The Genetic and Functional Diversity of Symbiodiniaceae on the Coral Reef of Rarotonga (Cook Islands)

The ecological success of tropical corals is facilitated by their mutualistic symbiosis with a family of dinoflagellate algae, called Symbiodiniaceae. Corals may have the ability to acclimatise to climate-driven ocean warming by ‘shuffling’ their symbiont community composition in favour of thermo-tolerant phylotypes. The proliferation of thermo-tolerant symbionts after bleaching may be inherently linked to alga-derived niche partitioning throughout the coral colony. This thesis aimed to test this ‘niche-differentiation hypothesis’: that individual coral colonies self-shade their own tissues causing intra-colony light gradients that facilitate different symbiont phylotypes to partition themselves within segregated ‘light-niche spaces’ according to their photo-acclimatory requirements.

The objectives of Chapter 2 were to characterise the extent of localised differences in light-availability across colony structures and determine whether variation in light-availability is correlated with differentiated Symbiodiniaceae community assemblages. Paired ‘shaded’ and ‘exposed’ samples were taken from individual colonies spanning 20 coral species on the coral reef of Rarotonga. Using pulse amplitude modulated (PAM) fluorometry, rapid light curves were performed to capture differences in the PSII photoacclimation strategy between habitats, characterised as the minimum saturating irradiance (Ek), and the extent of photochemical [1 – C] vs. non-photochemical [1 – Q] quenching. Symbiodiniaceae diversity within each sample was determined with high-throughput sequencing of the ITS2 region. Exposed samples had 50% larger Ek values than shaded samples and demonstrated a shift toward preferential non-photochemical quenching; signatures consistent with higher overall light exposure. Between light-exposed and shaded regions, most coral species harboured an assortment of differentially abundant Symbiodiniaceae amplicon sequence variants (ASVs), the majority of which were rare in relative abundance. For one coral species, Hydnophora microconos, the extent of rare symbiont community differentiation within a single colony was positively correlated with the magnitude of difference in NPQ utilisation [1 – Q] between light habitats.

Chapter 3 aimed to develop and test an entirely open-source method for reconstructing coral structures in 3D, modelling symbiont distributions, and estimating surface irradiance gradients using Structure-from-Motion (SfM) and RADIANCE lighting analysis software. A total of 48 coral tissue fragments were sampled across a single Hydnophora microconos colony and the Symbiodiniaceae diversity within each sample determined with high-throughput DNA barcoding. After sampling, a high-resolution digital mesh of the colony was produced using photogrammetry and the expected irradiance exposure across the mesh was estimated as a function of colony orientation and the local diel solar path preceding the sampling date. Correlating symbiont diversity with local illuminance estimates revealed that certain rare Symbiodiniaceae phylotypes were more likely to be found within regions exposed to high average irradiance.

I discuss how intra-colony light gradients may encourage the persistence of rare opportunistic symbiont phylotypes within optical niches that align with their specific photo-acclimatory requirements/tolerances. Integrating light-niche partitioning within our understanding of how environmental change influences the coral holobiont may explain variability within the symbiont shuffling process.