Mutualistic dinoflagellates with big disparities in ribosomal DNA variation may confound estimates of symbiont diversity and ecology in the jellyfish Cotylorhiza tuberculata

The precise identification of mutualistic dinoflagellates is critical for understanding the physiology, ecology and evolution of their mutualisms with animals. Cotylorhiza tuberculata (Macri 1778) is a common scyphozoan endemic to the Mediterranean Sea and relies in part on endosymbiotic dinoflagellates (zooxanthellae) for survival and growth. To further study the diversity of symbionts associated with these animals, we analyzed specimens of C. tuberculata collected across the western Mediterranean Sea and from public aquaria, using a combination of next generation sequencing (NGS) of ITS2 rDNA and direct Sanger sequencing of partial 28 S rRNA and mitochondrial cob genes. Two diagnostic ITS2 profiles were characterized during our analysis of NGS data. Combined with information from additional genetic markers, each profile corresponds to a single species of symbiont, not diverse community assemblages as are sometimes inferred. Breviolum psygmophilum was common in all specimens, while Philozoon medusarum occurred at lower abundances in many individuals. The ribosomal array of B. psygmophilum was highly heterogeneous and contained ~ 15 co-occurring sequence variants found in the same relative proportions across all samples obtained in this study, while the ribosomal array in the genomes of P. medusarum was relatively homogeneous represented mostly by one abundant sequence variant. This precise interpretation of rDNA data improves understanding of the ecology and evolution of these mutualisms. Cotylorhiza tuberculata’s association with dinoflagellate symbionts from different genera is consistent with previous findings and suggests that evolutionary divergent symbionts with dissimilar niches are better able to coexist in hospite.