Research Update - The Self-Healing Earth

Microarray

The ground beneath our feet is a complex thing. It holds many meanings and uses for different people. When your boots or clothes become soiled with it, it is just dirt; farmers and gardeners prefer to call it soil. Geologists rely on soil geochemistry when prospecting for precious metals and gemstones such as platinum and diamonds, assaying soil samples hoping to find telltale "indicator" minerals and elements known to be associated with these targets. 

Ask Dr. Charles Greer of the NRC Biotechnology Research Institute (NRC-BRI in Montréal) the same question and he's likely to describe the vast numbers of microorganisms that live in just a single gram of soil. Greer also looks to the soil with the same intent as a prospector (he sees value) but, in this case, he is looking to harness the unique capabilities of these microorganisms to actually break down and neutralize harmful pollutants introduced into the soil by humans and man-made processes.  "Ultimately, we are trying to make use of these organisms to naturally clean up contaminated sites," he notes, a process which is paying dividends in Greer's efforts to clean up a site in Canada's High Arctic region on Ellesmere Island (see sidebar).

Clean up site at Eureka, Ellesmere Island

For several years Greer's team has been working to clean up a contaminated site at Eureka, on Ellesmere Island. A spill of diesel fuel had jeopardized the water supply for the weather station. Following testing of the soil to look for naturally-occurring microorganisms that could be used to clean up the soil, a pilot study was set up and a program of tilling and fertilizing the soil began to ensure the growth of certain microorganisms known to be effective in treating this type of pollution. Several years later, ongoing testing with DNA microarray technology has shown increasing activity levels of these "good" bacteria in the soil. Other testing has shown reduced concentrations of diesel fuel in the affected area. Greer predicts that in several more years, the site will be completely rehabilitated, an accomplishment achieved completely through natural biological processes.

The potential impact of this work is enormous, considering the large number of sites in Canada with contaminated soil, which in urban areas are commonly known as brownfield sites. There are potentially thousands of brownfield sites across Canada and, with growing efforts to restrict development in existing urban areas, there will be even more pressure to bring these lands back into use.

Known formally as: "A Genomics-Based Approach to Enhancing Bioremediation through Microbial Identification and Community Profiling", Greer's ongoing research in this area rests on several key concepts.

The Approach

To begin, Greer acknowledges that, at the present time, scientists are missing information about the identity of these microorganisms.  "From a microbial point of view, we are only familiar with about one per cent of what is actually out there," he notes. 

Nevertheless, according to Greer, trying to identify all of these microorganisms would be an enormous undertaking, similar to taking apart an unthinkably large and complex engine in order to understand all of its individual parts and functions and then putting it back together again. Instead, the team is focused on what is understood about the observed effects of these microorganisms on their environment and their role in the ecosystem. He adds that, because nature involves a high level of redundancy (many organisms share a number of common traits), this information can go a very long way.

For example, that same gram of soil and, more importantly, the microorganisms contained within, play a key role in driving what are known as biogeochemical cycles, natural processes in which elements are broken down, transformed and recycled in a continuous and ongoing cycle. Basic research by the environmental biotechnology community has produced an understanding of which microorganisms are involved in these processes and are capable of breaking down pollutants, for example, turning organic petroleum hydrocarbons into a harmless inorganic mineral form. Greer offers another example of a gene that initiates the oxidation of components in diesel fuel, which essentially starts the process to "burn it up biologically."

Additional research has identified specific genes and gene signaling pathways involved in these breakdown processes. Signaling pathways are used by organisms to communicate messages and relay orders, often involving numerous other genes and proteins in the process of getting the work done. 

The Tools

Greer's team has built upon this research and has developed DNA microarray technology that will accelerate the speed and accuracy of "prospecting" the soils of contaminated sites for microbes that can, with help, clean up the soil. A microarray is a silicon chip imprinted with large amounts of specific genetic material as opposed to electronic circuitry. Microarray technology is widely used in the biotechnology community for conducting genetic testing, such as seeing what genes are "turned on" when exposed to certain conditions, or testing to see if there is a match between a sample and the genetic material found on the microarray. NRC-BRI is the first to use microarrays to analyze contaminated sites and study changes in these genes during the remediation process.

"We have developed specialized tools such as microarrays to study what is going on in complex environments, for example, to be able to pick out a gene and, more specifically, an enzyme that is responsible for an important function. For example, it could be involved in converting a pollutant into a useable compound or it may be involved in geochemical cycling processes," Greer notes. Using the tools designed by Greer's team, users can take a soil sample, extract all the DNA and using the microarrays, determine if any of these target genes are present. Armed with this information, users can design a useful and focused remediation program.

Greer's experiences on Ellesmere Island and at other contaminated site across Canada have also used strategies to actually change the balance of microorganism populations in soils to accelerate bioremediation. Sometimes this involves adding nutrients to increase the activity levels of these bacteria or, in other cases; it could entail introducing natural microorganisms with the desired properties into a site.  "What we are trying to do is manipulate the microorganisms in sites to work better, to work more efficiently, to work faster," he notes.

Work is continuing and, in the process, giving nature a helping hand to do its work.

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