Barcoding and Bio‐tracers: Methods in monitoring ecosystem change in Georgian Bay

Neil Rooney1, Kevin McCann2, Jeremy DeWaard3, Chelsea Moore1, Reilly O’Connor1 and Jamie Simpson2


The Great Lakes are a phenomenal set of highly complex, interconnected ecosystems that are a gift from the retreating glaciers of 14,000 years ago. In the millennia since, they have developed structurally baroque food webs that provide natural, economic, social and cultural services to the millions of people that reside within their catchment.

Catching and processing fish for sampling

As we all know, however, the past several decades have seen these systems confronted with local and global stressors that affect both their structure and functioning. In order to understand the effects of these stressors on the Great Lakes, we need to undertake two separate but related endeavors. First, we must document the state of the ecosystems as they stand. Second, we must develop time and cost effective ways to quantify the effect of human activities on ecosystem structure and function. Towards these ends, the University of Guelph Aquatic Ecology Research Group has been working with Georgian Bay Forever over the past 6 years to employ the latest in molecular barcoding tools to document the biodiversity of Georgian Bay and to develop novel biotracer assessment tools to quantify the effect of human activities on ecosystem structure and function in Georgian Bay.

Barcoding Life

Figure 1

The University of Guelph is home to the Centre for Biodiversity Genomics which is the world leader in DNA barcoding. This technology uses a fragment of an organism’s DNA to identify the taxonomic group to which it belongs. Under Dr. Paul Hebert, scientists here lead national and international work aimed at developing a complete catalogue of the Earth’s life forms.

Together, the University of Guelph and Georgian Bay Forever have helped grow the global DNA barcode library which will assist other groups in identifying taxonomic groups in their local freshwater ecosystems. Of more immediate importance, it has documented the abundance and distribution of over 175 taxonomic groups (a measure of biodiversity) in Georgian Bay.

As can be seen from Figure 1, we are adding new taxonomic groups to our list every year. These results show us that we are still in the early stages of identifying all members of this ecosystem and continued effort will identify additional taxonomic groups. This process of creating an inventory is essential for establishing a baseline for Georgian Bay, a baseline which we can refer to in the future as the ecosystem is challenged by environmental change. Additionally, this information will be used to develop an assessment methodology for evaluating ecosystem health. We look forward to continuing this important work in the years to come.

Bio-tracers: Towards developing a method of rapid assessment of ecosystem health

Monitoring changes in ecosystem health can be slow and expensive. Developing a method to assess or monitor ecosystem changes quickly and inexpensively would be an exceptionally useful tool. The use of bio-tracers such as stable isotopes and fatty acids are showing promise as indicators of changes in the ecosystem, particularly those associated with human activities.

Figure 3

In earlier work, our research group has shown that these tools can be useful for quantifying the effect of increased lake temperatures and nutrient loading on food web structure and sustainability. More recently, we have brought these tools to Georgian Bay to examine the influence of fish farms on local wild fish populations. Our research program uses biochemical tracers to quantify the extent of aquaculture waste (feed and faeces) derived subsidies to wild fish and, importantly, link these metrics to individual and population based measurements of wild fish health (reproductive capacity, metabolic stress, foraging behaviour and food web structure). While the research program is just beginning, we do have some interesting preliminary findings. When we set out to look for effects of fish farming on wild fish, we selected sites that were close to the aquaculture operations and sites that were 10km away to serve as control sites. Interestingly, lake trout samples from sites both near and ‘control’ sites showed signals of fish farm feed for both stable isotopes and fatty acids (Figure 2). These preliminary results suggest that lake trout may be travelling further than we initially predicted (i.e. our control sites are not really control sites as lake trout caught there may be travelling among fish farms). We are awaiting results from sulfur isotope analysis which will provide a good test for this hypothesis, as fish feed is significantly higher in the stable sulfur isotope compared to the local flora and fauna. We are also in the process of analyzing other fish species right now that will give us additional insights into effects at the fish community level.

Future Work

The University of Guelph Aquatic Ecology Research Group is committed to continued research on both documenting biodiversity and quantifying the effects of human activities on the health of the Georgian Bay ecosystem. With respect to the aquaculture research, we will work with Georgian Bay Forever as well as the Ontario Aquaculture Association and Wikwemikong First Nation and to further develop and refine our biotracer tools. We also envision this research incorporating telemetry work on fish populations with our research partners at GLATOS ( which would rigorously test the hypothesis that lake trout are travelling great distances to obtain resources from fish farms.

Regarding the genetic work that we have carried out in Georgian Bay, we think that it is essential to carry on this work in the coming years. We would like to engage GBF moving forward to explore opportunities to build the inventory of biological diversity within the Bay.

We would like to thank GBF for continued support throughout the years and we look forward to future work together.

Dr. Neil Rooney

1. School of Environmental Sciences, University of Guelph.
2. Department of Integrative Biology, University of Guelph
3. Centre for Biodiversity Genomics, University of Guelph