Global threats to coral reefs demand novel strategies for conservation and restoration. In particular, interest in increasing the use of corals with robust phenotypes in restoration and captive breeding programs has grown. Recent work has documented intraspecific variation in phenotype among known genotypes of the threatened staghorn coral Acropora cervicornis in a common garden. Phenotypes identified include those that may be desirable to restoration practitioners, such as rapid growth and high skeletal density. Determining phenotype in A. cervicornis often requires painstaking repeated measures, which can be time-consuming, expensive, and logistically challenging. Metabolomic profiling detects the full set of metabolites in an organism, and, when linked to metabolic pathways, can provide a snapshot of an organism’s physiological state. Identifying metabolites associated with advantageous traits has the potential to streamline selection of corals for use in restoration. However, little information exists to illustrate intraspecific variation in coral metabolite profiles. To address this gap, we applied untargeted 1H-NMR and LC-MS metabolomic profiling to three genotypes of the threatened coral Acropora cervicornis that have been shown to possess unique growth and thermotolerance phenotypes. Both methods revealed distinct metabolite “fingerprints” for each genotype examined. A number of metabolites driving separation among genotypes were putatively identified, including compounds with key osmotic and antioxidant functions. For the first time, these data illustrate intraspecific variation in metabolomic profiles for corals in a common garden. These results contribute to a growing body of work on coral metabolomics and also suggest future work could identify specific links between phenotype and metabolite profile.

Precipitous declines in coral reef and mangrove habitats worldwide threaten food security, livelihoods, and infrastructure for coastal societies. Is it possible to restore the ecological functionality of damaged habitats? What factors mediate the success of restoration efforts? Here I describe why meta-community theory, which conceives local biological communities as part of a network of interconnected communities, is the foundation for a promising framework in which to design coastal habitat restoration and set expectations for recovery following intervention. To do this, I will summarize what three decades of research on habitat loss in tropical marine systems globally has revealed about the properties of coral and mangrove meta-communities (e.g. species equivalence, migration rates, habitat heterogeneity) that mediate key ecological processes (e.g., magnitude and stability of species diversity, biomass, and productivity) across space and time. I will then highlight opportunities for incorporating meta-community properties into the spatial and temporal design of in situ coral and mangrove restoration, and evaluating the trajectories and magnitude of ecological change following intervention. Finally, I will discuss the potential for emerging meta-community network modelling techniques—which dynamically incorporate variation in habitat size and spacing, and species’ traits such as home range size, size-based trophic interactions, and ontogenetic migration ability to predict diversity and stability across the system—to serve as tools for restoration design and evaluation.

Reef habitat microbiomes play a vital role in coral reef ecosystem health and function. Characteristics of the physical habitat of a reef may help drive the evolution of the host organism, its algal symbionts, and associated microbiomes. In southern Florida in particular, reef marine microbiome communities may be influenced by fine-scale patchiness in sea temperature and available light, connectivity patterns in ocean circulation, microbial contaminants from wastewater, coastal inlet discharges, terrestrial runoff, and coastal tidal or storm flooding. We sequenced samples from coral tissue, water, and sediments at both near- and offshore reefs of the Florida reef tract. Sites included both near-urban southeast Florida shelf and more isolated reefs of the Florida Keys. We report on associations between the community structure and biodiversity of these microbiomes, and the observable characteristics of their environment, notably sea temperature variability and seafloor topography, tides, ocean currents, waves, and relative turbidity. The microbiomes were characterized by 16S rDNA amplicon Next-Generation-Sequencing (NGS) of total microbial metagenomic DNA extracts. We investigated connectivity using combined outputs of a quasi-operational ocean-circulation model with data on waves and surface winds. We estimated sea temperature variability from long-term in situ measurements and a reef ocean heat budget based on depth, slope, light, and waves. Relative turbidity change over time was estimated from a multiyear record of high-spatial-resolution satellite ocean-color.

