Thompson Rivers University

Sifting through dirt’s DNA

December 9, 2020

Dr. Lauchlan Fraser, NSERC Industrial Chair in Ecosystem Reclamation

When it comes to biodiversity in soil, sometimes too much information is a bad thing.

Thompson Rivers University faculty members Drs. Lauchlan Fraser and Jonathan Van Hamme are leading novel research to enable more precise measurements of soil biodiversity which allows accurate environmental assessments at mine sites and leads to healthier, more productive soils overall.

Genomics reveal relic DNA

Genomic testing has provided countless scientific insights; however, using such sensitive tools means scientists are finding environmental DNA in soils from dead organisms that no longer contribute to soil health.

Supported by a $250,000, two-year grant from Genome BC through its Sector Innovation Program, the project will standardize how environmental DNA is measured in microbial soil communities, removing what is referred to as relic DNA, which can exaggerate microbial diversity.

Read: Genomics will support accurate environmental assessments at mine sites, Genome BC

Before genomic testing was available, researchers would cultivate the bacteria and fungi within the soil samples to determine soil health, but this method would often only identify a small fraction of the microbes in the soil. New testing allows researchers to find virtually all of the DNA from all of the microbes in the soil.

“A dead organism is not a functioning organism,” says Fraser. “We want to know how that soil is functioning here and now. We estimate that about 33 percent of the DNA is dead, or relic DNA, and it could be as high as 80 percent. If we are trying to attribute microbes to soil health, we might be wildly overestimating the function of that system,” explains the Natural Sciences and Engineering Research Council Industrial Research Chair in Ecosystem Reclamation.

Environmental assessment accuracy is essential

“This work will support one of our province’s most active economic sectors,” says Dr. Federica Di Palma, chief scientific officer and VP Sectors at Genome BC. “Genome BC’s investment will support better tools and guidelines for environmental assessment which will be validated by industry partners.”

Work on this project has already begun. The research team is working with two mining partners: Tech Highland Valley Copper and Copper Mountain Mine. Soil samples have been collected and the team is developing testing procedures in the lab to determine proof-of-concept protocols for removing relic DNA. This spring, additional samples will be collected to determine the effectiveness of those protocols.

“This will provide a better estimation of microbial diversity by increasing sensitivity and reliability,” says Fraser. “This tool will be incredibly useful for the mining industry, BC Ministry of Energy and Mines, BC Ministry of Environment, and Environment and Climate Change Canada.”

Environmental assessment is a critical step in evaluating the health of reclaimed mine sites and is vital to the local community, because it has direct implications for human and environmental health.

Canada has approximately 10,000 abandoned mines that never achieved regulatory compliance, largely a result of mining practices before mine closure regulation. This can directly translate into saving dollars by ensuring the return of environmental security deposits, which can run into many millions of dollars, after clearing the environmental assessment. In the past, lack of reclamation compliance means most bonds are never returned.


Dr. Lauchlan Fraser
Professor and NSERC Industrial Research Chair in Ecosystem Reclamation
Thompson Rivers University

Jennifer Boon
Communications Manager, Sectors
Genome BC
778-327-8374 |

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