Abstract
Understanding how organisms respond to chemical stress requires disentangling genetically encoded (constitutive) adaptations from environmentally induced (plastic) responses. This challenge is particularly acute for polycyclic aromatic hydrocarbons (PAHs), widespread aquatic pollutants with well-documented toxicity, where mechanisms of tolerance, including host-microbiome interactions, are unexplored. We used Daphnia magna, a keystone freshwater species with clonal reproduction and dormant egg banks to test population-specific (constitutive) responses to phenanthrene (PHE), a common PAH. Populations resurrected from contrasting historical environments were exposed to sub-lethal PHE concentrations, and both host transcriptomes and gut microbiomes were profiled to assess induced responses. Transcriptomic analysis revealed distinct, population-specific responses in detoxification, stress signalling, and endocrine regulation. Unexpectedly, the semi-pristine (pollution-naïve) population showed higher tolerance, with robust induction of cytochrome P450 and hormonal pathways, while populations historically exposed to pollution exhibited chronic stress signatures and reduced plasticity. Gut microbiome profiling revealed PHE-induced functional shifts across populations, with the pollution-naïve population showing broader stress-associated responses and historically exposed populations to pollutants exhibiting more detoxification-focused microbiome profiles. Both host and microbial datasets consistently showed enrichment in pyruvate and carbon metabolism, indicating coordinated energy mobilisation and detoxification responses. Our results show that historical exposure to chemical stress and wider pollution does not necessarily confer enhanced physiological tolerance to PHE. Instead, hydrocarbon stress elicits coordinated, functionally linked responses across the host and its associated microbiome. By leveraging Daphnia's unique ecology and evolutionary history, we disentangle constitutive from plastic responses and show that microbiome functional reconfiguration under PHE exposure is coordinated with host responses, contributing to population-specific profiles.