A PCR‐based method for diet analysis in freshwater organisms using 18S rDNA barcoding on faeces

Abstract

The development of DNA barcoding from faeces represents a promising method for animal diet analysis. However, current studies mainly rely on prior knowledge of prey diversity for a specific predator rather than on a range of its potential prey species. Considering that the feeding behaviour of teleosts may evolve with their environment, it could prove difficult to establish an exhaustive listing of their prey. In this article, we extend the DNA barcoding approach to diet analysis to allow the inclusion of a wide taxonomic range of potential prey items. Thirty-four ecological clade-specific primer sets were designed to cover a large proportion of prey species found in European river ecosystems. Selected primers sets were tested on isolated animal, algal or plant tissues and thereafter on fish faeces using nested PCR to increase DNA detection sensitivity. The PCR products were sequenced and analysed to confirm the identity of the taxa and to validate the method. The methodology developed here was applied to a diet analysis of three freshwater cyprinid species that are assumed to have similar feeding behaviour [Chondrostoma toxostoma toxostoma (Vallot 1837), Chondrostoma nasus nasus (Linnaeus, 1758) and Barbus barbus, (Linneaus 1758)]. These three species were sampled in four different hydrographic basins. Principal Component Analysis based on prey proportions identified distinct perilithon grazer and benthophagous behaviours. Furthermore, our results were consistent with the available literature on feeding behaviour in these fish. The simplicity of the PCR-based method and its potential generalization to other freshwater organisms may open new perspectives in food web ecology.

Angling baits and invasive crayfish as important trophic subsidies for a large cyprinid fish

“…Classical dietary studies have reported that B. barbus is omnivorous, eating benthic invertebrates (Cherghou et al 2002;Piria et al 2005;Corse et al 2010) and small fish (Kottelat and Freyhof 2007), with algae also present in their diet (Cherghou et al 2002;Piria et al 2005). Our stable isotope data revealed a different story with little evidence that benthic macro-invertebrates (excluding P. leniusculus) were as important to diet when compared to fishmeal pellets and P. leniusculus.…”

The use of DNA barcodes in food web construction—terrestrial and aquatic ecologists unite!

“…Diet studies of these types have been applied extensively to marine taxa ranging from higher trophic levels (e.g., Deagle et al 2005;Dunn et al 2010;Méheust et al 2015) through marine birds (e.g., Deagle et al 2007;Bowser et al 2013) and fish (e.g., Moran et al 2016) to different invertebrates and lower trophic levels (e.g., Jarman et al 2002;Nejstgaard et al 2003;Blankenship and Yayanos 2005;Leal et al 2014b;Olsen et al 2014;Hu et al 2015;reviewed in Calado and Leal 2015). DNA-based approaches have also yielded breakthrough dietary analyses in complex freshwater systems (e.g., Corse et al 2010;Carreon-Martinez et al 2011;Bartley et al 2015). Most of the studies to date attest to the effectiveness of DNA-based analysis, especially when combined with morphological analysis (e.g., Casper et al 2007;Braley et al 2010;Alonso et al 2014), and they offer new insights in trophic ecology.…”

Unrevealing Parasitic Trophic Interactions—A Molecular Approach for Fluid-Feeding Fishes

“…In most animal groups, the cytochrome oxidase subunit 1 (COI) is the reference for the DNA barcoding system (Hebert et al, 2003). COI sequences libraries are available through on-line systems (such as GenBank, Bold), enabling its use in the identifications of host or prey species (Valentini et al, 2009;Corse et al, 2010;Leray et al, 2013a;Jo et al, 2014). DNA barcode techniques have been used to determine host-parasitoids webs in arthropods (Hrček and Godfray, 2014), as in Lepidoptera (Janzen et al, 2009) and Hemiptera (Gordon and Weirauch, 2015).…”