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

  • Sherlyn Sher Qing Lim
  • Danwei Huang
  • Keryea Soong
  • Mei Lin NeoEmail author


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.


Community structure Coral reef High-throughput sequencing ITS2 Symbiodiniaceae Tridacna 



We thank members of the Reef Ecology Laboratory for their support and assistance, especially Sudhanshi Jain for help in the lab, as well as Lutfi Afiq-Rosli, Ywee Chieh Tay and Samuel Chan for advice on data analyses. Author M.L. Neo acknowledges National Research Foundation (NRF), Prime Minister’s Office, Singapore for supporting her research endeavours at the St John’s Island National Marine Laboratory. This work was supported by the L’Oréal-UNESCO For Women in Science National Fellowship (2015), a Research Award for the Dongsha Atoll Research Station (2016), a Visiting Scientist Award for the South-East Asia Network for Education and Training (2016), and NRF Singapore under its Marine Science R&D Programme (MSRDP-P03).

Compliance with ethical standards

Conflict of interest

All authors declare that they have no conflicts of interest.

Research involving human participant and/or animals

All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Department of Biological SciencesNational University of SingaporeSingaporeSingapore
  2. 2.Tropical Marine Science InstituteNational University of SingaporeSingaporeSingapore
  3. 3.Department of OceanographyNational Sun Yat-Sen UniversityKaohsiungTaiwan

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