Diversity of endosymbiotic Symbiodiniaceae in giant clams at Dongsha Atoll, northern South China Sea

Despite the importance of endosymbiotic dinoflagellates in the ecology of giant clams, the diversity and distribution of Symbiodiniaceae in different tridacnine species remain relatively poorly studied. Using a DNA metabarcoding approach based on the nuclear ribosomal ITS2 marker, this study examined the patterns of Symbiodiniaceae diversity and composition in two giant clam species, Tridacna maxima ( n = 32) and Tridacna noae ( n = 41) found at Dongsha Atoll, the largest atoll in the northern South China Sea. Both species of giant clams hosted Symbiodiniaceae from genera Symbiodinium (formerly Clade A), Cladocopium (formerly Clade C) and Durusdinium (formerly Clade D). Tridacna maxima harboured Cladocopium preferentially, followed by Symbiodinium and Durusdinium , while T . noae hosted Durusdinium most abundantly, followed by Symbiodinium and Cladocopium . Endosymbiont diversity also varied between host species— T. maxima contained 11 species while T . noae had 13 species. Among the endosymbionts, Cladocopium goreaui (ITS2 type C1) was most common in both host species. Further analyses revealed that endosymbiont species richness was influenced primarily by depth, size, and, to some extent, geographic locality of giant clams. Endosymbiont community structure was significantly different between host species and this variation was primarily driven by depth. Even though both tridacnine species share similar habitats on coral reefs, the contrasting diversity and composition of Symbiodiniaceae present in each species may underlie the host’s adaptability to micro- and macro-environmental changes. These results not only provide a baseline of the various endosymbionts occurring in giant clams on an isolated reef ecosystem, they provide useful information for predicting impacts on these host species that could arise due to climate-related environmental stressors.