Bioremediation: What is it? Why is it so Important?

The fallout of heavy pollution is very plain to see. When an ecosystem is full of heavily pollution, the natural systems of the earth can not adapt to the change. Some of the bacteria, fungi, protists, and other microorganisms capable of eating pollutants may die. However, there are some that may also survive and continue on their mission of eating the pollutants. Bioremediation works by supplying these select pollution eating organisms with the proper tools to strive and grow rapidly. These organisms are then able to break down the organic pollutant at a much faster rate. To explain bioremediation, you have to understand everything that happens and goes into it.


What is Bioremediation

Bioremediation occurs as part of Earth’s clean up system. It is a natural process used to clean up organic pollutants and contaminants. This happens when microbes come in contact with a substance that registers as a contaminant like oil, gas, or diesel. Ideal conditions for this process to be greatly effective include temperature balance, surface pH levels, available moisture and others.


To begin this process, microbes release enzymes to break down contaminants into smaller pieces. Those microbes are then able to eat the broken down contaminants as a source of food and energy. The byproduct of this process is water, carbon dioxide, and other harmless amino acids. In ideal environments with enough tools for these organisms to thrive, the microbes will reproduce and create more microbes to help aid their efforts in the removal of other contaminants. This cycle will continue to repeat until the food source is gone.

How We Help The Natural Process

Bioremediation is a natural process that is always happening in ecosystems. Whenever a contaminant is introduced into an ecosystem, the correct microbes will get to work on getting rid of it. When a man-made disaster strikes, these microbes are already at work. But, the sheer amount of pollution that takes place can hinder their work. This is where certain cleanup companies come into the fold. Even nature needs help sometimes. Their job is to use these pollution-eating organisms to clean up the mess. Instead of adding organisms to the environment, which can actually harm the natural balance even further, the best way to clear chemical pollutants is to help the already existing organisms. This happens by adding nutrients near the affected area.


Additional Steps

An environment like an oil spill is not an ideal environment for these microbes to thrive. Therefore, it may be impossible for them to completely clear the contaminant on their own. Adding nutrients to the environment may not be enough. If the spill or the amount of pollutant is great enough, they take additional steps. A great example is the clean up of the Deepwater Horizon oil spill. During the cleanup, responders dumped a lot of chemical dispersants on the spill in an attempt to break up the oil in the Gulf of Mexico. This is done because it is easier for the microbes to consume the oil when the surface area is larger. Instead of all of the contaminant congregating in a smaller area.


Methods of Bioremediation

There are three types of bioremediation, each for a different condition.


Biostimulation- This method is when bacteria are made to start the bioremediation process. Nutrients and other important substances are released into the soil or water. These will increase the growth of microbes in that environment. As a result, the bacteria will replicate more quickly and thus will be able to clear the contaminants much more quickly and efficiently.


Bioaugmentation- This is when a certain area is in desperate need of microorganisms to remove contaminants. Instead of adding nutrients to aid already existing bacteria and other microorganisms, microorganisms will actually be added to the affected area.


Intrinsic Bioremediation- Also known as Natural Attenuation. Defined by the Environmental Protection Agency as “a variety of physical, chemical, or biological processes that, under favorable circumstances, act without human intervention to reduce the mass, toxicity, mobility, volume, or concentration of contaminants in soil or groundwater. These in situ processes include biodegradation; dispersion; dilution; sorption; volatilization; radioactive decay; and chemical or biological stabilization, transformation, or destruction of contaminants.”


Bioremediation Microbes

There are many different microorganisms that are active in bioremediation. Each one has a specific trait that makes it crucial to the processes.


Bacteria- They are very diverse, which makes them extremely valuable for bioremediation. Some toxins are universal to bacteria. Meaning that there is likely an organism able to break down any toxin that it comes in contact with. However, there are some specific bacteria that are known to help more than others.


