Coral reefs are undergoing degradation due to overexploitation, pollution, and climate change. Management and restoration efforts require that we gain a better understanding of the complex interactions between corals, their microbiomes, and their environment. For this purpose, Varadero Reef near Cartagena, Colombia, serves as an informative study system located at the entrance of the Bay of Cartagena adjacent to the Canal del Dique, which carries turbid and polluted water into the bay. Varadero’s survival under poor environmental conditions makes it a great study site for investigating the relationship between the microbiome and coral resistance to environmental stressors. To determine whether the microbiomes of Varadero corals differ from those in less impacted sites, we conducted a reciprocal transplant experiment by relocating coral fragments from Varadero as well as a geographically proximate reef that is less affected by plume dynamics (Rosario) across a gradient of turbidity (low, medium, and high). After 6 months of acclimatization, transplanted corals developed site-specific microbiomes that differed significantly from pre-transplant microbiomes, and corals transplanted to the highly impacted site from both Varadero and Rosario site saw higher mortality and an increase in overall microbial diversity. In combination with physiology and survivorship outcomes pointing to a limit in the corals’ photoacclimative capacity, our results indicate that, rather than surviving, Varadero Reef is experiencing a slow decline, and its corals are likely on the brink of dysbiosis. With continued anthropogenic interference in marine environments, sites such as Varadero will become increasingly common, and it is imperative that we understand how corals and their microbial symbionts are changing in response to these new environmental conditions.

Degradation of water optical properties due to anthropogenic disturbances is a common phenomenon in coastal waters globally. Although this condition is associated with multiple drivers that affect corals health in multiple ways, its effect on light availability and photosynthetic energy acquisition has been largely neglected. Here, we describe how declining the water optical quality in a coastal reef exposed to a turbid plume of water originating from a man-made channel compromises the functionality of the keystone coral species Orbicella faveolata. We found highly variable water optical conditions with significant effects on the light quantity and quality available for corals. Low-light phenotypes close to theoretical limits of photoacclimation were found at shallow depths as a result of reduced light penetration. The estimated photosynthetically fixed energy depletion with increasing depth was associated with patterns of colony mortality and vertical habitat compression. A numerical model illustrates the potential effect of the progressive water quality degradation on coral mortality and population decline along the depth gradient. Collectively, our findings suggest that preserving the water properties seeking to maximize light penetration through the water column is essential for maintaining the coral reef structure and associated ecosystem services.

The biodiversity in coral reef ecosystems is distributed heterogeneously across spatial and temporal scales, being commonly influenced by biogeographic factors, habitat area and disturbance frequency. A potential association between gradients of usable energy and biodiversity patterns has received little empirical support in these ecosystems. Here, we analyzed the productivity and biodiversity variation over depth gradients in symbiotic coral communities, whose members rely on the energy translocated by photosynthetic algal symbionts (zooxanthellae). Using a mechanistic model we explored the association between the depth-dependent variation in photosynthetic usable energy to corals and gradients of species diversity, comparing reefs with contrasting water clarity and biodiversity patterns across global hotspots of marine biodiversity. The productivity-biodiversity model explained between 64 and 95% of the depth-related variation in coral species richness, indicating that much of the variation in species richness with depth is driven by changes in the fractional contribution of photosynthetically fixed energy by the zooxanthellae. These results suggest a fundamental role of solar energy availability and photosynthetic production in explaining global-scale patterns of coral biodiversity and community structure along depth gradients. Accordingly, the maintenance of water optical quality in coral reefs is fundamental to protect coral biodiversity and prevent reef degradation.

This study documents the first validation of the suitability of the most common parameters and protocols used in marine ecophysiology to characterise photosynthesis by means of chlorophyll a fluorescence tools. We demonstrate that the effective yield of PSII (ΔF/Fm′) is significantly underestimated when using short inductions times (≤1 min) following the rapid light curve protocol (RLC). The consequent electron transport rates (ETR) underestimations are species-specific and highly variable with irradiance and the photoacclimatory condition of the sample. Our analysis also questions the use of relative descriptors (relETR), as they not only overestimate photosynthesis, but overlook one of the fundamental components of the photosynthetic response: light absorption regulation. Absorptance determinations were fundamental to characterise the ETR response of low-pigmented seagrass leaves, and also uncovered relevant differences between two coral species and the accclimatory response of a cultured dinoflagellate to temperature. ETR and oxygen evolution determinations showed close correlations for all organisms tested with the expected slope of 4 e– per O2 molecule evolved, when correct photosynthesis inductions and light absorption determinations were applied. However, ETR curves cannot be equated to conventional photosynthetic response to irradiance (P vs E) curves, and caution is needed when using ETR to characterise photosynthesis rates above photosynthesis saturation (Ek). This validation strongly supports the utility of fluorescence tools, underlining the need to correct two decades of propagation of erroneous concepts, protocols and parameters in marine eco-physiology. We aim also to emphasise the importance of optical descriptions for understanding photosynthesis, and for interpreting fluorescence measurements. In combination with conventional gross photosynthesis (GPS) approaches, optical characterisations open an extraordinary opportunity to determine two central parameters of photosynthesis performance: the quantum yield (φmax) of the process and its minimum quantum requirements (1/φmax). The combination of both approaches potentiates the possibilities of chlorophyll a fluorescence tools to characterise marine photosynthesis biodiversity.

Degradation of water optical properties due to anthropogenic disturbances is a common phenomenon in coastal waters globally. Although this condition is associated with multiple drivers that affect corals health in multiple ways, its effect on light availability and photosynthetic energy acquisition has been largely neglected. Here, we describe how declining the water optical quality in a coastal reef exposed to a turbid plume of water originating from a man-made channel compromise the functionality of the keystone coral species Orbicella faveolata. We found highly variable water optical conditions with significant effects on the light quantity and quality available for corals. Reduction of light penetration into the water column elicits the development of low-light phenotypes close to theoretical limits of photoacclimation despite their occurrence at shallow depths. Predicted photosynthetic energy depletion with increasing depth is associated with patterns of colony mortality and contraction of the habitable space for the population. A numerical model illustrates the potential effect the progressive degradation of water optical properties on the gradual mortality and population decline of O. faveolata. Our findings suggest that preserving the water optical properties seeking to maximize light penetration into the water column may have an extraordinary impact on coral reefs conservation, mostly toward the deeper portions of reefs.