High-throughput physiological profiling of endosymbiotic dinoflagellates (Symbiodiniaceae) using flow cytometry

Endosymbiotic dinoflagellates (Family Symbiodiniaceae) are directly responsible for coral survival during climate change, as the breakdown of the coral-dinoflagellate symbiosis leads to coral bleaching and often mortality. Despite methodological progress, assessing the physiology of Symbiodiniaceae in hospite remains a complex task. Bio-optics, biochemistry, or “-omics” techniques are expensive, often inaccessible to investigators, or lack the resolution required to understand single-cell physiological states within endosymbiotic dinoflagellate assemblages. To help address this issue, we developed a protocol that generates a physiological profile of Symbiodiniaceae cells while simultaneously determining cell densities using an entry-level benchtop flow cytometer. Two excitation/emission profiles in the red spectrum target light harvesting complex (LHC)-associated pigments, while green and yellow autofluorescence provides insight into antioxidant-associated pigments. Excitation/emission profiles are generated for each individual cell, simultaneously profiling thousands of Symbiodiniaceae cells, thus increasing statistical power to discriminate between groups even when effect sizes are small. As flow cytometry is adopted as a robust and efficient method for endosymbiont cell counting, integration and expansion of our protocol into existing workflows allows quantification of endosymbiont photophysiology and stress-signatures with minimal additional effort.