Total biodiversity: using genomics to see how it all comes together


- Ottawa, Ontario

About an hour's drive east of Ottawa, federal researchers have carried out what they refer to as the "catastrophic removal of riparian zone habitats" in an experimental watershed in the South Nation River basin. It is a controlled, but realistic habitat disturbance researchers are using to show how new genomics technologies can deepen our understanding of the ways different agricultural and water management practices can impact on both ecosystem and human health.

Sharing resources

Researchers from 3 departments are involved in the project, co‑led by Dr. David Lapen of Agriculture and Agri‑Food Canada (AAFC), Environment and Climate Change Canada (ECCC) research scientist Dr. Donald Baird and veterinarian Dr. Nick Ogden from the Public Health Agency of Canada (PHAC). It is one of 16 separate, but interlocking research projects funded through the federal Genomics Research and Development Initiative (GRDI) that, together, make up the GRDI Ecobiomics Project—a 5‑year, collaborative effort involving 64 scientists from seven federal departments and agencies.

Public health

In the South Nation project, Dr. Ogden is demonstrating how metagenomics technologies acquired with the support of GRDI funding can enhance the PHAC's capacity to track zoonoses—infectious diseases that are passed from animals to humans, such as West Nile fever and Lyme disease.

"West Nile, for example, is spread by a small number of species of mosquito, so we are looking at how changes in habitat may affect their populations," explains Dr. Ogden, "Until recently, we would have to  identify the insects in a surveillance trap one at a time—and a lot of mosquitoes look very much alike.

"With this technology, we get the DNA of everything in the trap at once, telling us exactly which species are in there, as well as an approximation of the proportions of each species—looking at the results over time, we can see relatively quickly and inexpensively how environmental change can affect species of concern in a specific area."

The environment

Among other activities, researchers from ECCC involved in the project are looking at how changes in land use can affect the size and composition of the avian community, and taking blood samples from birds in the area and testing them for a variety of diseases—contributing to Dr. Ogden's part of the project.

"It's not just about how many birds may be carrying disease, but also the species," says Dr. Ogden. "Robins and sparrows, for example, are the most common reservoirs for the West Nile virus, and are the species that often move in when other species move out due to habitat change. Since more robins and sparrows is associated with higher risk for West Nile, this project is helping us understand how activities that impact avian biodiversity can also impact public health."

Food production

Metagenomics technologies are also giving the researchers the opportunity to see inside what has long been considered a "black box"—the microbial community that is crucial to the health and productivity of soil—and how different agricultural practices affect that community.

ECCC research scientist Dr. Greg Mitchell says the project is looking at other ways agricultural practices can affect productivity. "Metagenomic analysis of their droppings is giving us new insight into what different species of birds like to eat—some are important predators of insects that can damage crops," says Dr. Mitchell. "If their habitat is destroyed or damaged, producers lose that benefit. The same is true for beneficial insects—like the pollinating bees that play a role in the productivity of a range of food crops."

Understanding how it all works together

Dr. Baird—who also co‑leads the GRDI Ecobiomics Project as a whole—says the South Nation River project exemplifies the kind of collaboration that characterizes the entire undertaking.

"The Ecobiomics Project really is unique internationally," says Dr. Baird. "We have environmental scientists, botanists, zoologists, microbiologists and others all working together to build an understanding of the whole system. We're not just looking at insects or birds or microbes in the soil and water. We're looking at the total biodiversity—all the species that are there, and how they interact with one another—and how, for better or worse, human activities impact on that biodiversity and those interactions."

At AAFC, Dr. Lapen says the ultimate goal is to enhance predictive capability. "In other words, we're assembling the evidence that will allow us to say, 'if these kinds of practices are employed, these are the probable impacts,'" says Dr. Lapen. "It will add an entirely new dimension to everything we do from recommending agricultural best management practices to environmental assessments to how we remediate damaged areas."

Benefits to Canadians

At the Canadian Agri‑food Policy Institute (CAPI) in Ottawa, Dr. Tülay Yildirim says the research conducted through the Ecobiomics Project has the potential to deliver significant benefits to agriculture and the environment.

"We know the microbes in the soil play a key role in maintaining the health and productivity of the soil," says Dr. Yildirim, Director of Policy Research Partnerships at CAPI, "Producers are always interested in knowing what they can do to make their soil healthier, and increasing our understanding of the links between what we do above the soil and what is happening in the soil is valuable knowledge—as is understanding more about the role of the microbial community in sequestering carbon."

At South Nation Conservation—a regional conservation authority—Special Projects Team Lead Ronda Boutz says the GRDI project continues a rich history of working with the Federal Government on a variety of environmental and agricultural issues. "The recent Ecobiomics activities have been instrumental in helping us understand how natural capital and anthropogenic stressors affect aquatic and terrestrial biodiversity," says Ms. Boutz. "And importantly, what we can do to reduce negative impacts in our watershed."