  • Pseudomonas Putida- a Gram-negative soil bacteria that are active in the bioremediation of toluene, a component of paint thinner. It is also able to degrade naphthalene which is a product of petroleum refining.
  • Dechloromonas Aromatica- This is able to oxidize aromatics including benzoate, chlorobenzoate, and toluene. It is the only organism able to oxidize benzene anaerobically. It is useful in situ bioremediation of benzene contamination in ground and surface water.
  • Deinococcus Radiodurans- This is a radiation resistant bacteria, engineered for the bioremediation of solvents and heavy metals. An engineered strain of this bacteria has shown to degrade ionic mercury and toluene in radioactive mixed waste environments.
  • Methylibium Petroleiphilum- This bacteria (PM1) is capable of degrading methyl tert-butyl ether (MTBE). This is done by using MTBE as the only source of carbon and energy.
  • Alcanivorax Borkumensis- A marine bacteria which consumes hydrocarbons like the ones found in fuel. It produces carbon dioxide as a result. This bacteria grows rapidly in environments damaged by oil and has been used in the cleaning of over 830,000 gallons of oil from the Deepwater Horizon oil spill.



Fungi- While bioremediation normally uses bacteria, fungi fundamentally have important roles due to their involvement in the cycle of elements through decomposition and transformation of organic and inorganic material. These attributes can be used in the bioremediation of organic compounds and reduce the risk of metals. Due to their metabolic versatility and their environmental resilience, fungi can oxidize many different chemicals and can survive in harsh conditions like low moisture and high amounts of pollutants.

bioremediation: fungi

  • White Rot Fungi- The most important thing about these fungi is their enzymatic functional ability to metabolize complex chemicals. They are highly useful for their ability to degrade lignin extracellularly through its hyphal extension. This allows for them to reach other soil contaminants that some organisms can not. They can also thrive in harsh conditions.
  • Phanerochaete Chrysosporium- Is used in the bioremediation of pesticides, PAHs, dioxins, carbon tetrachloride, and others.
  • Other Applications- Bioremediation of hydrocarbon pollutants, remediating metals, pesticide degradation, and other instances where bacteria can not perform.


Archaea- This organism has been shown to be very valuable in bioremediation, more so than fungi. Archaea is able to adapt to extreme environments. In fact, they adapt naturally to cold environments which make them important in the degradation of hydrocarbons in those environments. Extreme halophilic archaea has the potential to be very useful in hypersaline environments where bacteria cannot thrive. They are also very resistant to antibiotics like penicillin, cycloheximide, streptomycin, and more.


Types of Bioremediation

There are a few different approaches to bioremediation. Each using a different organism to work at clearing pollutants and contaminants.


Microbial Remediation

The Microbial Remediation approach uses microorganisms to do one of two things. Either degrade organic contaminants or bind heavy metals in more inert and less bioavailable forms. These organisms will break down the pollutants by using them as their food source or using them with a food source. Think of it like their regular food source with a side of pollution. These microorganisms include both aerobic and anaerobic bacteria. Aerobic uses oxygen and creates carbon dioxide. Anaerobic does not require oxygen and end up creating methane, hydrogen gas, sulfides, elemental sulfur, and dinitrogen gas.

Microbial remediation can be done by either adding high numbers of bacteria to a contaminated area or adding nutrients to the affected area, creating ideal conditions for bacterial growth. A very popular grassroots remediator method to this is using actively aerated compost tea. This can inoculate a site with very beneficial bacteria. This tea takes all of the bacteria and fungi that have grown in the compost pile and extracts them into liquid. Then spread it over the affected soil. Whatever you do, just do not drink the tea.



This approach to bioremediation works with the natural ability of plants to repair and regenerate toxic soils, groundwater and surface waters. They help to bind, extract, transform, and clear many kinds of contaminants like metals, pesticides, chlorinated solvents, polychlorinated biphenyls, explosives, radionuclides, and petroleum hydrocarbons. By doing this, plants can help prevent the pollutants from being spread to another area by the wind or rain. This approach is best used in areas with low to medium amounts of pollution.

