Applying cutting-edge tech to birds and bugs in prairie pothole wetlands

A vial containing aquatic invertebrates sampled from a prairie pothole.

From a birds-eye-view, the prairies of Canada are dotted with glittering pools of water. These small to medium-sized shallow ponds – known as prairie potholes – are scattered across 700,000 km² of North America and were created by the melting of ancient glaciers. While these shallow waterbodies may not seem like ideal vacation destinations, prairie potholes are essential habitat for migrating waterfowl, of which millions use these wetlands each spring for nesting and rearing their young.

North American waterfowl populations are declining, and one proposed driver is increased pesticide runoff from crops, which may harm aquatic invertebrates living in the potholes. These invertebrates—such as beetles, fairy shrimp and fly larvae—are particularly important to waterfowl during nesting and brood-rearing, when their energy demands are highest. However, to understand whether pesticides and other agrichemical materials have impacted this critical food source, researchers first need better data on what invertebrate species are present in wetlands being used by waterfowl, and how these invertebrate communities change with wetland size, hydroperiod (how long a wetland holds water) and surrounding land use.

“There have been very few large-scale invertebrate sampling projects related to waterfowl productivity to date,” says Matt Dyson, researcher and field lead at the Institute for Wetland and Waterfowl Research at Ducks Unlimited Canada (DUC). “This is primarily because it takes a lot of work to sample invertebrates and subsequently identify them.”

To fill this gap, research teams from DUC, the Alberta Biodiversity Monitoring Institute (ABMI) and InnoTech Alberta (ITA) have teamed up to better understand the relationships between aquatic invertebrates and waterfowl communities under intensifying agriculture. The project, with funding from Alberta Innovates among other sources, combines both conventional and cutting-edge technologies for aquatic invertebrate and waterfowl identification to develop more time and cost-effective approaches for large-scale wetland monitoring.

Dried and sorted invertebrate samples. The small spheres in the tubes are grinding beads that help in the blending process.

DUC field researchers begin by collecting aquatic invertebrate samples from prairie potholes across Alberta, which are then sent to the ABMI's Freshwater Invertebrate Lab for identification. Here, experienced taxonomists carefully sort and identify thousands of individual invertebrates. While this method can provide precise identification and count estimates for intact specimens, it requires a high level of expertise and a fair amount of time and patience. Damaged specimens can be difficult or even impossible to identify. To make matters more challenging, most identification guides are designed for invertebrates at their latest life stage, meaning that the identities of young individuals often remains a mystery.

Along with this conventional approach, the research team implements two genomic identification tools: bulk tissue sequencing and environmental DNA (eDNA). To conduct bulk tissue sequencing, the ABMI taxonomic team provides the dried invertebrate samples from each wetland sample to the molecular biologists at ITA. While these specimens have already been identified and weighed by ABMI staff, this information is withheld from the ITA biologists to ensure they remain unbiased when making their own identification. Once received, the ITA team grinds each sample into a ‘bug milkshake’. The DNA from the resulting mush is analyzed and compared to reference databases to match the sampled DNA to corresponding species through a process known as metabarcoding.

The second genomics tool involves taking water samples from the potholes for eDNA analysis, which identifies species based on trace DNA fragments. The presence of genetic material floating in the water can indicate what species were recently present in the waterbody. The concentration of genetic material may also give a rough idea of how abundant different species are. These data allow researchers to estimate how much invertebrate prey may be available to waterfowl on the landscape.

Each molecular method provides a unique advantage. Bulk samples produce higher-quality DNA than the eDNA, while the eDNA is much faster to collect. When used together alongside conventional identification, the team can produce a comprehensive set of data.

“With ABMI’s team of taxonomic specialists, ITA’s team of molecular biologists and DUC’s expertise in waterfowl field research, this collaboration offers a unique opportunity to directly compare conventional and molecular approaches to studying freshwater invertebrates,” says Tyler Cobb, director of the ABMI's Processing Centre and adjunct professor at the University of Alberta. “Combining the methods in a single analysis offers a more comprehensive and scalable picture of waterfowl prey.”

A ‘bug milkshake’ (left) represents what’s left of specimens after grinding to enable DNA extraction. A vial (right) contains an extracted DNA sample.

In addition to sampling invertebrates, DUC has been using new technologies to count and identify waterfowl. Drones equipped with infrared and high zoom powered cameras not only allow the team to identify adult ducks during the nesting period, but also their well-hidden ducklings during the brood rearing period.

“The ducklings shine brightly on the infrared camera because they don’t have well developed feathers yet to help them thermoregulate," says Dyson, who likens the images of the ducklings to “little fireballs.”

The first two years of the project focused on sites in Alberta, with a further expansion within the province and into Manitoba and Saskatchewan planned for this summer. The team hopes their findings on the abundance, diversity and distribution of waterfowl and their prey will help inform habitat conservation programs across the prairies. In addition, their work is helping to develop a suite of tools which could make wetland management and biomonitoring more robust and cost-effective.

“An important goal of the project is improving the generalizability of the findings across the prairie pothole region. Hopefully, some of the methods we’re developing here can be used elsewhere,” says Cobb.

This article is part of Making Waves, an annual Alberta Innovates publication highlighting water solutions we support. You can read more stories from this issue below.