Development of clade-specific Symbiodinium primers for quantitative PCR (qPCR) and their application to detecting clade D symbionts in Caribbean corals
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We developed quantitative PCR (qPCR) assays to distinguish each of the four clades (A–D) of dinoflagellate endosymbionts (genus Symbiodinium) commonly found in Caribbean corals. We applied these primer sets, which target portions of the multi-copy ribosomal DNA (rDNA) gene family, to assess the presence/absence of symbionts in clade D (as indicated by the detection of clade D DNA). We detected these symbionts in five of six Caribbean host species/genera (21% of samples analyzed, N = 10 of 47 colonies), from which clade D had rarely or never been observed. This suggests that Symbiodinium in clade D are present in a higher diversity of coral species than previously thought. This qPCR-based approach can improve our understanding of the total microbial diversity associated with corals, particularly in hosts thought to be relatively specific, and has many other potential applications for studies of coral reef ecology and conservation.
This work was conducted in the Bahamas under CITES permit #252, in the Florida Keys (USA) under National Marine Sanctuary permits FKNMS-2001-030 and FKNMS-2002-073, and Florida Fish and Wildlife Conservation Commission permit 01S-620 (all to A.C.B.), and in Panama under permit DNAPVS #3-95 (to the Smithsonian Tropical Research Institution). Collections in Bermuda were made under permits 020203 and 020701 (to C.J. Starger) and in the Dominican Republic under a permit from the Subsecretaria de Areas Protegidas y Biodiversidad (to R. Torres). We are grateful to S. R. Santos, M. A. Coffroth, R. A. Kinzie, and M. Hidaka for providing us with cultured Symbiodinium material. We thank M. A. Coffroth, P. W. Glynn, D. M. Poland, and three anonymous reviewers, whose comments improved previous versions of this manuscript. A.M.S.C. is supported by a Columbia University Graduate Fellowship, M.D.M. is supported by the National Science Foundation (IOS-0455904) and A.C.B. is supported by the National Science Foundation (OCE-0099301 and 0527184), the Pew Charitable Trusts, and the Wildlife Conservation Society.
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