There are six ways that plants act in bioremediation.


  • Phytoextraction- This is when plants pull the contaminants through their roots and assimilate them into their stems and leaves. Hyperaccumulators are plants that are especially good at phytoextraction.
  • Photodegradation- This is the process of pulling up and breaking down chemicals through the release of enzymes and metabolic processes.
  • Phytovolatilization- Volatile chemicals are either transformed into the plant into less harmful states and released, or released and degraded by the sun.
  • Rhizodegradation- Roots of some plants create the ideal environment for bacteria.
  • Rhizofiltration- Plant roots filter contaminated water by absorbing contaminants.
  • Phytostabilization- Referred to as the “green cap.” This is when plants bind pollutants by absorbing them into their roots. Then they release a chemical that converts the pollutant into a much less toxic state. This also stops contaminants from spreading in the soil.




Fungi, as said before, are very useful for bioremediation. This is because they are nature’s decomposers. They are able to break down numerous materials from plants and wood to complex compounds like lignin and cellulose. Certain fungi can break down even more complex materials like hydrocarbons, pesticides, and heavy metals. Mycelium is what is used for bioremediation and the repair of earth systems by fungi. Mycelium is the vegetative part of fungi. It sends out enzymes that break down chemicals, as well as acts as a filter.


Here are examples of common fungi usage in remediation and the pollutants that they work with.


  • Shaggy Mane- Arsenic, cadmium, and mercury
  • Elm Oyster- Dioxins, and wood preservatives
  • Phoenix Oyster- TNT, cadmium, mercury, copper
  • Pearl Oyster- PCBs, PAHs, cadmium, mercury, dioxins
  • King Oyster- Toxins, agent orange
  • Shiitake- PAHs, PCBs, PCPs
  • Turkey Tail- PAHs, TNT, organophosphates, mercury
  • Button Mushrooms- Cadmium
  • King Stropharia- E-coli and other biologicals

bioremediation: fungi


Examples of Bioremediation

There are many instances where bioremediation can be very useful. It is a much safer alternative than incinerating or using more chemicals to clean polluted areas. There are 3 very common uses for bioremediation.



  • Crime Scene Cleanup- The use of bacteria and other microorganisms can be very useful when cleaning up blood and bodily fluids. These fluids could pose significant health risks like hepatitis, HIV, and MRSA. Crime scene cleaners will use enzyme cleaners, in place of bleach or ammonia to get rid of harmful contaminants.
  • Contaminated Soil- This is a very common example and is mentioned many times above. Microorganisms will use the chemical contaminants as an energy source and will metabolize the pollutant into useable energy.
  • Oil Spill Cleanup- This is the most common use for bioremediation. Again as mentioned before, bioremediation was the primary use in the Deepwater Horizon spill cleanup. This was due to the effectiveness of it and the low cost. Two methods are used in this instance. Bioaugmentation, which is the addition of microbes to an affected area. The other is biostimulation, which is the addition of nutrients to aid the already existing microbes.

bioremediation: oil


Nature’s Cleaner Uppers

Bioremediation happens naturally and all of the time. It is part of the natural cycle of elements. It only makes sense to use the tools we already have to our advantage. Bacteria and other microorganisms help maintain the balance of chemicals in their respective ecosystems. When humans mess up, like we usually do, and end up greatly harming our environment, bioremediation is there to clean up. But even nature can use a little bit of help sometimes.



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Patrick Sands

Hey, I'm Pat. I am a Millersville grad with a Bachelors of Arts in English. I love to write, play video games, watch movies and TV, basically be a total nerd whenever I can. Green and Growing is important to me because it allows me to help others be as green and eco-friendly as possible. With Climate Change being what it is, it is even more important for people to get educated about their environment. This website allows me to do my part in that. Also, I'm a huge goof who tries to add some humor into anything I write. Stay Excellent out there!

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