We previously reported the occurrence of genetically‐diverse symbiotic dinoflagellates (zooxanthellae) within and between 7 giant clam species (Tridacnidae) from the Philippines based on the algal isolates' allozyme and random amplified polymorphic DNA (RAPD) patterns. We also reported that these isolates all belong to clade A of the Symbiodinium phylogeny with identical 18S rDNA sequences. Here we extend the genetic characterization of Symbiodinium isolates from giant clams and propose that they are conspecific. We used the combined DNA sequences of the internal transcribed spacer (ITS)1, 5.8S rDNA, and ITS2 regions (rDNA‐ITS region) because the ITS1 and ITS2 regions evolve faster than 18S rDNA and have been shown to be useful in distinguishing strains of other dinoflagellates. DGGE of the most variable segment of the rDNA‐ITS region, ITS1, from clonal representatives of clades A, B, and C showed minimal intragenomic variation. The rDNA‐ITS region shows similar phylogenetic relationships between Symbiodinium isolates from symbiotic bivalves and some cnidarians as does 18S rDNA, and that there are not many different clade A species or strains among cultured zooxanthellae (CZ) from giant clams. The CZ from giant clams had virtually identical sequences, with only a single nucleotide difference in the ITS2 region separating two groups of isolates. These data suggest that there is one CZ species and perhaps two CZ strains, each CZ strain containing individuals that have diverse allozyme and RAPD genotypes. The CZ isolated from giant clams from different areas in the Philippines (21 isolates, 7 clam species), the Australian Great Barrier Reef (1 isolate, 1 clam species), Palau (8 isolates, 7 clam species), and Okinawa, Japan (1 isolate, 1 clam species) shared the same rDNA‐ITS sequences. Furthermore, analysis of fresh isolates from giant clams collected from these geographical areas shows that these bivalves also host indistinguishable clade C symbionts. These data demonstrate that conspecific Symbiodinium genotypes, particularly clade A symbionts, are distributed in giant clams throughout the Indo‐Pacific.

To understand the flexibility of symbiotic associations in coral reefs, we investigated the specificity of the Aiptasia (cf. insignis)-Symbiodinium association in the laboratory by rendering the anemones aposymbiotic and inoculating them with different isolates of SYMBIODINIUM: Infective algal symbionts were monitored over 3 months by re-isolation and identification using denaturing-gradient gel electrophoresis and sequence comparison of their amplified 18S rRNA hypervariable V1 + V2 gene region. Despite similarity in their external morphology, the algal isolates differed in their infectivity towards the host. Within days of single-isolate inoculation, aposymbiotic anemones formed associations with fresh or cultured isolates (clade B) from the anemones Aiptasia sp. or A. tagetes, respectively. They associated to a limited extent with cultured isolates (clade A) from the tridacnids Tridacna crocea or Hippopus hippopus, and not at all with a cultured isolate (clade C) from the stony coral Montipora verrucosa, nor with a free-living isolate (clade A) from subtidal sands. Aposymbiotic anemones inoculated with a mixture of all isolates had only the anemone taxon as their detectable symbionts. Re-inoculation of induced symbioses with a mixture of all isolates and incubation with wild anemones showed that the initial induced symbioses with the anemone taxon were stable. Anemones originally infected with tridacnid isolates either additionally acquired the anemone taxon or had the former outgrown by the latter. These results demonstrate the presence of a host-symbiont recognition mechanism, and possibly competition among potential algal symbionts in the Aiptasia-Symbiodinium association. Here we present a method that may be useful in monitoring the algal population dynamics in symbiotic corals in the field, along with an efficient method of rendering Aiptasia aposymbiotic for further laboratory investigation of Aiptasia-Symbiodinium symbioses.

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