Many seabird species are in decline, both globally and nationally, largely attributed to anthropogenic changes in the environment. Understanding the drivers of these declines requires detailed knowledge of population demographics and diet. However, long-term, multi-colony studies of seabird diet remain scarce. This study aimed to evaluate the feasibility of using DNA metabarcoding to obtain colony-level diet data from seabird faeces collected opportunistically during the breeding season.

We collected 45 Black-legged Kittiwake Rissa tridactyla and 43 European Shag Gulosus aristotelis faecal samples from four locations on the west coast of Scotland (Colonsay, Canna, the Treshnish Isles and the Shiant Isles). Prey DNA was successfully extracted from 76 (86%) samples, providing diet data for a region with limited diet monitoring. Across species and locations, we identified 20 prey fish taxa and nine likely invertebrate prey taxa, indicating that a broad range of prey was consumed. Sample sizes from Canna and Colonsay were sufficient to detect evidence for differences in diet composition of Kittiwakes between locations, and between Kittiwakes and Shags on Canna.

DNA metabarcoding offers a non-invasive, practical, complimentary approach to conventional diet monitoring methods, reducing biases associated with visual identification of prey while enabling higher taxonomic resolution. Opportunistically collecting faeces also increases the capacity of obtaining spatially and temporally representative diet monitoring, even in logistically challenging locations. These findings demonstrate the use of faecal DNA metabarcoding for seabird diet monitoring and consequently its potential to inform effective management and conservation decisions.

The UK holds internationally important populations of seabird species, many of which are declining, with further losses predicted with future likely climate change scenarios (Davies et al. 2023). Understanding the drivers of these declines requires an understanding of population demographics among regions, as well as diet (Barrett et al. 2007; Karnovsky et al. 2012). Prey availability is a major factor driving seabird breeding success (Frederiksen et al. 2005), and the greatest impact of climate change on seabirds is likely indirect through temperature-mediated changes on prey populations (Renner et al. 2024; Johnston et al. 2025). However, despite the known links between food availability, diet, and seabird demography, long-term and multi-colony studies on seabird diet are rare. Much of our understanding of the links between diet, behaviour, and demographic rates comes from studies focussed on the northern North Sea (e.g. from long-term studies on the Isle of May based on five main study species; Newell et al. 2024). Therefore, it is of high priority to collect long-term diet information across broader ranges of geography and species to better understand the impacts of changes in the marine environment, particularly those associated with climate change. The development of any method that has the capacity to augment data collection will also create the opportunity for the setting up of long-term, multi-colony studies.

Conventional diet monitoring during the breeding season has largely involved visual observations of prey being delivered to chicks, collecting regurgitates opportunistically when handling individuals or collecting pellets from nest sites (Barrett et al. 2007). Although these methods have their advantages, being relatively non-invasive and allowing large sample sizes to be collected, they can also result in identification biases. Identifying prey species being delivered to chicks by observation can result in misidentification and the overlooking of small items, although this can be reduced through the use of photographs (Gaglio et al. 2017). Observations and photographs are only useful for prey-loading species, such as terns and auks. On the other hand, determining diet from pellets or regurgitates can over-represent prey items with indigestible hard parts and therefore under-represent soft food items (Barrett et al. 2007). All these methods require specialist knowledge and can require considerable time in the colony or laboratory identifying prey items.

An alternative technique that can reduce biases in prey items identified is the use of DNA metabarcoding to detect prey DNA in regurgitates or faeces (Barrett et al. 2007). This technique is increasingly being used to successfully study the diet of a range of seabirds; Macaroni Penguins Eudyptes chrysolophus (Deagle et al. 2007), Atlantic Puffins Fratercula arctica (Bowser et al. 2013; Fayet et al. 2021), and European Storm Petrels Hydrobates pelagicus (Carreiro et al. 2020). DNA metabarcoding can detect a broad range of prey items, including soft-bodied species that can be difficult to identify with conventional methods, and can identify prey items to a higher taxonomic resolution (Deagle et al. 2007; McInnes 2016; Ceia et al. 2022). It also provides a relatively non-invasive method to study seabird diet, especially if sampling faeces from the environment (de Leeuw et al. 2024; Good et al. 2024). Given the logistics involved in monitoring seabird diet through more conventional approaches, the potential of using DNA metabarcoding to analyse seabird faeces collected opportunistically from colonies may provide a more feasible way of obtaining diet information from a wider range of locations and species (de Leeuw et al. 2024; Good et al. 2024).

The main aim of this study was to determine the feasibility of using DNA metabarcoding to obtain colony-level diet data through opportunistically collecting seabird faeces during the breeding season from several locations on the west coast of Scotland: a region of the UK where the collection of diet data is currently limited. We focused on two seabird species: the Black-legged Kittiwake Rissa tridactyla (hereafter Kittiwake) and European Shag Gulosus aristotelis (hereafter Shag), both of which are, respectively, on the Red and Amber list of the UK Birds of Conservation Concern (Stanbury et al. 2024). We selected these two species due to their contrasting foraging strategies, with Kittiwakes being surface feeders and Shags benthic feeders, providing a wide array of prey species consumed. While the diets of both species have been studied at a limited number of UK sites using conventional methods, their diet has not yet been examined using DNA metabarcoding. Where sample sizes allowed, we carried out statistical comparisons of diet between species and locations. For one location, where conventional diet sampling methods were also used (regurgitates and pellets on Canna), we compared those results with those obtained by DNA metabarcoding of the faecal samples to evaluate the consistency between methods in identifying diet composition.

Thanks to Mark Constantine for funding this project, and to David Agombar for facilitating this process. Thanks to everyone who helped collect faecal samples in the field including members of Highland Ringing Group on Canna and members of the Treshnish Isles Auk Ringing Group and Shiants Seabird Research Group. Thanks also to Gemma Clucas for invaluable advice when planning this project and Ian Cleasby for help with the R scripts. Thanks to the editors and reviewers for providing constructive feedback that improved this manuscript.

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