Description:
<jats:title>Abstract</jats:title><jats:p>Microbes play a critical role in the development and health of marine invertebrates, though microbial dynamics across life stages and host generations remain poorly understood in most reef species, especially in the context of climate change. Here, we use a 4‐year multigenerational experiment to explore microbe–host interactions under the Intergovernmental Panel on Climate Change (IPCC)‐forecast climate scenarios in the rock‐boring tropical urchin <jats:italic>Echinometra</jats:italic> sp. <jats:italic>A</jats:italic>. Adult urchins (F<jats:sub>0</jats:sub>) were exposed for 18 months to increased temperature and <jats:italic>p</jats:italic>CO<jats:sub>2</jats:sub> levels predicted for years 2050 and 2100 under RCP 8.5, a period which encompassed spawning. After rearing F<jats:sub>1</jats:sub> offspring for a further 2 years, spawning was induced, and F<jats:sub>2</jats:sub> larvae were raised under current day and 2100 conditions. Cross‐generational climate effects were also explored in the microbiome of F<jats:sub>1</jats:sub> offspring through a transplant experiment. Using 16S rRNA gene sequence analysis, we determined that each life stage and generation was associated with a distinct microbiome, with higher microbial diversity observed in juveniles compared to larval stages. Although life‐stage specificity was conserved under climate conditions projected for 2050 and 2100, we observed changes in the urchin microbial community structure within life stages. Furthermore, we detected a climate‐mediated parental effect when juveniles were transplanted among climate treatments, with the parental climate treatment influencing the offspring microbiome. Our findings reveal a potential for cross‐generational impacts of climate change on the microbiome of a tropical invertebrate species.</jats:p>