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

• Published in: Environmental microbiology Vol. 27; no. 8; pp. e70161 - n/a
• Main Authors: Uchida, Taiga, Li, Yanxiu, Yamashita, Hiroshi, Shimada, Go, Shinzato, Chuya
• Format: Journal Article
• Language: English
• Published: Hoboken, USA John Wiley & Sons, Inc 01.08.2025; Wiley Subscription Services, Inc
• Subjects: Algae; Animals; Anthozoa - microbiology; Bacteria; Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; Bacteria - metabolism; Bivalvia - microbiology; Bivalvia - physiology; Bleaching; carotenoid; Carotenoids; Cell density; coral reef; Coral reef ecosystems; Coral Reefs; Corals; Endozoicomonas; Environmental stress; giant clam; Gills; Mantle; microbiome; Microbiomes; Microbiota; Microorganisms; Phylogeny; Resilience; RNA, Ribosomal, 16S - genetics; rRNA 16S; Stress, Physiological; Symbionts; Symbiosis; Thermal stress; Tridacna; Upper mantle; giant clam; Endozoicomonas; symbiosis; Tridacna; carotenoid; coral reef; microbiome
• ISSN: 1462-2912; 1462-2920; 1462-2920
• DOI: 10.1111/1462-2920.70161

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. The microbiome of the boring giant clam, Tridacna crocea, varies among tissues, with Endozoicomonas dominating most tissues and putative carotenoid‐producing bacteria (Rubritalea, Muricauda) enriched in the outer mantle. Using dark‐induced bleaching, we examined the impact of symbiont loss on bacterial communities and found that the overall bacterial diversity of the outer mantle remained stable, even after the loss of symbiotic algae. These findings highlight the potential role of Endozoicomonas and carotenoid‐producing bacteria in maintaining holobiont resilience under coral reef environmental stress.