Novel real-time PCR species identification assays for British and Irish bats and their application to a non-invasive survey of bat roosts in Ireland

Abstract

Novel real-time PCR species identification assays for British and Irish bats and their application to a non-invasive survey of bat roosts in Ireland,

One Bat’s Waste is Another Man’s Treasure: A DNA Metabarcoding Approach for the Assessment of Biodiversity and Ecosystem Services Using Bat Faeces

“…1) under license from NPWS (licence number DER/BAT 2016-29). Each DNA extract was identified to species and sex using real-time PCR assays (Harrington 2018;Harrington et al 2019) and identified to individual level using a panel of seven microsatellite markers originally designed by Puechmaille et al (2005) and re-designed and optimised by Harrington (2018). Twenty-four R. hipposideros samples were used as part of this DNA metabarcoding work and evenly represented sex (n = 12 for male and female samples) and location (n = 4 samples from each of the six roosts with sex evenly represented at each roost).…”

“…Indirect monitoring of biodiversity via environmental sources or the diet of a predator, such as insectivorous bat species, can provide data regarding the composition and interactions of species within a community (de Sousa et al 2019), providing a more holistic approach to assessment. Bats are described as indicators of diversity and can be studied relatively easily across landscapes using well-established surveillance methods (Jones et al 2009;Park 2015;Russo and Jones 2015;Russo et al 2018;Harrington et al 2019). Bats are considered specialised hunters, with different species seeking areas of open, narrow and edge space habitats to hunt (Denzinger and Schnitzler 2013;Heim et al 2016).…”

“…A degree of functional flexibility was also evident within the trophic niche of R. euryale, as it consumed a wide range Lepidoptera which varied in their energy content throughout the season (Arrizabalaga-Escudero et al 2019). Browett et al (2021) optimised a dual primer approach for the DNA metabarcoding of bat diet using DNA previously extracted from non-invasively collected faeces, previously identified to species, sex and individual level using real-time PCR and microsatellite genotyping (Harrington 2018;Harrington et al 2019). This approach uses proven good quality and quantity DNA, and excludes low quality samples, and facilitates the inclusion of questions related to sex and individual level dietary preferences.…”

Primer biases in the molecular assessment of diet in multiple insectivorous mammals

“…Large sheets of plastic were laid on the ground within each roost and left for a period of one to two weeks. Droppings were collected and stored frozen at -20°C or DNA extracted within 24 hours using the Zymo Research Genomic DNA TM -Tissue MicroPrep kit following the protocol used for faecal DNA extraction in Harrington et al (2019). Each DNA extract was identified to species level using a species-specific real-time PCR assay (Harrington et al 2019) and identified to individual level using a panel of seven microsatellite markers originally designed by Puechmaille et al (2005) and redesigned and optimised to work efficiently with faecal DNA by Harrington (2018) via two multiplex PCRs.…”