Gene‐to‐Population Level Responses to Multiple Stressors on the Rocky Shore

ABSTRACT Coastal ecosystems are exposed to both global and local stressors operating across multiple scales. However, research rarely considers how their combined effects propagate over time and across levels of biological organisation. Here, we employ an in situ warming experiment across two rocky shore sites with contrasting sewage pollution to quantify independent and interactive effects of warming and nutrient pollution from genes to populations. Passively warmed and control settlement plates were deployed at polluted and non‐polluted sites and surveyed across a summer to quantify temporal dynamics in the responses of key intertidal taxa. Barnacles were further employed as a model for comparing responses across biological levels, including body size, stable isotope analysis and RNA sequencing. Pollution consistently increased invertebrate abundance and macroalgal cover, alongside transient positive effects on barnacle size, whereas warming reduced barnacle abundance and suppressed macroalgal cover late in the season. Warming and pollution interacted synergistically on barnacle abundance, with pollution remaining the dominant stressor. Microphytobenthos groups similarly showed distinct pollution‐driven increases with warming primarily modifying temporal trajectories; cyanobacteria showed both date‐specific and season‐wide synergistic interactions, against a backdrop of temporal variability across stressor treatments. Consistent with these patterns, pollution shifted barnacle δ 13 C and δ 15 N towards values indicative of greater assimilation of sewage‐derived material, while warming increased elemental C:N ratios, consistent with altered nutritional stress. Barnacle transcriptomic responses mirrored this dominance of pollution, broadly regulating gene expression linked to protein turnover, DNA repair and protein folding; combined warming and pollution further intensified proteostasis‐related changes and produced predominantly reversal and antagonistic interaction types. Our results show that sewage pollution can overwhelm and reshape warming effects over time and across biological levels, linking group‐level responses with parallel shifts in trophic biomarkers and gene regulation. Our scalable field approach provides a template for in situ marine multiple stressor experiments across wider spatiotemporal scales.