Sustainable development of the Canadian economy requires wise stewardship of our environment and natural resources; this is particularly true given the anticipated impacts of climate change. Biomonitoring seeks to describe and understand biological diversity at multiple ecological levels, both as a means to learn the typical mix of species that can be found in different habitats, and to establish “biological early-warning systems” that can tell us when environmental stresses are reaching a critical point. Canada is recognised as a world leader in biomonitoring, however, current practices have limitations. They are personnel-intensive, which limit the frequency and intensity of sampling, particularly in remote areas. Also, present biomonitoring methodologies focus on a very limited subset of all species that can be found at a given location.
Our project introduces ‘Biomonitoring 2.0′, a system based on cutting-edge DNA-sequencing technologies and state-of-the-art computational analysis, which will simultaneously reduce sample costs while dramatically increasing the knowledge gained from biological samples. The first test bed for this new system is Wood Buffalo National Park, a globally unique region spanning Alberta and the North West Territories that is under considerable threat from oil sands activities and other human impacts, in spite of its remoteness and protected status. Following testing, the protocol will be applied at other global locations. By integrating our new genomics tools and technologies into a well-established Canadian biomonitoring framework, the Canadian Aquatic Biomonitoring Network (CABIN), we will greatly increase our potential to manage our cherished national resources. The project team has been working closely with stakeholders including industry, government departments, First Nations and Metis, and environmental organizations. By developing a sophisticated, yet user-friendly Web-based portal, with client-based customized tools, we will be able to communicate much richer summaries of environmental health and impacts to society, through direct interactions with local stakeholders.
The Biomonitoring 2.0 project is divided into four, separate, but interdependent, spheres:
The first real-world, large-scale test bed for this new system is Wood Buffalo National Park, a globally unique region spanning Alberta and the Northwest Territories that is under considerable threat from oil sands activities and other human impacts. We are working with national and international collaborators to implement similar systems in other socio-economically important locations.
Sample sites have been chosen in two wetland complexes. The more northerly region is in the vicinity of Whooping Crane nesting sites. The more southerly region is in the Peace-Athabasca river delta. Within each region, eight sampling sites have been carefully chosen. At each site, samples will be collected across a 100m lateral wetland transect covering both aquatic and terrestrial habitats. These samples include soil cores, water samples, benthic samples, and terrestrial malaise trap samples. Biodiversity sample units will be collected in June and August of each year, beginning in August 2011 and ending in August 2013 (5 sampling periods). Historical trend information, GIS data, and local physico-chemical analysis is also being compiled for each sample site.
An example of a proposed “biological sampling unit” (BSU) comprised of 18 samples taken from soil (S), Malaise traps (M), water (W), and benthos (B).
The genomic sequencing sphere focuses on gathering sequence information through 454-pyrosequencing and Illumina MiSeq sequencing of various environmental samples. From our previous work in a Genome Canada Technology Development project we have established standard operating procedures for a sample-to-sequence workflow in all environmental samples targeted in this project. Typically, for each environmental sample we use a specific DNA extraction approach using multiple independently isolated vials of DNA that will be pooled prior to PCR amplification and sequencing. Each of these sequencing runs generate over a million DNA sequences from the organisms of the park. Multiple target gene regions have been chosen for each kingdom of life, from bacteria, to plants, to fungi, to invertebrates. New protocols are being developed to increase the efficiency of sequencing large mixtures of thousands of different organisms.
Bioinformatic techniques are necessary at every step, from raw sequence data through to the assessment of biodiversity and the development of models of ecosystem health. The bioinformatics sphere of the Biomonitoring 2.0 project builds on research already being carried out by project members The practical solutions developed rely heavily on recent advances from these projects. A key problem in the translation of DNA sequences to ecological knowledge is that of taxonomic sequence assignment, whereby barcode sequences must be correctly associated with their species of origin. This sphere includes refining current best-practice, homology-based approaches for assigning sequences to species, and validating their use (in terms of speed and accuracy) on relevant WBNP data sets.
Another aspect of the project is the integration of data from disparate sources, including taxonomic attribution, environmental data collected alongside the sequence samples, environmental data from external sources, and other geospatial data. Key data sources are then identified and pipelines developed to acquire and combine these data in specialized geospatial analysis software known as GenGIS. Within GenGIS, established statistical and visual methods are implemented to assess biodiversity and its relationship with key environmental factors such as location, concentration of chemicals, and time.
