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DNA sequencing changes the way we study ecosystem health

Canada is a country of unparalleled natural resources and unique wildlife: First Nations peoples and later arrivals were drawn here by the promise of fish, furs, forests and precious metals. In 2012 we are a still a country that is heavily dependent on resource revenues, but technological advances that allow resource exploitation on a massive scale also have the potential to do catastrophic and irreversible damage to the environment. Prevention and protection are essential components of environmental preservation, but another important component is monitoring, which allows us to track changes in the environment over time. Biomonitoring involves the collection of living organisms from a habitat of concern, based on the idea that some species are sensitive to environmental conditions and can serve as early indicators of change.

"Traditional" biomonitoring has been carried out for many decades across Canada and around the world. In this process, samples of water, soil and airborne insects are collected from the wild and brought back to the lab for identification. This identification process is labour-intensive and time consuming, because each specimen from a sample must be examined under the microscope to identify the key features that distinguish, say, caddisfly A from caddisfly B. Identification is laborious, error-prone and can be imprecise; furthermore, these protocols can only be applied to species that can be manipulated and distinguished under a light microscope. Larval forms, seeds, and bacteria cannot be typed at all using these techniques. Bacteria are particularly important in the bigger picture, because they can be extremely sensitive indicators of changes in habitat conditions, and because they are the primary producers that support everything else in the ecosystem, both directly and indirectly.

The DNA sequencing revolution that gave us a complete map of the human genome has now made its way into the environment: "metagenomic" projects aim to describe habitats from the human gut to soil in terms of the microbes that live there, and the key tasks they perform. A project recently funded by Genome Canada, with strong support from Parks Canada, Environment Canada and other stakeholders, aims to bring these techniques into the wild where they can revolutionize biomonitoring. Instead of laborious identification of a subset of the organisms in a particular habitat, the sequencing of DNA "marker genes" can quickly determine the presence and relative abundance of bacteria, other single-celled organisms, plants, animals and fungi. This "Biomonitoring 2.0" (Bio2.0 for short) approach will revolutionize the way we keep track of ecosystem health and will ultimately allow us to monitor more sites more often. Most importantly, the rapid turnaround time will allow for quick recognition and response for emerging threats to important habitats.

The Bio2.0 team includes scientists from the Canadian government who are collecting samples from out pilot project site in Wood Buffalo National Park, molecular biologists to isolate and sequence DNA, and bioinformatics researchers including Rob Beiko from FCS who are tasked with making sense of a huge pool of DNA. Important computational challenges including determining which DNA sequence came from which organism, finding new ways to quantify the biodiversity at our different sample locations, and using GIS applications developed in the Beiko lab to relate biodiversity back to geographic and habitat information. After a small study at two locations in 2010, we have expanded our work to cover sixteen locations in Wood Buffalo, including eight locations in Alberta near the Athabasca Oil Sands, and eight sensitive whooping crane nesting sites. Sequencing of a wide range of samples from these sites is now underway, and soon we will be able to present our first full snapshot of biodiversity in Canada's largest protected area. In the longer term, the samples we collect in the coming years will constitute a DNA-based early warning system for Canada's most important natural habitats.