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Dietary studies are critical for understanding foraging strategies and have important applications in conservation and habitat management. We applied a robust metabarcoding protocol to characterize the diet of the critically endangered freshwater fish Zingel asper and conducted modelling and simulation analyses to characterize and identify some of the drivers of individual trophic trait variation in this species. We found that intra-specific competition and ontogeny had minor effects on the trophic niche of Z. asper. Instead, our results suggest that the majority of trophic niche variation was driven by seasonal variation in ecological opportunity (in our case, the seasonal variation in the availability of preferred prey types). Overall, our results are in line with the optimal foraging theory and suggest that Z. asper is specialized on a few ephemeropteran prey species (Baetis fuscatus and Ecdyonurus) but adapts its foraging by becoming more opportunistic as its favoured prey seasonally decline. Despite the now widespread usage of metabarcoding, very few studies have attempted to study inter- and intra-populational individual trophic traits variation with metabarcoding data. This study illustrates how metabarcoding data obtained from feces can be combined with modelling and simulation approaches to test hypotheses in the conventional analytic framework of trophic analysis.

Pour guider les actions de gestion et de conservation d’une espèce menacée, il est indispensable d’acquérir des connaissances sur son écologie, et en particulier sur son régime et son comportement alimentaires. Dans le cadre du Plan national d’actions en faveur de l’apron du Rhône, des scientifiques d’Irstea et d'Aix-Marseille Université ont identifié certains paramètres clefs pour améliorer ou restaurer la capacité d’accueil du milieu sur le plan de la disponibilité des ressources trophiques. Ils ont pour cela mobilisé une approche très innovante qui associe d’une part le métabarcoding pour déterminer et quantifier le régime alimentaire de l’apron, et d’autre part un échantillonnage intensif des macroinvertébrés aquatiques benthiques de quatre rivières.

International audience

CorrespondAnce: Emmanuel Corse, E-mail: emmanuel.corse@ univ-provence.fr; André Gilles, E-mail: andre.gilles@univ-provence. fr; International audience; 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