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Abstract Active chlorophyllafluorometry is a well‐established tool for noninvasively diagnosing coral functional state, but has not yet been developed as a rapid phenotyping (functional screening) platform as for agriculture and forestry. Here, we present a proof‐of‐concept using Light‐Induced Fluorescence Transient‐Fast Repetition Rate fluorometry (LIFT‐FRRf) to identify coral photobiological‐based phenotypes in the context of rapidly scaling coral propagation practices on the northern Great Barrier Reef. For example, resolving light niche plasticity to inform transplantation, and identifying functionally diverse colonies to maximize stock selection. We first used optically diverse laboratory‐reared corals and coral endosymbiont (Symbiodiniaceae) isolates to develop a phenotyping approach integrating FRRf instantaneous kinetic parameters (light harvesting, electron turnover rates) and light‐dependent parameters (dynamic “quenching” terms, saturating light intensity [E_K]). Subsequent field‐based LIFT‐FRRf phenotyping of coral from a selective (2‐4 m depth) reef habitat revealed that widely topographically dispersed platingAcroporataxa exhibited broad light niche plasticity (E_Kvariance) underpinned by multiple phenotypes that were predominantly differentiated by minimum electron turnover capacity; fluorometer configurations that cannot resolve kinetic parameters will thus likely have more limited capacity to resolve phenotypes. As such, platingAcroporahave broad propagation potential in terms of multiple functional variants for stock and across diverse light environments (growth, transplantation). In contrast, coral taxa (Pocillopora verrucosa,Echinopora lamellosa) with relatively restricted topographic dispersion exhibited less light niche plasticity and only single phenotypes, thereby imposing more constraints for propagation. We discuss the core technical, operational, and conceptual steps required to develop more sophisticated coral phenotyping platforms.