Eastern oyster larvae recruit a core bacterial microbiome distinct from hatchery water treatment systems

Eastern oyster (Crassostrea virginica) larvae can exhibit high mortality rates in hatcheries, and microbial colonization during early development is a potential contributing factor to larval health and survival. However, the sources and assembly mechanisms of larval-associated bacterial communities remain poorly understood, constraining our ability to develop evidence-based strategies for managing larval microbiomes to improve hatchery outcomes. We characterized bacterial community composition in 5-day post-fertilization C. virginica larvae and sampled water sources throughout the hatchery treatment system using 16S rRNA gene V3-V4 amplicon sequencing. Larval microbiomes were statistically distinct from all sampled water sources, exhibiting 1.9-fold lower Shannon diversity, and showed no relationship to water sampled from sequential treatment steps, which themselves did not differ in bacterial composition. We identified 39 core bacterial genera present in majority of larval samples, collectively representing 90% of larval sequences and dominated by Rhodobacteraceae/Paracoccaceae (39.5% abundance) and Alteromonadaceae/Marinomonadaceae (24.1%). Critically, 46.2% of core larval sequences belonged to genera highly abundant but rare in all water sources, indicating selective recruitment mechanisms beyond passive environmental acquisition. This core microbiome composition closely parallels that of sea cucumber early life stages, where the same bacterial families dominate across development, suggesting phylogenetically conserved associations beneficial to marine invertebrate larvae. Our findings indicate that hatchery water treatment has minimal impact on larval microbiome assembly compared to host-mediated selection. Understanding the functional dynamics of this core microbiome can enable targeted interventions to optimize larval health outcomes. Management strategies should focus on manipulating conditions to promote beneficial microbial functions and direct supplementation of larval-associated communities, rather than solely optimizing water treatment.