Coastal urbanisation negatively affects marine ecosystems through habitat degradation and pollution. Cory’s (Calonectris borealis) and Scopoli’s (C. diomedea) shearwaters are closely related species inhabiting the Northeast Atlantic Ocean and the Mediterranean Sea, respectively. This study assesses the fatty acid profile, with the trophic and foraging ecology, of Cory’s and Scopoli’s shearwaters breeding at Berlenga (Atlantic Ocean) and Chafarinas (Mediterranean Sea) Islands. The diet quality of Scopoli’s shearwaters is expected to be generally lower, characterised by reduced levels of ω-3 fatty acids. Additionally, higher concentrations of specific fatty acid trophic markers are anticipated, reflecting the Mediterranean's semi-enclosed environment, low productivity, and pollution challenges. These markers include oleic acid, vaccenic acid, trans fatty acids (indicative of urban and industrial discharges), and odd-chain fatty acids (indicative of bacterial presence). This study supported these predictions, with Scopoli’s shearwaters foraging in the Mediterranean having higher concentrations of oleic and vaccenic acids, odd-chain fatty acids, and trans-palmitoleic acid in their plasma. Yet, concentrations of ω-3 were also higher in Scopoli’s shearwaters. This may result from diverse prey availability and selection, and different habitat exploitation, partially supported by differences in the trophic ecology and foraging patterns of both species; or from an enhanced immunological basal response of Scopoli’s shearwaters to cope with higher anthropogenic pressure in the western Mediterranean Sea. Further studies including specific diet and contaminant analyses are crucial to understand differences in fatty acid profiles of seabirds inhabiting both oceanic basins and the implications of diet quality for seabird populations.
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