The Role of Microorganisms in Bioremediation

1. The Role of Microorganisms in Bioremediation

Bacteria, fungi, and microalgae are widely distributed in the biosphere and are referred to as the main bio-remediators,

This is due to their fast replication rate and ability to grow in a wide range of environmental conditions. By using their enzymatic abilities to modulate the breakdown and conversion of toxins, these organisms can be used alone or in a consortium to repair the natural environment and stop future pollution. 

Depending on the type of pollutants (heavy metals, agrochemicals, dyes, hydrocarbons, plastics, greenhouse gases, sewage, wastewater, or agro-industrial waste), bioremediation techniques can be applied ex situ or in situ. These techniques primarily involve degradation, detoxification, mineralization, or transformation. 

2. Factors affecting microbial bioremediation

The physicochemical properties of the environment, the availability of pollutants to microorganisms, and the chemical makeup and concentration of pollutants all of these affect the effectiveness of  bioremediation .

The presence of a microbial population that can break down the pollutants, the accessibility of the contaminants to the microbial population, and environmental conditions such as soil type, temperature, pH, oxygen or other electron acceptors, and nutrients are the some of the factors that affect the  bioremediation processes.

Biological factors

Biologic variables can influence the breakdown of organic molecules by causing microbes to compete for scarce carbon sources, interact antagonistically, or be preyed upon by bacteriophages and protozoa. The expression of specific enzymes by the microbial cells can increase or decrease the rate of contaminant degradation.

Environmental factors

Potential interactions during the Bioremediation procedure are determined by the physicochemical features of the targeted pollutants and the metabolic traits of the microorganisms.

pH, temperature, moisture, soil structure, solubility in water, nutrients, site characteristics, redox potential, oxygen content, and the physical-chemical bioavailability of pollutants (contaminant concentration, type, solubility, chemical structure, and toxicity) all have an impact on the growth and activity of microorganisms. 

Availability of nutrients

The addition of nutrients modifies the vital nutritional balance for microbial growth and reproduction. By adjusting the bacterial C: N: P ratio, nutrient balancing—particularly the provision of vital nutrients like N and P—can increase the biodegradation efficiency. Microorganisms require a variety of nutrients, including carbon, nitrogen, and phosphorus, in order to live and carry out their microbiological functions. 

Temperature

Temperature is the most crucial physical factor in regulating the content of hydrocarbons and the survival of microbes. In cold environments such as the Arctic, oil degradation via natural processes is very slow and puts the microbes under more pressure to clean up the spilled petroleum. Most oleophilic microorganisms become metabolically inactive due to the sub-zero water temperature in this area, which shuts off the transport channels inside the microbial cells or may even freeze the entire cytoplasm.Biological enzymes are participated in the degradation pathway have an optimum temperature and will not have the same metabolic turnover for every temperature. 

Concentration of oxygen

 Biological degradation occurs under both aerobic and anaerobic conditions. In most situations, oxygen can improve the metabolism of hydrocarbons.

Moisture content

Microorganisms require adequate water to accomplish their growth

pH

pH has its own impact on microbial metabolic activity and also increase and decrease removal process. The measurement of pH in soil could indicate the potential for microbial growth 

Site characterization and selection

Sufficient remedial investigation work must be performed prior to proposing a bioremediation remedy to adequately characterize the magnitude and extent of contamination.

Metal ions

Metals are important in small amount for bacteria and fungus, but in high quantity inhibit the metabolic activity of the cells. Metal compounds have direct and indirect impact on rate of degradation.

Toxic compounds

When in high concentrations of toxic nature of some contaminants, can create toxic effects to microorganisms and slow down decontamination. The degree and mechanisms of toxicity vary with specific toxicants, their concentration, and the exposed microorganisms. 

3. Role of Bacteria in bioremediation

Bacteria are essential agents for eliminating a variety of pollutants, such as heavy metals, hydrocarbons, pesticides, and nutrients, due to their metabolic diversity, adaptability, and engineering potential.

