Microbial communities experienced during early development shape the host immune system and epigenome.

Shaping of the epigenomic landscape by local environments during early life stages could initiate adaptive developmental plasticity, allowing organisms to optimize their phenotypes for local conditions. Elevated seawater temperature can increase bacterial loads and pathogen spread, making it imperative to understand how physiological and molecular traits of marine organisms are impacted, especially the immune system. Experimentally manipulated temperatures and microbial environments during embryogenesis resulted in changes in larval morphology, immune cell development, and the epigenome of the purple sea urchin (Strongylocentrotus purpuratus). Development amid high microbial richness led to increased chromatin accessibility, predominantly in promoter regions, whereas elevated temperature altered very few chromatin regions but was associated with more differentially expressed genes. Larvae raised in high microbial richness also exhibited delayed immune system development. Overall, we show that early developmental environments strongly influence whole-organism and molecular phenotypes, with early exposure to microbes altering the host immune system and epigenome.