Comparison of fish prey contribution in the diet of European hake by visual assessment of stomach contents and DNA metabarcoding

Increasing marine trophic web knowledge through DNA analyses of fish stomach contents: a step towards an Ecosystem Based Approach to fisheries research

“…It provided a comprehensive and detailed view of fish prey while successfully limiting the amplification and detection of predator DNA for all targeted species—the only exception was European sardine, from which a significant proportion of predator reads was obtained in real stomachs, although still lower than the proportion obtained in other studies not using BP and extracting the contents from the stomachs (Bessey et al, 2019; Piñol et al, 2014). Overall, the results obtained agree with previous knowledge: preference for arthropods by small pelagic fish (Bachiller et al, 2020; Bachiller & Irigoien, 2015) and dominance of fish DNA in the stomachs of European hake (Gül et al, 2023; Philips, 2012). We also identified overlap in the diet of pelagic species (Bachiller & Irigoien, 2015), and variation of prey composition in the stomachs of pelagic fish along the study area reflecting dietary plasticity and opportunistic feeding behaviour (Bachiller et al, 2020; Bogstad et al, 1995).…”

“…Fish feeding behaviour is known to change temporally and spatially (Gül et al, 2023; Jansen et al, 2019; Olaso et al, 2005), and these variations should be accounted for by multispecies and ecosystems models to optimise the application of EBFM approaches—especially in the current context of climate change and poleward migration of many planktonic and nektonic species (Richardson, 2008), which is expected to impact currently established trophic webs. Our results indicate that DNA metabarcoding is capable of reporting such spatial and temporal dietary changes in great detail.…”

“…In European marine regions, DNA metabarcoding has only been applied to assess the diet of few commercially relevant fish species: European hake ( Merluccius merluccius ) (Gül et al, 2023; Riccioni et al, 2018), polar cod ( Boreogadus saida ) (Maes et al, 2022), Atlantic bluefin tuna ( Thunnus thynnus ) (Günther et al, 2021), European sardine ( Sardina pilchardus ), European anchovy ( Engraulis encrasicolus ), Round sardinella ( Sardinella aurita ), and European sprat ( Sprattus sprattus ) (Albaina et al, 2016; Bachiller et al, 2020; Bachiller et al, 2021), from which only two studies have been conducted in ICES ecoregions (Albaina et al, 2016; Maes et al, 2022). Although DNA metabarcoding has great potential for providing large-scaled fish trophic data, its incorporation into data collection routinary programs is hampered by, among other reasons, the lack of standardised method.…”

Assessing the trophic ecology of Southern Ocean Myctophidae: the added value of DNA metabarcoding

“…Again, the DNA metabarcode sequencing approach showed a higher diversity and higher taxonomic resolution than morphological identification, though in this case some species were missed by the DNA metabarcode sequencing approach, likely due to primer mismatch. Similar results of broadly comparable diet with increasing taxonomic resolution have been observed in method comparisons with European hake and polar cod (Gül et al 2023, Maes et al 2023. Several of the studies published to date however do not include direct individual level comparisons (Gül et al 2023, Berry et al 2015, or only compare presence/absences (Maes et al 2023) leaving D r a f t 5 some additional uncertainty around the ways in which method choice affects the detection and quantification of different prey types.…”

Ectopleura crocea (Cnidaria: Hydrozoa) Identified as a Predator of Pelagic Fish Eggs through Cytochrome c Oxidase I Metabarcoding

“…Among the DNA-based methods, metabarcoding is applied for the sequencing and identification of bulk samples. Metabarcoding has been used to investigate species compositions in various fields such as fish eggs and larvae, zooplankton, and gut contents [14][15][16][17].…”