Abstract
Recent advances in molecular phenotyping have driven the rapid growth of untargeted, multi-dimensional approaches such as epigenomics, transcriptomics, proteomics, and metabolomics. When applied to ecology, these high-throughput omics tools offer powerful new molecular trait descriptors for investigating biological and environmental processes. Using UHPLC-HRMS/MS, we analyzed metabolome variations in gut, liver, and muscle tissues of chubs and gudgeons collected in summer 2019 from French rivers affected by benthic cyanobacterial blooms. Tissue-specific metabolomic profiles were evident, with muscle metabolomes showing the most distinct species differentiation. The different tissue metabolomes of both fish species also varied by sampling location, indicating local environmental influences. Notably, fish from the Vienne site exhibited molecular signatures of metabolic stress, including elevated oxidized glutathione and bile acids, and decreased purines, amino acids, peptides, and lipids—potentially linked to anatoxin-a-producing cyanobacterial mats. These findings underscore the potential of environmental metabolomics as a sensitive tool for assessing ecological stress and support its integration into routine environmental bio-indicator programs.