Bacteria can break down or transform pollutants such as hydrocarbons, heavy metals, and xenobiotic compounds through their natural metabolic pathways, making them less toxic or easier to remove from the environment.

Biofilm Formation: Many bacteria form biofilms—structured communities that enhance their ability to degrade persistent organic pollutants by providing stability and increased resistance to environmental stresses

Community Interactions: Bacterial consortia (mixed communities) often outperform single strains due to synergistic interactions, substrate specificity, and adaptability to complex waste mixtures.

 Modern techniques in systems biology and metabolic engineering allow for the design of bacteria with enhanced or novel pollutant-degrading abilities, including the construction and optimization of catabolic pathway

 Encapsulating bacteria in hydrogels or other matrices improves their stability, reusability, and efficiency in bioreactors, making the process more cost-effective and sustainable

Common Bacteria Used in Bioremediation

• Pseudomonas: Known for breaking down hydrocarbons and heavy metals in soil and water.
• Bacillus: Effective in degrading oil, heavy metals, and other organic pollutants.
• Flavobacterium: Involved in the removal of heavy metals.
• Arthrobacter, Corynebacterium, Rhodococcus, Streptomyces, Nocardia, Microbacterium: These Actinobacteria are notable for degrading pesticides, polycyclic aromatic hydrocarbons (PAHs), and heavy metals.
• Cupriavidus, Paenibacillus, Burkholderia, Ensifer: Identified as resistant to and capable of removing heavy metals like cadmium, chromium, and nickel from contaminated soils.
• Alcanivorax, Halomonas: Marine bacteria effective in degrading petroleum hydrocarbons and removing heavy metals from marine environments

4. Role of Fungi in Bioremediation

Fungi are particularly effective  in bioremediation because of their metabolic diversity, capability to accumulate or change organic molecules and hazardous metals, and ability to breakdown complex contaminants.

Fungi produce a wide range of enzymes (e.g., laccases, peroxidases) that break down complex organic pollutants such as hydrocarbons, pesticides, pharmaceuticals, plastics, and persistent organic compounds into less harmful substances.

Fungi often work in synergy with bacteria, enhancing the breakdown of pollutants through cooperative metabolic processes

Fungi can remove heavy metals from contaminated environments through biosorption, bioaccumulation, biotransformation, and bio volatilization, making them effective for soils polluted with toxic metals.

Fungi are used to clean up both terrestrial and aquatic environments, including soils contaminated with petroleum hydrocarbons, heavy metals, and persistent organic pollutants, as well as water bodies polluted with pharmaceuticals and plastics.

White rot fungi are particularly noted for their ability to degrade a wide range of toxic xenobiotics, including synthetic dyes, PAHs, and emerging pollutants.

Combining fungal bioremediation with other methods (physical, chemical, or biological) increases efficiency, cost-effectiveness, and adaptability for large-scale or on-site applications.

Examples of Fungi in Bioremediation

• White Rot Fungi (WRF):

  • Notable species: Phanerochaete chrysosporium, Pleurotus ostreatus, Trametes versicolor, Lentinula edodes
  • Capable of degrading a wide range of pollutants, including synthetic dyes, polycyclic aromatic hydrocarbons (PAHs), pesticides, pharmaceuticals, and phenolic compound.
  • Their powerful enzymes (like laccases and peroxidases) break down complex and toxic chemicals.

• Aspergillus Species:

  • Examples: Aspergillus hiratsukae, Aspergillus terreus
  • Effective in removing heavy metals such as copper from contaminated soils, with A. terreus showing high tolerance and accumulation capacity.
  • Also involved in the degradation of various organic pollutants.

