Monitoring Mammals with a Drop of Water
Student Spotlight - Holly Broadhurst
PhD Research at University of Salford
Email: h.a.broadhurst@edu.salford.ac.uk Twitter: @BroadhurstHolly Instagram: @PinkHaired_Scientist Lab website: https://sites.google.com/view/mcdevittlab/home
I have just entered the 2nd year of my PhD at the University of Salford, in collaboration with NatureScot as an iCASE partnership. My research focuses on the use of environmental DNA (eDNA) for detecting and monitoring terrestrial and semi-aquatic mammals throughout the UK.
Research background
Environmental DNA applications have transformed the field of Molecular Ecology and how we detect species within freshwater habitats. The use of eDNA provides an alternative non-invasive method for monitoring mammals as it utilises traces of DNA that can be collected through an environmental sample (e.g., water or soil), so doesn't require sighting or capturing the animal(s) in question. The coupling of eDNA surveys with next-generation sequencing of DNA has the potential to detect, and thus provide data on the distribution of, several elusive mammal species simultaneously. To test the efficiency of eDNA surveys it is vital to compare the results to other traditional mammal monitoring methods such as camera traps and field signs.
Over summer 2020, I was lucky enough to visit Assynt, North West Scotland, to carry out my first fieldwork season. I joined a wonderful team from the University of Aberdeen who has been monitoring the water vole (Arvicola amphibius) metapopulation for 20 years! I am contributing to this large dataset with the addition of comparing long-term eDNA sampling with camera trap data for detecting water voles as well as the whole mammalian community. (Click here to read Victoria Curley's student blog on water vole predation by weasels at this site).
Fieldwork in Assynt
Fieldwork is where the magic starts and it is a huge component of my PhD. Mainly it involves the collection and filtration of eDNA water samples that contain complex biological information of many species. Assynt’s picturesque scenery is one of the biggest perks of fieldwork, but unfortunately, you spend the majority of the time looking at your feet, so you don’t fall into a bog. Half of the team had been in Assynt for two weeks longer than me, and after 3 months of lockdown, I had not established my ‘Assynt legs’ quite yet. Hopping from tussock to tussock with the dreaded fear I will lose my footing and kneel over in the boggy marsh that acts as a moat in between the compact mounds, eventually, I decided to plod through the bog than hop on the wobbly tussocks like steppingstones.
After trekking over Assynt’s boggy landscape looking for camera traps that are placed along rivers and streams that are known water vole patches, I find where to collect my eDNA samples. Whilst sitting on the edge of the waterbody on a beautiful summer’s day, we get our required equipment ready. Gloves first, syringe, filter, and the big guns. Lucky for us, the majority of Assynt’s water bodies are clear and easy to filter, but when it‘s murky you get the extra workout of trying to push debris through the filter and on a wind-free day you are accompanied by swarms of midges.
Collecting and filtering the water sample is simple, the most difficult aspect is avoiding contamination of the samples. Contamination can be a huge risk when working with eDNA, especially when you are targeting rare species of conservation concern or invasive/non-native species. Cross-contamination between sampling sites can have a detrimental effect by showing false positives. This is when a species is detected at a site where it is in fact absent. Therefore, being vigilant throughout the sampling period is essential for reliable and accurate eDNA samples. Contamination doesn’t just happen in the field; it can occur at any stage of the process from field to the laboratory.
What’s next in my research?
Most of my time at the moment is spent in Cockcroft laboratory at the University of Salford where I am processing my eDNA samples. I am using a genetic technique called eDNA metabarcoding that can identify multiple mammal species from an environmental sample. My next field work season will be focusing on collecting eDNA data with the goal to answer questions relating to the origin, fate and persistence of mammalian eDNA in flowing water systems as well as other exciting research questions.
Acknowledgements
A massive thanks to Victoria Curley for volunteering to help me collect and filter eDNA samples in Assynt and Ellen Bielenski, Laura Mackenzie and George Porton for making my field fieldwork season a highlight of 2020. A huge thanks to my research group at the University of Salford for supporting me through my lockdown-PhD and keeping me sane throughout.