Obtaining quantitative information on fundamental aspects of ecology such as diet can be challenging for pelagic seabird species. DNA metabarcoding of faecal samples is a non-invasive method of dietary analysis, with potential to identify prey at high taxonomic resolution. We apply this method to understand the diet of the Manx Shearwater Puffinus puffinus, a highly pelagic species where little quantitative information on diet is available. Using DNA metabarcoding analysis on faecal samples for this species, we identified six species of fishes: European Sprat Sprattus sprattus, Blue Whiting Micromesistius poutassou, Atlantic Herring Clupea harengus, Northern Rockling Ciliata septentrionalis, sandeel Ammodytes sp and a species of Cottoidei (sculpins and allies). Of 153 dietary samples, only 19 produced sufficient DNA to identify prey species. We speculate that our low success rate may be the result of long foraging trips early in the breeding season, where excretion prior to sampling may reduce the amount of prey matter in faecal samples and prey DNA degradation during prolonged residence in the gastrointestinal tract may reduce the detectability of prey matter. We discuss improvements in sample collection for future dietary studies of this and other highly mobile species with similar traits.

Many seabird species face declines due to fish stocks being depleted via over-fishing, pollution, and climate change (Kowalczyk et al. 2014; Wanless et al. 2018). With recent reports suggesting almost half of UK seabird species have declined over the last 20 years (Burnell et al. 2023), it is becoming increasingly important to study diet—an often-overlooked but fundamental aspect of a species’ ecology. This is especially true of wide-ranging pelagic seabirds, where direct observation of at-sea foraging behaviour is challenging, and the identification of prey in regurgitated food brought to offspring is often difficult (Weimerskirch et al. 2005; Kane et al. 2020). As seabirds return to land to breed, they are more accessible as study organisms than most pelagic foragers. Changes in seabird foraging behaviour can therefore provide insights into the productivity of remote marine ecosystems (Thompson et al. 1998; Piatt et al. 2007; Grémillet & Boulinier 2009).

Innovations in biotelemetry have allowed the remote observation of foraging behaviour (Dean et al. 2015; Whitford & Klimley 2019; Bolton 2021); however, until recently, only traditional methods of understanding diet itself were available (Weiser & Powell 2011; Nielsen et al. 2018; Whitford & Klimley 2019). For species that carry whole prey to their offspring, some prey identification can occur through field observation (Baillie & Jones 2003). In cases where feeding occurs through regurgitation, this requires forcing regurgitation (Thompson 1987; Weiser & Powell 2011), a method that is both invasive and does not allow for clear identification of prey species (Nielsen et al. 2018). Stable isotope analysis is a less invasive method for investigating diet, but the results of which can only indicate the trophic position of prey, and approximate foraging locations (Navarro et al. 2007; Meier et al. 2017; Austin et al. 2019). Here we employ an alternative approach for sampling seabird prey, using DNA metabarcoding of faecal samples. This method has potential to provide both quantitative and qualitative information and can distinguish between morphologically similar prey types (Deagle et al. 2007, 2019). DNA metabarcoding has been applied to the faecal samples of multiple seabird species to understand diet and assess conservation risks (McInnes et al. 2017; Komura et al. 2018; Marcuk et al. 2024). For example, in Brown Boobies Sula leucogaster and Cape Verde Shearwaters Calonectris edwardsii, DNA metabarcoding was used to identify prey overlap with commercially targeted fish to assess bycatch risk (Carreiro et al. 2023). In Atlantic Puffins Fratercula arctica, DNA metabarcoding was applied to investigate how adult and chick diets differ and how foraging behaviour links to diet across colonies of differing productivity (Fayet et al. 2021; Kennerley et al. 2024).

Despite being a well-studied bird, very little is known about the diet of the Manx Shearwater Puffinus puffinus, an apex predator that is believed to specialise in the active subsurface pursuit of small fish and some cephalopods (Brooke 1990). Most of the global population of Manx Shearwaters breeds on islands around the UK, with foraging efforts centred in the Irish and Celtic seas, both of which are sites for significant offshore wind development in the next decade (Guilford et al. 2008; Crown Estate 2024). It is unclear how large-scale modifications to foraging areas may impact seabirds, and it is therefore important to understand and quantify any dietary specificities for this species (Masden et al. 2010; Warwick-Evans et al. 2018).

The last investigation of Manx Shearwater diet was conducted in the 1980s on a small number of samples, the results of which suggested pre-laying diet might be different to other breeding season stages (Thompson 1987). However, as diet was investigated through forced regurgitation, most fish could not be identified to a species level. Other dietary studies in seabirds suggest that prior to laying, females may require specific nutrients for egg synthesis (Boersma et al. 2004; Sorensen et al. 2009; Phillips et al. 2011). Here, we aim to provide novel dietary information; establishing the prey species present in the diet of Manx Shearwater and comparing diet between pre- and post-laying periods to understand how diet may vary with breeding stage. To understand how diet links to foraging sites, we additionally compared pre- and post-laying foraging areas using geolocator (GLS) devices. We also aimed to investigate sex differences in diet between males and females.

We would like to thank the Wildlife Trust of South and West Wales, in particular Leighton Newman and Ceris Aston. Also, we would like to thank Alice Skehel for her assistance in sample collection. We would like to additionally acknowledge the funders of this project, a Merton College D.Phil. studentship (KSD, TG), the Mary Griffiths award (TG), the Leverhulme Trust (LFR) and the Elizabeth Hannah Jenkinson Fund (KSD). We would also like to thank the Brettschneider Fund (KSD) for enabling the exchange between Oxford and Cornell University.

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