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.

1. The objective of this study was to assess barcoding of environmental DNA (eDNA) as a method for monitoring invertebrate ecosystem service providers (IESP) in soil samples.2. We selected 26 IESP that occur in New Zealand kiwifruit or apple orchards and produced mitochondrial cytochrome c oxidase gene subunit I (COI) and/or 28S ribosomal DNA sequences for each. Specific barcode primers were designed for each IESP and tested along with generic barcoding COI primers for their ability to detect DNA from IESP that had been added to sterilised and unsterilised soil samples.3. While the specific primers accurately detected the IESP in more than 96% of the samples, the generic COI primers detected only 33% of the IESP added to the sterilised samples, and none in the unsterilised samples.4. In a field test, we compared metabarcoding with traditional invertebrate trapping methods to detect the IESP in ten kiwifruit and ten apple orchards. All IESP were 2 collected in traps in at least one orchard, however very few were identified by metabarcoding of soil eDNA. 5. While the specific primers can be used as a tool for monitoring IESP in soil samples, methodological improvements are needed before metabarcoding of soil eDNA can be used to monitor these taxa.

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 (the Rhone streber). We conducted modelling and simulation analyses to identify and characterize some of the drivers of individual trophic trait variation in this species. We found that population density 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. The total trophic niche width of Z. asper seasonally expanded to include a broader range of prey. Furthermore, null model simulations revealed that the increase of between-individual variation in autumn indicates that Z. asper become more opportunistic relative to summer and spring, rather than being associated with a seasonal specialization of individuals. Overall, our results suggest an adaptive variation of individual trophic traits in Z. asper: the species mainly consumes a few ephemeropteran taxa (Baetis fuscatus and Ecdyonurus) but seems to be capable of adapting its foraging strategy to maintain its body condition. This study illustrates how metabarcoding data obtained from faeces can be validated and combined with individual-based modelling and simulation approaches to explore inter-and intrapopulational individual trophic traits variation and to test hypotheses in the conventional analytic framework of trophic ecology.