As natural habitats are increasingly lost or degraded, there is a need to determine the mechanisms that organisms use to locate suitable habitats and to identify if adaptation is possible to new or altered locations. The importance of chemical cues during the settlement process is becoming well recognized for many invertebrate larvae, including coral larvae; however, the chemical nature of these cues is poorly understood. Coral settlement studies have mostly focused on surface-bound chemical cues and the role these play once contacted by settling larvae. Although coral larvae do not possess the same chemical detection systems or similar swimming ability as fish larvae, chemical cues can both positively and negatively influence their substrate preferences. We will describe methods developed and used to understand the types of compounds released by coral reef organisms as extracellular metabolites, with an emphasis on those compounds involved in settlement site selection by coral larvae. Understanding these chemical cues could facilitate settlement and recruitment of coral larvae for restoration purposes.

The endangered species listing of Acropora cervicornis has prompted the need for restoration. Since resources are limited, sites selected for restoration should not only be suitable for outplant survival, but also contribute larvae to replenish surrounding reefs. However, coral larval dispersal patterns and reef connectivity remain poorly studied. Here, we measured long term larval survival and competency of Acropora cervicornis to calibrate a high resolution (100m) biophysical larval dispersal model of Acropora in the Florida Reef Tract. The resulting connectivity matrix was used to develop a metapopulation model to identify areas of higher interest to restore and protect. Larvae experienced high mortality during early development, but once the planula stage was reached, mortality rates decreased considerably. Larvae reached competency after day 5. The model predicts that most larvae are lost from the system, but the ones that settle are primarily transported from south to north. However, some of the northernmost reefs can still act as sources, with eddies pushing larvae southward. Reefs within the Middle Keys are some of the most important larval sources within the system and thus should be prioritized for restoration. Reefs with high self-recruitment, such as some in the Lower and Upper Keys, should be prioritized for protection, as they are more isolated and thus vulnerable to disturbance. More importantly, this model allows managers to compare the capacity of suitable sites for restoration to recolonize other reefs through sexual recruitment. Taking reef connectivity into account would enhance genetic diversity, hasten coral recovery, and boost resilience across the entire reef system.

Coral restoration is gaining momentum globally in response to stressors such as bleaching and disease. Along with restoring threatened species and ecological condition of reefs, there is growing interest from a variety of sectors for restoration that supports specific social benefits (e.g., tourism). This has implications for restoration as site selection will vary substantially as we prioritize different benefits. Ecological parameters such as bathymetry, historic distribution and abundance, temperature and light conditions are important for maximizing the likelihood of survival and growth of out-planted corals. Additional factors come into play when selecting sites specifically to return benefits like wave attenuation, local fisheries, or tourism. Global and regional-scale models that predict the spatial availability of such social benefits have been developed for different geographies through the Mapping Ocean Wealth initiative, an ongoing effort to develop spatially-explicit and quantitative data on a range of ecosystem benefits for a range of habitat types. This information is increasingly high-resolution, and innovative new tools are being developed in tandem to enable environmental managers to predict the changes in societal benefits that could be associated with reef loss or reef recovery in specific locations. Resource constraints in the conservation and management community demand smart investments, and the return on investment is an important consideration for both policy makers and business leaders of for-profit and not-for-profit organizations alike. Spatially-explicit models that link various coral reef attributes (location, vertical relief, coral cover) to social can be used to assess return on investment (ROI) and other socially-relevant metrics under different scales and timeframes of restoration investment. These models can also be used to test assumptions and trade-offs among different management actions. For example, maps of fishing impact and fish biomass in Micronesia allow the comparison of the increases in standing stocks from reducing fishing versus increasing coral cover in any 1 ha reef area in the region, and potentially the ROI of each management action. Looking forward, we suggest that analysis of social benefits and potential tradeoffs can attract new restoration investment that supports multiple objectives and outcomes.

The success of restoration efforts is usually measured on the basis of coral survival and growth rates, but that approach may be improved by taking in consideration specific evaluations of the ecological role that transplanted colonies play in the reef. Corals are ecological engineers and offer shelter to numerous species, and also provide food in form of mucus; these functions are in direct relation to the size of the colony, and thus it is relevant to determine the minimum size that a fragment needs to fulfill its role in a reef. The objective of the study was to detect the size that colonies of naturally settled Pocillopora spp. require to host a full set of associated reef fishes, and use that information as a proxy indicator of success for restoration projects. The study was carried out at three locations in the southern Gulf of California, Mexico. We measured the largest diameter, perpendicular diameter and height in cm of 1,144 colonies, and calculated its volume; at the same time, visual censuses of associated fish were conducted observing individuals inside the colonies or in a perimeter of 30 cm around them. From these data, fish richness and abundance were calculated, and these response variables were introduced in non-linear regression models to determine the minimum volume that a colony should have to reach its maximum number of individuals and species richness (considering this as a measure of ecological functionality). The resulting models presented an asymptote, and we estimated that the volume that a Pocillopora colony requires to have its complete fish collection is between 30,000 and 40,000 cm 3, which according to local estimations of growth rate represents an approximate age of 6-7 years. We suggest that managers apply these results to plan more efficient restoration efforts.

