Gaining ecological insight on dietary allocation among horseshoe bats through molecular primer combination

Abstract

Knowledge on the trophic interactions among predators and their prey is important in order to understand ecology and behaviour of animals. Traditionally studies on the diet composition of insectivorous bats have been based on the morphological identification of prey remains, but the accuracy of the results has been hampered due to methodological limitations. Lately, the DNA metabarcoding and High Throughput Sequencing (HTS) techniques have changed the scene since they allows prey identification to the species level, ultimately giving more precision to the results. Nevertheless, the use of one single primer set to amplify faecal DNA produces biases in the assessed dietary composition. Three horseshoe bats overlap extensively in their distribution range in Europe: Rhinolophus euryale , R . hipposideros and R . ferrumequinum . In order to achieve the deepest insight on their prey list we combined two different primers. Results showed that the used primers were complementary at the order and species levels, only 22 out of 135 prey species being amplified by both. The most frequent prey of R . hipposideros belonged to Diptera and Lepidoptera, to Lepidoptera in R . euryale , and Lepidoptera, Diptera and Coleoptera in R . ferrumequinum . The three bats show significant resource partitioning, since their trophic niche overlap is not higher than 34%. Our results confirm the importance of combining complementary primers to describe the diet of generalist insectivorous bats with amplicon metabarcoding techniques. Overall, each primer set showed a subset of the prey composition, with a small portion of the total prey being identified by both of them. Therefore, each primer presented a different picture of the niche overlap among the three horseshoe bats due to their taxonomic affinity.

DNA metabarcoding and spatial modelling link diet diversification with distribution homogeneity in European bats

“…5) that is known to affect the Zeale primers 20,21 . Our results complement the existing broad-scale molecular dietary data of Miniopterus schreibersii 17 , and provide geographically widespread molecular insights into the dietary ecology of Myotis daubentonii, Myotis myotis, Myotis emarginatus, Myotis capaccinii, Rhinolophus euryale and Rhinolophus ferrumequinum, which to our knowledge had only been studied at local scales previously 16,[22][23][24][25] .…”

eDNA metabarcoding reveals a core and secondary diets of the greater horseshoe bat with strong spatio‐temporal plasticity

“…Using eDNA metabarcoding, we have shown that R. ferrumequinum diet is much more diversified than previously described by microscopic (Flanders & Jones, 2009; Jones, 1990) and molecular analyses (Alberdi et al., 2020; Aldasoro et al., 2019; Galan et al., 2018). We revealed a broader ecological and taxonomic variety of prey from the order to species levels of taxonomic resolution (519 species; 76% of the taxa affiliated at the species level).…”

“…Because it is important to minimize disturbance and stress for bats, the number of samples is critical to assess prey diversity when using eDNA metabarcoding. Future bat diet studies should rather rely on a large number of guano collected beneath colonies rather than on feces collected from captured bats (usually < 30 samples; Alberdi et al., 2020; Aldasoro et al., 2019; Bohmann et al., 2018; Galan et al., 2018; Vallejo et al., 2019).…”

Body Size Variation in Italian Lesser Horseshoe Bats Rhinolophus hipposideros over 147 Years: Exploring the Effects of Climate Change, Urbanization and Geography

“…The lack of temporal trends in body size also rejects alternative interpretations, such as, for instance, the possible occurrence of any response to changes in land use, and consequently, productivity, according to the “resource rule” pattern [ 18 ]. Rhinolophus hipposideros mostly prey on dipterans and moths, which in many cases have declined due to land use change [ 40 ], so factors such as agricultural intensification, urban expansion and forest reduction and fragmentation have likely contributed to a reduction in food availability for this bat [ 41 ]. As a pest suppressor [ 42 ], R. hipposideros is also exposed to the direct and indirect effects of pesticides [ 43 ].…”