Microbiome of the Boring Giant Clam Provides Insights Into Holobiont Resilience Under Coral Reef Environmental Stress

Abstract

Giant clams are key denizens of coral reef ecosystems, forming holobionts through symbiotic relationships with algae of the family Symbiodiniaceae, as in reef-building corals. In this study, we performed a tissue-specific microbiome analysis of the boring giant clam, Tridacna crocea and evaluated the impact of dark-induced bleaching on its outer mantle bacterial community. Using 16S rRNA metabarcoding, Endozoicomonas was identified as the dominant bacterial genus in most tissues, particularly in gills, implying an important contribution to the giant clam holobiont. In contrast, in the outer mantle, where algal symbionts reside, the microbiome exhibited greater diversity, with a significant presence of carotenoid-producing bacteria such as Rubritalea (Rubritaleaceae) and Muricauda (Flavobacteriaceae). These bacteria may protect symbiotic algae from light and thermal stresses, potentially enhancing holobiont resilience in coral reef environments. Although dark-induced bleaching significantly reduced algal cell density, bacterial diversity remained largely unaffected, suggesting a robust bacterial association, independent of algal dynamics. This study highlights the potential ecological significance of Endozoicomonas and carotenoid-producing bacteria in sustaining giant clam holobiont health and provides insights into microbial mechanisms that support stress tolerance in coral reef organisms.