To predict restoration success requires an understanding of the factors influencing growth and survivorship of coral species. Here we use empirically-derived matrix population models to generate estimates of stage-specific growth, survivorship, and fertility for Acropora palmata, A. cervicornis, and Orbicella annularis inhabiting the wider Caribbean. Growth and survivorship data were generated from repeated benthic transect surveys spanning from 2011-2015, while estimates of fertility were generated with a meta-analysis of the relevant primary literature. Preliminary results suggest that O. annularis in the wider Caribbean is experiencing declines of ~4% per year (lambda = 0.96), and in terms of future population growth, survivorship of individuals within the two smallest size classes (i.e.

The goal of restoration programs is to ensure long-term success. In Mexico, coral restoration programs began 12 years ago, nevertheless, there is no reliable information on the location and characteristics of the restoration sites, and no monitoring data post out-planting. To determine if there are any interactions between the characteristics of out-planting sites and the condition of A. palmata recruits, we evaluated 18 sites where restoration had taken place. For sites restored with sexual recruits, we evaluated 50% of the restored area using 1 by 1 m randomly-placed quadrats, whereas for sites restored with fragments, we evaluated 10% of the total area, using 2 by 10 m randomly-placed transects. In both cases, we assessed the condition of the recruits by registering mortality, overgrowth, predation, and out-planting density. Additionally, we recorded benthic composition and water depth. Using these parameters, we developed a restoration status index. The use of coral fragments has been the most common practice (91% of evaluated sites), while restoration utilizing sexual recruits is notably less (6% of evaluated sites), and in one case, a combination of both techniques was used. According to the restoration status index, most of the restoration areas are in poor condition due to high mortality. In most cases, it is unclear whether this is due to the out-planting techniques that were used or due to degradation of the environment after the out-planting. Regardless of the technique that has been applied, all the restoration efforts to date have been applied on a small scale. Given that the actual area of Acropora spp. that has been lost is orders of magnitude higher than the restoration areas, there is an urgency to upscale coral restoration and to increase the success of restoration programs by better understanding the conditions that could favor out-planting of sexual recruits and fragments.

Florida’s corals have suffered tremendous recent declines from climate change (bleaching) and disease, and there is an urgent need to safeguard remaining genotypic diversity from further loss. Because gametes cannot yet be reliably collected and/or cryopreserved, field gene banks must be created to preserve remaining diversity. Current efforts focus on doing this in coral nurseries or large land-based facilities, but an alternative approach leverages the enormous growth of the reef aquarium industry over the last 25+ years, which has created a highly skilled nationwide community of reef aquarists who can be enrolled to maintain and propagate Florida’s valuable coral genetic resources. Priority coral species and genotypes collected by federal and state agencies can be transported to a National Resource Facility “hub” in Miami that fragments and distributes (“uploads”) these genotypes to the network (the “Coral Cloud”). In turn, using an app-based technology platform, the Cloud shares data and photos on growth rate, wound healing, survivorship, and susceptibility to bleaching/disease, which can then be used to inform subsequent genome-enabled experiments on these curated genotypes at the Miami hub. This approach leverages vast yet unexploited expertise in coral husbandry to help solve the problem of how to conserve genotypes long-term at low cost across a dispersed network of ex situ facilities, and could also be used to crowdsource other problems (such as how to improve the long-term survivorship and grow-out of coral recruits) by challenging the Coral Cloud to identify and test novel solutions. The Coral Cloud represents a radical departure from established coral reef conservation practices, but such approaches are now needed to help confront Florida’s growing crisis. In addition, by enrolling an untapped public resource to help coral reef conservation in a meaningful way, the Coral Cloud represents a tremendous opportunity to engage in outreach, activism, and citizen science nationwide.