Coral skeletal cores as windows into past Symbiodiniaceae community dynamics

The symbiosis between the dinoflagellate Symbiodiniaceae family and reef-building corals underpins the productivity of coral reefs. This relationship facilitates the deposition of calcium- carbonate skeletons that build the reef structure thanks to the energy derived from photosynthesis. The loss of Symbiodiniaceae from coral tissues—resulting in coral bleaching—impedes coral growth and can lead to mass mortality if the symbiosis fails to recover. Given that Symbiodiniaceae communities are dynamic and can shift in response to environmental stressors in the decades- to centuries-long lifespan of coral colonies, understanding these changes is crucial. Although the reconstruction of Symbiodiniaceae communities from coral skeleton records has recently been demonstrated as feasible, no studies have yet assessed reconstructions across different species and locations. Here, we present an approach to use coral skeletons for reconstructing the Symbiodiniaceae community on decadal and centennial scales and resolving dynamics related with coral species and environmental history of sampling locations. For this, we used dated coral skeleton cores from Porites Iobata and Diploastrea heliopora , species commonly used as climate archives, sampled in Palau and Papua New Guinea. We also examined the effect of various DNA extraction protocols on community reconstruction. Here we show that the reconstructed Symbiodiniaceae communities significantly varied across all cores and DNA extraction methods, with decalcification-based protocols enhancing the retrieval of skeletal-bound DNA. Moreover, we observed distinct community dynamics related to the specific coral host and sampling location. Notably, associations of Symbiodiniaceae dynamics with past heat stress events were apparent in cores of both species from Palau. Our findings enable a deeper understanding of the temporal and spatial variability in Symbiodiniaceae communities, offering insights that may refine the use of paleobiological proxies in climate studies and reveal broader ecological trends and microbially-aided adaptation pathways in corals.