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What were you hoping to learn when you set out on the research that led to your highly cited 2003 paper in Applied Environmental Microbiology, "Characterization of hydrocarbon-degrading microbial populations in contaminated and pristine alpine soils," (Margesin R, et al., 69[6]: 3085-92, June 2003)?

We had developed some molecular techniques to look for hydrocarbon-degrading bacteria directly in the soil, so we wouldn't rely on having to isolate and culture them under laboratory conditions. Our main interest in that particular piece of work, and by extension several other comparable studies, was to use these tools to differentiate between types of bacteria present in contaminated soil verses non-contaminated soil. What we were looking for specifically was the presence of key genes involved in the breakdown of hydrocarbons, when these bacteria use hydrocarbons as a source of nutrients.

Can you describe the molecular techniques?

We were targeting key genes involved in the degradation of alkanes and aromatic hydrocarbons—in particular, alkane monooxygenase and naphthalene dioxygenase genes. We used a variety of molecular approaches to detect these genes directly in environmental samples. We could do hybridization with the gene itself; we could use PCR with specific primers for the genes.

Was it a new idea to use the bacterial genes to look for these bacteria, or had it been done elsewhere and you were just applying it?

I'm not going to say it was my idea, that I initiated this kind of research, but I certainly did at our institute. There were already some other people talking about it in the literature. What I did here at the institute was develop a program that was larger and broader than others. Rather than just focusing on an individual pathway or organism, we started to look more broadly at all types of pollutants—pesticides, chlorinated solvents, polychlorinated biphenyls (PCBs), explosives etc.—and lots of different hydrocarbon-degradation genes.

We were doing work at that time, or had done work at that time on a fairly broad range of different types of compounds. So I wanted to put together what you might call a toolbox that would have representatives from a variety of these different bacterial pathways.

An aerial picture of the Canadian Forces Station at Alert, top of Ellesmere Island, Nunavut (taken in August 2008), where we are currently doing a lot of our research and bioremediation work"

View larger image in the tab below.

We basically used a variety of different types of molecular techniques to develop a better understanding of what goes on during a practical remediation project. Some of the studies were done in the lab, but we tried to do more and more in the field under real-life conditions. We'd get samples, bring them back to the lab, and apply our tools to their analysis. And this was giving us a much deeper understanding of the microorganisms involved in these processes and what types of conditions have the largest effect on their biological activity.

What we want to do ideally is figure out ways to stimulate the bacteria in the soil, for example, that are responsible for degrading whatever pollutant is present, without stimulating the other microorganisms present, and so without a need to provide a lot of additional nutrients to organisms using those nutrients for some other purpose. The goal was to make the bioremediation process more efficient and more cost effective, and one way to do that is to target only those organisms that are providing the useful function.

Are there always organisms in the soil that will degrade hydrocarbons and other pollutants?

There are almost always organisms in soil that have these functions. Bacteria that can degrade different compounds present in crude oil, for example, are pretty much ubiquitous. That's because crude oil is not a man-made product. It's a natural product. There are seepage points from the ocean continuously spewing hydrocarbons out. The oil sands in northern Alberta, Canada, for instance, are sand saturated with crude oil, and people mine this sand and extract the oil from it. These sands are often found along rivers and erosion then carries the hydrocarbons into the river.

There have always been bacteria and other organisms exposed to oil and some of them are obligate oil eaters. That's all they eat. They're a very specialized group of naturally occurring organisms.

Man-made compounds are a different story. PCBs are a good example. The reason they were used so widely was essentially because they're resistant to decomposition and breakdown. We wanted them to last for a long time. If you put PCBs in a transformer, it would be permanent. So as a result of this desire to make compounds that would not be subject to breakdown by light or oxygen or some chemical or biological means, we ended up with compounds that are extremely resistant to microbial breakdown.

For some of these man-made compounds, there are no organisms currently known that can break them down. Although, now that I think about it, PCBs may have been a poor example, because there are actually organisms that are now known to be able to do it.

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