LAUSR

Reef-building corals are nutritionally dependent on the symbiotic alga Symbiodinium and may therefore select for high-performing symbiont lineages. However, the effects of fine-scale genetic variation within symbiont populations on host performance are not well understood. Applying quantitative PCR (qPCR) to Pocillopora damicornis colonies from Lord Howe Island (Australia), we estimated the relative abundance of intra-genomically variable (IGV) Symbiodinium cells and those with homogeneous rDNA sequence repeats. We then analysed their physical status and photosynthetic performance at both ambient and extreme summer temperatures (25 and 29 °C, respectively) in a closed-system oxygen flux chamber. The proportion of IGV Symbiodinium was negatively correlated with photosynthetic production and efficiency, and under thermal stress, colonies dominated by IGV cells could only meet respiratory demands at high irradiance (> 250 µmol photons m−2 s−1). IGV Symbiodinium were also estimated to be 50% larger by volume, occurred at lower density, and had higher chlorophyll c2/a ratios. The comparatively poor performance of heterogeneous Symbiodinium cells suggests either a direct deleterious effect of IGV or reduced performance in putative inter-lineage recombinants, whose genomes feature ITS2 variants from both parental ribotypes. While it remains unclear whether the mixed rDNA arrays result from somatic mutation or recombination, our results demonstrate that the beneficial capacity of symbionts can vary within Symbiodinium populations, with potential implications for host fitness.