Revealing the diet of the lesser horseshoe bat (Rhinolophus hipposideros) via DNA metabarcoding

R. hipposideros has the most restricted range of any resident bat species in Ireland, with the next closest population occurring on the west coast of Britain resulting in the isolation of the Irish population from all other European populations. In Ireland, R. hipposideros is protected by Irish and European law (Wildlife Act 1976; EU Habitats Directive, Annex II). Understanding the diet of R. hipposideros is important for making informed conservation management decisions, and to understand the role it plays in the provision of ecosystem services. Traditional morphological approaches to dietary analysis of bat faeces can result in the over-representation of hard bodied versus soft bodied insects but DNA metabarcoding approaches employing next generation sequencing (NGS) facilitate the simultaneous and unambiguous identification of multiple taxa/species from a single DNA extract. In this study, we used DNA that was extracted from faecal samples collected at R. hipposideros roosts. The collected DNA samples had previously been species and sex-typed using real-time PCR and individuals identified via genotyping. Using an NGS approach to DNA metabarcoding, the dominant prey groups revealed in the diet were Diptera and Lepidoptera, with Hymenoptera, Coleoptera, Neuroptera and Trichoptera also identified. Female bats had a greater amount of Lepidoptera in their diet in comparison to males, suggesting sex-specific hunting strategies. Pest species such as mosquitoes (Culiseta spp., Culex pipiens) and midges (Culicoides punctatus) implicated in the spread of disease were detected, highlighting the role of R. hipposideros in the provision of ecosystem services relevant to human and animal health. The combination of these molecular techniques can be used to understand the individual and gender-specific prey preferences of R. hipposideros.