Mammal eDNA Sampling!

Mammals are one of the most exciting taxa, but often most elusive groups of animals found in the UK. Many people do not often, or ever, get to see mammals for themselves. To try and monitor mammals in the UK our research group is taking a slightly alternative approach by looking for mammals in the water. By taking water samples we are hoping to extract DNA that has been left behind by mammals (which is defined as environmental DNA - eDNA) in our lab back at the university which we can later match to specific species.

To research and monitor mammals methods such as camera traps, visual surveys and other types of humane traps are generally used to gather information on their communities. The main disadvantage with camera traps is that they are time and cost consuming with a limited photographic range. Ideally eDNA will be able to tell us about an entire community from one bottle of water, including rare or elusive species which can be missed by camera traps. Whilst the process is still being defined, it is a very exciting new field.

With this in mind the McDevitt Lab research group has now been exploring the use of eDNA in detecting mammal species in the Scottish Highlands. In this study we are trying to detect water voles, Arvicola amphibius, a species that is under threat from the invasive american mink, Neovison vison, and habitat loss.

Each day we prepared all of our equipment and labelled our sample collection bottles before we set off into the field. On arrival at each site one person would take the water samples, 2 upstream from the camera, 1 at the camera and 2 downstream, whilst the other person would record the time, date, pH and temperature. We had to be careful to prevent any contamination from site to site, wearing new sterile gloves at each sampling point and before using any equipment. We also had to ensure we never came in contact with the water, only our gloved hand and bottle where allowed to to prevent contamination.

At the end of each day we would spend the next few hours filtering each bottle of water. To do this we would pour part of the bottled river water in to a 60ml syringe with a filter on the end and push the water through. A membrane in the filter collects all the DNA whilst letting the rest of the water pass through, the membrane is the only part we will need for our DNA extractions back in the lab. This was the most exhausting part of the trip as we realised that as there were only two of us collecting all of the samples and filtering it would take us a lot longer than the previous field trip in the summer. We powered through during the days getting as many samples as we could and then stayed up till late getting through all the filtering.

We stored our samples in a cool box in the fridge for preservation until we got back to the University where they were then frozen.

What's next?

After the Christmas break we were back in the eDNA lab to start the long process of DNA extractions. Although we managed to finish all the DNA extraction, by the time we were able to move on to the next step towards species identification the Covid-19 outbreak happened so all work has halted. As soon as it is safe to return to our labs and Scotland work will be continued on this project.

At the end of this study, alongside other eDNA mammal studies currently being conducted within this research group, we would like to validate eDNA as a reliable detection method for different mammal species. Specifically we want to target elusive and invasive species that may be missed by camera traps. We have two more sampling seasons to conduct so hold this space to see any updates from the field and lab from Holly Broadhurst.