Autumn 2016 / Leading Edge
Hungry for Hazardous Waste

How pollution-eating microbes could help clean up toxic sites

Illustration of a metal can with a poison symbol sitting on its side on top of a field of flowers

Illustration: Brian Stauffer

Professor Elizabeth Edwards of chemical engineering and her team have developed a secret weapon in the war against pollution: a mix of micro-organisms that eat toxic chemicals for breakfast. Now, funding from Genome Canada will help Edwards and her industrial partners bring the unique microbial culture to market.

Everywhere tanks of oil or gasoline are stored underground, hazardous chemicals leak into soil and groundwater. “The owner of every gasoline station on the planet probably has some contamination issues,” says Edwards, who holds the Canada Research Chair in Anaerobic Biotechnology.

To clean up the site, crews have to dig, wash or aerate the soil to encourage the growth of oxygen-loving micro-organisms that break down the pollutants – a labour-intensive, time-­consuming and expensive remediation process. Edwards and her team have discovered another set of organisms that live without oxygen and could do the job without having to churn up and process all the soil.

The microbial cultures Edwards works with now have evolved from soil samples taken at contaminated oil refinery and gas station sites more than 15 years ago. Since then, Edwards and her team have been enriching the cultures by feeding the organisms oil-derived chemicals that are difficult to degrade and selecting the samples that are most effective at breaking them down.

“What we have is a culture that can chow down on these chemicals when there’s no oxygen around,” says Edwards. Adding this culture to a contaminated site, a process known as bio-augmentation, may speed up the degradation of pollutants with minimal disruption to the environment.

In addition to demonstrating the effectiveness of the process in the lab, the team has done extensive genomic sequencing to understand which individual species in the culture are responsible for each step in the chemical breakdown. “We think it’s ready to be tested in the field, but to do that we have to scale it up,” says Edwards. Her team is partnering with SiREM, an environmental remediation laboratory in Guelph, Ontario, that specializes in bio-augmentation. The lab has already commercialized another one of Edwards’ microbial cultures, which is optimized to clean up chlorinated solvents such as those used in dry cleaning and other industrial applications. Adding more chemicals to the list of treatable ones could help increase SiREM’s share of the global market for bio-remediation, which is estimated in the billions of dollars.

“This project is a great example of the way our researchers work across disciplines to address challenges in sustainability,” says Prof. David Sinton, interim vice-dean, research, for the Faculty of Applied Science and Engineering. “Together with industrial partners, engineering researchers are bringing leading-edge solutions from the lab to the global marketplace.”

Other partners include Mitacs, a Canadian non-profit that’s funding a post-doctoral researcher on the project, and the Ontario Ministry of Research and Innovation, which will provide matching financial support.

If the pilot project is successful, the bio-augmentation culture could be used at contaminated sites around the world. “It’s a brand new tool to deal with difficult remediation,” says Edwards.

Reader Comments

# 1
Posted by Scott Anderson on September 11th, 2016 @ 1:24 pm

I appreciate that U of T Magazine is trying to positively report on the important researching taking place at the university. However, I think it is vitally important for a university magazine to promote critical thinking and ask questions of research, rather than simply accepting the claims of researchers at face value.

For instance, are there direct risks of this application of biotechnology? (It is actually unclear to what extent the organisms in question result from biotechnology techniques, and how these have been applied, but the article states that Prof. Elizabeth Edwards is the Canada Research Chair in Anaerobic Biotechnology.)

Are there uncertainties about how the organism will impact the ecosystem into which it is released and the organism’s potential to evolve in unforeseen ways?

Why is a biotechnological approach needed? Are there lower-tech approaches that would be equally effective at the remediation in question?

How are the bio-safety and bioethics questions related to this research being considered and addressed?

I am not opposed to the use of biotechnology, and this case may represent a very helpful use. However, I am opposed to the lack of critical thought present in this type of reporting about biotechnology.

Matthew Legge
BA 2006 Victoria
Richmond Hill, Ontario

# 2
Posted by Scott Anderson on September 14th, 2016 @ 9:36 am

Prof. Elizabeth Edwards responds:

Thank you for your important questions and I am happy to try to answer and clear up any confusion.

Biotechnology refers to any use of living systems to develop or make products, but does not necessarily mean that organisms are genetically or otherwise modified. In our case, we are using naturally-occurring microbes found in soil and groundwater. We grow them in the lab to boost the numbers of the most active benzene-degrading microbes, which allows them to do the same job as the resident microbial population, but more quickly. Since these more active organisms only grow on petroleum hydrocarbons, as soon as the contamination is gone, they will die back.

We are also taking the steps to obtain Environment Canada approval of our enriched cultures. My partners at SiREM and I have done this previously for another culture of microbes for treating chlorinated-solvent contaminated wastes, which we market under the name KB-1.

We worked with Environment Canada to ensure our cultures comply with the same regulations as other specialized microbial cultures such as those used to make beer and cheese. (See:

In terms of alternatives, our approach is actually the lowest-tech option possible, other than to do nothing and let nature takes its course. Conventional treatment requires extensive digging and dumping and just moves the contamination from one location to another, whereas bioremediation actually destroys the contaminant in place. As with any remediation effort, regardless of the technology, careful monitoring is required to understand what is happening to the chemicals below the ground.

# 3
Posted by George Heighington B.A%201972%20UTSC,%20B.Ed%201973 on September 15th, 2016 @ 3:16 pm

The article is very interesting. Much of the concern for waste on land has mushroomed since “Heighington V Ontario.” That case began on Scarborough’s McClure Crescent (close to UTSC) on November 20, 1980 when radioactive waste was uncovered in the yards and under the homes.

Resistance to move the soil or the residents resulted in a precedent legal action before Justice R.E. Holland, who found the Crown liable for the radioactive waste. The ensuing judgement cost bank mortgage departments and land investors lots of money, as they had to clean up the land. The legal action made ‘case law’ as it applies to waste clean-up. Afterward, industry tried to find the most inexpensive way to clean up the land, spawning a completely new industry.

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