Clade D Symbiodinium are thermally tolerant coral endosymbionts that confer resistance to elevated sea surface temperature and bleaching to the host. The union between corals and clade D is thus important to management and coral conservation. Here, we review the diversity and biogeography of clade D Symbiodinium, factors linked to increasing abundances of clade D, and the benefits and drawbacks of associating with clade D for corals. We identify clade D Symbiodinium as uncommon pandemically distributed generalists found in higher abundances on reefs exposed to challenging sea surface temperatures and local stressors or with a history of bleaching. This distribution suggests that clade D Symbiodinium are mostly opportunistic endosymbionts, whereby they outcompete and replace optimal symbionts in health-compromised corals. We conclude by identifying research gaps that limit our understanding of the adaptive role clade D Symbiodinium play in corals and discuss the utility of monitoring clade D Symbiodinium as indicators of habitat degradation in coral reef ecosystems. 1. Introduction Scleractinian corals form obligate endosymbioses with uni-cellular photosynthetic dinoflagellates in the genus Symbiodinium [1, 2]. The Symbiodinium translocates newly fixed organic carbon to the host coral and, in return, receive inorganic waste metabolites from host respiration and an environment free from predators [3].This mutually beneficial symbiosis contributes to the productivity of coral reef ecosystems, promotes deposition of calcium carbonate skeletons, and creates the structural framework that protects coastlines and serves as habitat for the extraordinary biodiversity found in coral reef ecosystems [4]. A consortium of bacteria, archaea, viruses, and fungi also forms close associations with corals and contributes collectively to the overall function and environmental thresholds of corals (e.g., [5–8]). These coral-microorganism communities are collectively described as the coral holobiont. Climate change and other anthropogenic impacts have already damaged an estimated 30% of the world’s coral reefs, and further declines in the integrity of coral reef ecosystems are projected for the near future [9]. A suite of often synergistic factors are contributing to the declining health of corals including global stressors such as elevated sea water temperatures and ocean acidification and local stressors like increased nutrient loading, sedimentation, and pollution [9]. The best documented and arguably most acutely damaging environmental conditions for corals are
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