My Experience in Forestry: The Microbial Ecology Lab

Megan Young, Adopt-A-Pond’s Wildlife Biologist, took part in an internship in Sault Ste Marie, Ontario, at the Great Lakes Forestry Centre for 12 weeks over the winter. She was working as a First Nations Intern with the Forest Ecosystem Research and Assessment Team within the Canadian Forestry Service/Natural Resources Canada. As she learned a lot about the soil and plant ecology side of the forest ecosystem, she’ll be sharing some aspects of what she’s learning on our blog! Check back for updates from her experience. 

Blog 2: The Microbial Ecology Lab

My second placement was in the Microbial Ecology Lab. There was a lot happening in the lab relating to the ecology and biodiversity of bacteria and fungi. 

When leaves fall in rivers, they are broken down by bacteria and fungi, releasing nutrients back into the ecosystem and acting as the base of the food web. To mimic this process, scientists put leaf packs in the rivers at their research sites for a number of weeks, giving fungal communities the chance to grow in the leaves. The leaves in the leaf packs are in a small mesh basket to prevent anything larger from degrading the leaves. When the leaves are removed, they are weighed to calculate the difference in leaf mass, and then are sampled to quantify ergosterol. 

Although genetic samples can be used to identify the biodiversity of species present, it can’t tell you the quantity or the biomass of each group. To estimate the quantity of fungal growth at a site, I quantified the amount of ergosterol in samples. Fungi have cell membranes, like plant and animal cells, that have sterols or lipids that control the properties of the membrane like the permeability. In animal cells, that sterol is cholesterol, but in fungi, it’s ergosterol. By measuring the amount of ergosterol in the sample, it gives scientists an idea of how much fungal biomass is in each sample.


The start of the ergosterol extraction process. The leaf litter samples have been soaked in a solution overnight, giving the solution a green colour from the leaves. At this point, the ergosterol should be extracted from the fungal cells and in the solution. The ergosterol will be filtered out of the solution by the white material in the bottom of the containers.

 To quantify the amount of ergosterol, there’s a chemical laboratory process to extract the ergosterol from the fungi cells, filter it out of a solution, and then transfer the ergosterol from the filter to a different solution. This solution is then put in a machine that reads the amount of ergosterol per sample. From there, a number of formulas are used to relate the amount of ergosterol per sample to the fungal biomass in the leaf litter. Since ergosterol plays a key role in regulating cell membrane properties, it makes sense that different fungi species will have  different amounts of ergosterol. Therefore, to estimate the fungal biomass, scientists use an average amount of ergosterol across many species. Although the process sounds simple, the preparation starts the night before and the process takes most of the day. Fortunately, I was able to do 12 samples at a time per day, but a more experienced scientist could probably do at least 24.

These videos show later stages in the ergosterol extraction/transfer process. The time lapse in the first video shows the ergosterol sample being transferred from the filter (not seen) to a solution in the tubes. The tubes are in a vacuum, which draws the fluid through the filter and pulls the ergosterol into the solution. The second video shows the final stage in the process. The ergosterol is in the yellow solution and a pipette is used to transfer it from the tube, through another filter to filter out large particles, and into a vial. The vial of solution is then put in the machine to quantify the amount of ergosterol per sample.

As someone with a background in wildlife ecology, I had never given much thought to the fungal biodiversity or biomass in an ecosystem. Similar to the soil properties, I knew it was an important factor but I didn’t know very much about it. For example, I always thought about fungi on trees or fallen logs, like those seen below, but never in rivers! It was so exciting to think about biodiversity and ecosystem processes from a different (much smaller) lens. I hope I can learn more about the relationship between fungi in different parts of the ecosystem.