Diet analysis of Kittiwake and Shag using DNA metabarcoding of faeces

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 ofobtaining 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.