Metabolomics in the wild: research opportunities, challenges, and regulatory potential for effects-based environmental monitoring

Abstract

Field-based environmental metabolomics offers a powerful tool for examining how organisms respond to complex mixtures of chemical and environmental stressors. When coupled with traditional ecotoxicology, metabolomics can help reveal mechanistic pathways; however, laboratory-based tests cannot fully replicate the dynamic, multifactorial conditions of natural ecosystems. This review synthesises current advances, challenges, and opportunities in applying metabolomics to ecotoxicology under real-world field conditions. We highlight the growing use of wild-caught organisms, caged exposures, mesocosms, and laboratory studies using field-collected samples to detect sub-lethal metabolic disruptions associated with contaminants such as PFAS, metals, organic pollutants, and wastewater-derived mixtures of compounds. Key themes include the sensitivity of metabolomics to early physiological changes, integration with complementary chemical and ecological data, the challenges in distinguishing natural variability from contaminant effects, the importance of establishing baselines and dose–response relationships, and the need for improved QA/QC and metadata reporting. As the methodological and logistical challenges are overcome, metabolomic profiles from field-exposed organisms are increasingly demonstrating value for environmental risk monitoring and forecasting. Environmental metabolomics has been successfully used for environmental monitoring, supporting regulatory frameworks, and identifying mechanistically grounded biomarkers of exposure and effects. However, to realise its full potential, coordinated efforts among current and future metabolomics practitioners are still needed to advance the current Metabolomics Standards Initiative (MSI) guidance. The MSI should, ideally, be expanded to include common standardised workflows, strengthen bioinformatics infrastructure, expand case studies, and fully embed and integrate metabolomics within routine environmental assessment and decision-making processes, thereby transitioning these ‘academic’ approaches into practical regulatory tools.