Bioremediation: Microbes Cleaning Up the Environment

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  • 0:07 Devastating Oil Spils
  • 1:09 Bioremediation
  • 2:05 Oil Spill Bioremediation
  • 3:07 Natural Bioremediators
  • 4:09 Bioaugmentation
  • 6:38 Lesson Summary
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Lesson Transcript
Instructor: Angela Hartsock

Angela has taught college Microbiology and has a doctoral degree in Microbiology.

Bioremediation uses living organisms to clean up pollution. In this lesson, we will examine the role of microbes in bioremediation and why it is not a perfect solution for degrading environmental pollutants.

Devastating Oil Spills

I still vividly remember the wreck of the Exxon Valdez oil tanker off the coast of Alaska that dumped millions of gallons of oil into Prince William Sound. But since that was back in 1989, I guess I should use a more contemporary example. How about the Deepwater Horizon oil spill? You all should remember when it spewed oil into the Gulf of Mexico in 2010. I will never forget the images of sea birds, both alive and dead, covered in oil.

Then there were the videos of the volunteers in hazmat suits attempting to clean up the mess and save the wildlife while at the same time risking their health through contact with the toxic oil. There must be a better way to clean up this pollution that doesn't endanger more human lives, a way to not just remove it from the environment but break it down into harmless compounds that can just disperse back into nature. Enter the exciting world of bioremediation.


Bioremediation is the use of organisms to metabolize pollutants. Instead of simply collecting the pollutant and storing it, bioremediation relies on living organisms to consume and break down the compound, turning it into harmless, natural substances. Bioremediators are any organism used for bioremediation. Typically, microbes like bacteria, archaea and fungi are the prime bioremediators.

There are lots of different types, they grow very rapidly, and they can be easily modified genetically. This doesn't mean plants and animals can't be used as bioremediators. It simply means that these microbes are much easier to use and often better suited to the tasks at hand. In order to better understand bioremediation, let's continue with the theme of oil spills.

Oil Spill Bioremediation

Many foods these days are touting the health benefits of 'all natural ingredients,' but crude petroleum oil is 'all natural' and far from a healthy compound. Millions of years ago, large numbers of microbes, predominantly algae and zooplankton, died, were buried under sedimentary rock and were subjected to the extreme temperatures and pressures deep in the earth.

Over the years, the tiny corpses changed in response to the extreme conditions, yielding a complex mixture of compounds composed mainly of carbon and hydrogen. What started as tiny dead bodies is now a smelly pool of dark, sludgy liquids and gases. If you could zoom in on each individual molecule, you would see huge variation in shapes and sizes. Some form long chains. Others form complex, circular molecules. Regardless of the molecular structure, during an oil spill, all of these molecules need to be broken down and rendered harmless.

Natural Bioremediators

Fortunately, microbes capable of breaking down nearly all of these compounds already exist. You can bet as soon as that oil started appearing on Earth, bacteria and archaea evolved ways to exploit it as an energy source. After countless billions of mutations and generations, a large, diverse community of microbes evolved. Each species targets one or a select few of the molecules, efficiently breaking them down, releasing energy.

Some species are able to take their compound down to carbon dioxide and water. Other species simply break large molecules into smaller chunks that are in turn broken down by a different species. The process is slow but nearly 100% effective. So, bioremediation is able to clean up these oil spills but not in a time frame that is acceptable to most environmentalists. Who has time to wait 1,000 years for nature's garbage men to take care of business? It's time to introduce another term.


Sometimes, natural species are not fast enough or even able to break down certain compounds. But I mentioned earlier that microbes like bacteria, archaea and fungi are able to be genetically modified. So, through DNA manipulation, scientists should be able to engineer microbes that target resistant compounds or break down pollutants much faster than natural species.

Bioaugmentation is the process of adding engineered microbes to a system to act as bioremediators. This sounds like a great idea to quickly and completely eliminate that oil. But there is a problem. If you take a lab rat that was born and lived its entire life in captivity and suddenly release it into a forest, it's going to struggle. It knows what to do with food but not where to find it or how to compete with wild rats for access to it.

The microbes respond the same way. They may be able to quickly break down a target pollutant, but so are the natural species. And those natural species evolved to these specific environmental conditions. At the end of the day, an engineered bacteria simply can't compete well enough to displace the naturally occurring species.

But bioaugmentation does have its place. Engineers and scientists are constantly striving to create new and better chemicals that have never existed before. These compounds don't have the close evolutionary relationship with naturally occurring microbes, so it is likely that one doesn't exist that can break them down. In this instance, engineering bacteria to break down these compounds can be the perfect solution.

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