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Context Coral reef resilience is the product of multiple interacting processes that occur across various interacting scales. This complexity presents challenges for identifying solutions to the ongoing worldwide decline of coral reef ecosystems that are threatened by both local and global human stressors. Objectives We highlight how coral reef resilience is studied at spatial, temporal, and functional scales, and explore emerging technologies that are bringing new insights to our understanding of reef resilience. We then provide a framework for integrating insights across scales by using new and existing technological and analytical tools. We also discuss the implications of scale on both the ecological processes that lead to declines of reefs, and how we study those mechanisms. Methods To illustrate, we present a case study from Kāneʻohe Bay, Hawaiʻi, USA, linking remotely sensed hyperspectral imagery to within-colony symbiont communities that show differential responses to stress. Results In doing so, we transform the scale at which we can study coral resilience from a few individuals to entire ecosystems. Conclusions Together, these perspectives guide best practices for designing management solutions that scale from individuals to ecosystems by integrating multiple levels of biological organization from cellular processes to global patterns of coral degradation and resilience.

Scleractinian coral recruitment provides critical support for reef persistence under the threat of global climate change. The high mortality rates exhibited in early life history stages are further increased under thermal stress, compromising reef recruitment. Tissue fusion with neighboring recruits is one potential early life history strategy that has been shown to support recruit survival (particularly in brooding species) by promoting rapid increases in colony size and potential opportunities for enhanced intracolonial genetic diversity. However, tissue fusion also presents risks in the cost of growth and maintenance of relationships between genetically distinct individuals. Although fusion is one potential strategy for recruit survival, the effects of colony size and enhanced genetic diversity achieved through fusion on survival under ocean warming conditions are not well understood. Here we tested the effect of tissue fusion on Pocillopora acuta recruit survival under ambient and high temperature stress by manipulating the size and parental genotypic richness in fused recruits. We provided opportunities for tissue fusion in groups of recruits with enhanced parental genotypic richness (1–4 parent genotypes) and size (1–4 recruits) and tracked subsequent growth and survival (N = 137). Under ambient temperature (1–15 days post-settlement), fusion significantly increased survivorship regardless of parental genotypic richness, while negative competitive effects existed between closely settled, but unfused recruits. Under high temperature (+ 2.5 °C; 16–47 days post-settlement), the median survival of fused recruits was 5 days longer than individuals, with 1.5 days added to median survival when composed of multiple parental genotypes. These results demonstrate that tissue fusion during coral recruitment can improve survival and provides insights on early life history strategies to increase tolerance to ocean warming.

Coral bleaching has a profound impact on the health and function of reef ecosystems, but the metabolomic effects of coral bleaching are largely uncharacterized. Here, untargeted metabolomics was used to analyse pairs of adjacent Montipora capitata corals that had contrasting bleaching phenotypes during a severe bleaching event in 2015. When these same corals were sampled four years later while visually healthy, there was a strong metabolomic signature of bleaching history. This was primarily driven by betaine lipids from the symbiont, where corals that did not bleach were enriched in saturated lyso-betaine lipids. Immune modulator molecules were also altered by bleaching history in both the coral host and the algal symbiont, suggesting a shared role in partner choice and bleaching response. Metabolomics from a separate set of validation corals was able to predict the bleaching phenotype with 100% accuracy. Experimental temperature stress induced phenotype-specific responses, which magnified differences between historical bleaching phenotypes. These findings indicate that natural bleaching susceptibility is manifested in the biochemistry of both the coral animal and its algal symbiont. This metabolome difference is stable through time and results in different physiological responses to temperature stress. This work provides insight into the biochemical mechanisms of coral bleaching and presents a valuable new tool for resilience-based reef restoration.

Thermal stress is a major contributor to loss of coral cover, significantly impacting reefs during the third global bleaching event between 2014 and 2017. The long-term persistence of coral reefs depends on acclimatization and adaptation to changing climate, which are influenced greatly by the interactions between bleaching and reproductive success. We observed a genotypically diverse population of Orbicella faveolata before, during, and after consecutive bleaching events in 2014 and 2015 in the Florida Keys. We documented less bleaching during the second event despite 40% more time above local bleaching thresholds and an association between bleaching severity and subsequent spawning. Approximately 75% of colonies experienced the same or less severe bleaching in the second event despite being metabolically compromised, with a substantial minority (~ 35%) faring better in the second event. The second bleaching event also resulted in smaller decreases in chlorophyll content per symbiont cell and symbiont-to-host cell ratio reef-wide, representing less damage to the coral–algal symbiosis. All colonies that recovered quickly (~ 1 month) or did not bleach in 2014 released gametes in 2015, while only 60% of colonies that recovered more slowly did. Bleaching also impacted the amount of gametes released, with more severe bleaching significantly associated with gamete release from

