Data from: Microbiota-mediated resistance: A co-evolved mechanism of pollution adaptation in Atlantic Killifish (Fundulus heteroclitus)

<strong>Data embargoed until publication of related article, or up to no more than 1 year from data upload</strong>

Evolutionary adaptations are typically examined through the lens of population genetics, although growing evidence suggests that co-evolved host-microbiome interactions can shape adaptive traits. Here, we investigated how such interactions contribute to evolved resistance to polycyclic aromatic hydrocarbons (PAHs) in Atlantic killifish (Fundulus heteroclitus) inhabiting a PAH-contaminated Republic (REP) site in the Elizabeth River, VA compared with a clean reference site, King’s Creek (KC). We previously showed that REP killifish harbor a distinct gut microbiome compared to KC, despite similar environmental microbial pools, suggesting host-driven selection. Recalcitrant aryl hydrocarbon receptor (AhR) signaling – a key xenobiotic metabolism pathway – is a hallmark of REP killifish PAH resistance. Therefore, we hypothesized that REP killifish harbor microbiota that promote AhR recalcitrance, contributing to their PAH resistance. We revealed REP gut inoculum contained elevated AhR activating metabolites. To test their effects on the AhR pathway and developmental resistance to PAHs, we generated germ-free (GF) embryos from both populations, cross-colonized them with KC or REP gut homogenates, and exposed them to benzo-a-pyrene (BaP), an AhR activating PAH. We then compared xenobiotic responses by measuring (i) cytochrome P4501A (CYP1A) induction, a canonical AhR target; (ii) transcriptome-wide changes, emphasizing AhR-related genes; and (iii) downstream physiological outcomes, including embryonic mitochondrial function and larval behavior. We found that REP microbiota induced CYP1A in KC, but not REP, embryos, confirming the presence of AhR agonists in REP microbiota, but revealing host-specific resistance to their effects. Notably, in the absence of microbiota or when colonized with KC microbiota, REP embryos increased AhR signaling upon BaP exposure, suggesting that absence of the native REP microbiota destabilized evolved resistance and heightened xenobiotic sensitivity. In the presence of BaP, the REP microbiota induced distinct transcriptional programs in REP embryos, particularly in mitochondrial and xenobiotic metabolism pathways. Functional assays confirmed REP microbiota conferred both mitochondrial resilience and behavioral tolerance to BaP in REP, but not KC, embryos. Together, these results indicate that REP killifish have co-evolved with their microbiota to achieve PAH resistance, potentially mediated through AhR signaling. This highlights microbial divergence as a partial driver, rather than a consequence, of rapid evolution to anthropogenic chemicals.