The photo-physiological characteristics of thermo-tolerant Symbiodinium types have been postulated to have negative effects on the energetics of the reef corals by reducing fitness. To investigate this, two key and inextricably coupled indicators of fitness, lipids and reproduction, were monitored in colonies of the broadcast-spawning coral Acropora millepora over a two-year period that included a natural bleaching event. In the absence of bleaching ITS1-type clade D predominant colonies had 26% lower stored lipids compared to C2 colonies. At spawning time, this correlated with 28% smaller eggs in type-D colonies. This energetic disparity is expected to have reduced larval duration and settlement-competency periods in type-D compared to type-C2 colonies. More importantly, irrespective of the effect of genotype, the fitness of all corals was adversely affected by the stress of the bleaching event which reduced prespawning lipids by 60% and halved the number of eggs compared to the previous year. Our results extend work that has shown that direct temperature stress and symbiont change are likely to work in concert on corals by demonstrating that the lipids and reproduction of the reef building corals on tropical reefs are likely to be impaired by these processes as our climate warms. 1. Introduction Reef-building corals are vulnerable to climate change as they live in a narrow thermal range and are extremely sensitive to variations. An increase of only 1-2°C above the coral’s normal summer maximum, in combination with light, can cause expulsion of the endosymbiotic algae (zooxanthellae) that live within their tissues, resulting in coral bleaching [1]. Such extremes are expected to occur regularly on reefs within the next century meaning that corals must adapt or acclimatize at a rate of 0.2°C every decade if they are to keep pace with even the lowest predicted temperature rise of 2°C by 2100 [2]. One way in which corals can increase their heat tolerance is by changing their endo-symbiont community to more thermally tolerant types like Symbiodinium type D [3]. Hosting a viable population of heat tolerant symbionts may give corals a better chance of surviving repeated bleaching events [4]. A recent study utilizing novel molecular methods has revealed previously undetectable levels (<5–10%) of thermally tolerant symbionts types in four species of reef corals [5], raising the possibility that many species may be able to acclimatize to climate change in this way [6, 7]. So far, symbiont changes have been transitory [8, 9], and it remains to be seen whether
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