Advances in fisheries management in the Bay of Biscay thanks to a genetic method for prey identification

The challenge

European policies — including the Marine Strategy Framework Directive and the Common Fisheries Policy — promote fisheries management that ensures the sustainability of fish stocks while moving towards an ecosystem-based approach. To achieve this, it is essential to gain a more accurate understanding of trophic relationships in the marine environment: who eats whom, which prey species are preferred, and how these relationships vary across space and time.

Historically, this information has been obtained through visual analysis of stomach contents, a slow and labour-intensive process that requires extensive taxonomic expertise and becomes particularly challenging — or even impossible — when prey is highly digested. In the case of cetaceans, obtaining this information is even more difficult. This limits both the quality and quantity of data available to support more realistic management models.

The solution

To address this need, a multidisciplinary AZTI team — bringing together specialists in genetics, marine ecology and ecosystem modelling — developed and validated a genetic method for identifying prey from DNA found in fish stomach contents and cetacean faeces.

Initially applied to five commercially important species in the Bay of Biscay — anchovy, sardine, hake, horse mackerel and Atlantic mackerel — the method is designed to:

• Reduce sample processing time and improve analytical efficiency.
• Analyse hundreds of stomach samples simultaneously, generating a list of identified prey species for each sample.
• Maintain a high level of accuracy even when stomach contents are highly digested.
• Be easily adapted to other species, extending its potential application to different contexts and monitoring programmes.

The results

Validation of the method demonstrated clear advantages over the traditional approach:

• Broader prey identification than visual inspection, including rapidly digested organisms such as jellyfish, which can easily go undetected.
• Greater ability to detect temporal and spatial changes in the diets of the species analysed, providing a more detailed picture of ecosystem dynamics.
• More robust and scalable trophic data, essential for developing and applying sustainable ecosystem-based management models, in line with European policies and with a direct impact on the sustainability of marine resources and the fishing sector.