• Other Fungi:

  • Non-ligninolytic fungi from the Ascomycota and Zygomycota phyla can degrade chlorinated hydrocarbons and PAHs, sometimes outperforming white rot fungi under certain conditions.
  • Filamentous fungi and yeasts are also used for degrading industrial effluents and can be engineered for specific bioremediation tasks

5. Role of algae in Bioremediation

Algae play a crucial role in bioremediation by removing a wide range of pollutants from water, including organic contaminants, heavy metals, phenolics, microplastics, and nutrients. Algae-based bioremediation is environmentally sustainable, cost-effective, and can be integrated with bioenergy and valuable product production.

Algae absorb and accumulate pollutants such as heavy metals, phenolics, and organic contaminants from wastewater, reducing their concentrations effectively.

Algae can break down complex organic pollutants and phenolics through metabolic and light-driven processes.

Algae remove excess nutrients (nitrogen, phosphorus) from wastewater, helping prevent eutrophication.

Algae can transform toxic substances like arsenic into less harmful forms through oxidation, reduction, and volatilization pathways.

Algal biomass from bioremediation can be used for biofuel, biofertilizer, and high-value compounds, supporting a circular economy

Algae-based systems are eco-friendly, avoid secondary pollution, and contribute to carbon dioxide fixation.

Examples of algae used in Bioremediation

Nannochloropsis oculata: Highly effective in removing petroleum hydrocarbons (kerosene, diesel, gasoline) from polluted marine water, achieving removal efficiencies up to 84.58% for kerosene, 65.51% for diesel, and 70.77% for gasoline. This species is particularly robust and reliable for hydrocarbon bioremediation in tropical marine environments

Porphyridium cruentum: Also used for petroleum hydrocarbon removal, though less efficient than Nannochloropsis oculata, with removal rates ranging from 46.64% to 58.94% depending on the fuel type.

Tetraselmis suecica: Successfully cultivated in aquaculture wastewater, this microalga efficiently removes dissolved inorganic nitrogen and phosphorus, while producing valuable biomass rich in proteins.

Microalgae and Cyanobacteria: These groups are broadly effective in removing a wide range of organic pollutants, heavy metals, nutrients, and even pharmaceutical compounds from wastewater. Their adaptability and ability to accumulate or degrade contaminants make them central to many bioremediation strategies.

6. Further Reading

Read the chapter on Water Pollution and Bioremediation from Microbiology: Canadian Edition

Read the Review article on "The Role of Microorganisms in Bioremediation- A Review" by Endeshaw Abatenh*, Birhanu Gizaw, Zerihun Tsegaye and Misganaw Wassie  from  Open Journal of Environmental Biology

Verma, S., & Kuila, A. (2019). Bioremediation of heavy metals by microbial process. Environmental Technology & Innovation. https://doi.org/10.1016/J.ETI.2019.100369.

Alazaiza, M., Albahnasawi, A., Ahmad, Z., Bashir, M., Al-Wahaibi, T., Abujazar, M., Amr, S., & Nassani, D. (2022). Potential use of algae for the bioremediation of different types of wastewater and contaminants: Production of bioproducts and biofuel for green circular economy.. Journal of environmental management, 324, 116415 . https://doi.org/10.1016/j.jenvman.2022.116415.

Ahmad, A., Banat, F., Alsafar, H., & Hasan, S. (2021). Algae biotechnology for industrial wastewater treatment, bioenergy production, and high-value bioproducts.. The Science of the total environment, 150585 .https://doi.org/10.1016/j.scitotenv.2021.150585. 

Vaksmaa, A., Guerrero-Cruz, S., Ghosh, P., Zeghal, E., Hernando-Morales, V., & Niemann, H. (2023). Role of fungi in bioremediation of emerging pollutants. , 10. https://doi.org/10.3389/fmars.2023.1070905.

Amobonye, A., Aruwa, C., Aransiola, S., Omame, J., Alabi, T., & Lalung, J. (2023). The potential of fungi in the bioremediation of pharmaceutically active compounds: a comprehensive review. Frontiers in Microbiology, 14.https://doi.org/10.3389/fmicb.2023.1207792.