The Biomonitoring 2.0 web portal will be the main means of disseminating project data to interested stakeholders, including government agencies, academia, non-governmental organizations, community groups, and industries. Research will be conducted to assess the effectiveness of this data-integration. By facilitating greater biodiversity discovery in a faster time, DNA-based NGS approaches will revolutionise biomonitoring programmes. The conventional, binary system (i.e., present/absent, impacted/not impacted) will be replaced with more nuanced appraisals of the full spectrum of potential environmental impacts, based on the entire biota. Huge volumes of DNA-based information will allow the isolation of specific responses from underlying natural variability.
Sustainable development of the Canadian economy requires wise, responsible stewardship of our environment and natural resources: this is particularly true given the anticipated impacts of human activities from urbanization to agriculture to the mining and energy sectors. Biomonitoring provides an “early warning system” for environmental degradation by using the differential sensitivity of certain groups of organisms (a.k.a. bioindicators) to environmental stressors. Canada is recognised as a world leader in biomonitoring, however, conventional biomonitoring approaches are personnel-intensive as they involve sampling organisms and identifying them from their physical appearance. Given the difficulties in accurate identification of bioindicator organisms, such as the larvae of aquatic insects, biomonitoring is performed with a limited frequency and intensity and has become a major bottleneck in environmental assessment programs. Working in close collaboration with Environment Canada, we have developed Biomonitoring 2.0, which uses DNA sequence information for identifying all organisms in an environment. Our approach can circumvent the identification bottleneck through bulk sampling and directly identifying organisms from mixtures. We obtain species-specific DNA fragments (DNA barcodes) from any environmental sample (soil, water, sediment, air) using cutting-edge, high-throughput next generation sequencing technologies rapidly and cost-effectively. By targeting multiple habitats in an environmental setting, we can provide a comprehensive (all taxonomic groups from mammals to microbes) and high-resolution (species-level) view of environmental change (Figure 1). Hence, the Biomonitoring 2.0 approach can simultaneously lower biological sampling costs while dramatically increasing the knowledge gained from those samples.
Biomonitoring 2.0 in Practice
We have successfully tested Biomonitoring 2.0 in a number of proof-of-concept studies (References 1-3). Since 2011, we have been conducting the first large-scale pilot project for this approach at Wood Buffalo National Park (WBNP), a globally unique region spanning Alberta and the Northwest Territories that is under considerable influence from oil sands activities. This project gained first ranking in a national Genome Canada Large Scale Applied Genomics competition and involves seven research groups at five universities as well as researchers and officers of Environment Canada and Parks Canada. Our project has now been included in the recently announced Integrated Monitoring Plan for the Oil Sands. Hence, our sampling will dramatically increase beyond WBNP boundaries and into the oil sands region of Alberta. The information gained in this project will significantly aid the implementation of an objective, comprehensive, scientifically credible environmental assessment program for the oil sands industry.
Fig 1: High-throughput, next generation sequencing ecological heat maps were generated to differentiate biodiversity in specimens obtained from two sampling sites (blue and green bars) in Wood Buffalo National Park. The six different genetic markers were chosen so as to capture the greatest diversity of taxonomic groups from the various samples. Environmental samples typically include soil, water, benthos and terrestrial arthropods.
The Future of Biomonitoring 2.0
In addition to continuing our biomonitoring program in WBNP and the oil sands, we are embarking on a number of international collaborations to promote the dissemination and adoption of the methodologies that we have pioneered, and to link ongoing projects currently underway in Canada, the USA, the UK, France and Australia. Our expanding network includes academia, industry, government and NGOs. In this way, Biomonitoring 2.0 is poised to play a significant role in informing crucial decisions on management and conservation in Canada and the world.
1. Baird DJ & Hajibabaei M (2012) Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing. Mol Ecol 21(8):2039-2044.
2. Hajibabaei M, Shokralla S, Zhou X, Singer GA, & Baird DJ (2011) Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS One 6(4):e17497.
3. Hajibabaei, M, Spall, JL, Shokralla, S and van Konynenburg, S. (2012) Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol. BMC Ecology 12:28
For further information, please contact the Biomonitoring 2.0 Project Leader:
Dr. Mehrdad Hajibabaei (University of Guelph); firstname.lastname@example.org