# From Sequences to Food Webs: DNA Metabarcoding Reshapes Fish Trophic Ecology

## TL;DR

DNA metabarcoding is transforming how scientists study what fish eat, offering detailed insights into aquatic food webs and ecosystem responses to environmental changes.

## Contribution

This review highlights how DNA metabarcoding improves understanding of fish diets, food web complexity, and ecological impacts of invasive species.

## Key findings

- DNA metabarcoding enables high-resolution identification of prey in fish diets, even when traditional methods fail.
- The method enhances understanding of trophic interactions, species coexistence, and food web organization.
- Challenges remain in quantification accuracy and reference database completeness, but multi-marker approaches offer promise.

## Abstract

Aquatic ecosystems rely on complex feeding relationships to function properly, and fish are an important part of these relationships. Knowing what fish eat helps reveal how ecosystems respond to pollution, climate change, and biological invasions. In recent years, DNA-based methods have changed how scientists study fish diets by identifying food remains from genetic traces, even when prey cannot be seen or identified by eye. This review summarizes the use of DNA metabarcoding in fish feeding ecology and the improvements it brings to diet analysis in complex aquatic environments. We highlight how these approaches have improved understanding of feeding strategies, species coexistence, food web organization, and the ecological impacts of invasive fish. We also discuss current challenges and future directions for making DNA-based dietary studies more reliable and ecologically meaningful. Overall, DNA metabarcoding represents a promising tool for improving dietary information that supports ecosystem protection, fisheries management, and responses to environmental change.

Fish occupy pivotal trophic positions in aquatic ecosystems, mediating energy transfer and shaping community structure through their feeding interactions. Unraveling these dietary relationships is therefore fundamental for understanding ecosystem functioning and supporting sustainable fisheries management. Traditional morphological analyses, while informative, often fall short in resolving fine-scale prey diversity and trophic linkages. In contrast, DNA metabarcoding has revolutionized dietary studies by enabling comprehensive, high-resolution, and non-invasive characterization of prey assemblages. This review synthesizes recent progress in applying DNA metabarcoding to fish trophic ecology, emphasizing technical innovations, methodological standardization, and ecological insights. We discuss how DNA metabarcoding has advanced the understanding of food web complexity, species interactions, and ecological responses to environmental change. However, challenges persist in quantification accuracy, reference database completeness, and cross-source contamination. Future research integrating multi-marker approaches, standardized workflows, and multi-method integration holds promise for transforming DNA metabarcoding into a powerful, reliable and mechanistic tool for trophic ecology. Collectively, these developments will bridge molecular data with ecological theory, strengthening the scientific foundation for ecosystem-based fisheries management.