Omics to Study and Manage Aquatic Environments: A Snapshot From the AquaEcOmics Meeting (Evian-les-Bains, 2025)

The AquaEcOmics meeting brought together 280 scientists applying omics tools to aquatic research in March 2025 (Evian-les-Bains, France). We synthesised here the main outcomes from the 167 presentations which were given. A similar number of presentations were about micro- and macroorganisms. While studies on macroorganisms mostly focused on stakeholder-driven research and methodology development, studies on microorganisms tended to focus on fundamental scientific questions. These questions mostly contributed to community ecology studies using metabarcoding; functional ecology studies using metagenomics, metatranscriptomics and metabolomics; and to a lesser degree population genomics studies using metabarcoding and RADseq, ddRADseq. Stakeholder-driven research presentations could be clustered in two groups: those using omics to replace existing standardised monitoring methods—also termed ‘retrofitting’—to meet regulatory frameworks (e.g., fish biomonitoring), and those investigating anthropogenic pressures by harnessing the full power of omics, for instance by sequencing the entire microbial diversity or by detecting resistance genes to antibiotics and metals in rivers. The carbon footprint and applicability of omics were also questioned, sparking animated debates among attendees. Finally, some presentations focused on methodological developments and encompassed sampling strategies and devices, issues related to reference libraries (completeness, curation), comparison of short reads versus long reads, and in situ detection and quantification of organisms (dPCR, models). The use of omics to study aquatic ecosystems is a fast-evolving field. Meeting attendees agreed to maintain the generated momentum to promote omics as tools to improve the monitoring and protection of our environment.