind for GMM development in the biodegradation application are:

  1. Enzyme specificity and affinity modifications.
  2. Regulation and construction of metabolic pathway.
  3. Development, monitoring, and control of Bioprocesses.
  4. Bioreporter sensory application for toxicity reduction, chemical sensing, and end-point analysis.

Construction of upgraded genetic modules and new catabolic pathways for biodegradation in microbes require separate plasmids for every toxic compound.  These plasmids are categorized into four groups:

  1. OCT plasmids – degradation of hexane, octane, and decane.
  2. XYL plasmids – degrade toluenes and Xylene.
  3. CAM plasmids – decomposition of Camphor compound.
  4. NAH plasmids – degradation of Naphthalene.

Examples of genetically-engineered microorganisms (GEM) include:

  • GMM Pseudomonas putida with multi-plasmid capabilities is often referred to as Superbug (Oil Eating Bug) that contains pKF 349 for salicylate toluene, pAC 25 (for 3-cne chlorobenxoate degradation), in addition to XYL, NAH, OCT, and CAM plasmids.
  • For the removal of Chromium in industrial wastewater, Alcaligenes eutrophus AE104 (pEBZ141) are used for degradation.
  • Rhodopseudomonas palustris, a recombinant photosynthetic bacterium, is used for mercury removal from wastewater.
  • PCB (polychlorinated biphenyls) are degraded by using GEM Achromobacter sp. LBS1C1 and A. denitrificans JB1.

The use of GMM strains for biodegradation and bioremediation purposes can cause competition with wild-type species in a mixed culture. The controversy surrounding GMM release into the environment must be overcome by proper field testing, biosafety, and the reduction in potential damage to the ecosystem.

Stages of Biodegradation

The biodegradation process can be subdivided into three processes – Biodeterioration, Bio-fragmentation, and Assimilation. Biodeterioration refers to the process of mechanical weakening of complex structures. In Bio-fragmentation, microorganisms break down toxic and complex compounds. And in Assimilation, old structures are transformed into new compounds.


The process involves the mechanical, physical, and chemical weakening of the compound structure. The abiotic factors, such as light, temperature, and chemicals of the environment, initiate these changes. 


After the weakening of the structure, the cleavage of polymeric bonds leads to the transformation of oligomers and monomers. The fragmentation is achieved in aerobic as well as in anaerobic conditions. Aerobic digestion of compounds leads to the formation of water, carbon dioxide, and simple molecules that are utilized as a nutrient source. Anaerobic digestion reduces the mass and volume of complex material, such as the production of natural gases. Anaerobic reactions are used widely used in waste management facilities as a source of renewable energy.


The newly formed molecules are taken up by the microorganisms via membrane carriers. The molecules are then used as an energy source in the form of ATP (Adenosine Triphosphate) or as cell structural elements.

Factors Affecting Biodegradation

Biodegradation of materials and its rate of degradation by microorganisms is influenced by nutritional requirements and environmental factors like soil, water, etc. The efficiency and rate of degradation depend on the compounds’ concentration, nature, bioavailability, and physicochemical properties. 

Environmental Factors

Biodegradation occurs at the ground, so the soil type and organic matter potentially affect the adsorption and absorption of pollutants on the soil surface. 

  • Absorption of the contaminant by the soil matrix reduces the bioavailability to microorganisms, and the proportion of metabolic breakdown is reduced consequently.
  • Porosity variations are seen in the saturated and unsaturated zone of the aquifer matrix, influencing the fluid movement and migration of pollutants in groundwater.
  • In fine-grained soil with water saturation, the transmission of gases such as CO2, methane, and oxygen gets reduced; hence the biodegradation process gets slower.
  • Microbes can oxidize pollutants in soil with more redox potential, thus increasing electron transport. This indicates aerobic conditions, hence low electron density.
  • In anaerobic conditions, high electron density can be observed in the soil, indicating the reduction potential of the microorganisms.

Biological Factors

The biological factor is the metabolic potential which includes the inhibition of enzymatic factors of an organism to degrade any contaminant. 

  • Inhibition of enzymatic activity can occur due to competition for the availability of limited carbon sources between microorganisms or predation by the bacteriophages and protozoa.
  • The degradation rate also depends on the concentration of the contaminant present in the surroundings and the number of microorganisms present with the ability to produce proper enzymes to degrade the contaminant.
  • The affinity of the contaminant to the specific enzymes can contribute to the rapid metabolism of pollutants by the organisms.
  • Biological enzyme-catalyzed reactions for biodegradation have an optimum pH of approx. 6.5 – 8.5, temperature and moisture influence the rate of metabolism, amount of soluble materials, and osmotic pressure in the terrestrial and aquatic systems.


The end goal is the same for both processes, which is to clean the environment and achieve sustainable development goals as much as possible. Since the beginning of industrialization and technological advancement, humans have been releasing toxic chemicals into the environment. These toxic compounds have become pollutants and have proven to be hazardous to human health and to the ecosystem in general, which has affected the balance of nature immensely. To curb this situation, nature has been doing its job of removing wastes via biodegradation employing microorganisms to metabolize these toxic chemicals. Microorganisms showed the super abilities and specific digestive machinery to transform synthetic compounds into a stable form. Microbes use the pollutants as their carbon source, which helps them gain energy and, in turn, cleans up the ecosystem.


  1. Biodegradation: Involved Microorganisms and Genetically Engineered Microorganisms –
  2. Biodegradation: Updating the Concepts of Control for Microbial Cleanup in Contaminated Aquifers –
  3. Polycyclic Aromatic Hydrocarbons (PAHs) Factsheet –
  4. Polychlorinated Biphenyls (PCBs) –
  5. Pesticide Biodegradation: Mechanisms, Genetics and Strategies to Enhance the Process –
  6. Jamee, Radia, and Romana Siddique. “Biodegradation of synthetic dyes of textile effluent by microorganisms: an environmentally and economically sustainable approach.” European journal of microbiology and immunology 9.4 (2019): 114-118.
  7. Removal and recovery of radionuclides and toxic metals from wastes, soils and materials –

About Author

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Nidhi Dewangan

Nidhi Dewangan has a bachelor’s and Master’s degree in Biochemistry from Pandit Ravishankar Shukla University, Raipur (C.G.), India. She is the author of the Chapter “Commonly found Bacteria and Drug-Resistant Gene in Wastewater” in the book “Antimicrobial Resistance in Wastewater and Human Health” published by Elsevier, under the guidance of Dr. Awanish Kumar, Assistant Professor at the Department of Biotechnology, NIT Raipur. She’s also a University and a National player in Squash. She has represented her University and won team events in the All India University Squash Championships. Her research interest is genetics and computational biology.

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