Using DNA as a tool to assess biodiversity
Student Spotlight - Thomas Curran
PhD Research at Waterford Institute of Technology (WIT)
Email: thomascurran303@gmail.com Twitter: @ThomasCurran01
I am a 3rd year Ph.D. student in Waterford Institute of Technology (WIT), in the southeast of Ireland where I work as a member of the Molecular Ecology Research Group. My project, supervised in WIT by Drs Denise O’Meara, David O’Neill and Catherine O’Reilly, primarily involves the development of DNA methods to aid the detection and surveillance of mosquitoes in Ireland. The direct surveillance of mosquitoes involves the collection of adult and larvae mosquitoes and their subsequent identification using keys and DNA based methods. I was also interested to see if I could develop an approach to indirectly detect mosquito DNA from the diet of insect consumers, such as bats. This took me on a journey to the University of Salford, Manchester to collaborate with Drs Allan McDevitt and Samuel Browett, where we used the exciting technique of DNA metabarcoding to reveal the diet of one of Europe’s most highly protected bat species, the lesser horseshoe bat (Rhinolophus hipposideros).
Background
The lesser horseshoe bat is one of 9 resident bat species in Ireland and is threatened due to a small population size and only occurs in some areas of the west of Ireland. This restricted range has resulted in its isolation from all other European populations, with the next closest population occurring in Wales.
Favourable habitats for the lesser horseshoe bat include hilly terrain with extensive areas of scrub and broadleaf trees with well-connected hedgerows, mountain valleys, limestone karst terrain and farmland. The lesser horseshoe bat is protected under European law (European Habitat’s Directive, Annex II & IV) and Irish law (Irish Wildlife Act 1976 (as amended)). Despite this high level of protection, the conservation status of this species is deteriorating due to a continual decrease in population range and an increase in population fragmentation.
All Irish bats are insectivorous, meaning that they predate on insects, including those bothersome to human and animal health and agriculture, such as mosquitoes and midges, thus providing an ecosystem service. Insect diversity is in decline throughout the world, and so studying the diet of bats is a useful way to not only monitor the ecosystem services that they provide, but to use it as an indirect tool to monitor insect diversity over space and time.
The aim of my work is to examine the diet of this species to provide insights into the ecosystem services provided by the lesser horseshoe bat and to explore the diversity of insects consumed by the species. The outputs from this work can be used to provide information relevant to habitat improvement and management of the species with a view to improving its overall conservation status.
What is DNA metabarcoding?
This is a molecular technique that can be used to identify multiple species/taxa from a single sample. To better explain this technique, I use shopping for chocolate as an analogy. On each chocolate bar there is a barcode and when this is scanned at the checkout, it assigns the barcode to a specific chocolate bar. This is a similar concept to DNA barcoding, i.e. single species identification using DNA. If we take a multipack of chocolate bars to the checkout, the barcode of that is scanned and it can detect all the bars that are in that multipack, i.e. multiple species identification. In the case of DNA metabarcoding here, we “scanned” DNA from bat faecal pellets and identified all the insects that were present in the dropping, just like a multipack!
What did we do?
Bat droppings were collected from known roosts within the lesser horseshoe bat's distribution range. The DNA was extracted, identified to species and sex-typed using real-time PCR and subsequently identified to individual level via genotyping by Dr Andrew Harrington for his Ph.D., which was earlier completed in my research group. A selection of these DNA samples was then taken forward for DNA metabarcoding at the University of Salford.
What did we find?
We used primers that target part of the mitochondrial DNA and were able to identify potential biases that occur when using this technique on multiple insectivorous mammal species including bats and shrews. Some of these biases include preferential amplification of certain orders over others and so we found that it can be useful to include multiple primers. We recently published this work in the journal of Mammalian Biology: https://doi.org/10.1007/s42991-021-00115-4.
Using this technique, pest insects within the diet of the lesser horseshoe bat were detected. Some of these pests were found to negatively impact agricultural activities elsewhere in Europe, while some are potentially linked to the transmission of disease to both humans and animals, such as mosquitoes and midges, highlighting several ecosystem services that the lesser horseshoe bat is providing to the environment and society. We also found an enormous variety of Lepidoptera and Diptera species, and some interesting detections within other orders, such as Araneae, Coleoptera, Hemiptera, Hymenoptera, Neuroptera, and Trichoptera. We anticipate using this data to help inform and direct future DNA barcoding studies for biodiversity assessment and to provide information to help inform policy for the conservation management of the lesser horseshoe bat. We hope to publish these findings soon!
Funding Acknowledgments
Thomas’s PhD is supported by a Waterford Institute of Technology and Environmental Protection Agency (EPA) cofund PhD Scholarship, funded under the EPA Research Programme 2014–2020. The EPA Research Programme is a Government of Ireland initiative funded by the Department of the Environment, Climate and Communications. It is administered by the EPA, which has the statutory function of co-ordinating and promoting environmental research. The laboratory work was financially supported by Bat Conservation Ireland and a University of Salford Internal Research Award.