Assessing the efficacy of coral restoration along Florida’s coral reef under the chronic persistence of stony coral tissue loss disease

Abstract

Stony coral tissue loss disease (SCTLD) has caused unprecedented coral mortality across Florida’s Coral Reef (FCR) since 2014, raising concerns about whether coral restoration can succeed under chronic disease conditions and whether outplanting activities may increase disease transmission risk. As the disease transitioned from epizootic outbreak to enzootic persistence, we conducted a large-scale experimental outplanting to assess coral restoration efficacy under chronic SCTLD persistence and to evaluate the relative importance of SCTLD versus non-disease drivers of restoration outcomes. From May 2021 through April 2023, we outplanted 1,165 colonies of three SCTLD-susceptible species (Montastraea cavernosa, Orbicella faveolata, and Pseudodiploria clivosa) sourced from land-based facilities and in-water nurseries across six regions spanning FCR and monitored survival and disease incidence. Concurrent surveys of natural coral communities assessed whether outplanting activities affected local SCTLD prevalence. Probabilities of infection per monitoring interval remained <1-2% across all species, regions, and propagation sources throughout the monitoring period. Importantly, outplanting activities did not increase SCTLD prevalence in neighboring natural coral communities. In contrast to the low and relatively uniform disease incidence, variation in coral survival was strongly structured by ecological and operational factors. The overall coral colony survival rate at the end of the study was 77.3% but was influenced by reef stratum (inshore vs. offshore reefs), geographic region, and colony source. M. cavernosa and P. clivosa exhibited higher survival at inshore sites compared to offshore sites, whereas O. faveolata showed no consistent reef stratum effect on survival. Across FCR, survival varied spatially between regions independent of latitude, suggesting local environmental drivers. Colony source effects varied by species. M. cavernosa and P. clivosa from land-based facilities exhibited significantly lower survival than colonies from in-water nurseries, whereas O. faveolata showed no significant differences between propagation sources. Our results indicate that under SCTLD-enzootic conditions, restoration outcomes are shaped more strongly by habitat suitability, geographic context, and propagation-related factors than by SCTLD itself. These findings suggest that coral restoration can proceed within SCTLD-enzootic zones without increasing disease risk to neighboring coral communities or substantially elevating SCTLD-related mortality of outplanted colonies.

1 Introduction

Coral reef ecosystems worldwide are experiencing declines in coral cover due to a suite of chronic stressors, including ocean warming (Cornwall et al., 2021), coastal pollution (Nalley et al., 2021), and eutrophication (Thanopoulou et al., 2022). Perhaps most conspicuously, the burgeoning number of coral diseases in recent decades has played a major driver of the decline of reef-building corals worldwide, resulting in cascading effects throughout these ecosystems (Hughes et al., 2017; Jackson et al., 2014).

Within this broader context, active coral restoration has emerged as a widely used intervention, particularly in disease-affected reef systems (e.g., Hein et al., 2020). However, key uncertainties persist regarding whether outplanting activities may inadvertently increase disease risk by enhancing host density or facilitating pathogen transmission (Weil et al., 2006), and whether restoration can produce sustained recovery under chronic disease pressure (National Academies of Sciences, Engineering, and Medicine, 2019). These concerns are central to ongoing discussions about the role and limits of active restoration in degraded reef environments, particularly where chronic diseases remain present (Walton et al., 2018; Muller et al., 2020).

The first reports of coral disease along Florida’s Coral Reef (FCR) date to the 1970s, and numerous diseases have since been documented in ever increasing numbers (Porter et al., 2001). During 2014, a new and highly virulent disease, later termed stony coral tissue loss disease (SCTLD), was observed on FCR and subsequently spread throughout the wider Caribbean (Swaminathan et al., 2024; Muller et al., 2020; Alvarez-Filip et al., 2019). Affecting at least 22 species of scleractinian corals (Florida Keys National Marine Sanctuary, 2018), SCTLD is highly contagious, resulting in rapid tissue loss and colony mortality in days or weeks (Precht et al., 2016).

The SCTLD epizootic has been among the most pervasive and consequential disease events documented on FCR, resulting in considerable changes to coral community structure and declines in coral species diversity and cover (Walton et al., 2018; Sharp et al., 2020; Hayes et al., 2022). Despite its severity and rapid spread, the etiological agent(s) responsible for SCTLD remain unresolved. This epidemic has resulted in an unprecedented concerted, collaborative, and organized effort among Florida’s resource managers, researchers, conservation practitioners, non-governmental organizations, veterinarians, and engaged citizens to document disease dynamics, impacts, and develop mitigation strategies (FKNMS, 2018). These efforts have suggested that SCTLD incidence is not consistently associated with water temperature or nutrient loading (Muller et al., 2020; Palacio-Castro et al., 2025). Current evidence suggests a bacterial component to the disease, as lesion progression can be slowed or halted through antibiotic treatments (Aeby et al., 2021; Neely et al., 2021; Walker et al., 2021), and microbial bioindicators associated with SCTLD have been identified (Becker et al., 2022). However, no single pathogen or consortium has been definitively confirmed as the causative agent (Ushijima et al., 2020). Manipulative experiments suggest that transmission among susceptible species is waterborne (Aeby et al., 2021; Eaton et al., 2021), with additional potential vectors including ship ballast water (Studivan et al., 2022) corallivory by butterflyfishes on affected coral colonies (Noonan and Childress, 2020). Transmission via microbial biofilms and reef sediments has also been proposed, whereby these benthic matrices may act as environmental reservoirs that concentrate and maintain SCTLD-associated microbial communities, increasing the exposure risk of SCTLD-susceptible corals (Evans et al., 2023; Studivan et al., 2022).

By 2018, portions of the FCR were thought to have become enzootic (i.e., the persistent low-level presence of SCTLD) (Neely et al., 2019), and an effort was initiated to test the efficacy of outplanting new coral colonies to restore ecological functions to areas affected by SCTLD and to develop a coral restoration strategy under the likely chronic persistence of SCTLD. This latter effort was initiated during 2018 with a short-term experimental outplanting of SCTLD-susceptible coral species at six, presumably enzootic, reef locations in the upper and middle Florida Keys regions of FCR (Smith et al., 2021). Throughout the 12-week monitoring period, no coral outplants exhibited signs of SCTLD. However, given the limited spatial and temporal scope of that effort, it remained unclear whether this pattern would persist under broader spatial and longer-term exposure across the FCR.

Building upon that effort, in 2021 a larger-scale and longer-term experimental coral outplanting effort of SCTLD-susceptible coral species was initiated along the length of the contiguous FCR, which was thought to now be entirely within the enzootic zone for SCTLD. The study presented here was designed to provide key information to resource managers charged with implementing coral restoration under chronic SCTLD conditions. Specifically, we aimed to i) determine the geographic and species-specific SCTLD incidence (i.e., the probability of infection through time) of these coral species outplanted along FCR and ii) assess whether the outplanting effort affects the SCTLD prevalence (i.e., the proportion of colonies exhibiting active disease) within the neighboring wild coral communities.

Other components of this project addressed coral growth dynamics, and the role of host genetics are presented in companion studies (Bell et al., 2025). SCTLD dynamics and survival patterns for the northernmost region of the reef tract have been examined in a regional analysis (Pantoni, 2024). The present study expands upon that work by evaluating these patterns across the full spatial extent of the reef tract, allowing assessment of whether regional findings are consistent across broader environmental and reef structural gradients.

We document the location-, species-specific, and coral source-specific SCTLD incidence and survival rates of three species of susceptible coral species, Montastraea cavernosa, