Watershed Metagenomics

In January 2012, the Program on Water Governance joined an interdisciplinary team of research scientists from across Canada including BCCDC Public Health Microbiology and Reference Laboratory, Simon Fraser University and McGill University. The objective of the project is to develop new tests to enhance our capacity to understand water quality in our watersheds. Using metagenomics the project aims to 1) develop microbiome profiles to assess and compare communities of microorganisms (the microbiome consisting of viruses, bacteria and protists) in different watersheds and 2) use these profiles to create novel tests to detect pollution and identify the specific source of the pollution.

Current drinking water testing collects samples from the tap, rather than at the source watershed, and testing for bacteria contaminants such as E. coli, often takes more than two days to complete. If a water supply has been contaminated, this processing time is simply too long as the water would already have reached people’s homes. Additionally, these tests do not always reflect contamination of water by non-bacterial pathogens such as parasites or viruses. By applying metagenomics, a much more robust method that can identify many pollutants at once, this research will improve current analysis methods by enabling faster testing at the watershed level. This simplified testing process will reduce days to hours, and provide profiles of all microbes present in a water sample rather than just E. coli bacteria. Furthermore, the test will characterize the “water profile” of a watershed, providing a picture of ecosystem health. Consequently, the new test is relevant for assessing both the safety of drinking water as well as the health of ecosystems.

As part of the GE3LS (Genomics and its Ethical, Environmental, Economic, Legal and Social Aspects) team, PoWG researchers are assessing stakeholder readiness for the uptake of these potential molecular water quality tests – identifying key challenges and opportunities for implementation. The research includes identifying, documenting and analyzing current microbial water quality risk assessment, management and communication practices in Canada (BC and Ontario). For further information visit the project website.

Watch the GLOBAL NEWS story here.

This work was supported by funding from Genome Canada, Genome BC, Simon Fraser University Community Trust Endowment Fund and in-kind funding from the Public Health Agency of Canada.


Study Findings: Metagenomics of the Watershed Microbiome

The Watershed Metagenomics approach is summarised in this infographic.

1. Ecological insights into watershed microbial communities

We looked at microbial community changes over hourly and monthly time scales in two of our polluted watersheds, gaining insight into the microbial changes at a level not previously examined. For example, few changes in the community were seen during the shorter sampling (i.e., hourly), with more changes occurring over different seasons. The timing of these shifts in the microbial communities will be important considerations for robust biomarker development.

2.  Identification of biomarkers of clean vs. affected water

Taxonomic and gene-group profiles were compared to identify biomarkers associated with clean vs. affected collection sites. We also looked at the correlations of gene families with specific environmental indicators of pollution. Several correlations were found between specific types of pollution (e.g., nitrogen-based or phosphate-based) and functional categories. In one of many complementary approaches, a gene-marker based taxonomic classification tool (MetaPhlAn) was used to identify bacterial species that were differentially abundant between the downstream and polluted samples versus the upstream samples in the agricultural watershed. PCR tests have been developed based on these targets (and others) and validated in the laboratory.

3. Microbial communities respond to changes in water chemistry indicative of contamination

Since we collected samples over a full year, we were able to characterize how microbial communities shifted within and between watersheds. The biggest differences were seen between sites that were affected or not affected by agricultural activity. Within these sites, there were large changes that corresponded with levels of rainfall. These changes were due to shifts in the communities’ compositions, as well as their complexity.

4. Viruses found in the water may be good indicators of land use

Virus communities found in freshwater ecosystems are complex and relatively unknown. They are often heavily influenced by the surrounding terrestrial and human environments and are therefore much more genetically diverse. Because of this close connection to the land, they are potentially good indicators of the effect that the land has on these freshwater environments. The virus communities in our samples were really complex and varied substantially from month to month, and we found quite a few viruses that have the potential to be good indicators of agricultural effects on local watersheds.


Project Publications

Dunn, G., Harris, L. and Bakker, K. (2015). Microbial risk governance: challenges and opportunities in freshwater management in Canada. Canadian Water Resources Journal. DOI:10.1080/07011784.2015.1043648.

Dunn, G., Bakker, K. and Harris, L. (2014). Drinking water quality guidelines across Canadian provinces and territories: jurisdictional variation in the context of decentralized water governance. International Journal of Environmental Research and Public Health 11(5), 4634-4651. DOI:10.3390/ijerph110504634

Dunn, G., Henrich, N., Holmes, B. and Harris, L. (2014). Microbial water quality communication: public and practitioner insights from British Columbia, Canada. Journal of Water and Health 12(3): 584-595.

Dunn, G., Harris, L. Cook, C. and Prystajecky, N. (2014).  A comparative analysis of current microbial water quality risk assessment and management practices in British Columbia and Ontario, Canada. Science of the Total Environment 468-469: 544-552.

Ngueng Feze I., Kirby E., Prystajecky N., Cook C., Knoppers B. M., Ozdenmir V., Dunn G., Isaac-Renton J., Joly Y (2014). The regulation of water quality assessment biotechnologies: Is Canada ready to surf the next wave? Journal of Environmental Law and Practice 201: 26:3.

Cook, C., Prystajecky, N., Ngueng Feze, I., Joly, Y., Dunn, G., Kirby, E., Özdemir, V. & Isaac-Renton, I. (2013). A comparative analysis of microbial drinking water quality testing in three Canadian provinces. Canadian Water Resources Journal 38(3): 185-195.