Marine environmental epigenetics: mechanisms, stress responses and applications to biomonitoring

The increasing exposure of coastal ecosystems to pollution, eutrophication, ocean acidification, hypoxia and accelerating climate change has highlighted the need for molecular tools capable of detecting sublethal and early biological responses before ecological deterioration becomes evident. In this context, epigenetic mechanisms such as DNA methylation, histone modifications and non-coding RNA expression provide sensitive and mechanistically informative indicators of organismal responses to environmental stress. This manuscript synthesizes current knowledge on how these epigenetic pathways respond to key anthropogenic and climate-driven stressors across marine taxa, emphasizing their roles in mediating plasticity, acclimatization and potential adaptive trajectories. We review methodological advances in environmental epigenomics, including high-throughput DNA methylation and chromatin-mapping techniques, and discussed the challenges posed by non-model marine species, including the scarcity of reference genomes. We also evaluate the practical application of epigenetic biomarkers as part of marine biomonitoring frameworks, with particular attention to their potential integration into effect-based assessment tools within the European Union Water Framework Directive. By connecting mechanistic insights with applied management perspectives, this manuscript highlights how epigenetic markers can improve early-warning capabilities, guide conservation planning and enhance the predictive power of coastal ecosystem assessments in the face of rapid environmental change.