Sexual reproduction in scleractinian corals is a critical component of species recovery, fostering population connectivity and enhancing genetic diveristy. The relative contribution of sexual reproduction to both connectivity and diversity in Acropora cervicornis may be variable due to this species’ capacity to reproduce effectively by fragmentation. Using a biophysical model and genomic data in this threatened species, we construct potential connectivity pathways on the Florida Reef Tract (FRT) and compare them to inferred migration rates derived from next-generation sequencing, using a link and node-based approach. Larval connectivity on the FRT can be divided into two zones: the northern region, where most transport is unidirectional to the north with the Florida Current, and the southern region that is more dynamic and exhibits complex spatial patterns. These biophysical linkages are poorly correlated with genetic connectivity patterns, which resolve many reciprocal connections and suggest a less sparse network. These results are difficult to reconcile with genetic data which indicate that individual reefs are diverse, suggesting important contributions of sexual reproduction and recruitment. Larval connectivity models highlight potential resources for recovery, such as areas with high larval export like the Lower Keys, or areas that are well connected to most other regions on the FRT, such as the Dry Tortugas.

Nearshore benthic habitats of Biscayne Bay fit the prediction of communities at risk due to their location adjacent to a large metropolitan center (Miami) and being influenced by changes in hydrology through the activities of the Comprehensive Everglades Restoration Plan (CERP). We examine whether the proposed programmatic expansion of mesohaline salinities through the introduction of additional fresh water would result in: (1) increases in seagrass cover; (2) expansion in the distribution and cover of Halodule; and (3) a reduction in the dominance of Thalassia, as hypothesized by CERP. Seagrasses were present at 98 % of sites where they covered 23 % of the bottom. Salinity was the only physical variable with a significant relationship to the occurrence of all SAV taxa. Occurrence of Thalassia, Halimeda, and Penicillus increased significantly with increasing salinity, but Halodule, Syringodium, Laurencia, Udotea, Batophora, Caulerpa, and Acetabularia showed a significant negative relationship with salinity. Mesohaline habitats had higher cover of seagrass and Halodule, and reduced dominance by Thalassia. Thus, we expect increases in the extent of mesohaline habitats to achieve the established CERP goals. We also examined the nutrient content of seagrass blades to evaluate whether: (1) nutrient availability is higher in areas close to canal discharges; and (2) tissue nutrient levels are related to seagrass abundance. The low abundance of Thalassia along the shoreline is not only due to its exclusion from low-salinity environments but also by higher nutrient availability that favors Halodule. Percent N and P, and N:P ratios in seagrass tissue suggest that Biscayne Bay receives high N inputs and is P-limited. Thus, increased P availability may facilitate an expansion of Halodule. The data presented suggest that increased mesohaline salinities will increase seagrass abundance and support co-dominance by Halodule and Thalassia as hypothesized, but raise concerns that current high N availability and increases in P may prompt a shift away from seagrass-dominated to algal-dominated communities under scenarios of enhanced fresh water inputs.

Coral reef restoration methods such as coral gardening are becoming increasingly considered as viable options to mitigate reef degradation and enhance recovery of depleted coral populations. In this study, we describe several aspects of the coral gardening approach that dem- onstrate this methodology is an effective way of propa- gating the threatened Caribbean staghorn coral Acropora cervicornis: (1) the growth of colonies within the nursery exceeded the growth rates of wild staghorn colonies in the same region; (2) the collection of branch tips did not result in any further mortality to the donor colonies beyond the coral removed for transplantation; (3) decreases in linear extension of the donor branches were only temporary and donor branches grew faster than control branches after an initial recovery period of approximately 3-6 weeks; (4) fragmentation did not affect the growth rates of non-donor branches within the same colony; (5) small branch tips experienced initial mortality due to handling and trans- portation but surviving tips grew well over time; and (6) when the growth of the branch tips is added to the regrowth of the fragmented donor branches, the new coral produced was 1.4-1.8 times more than new growth in undisturbed colonies. Based on these results, the collection of small (2.5-3.5 cm) branch tips was an effective propagation method for this branching coral species resulting in increased biomass accumulation and limited damage to parental stocks.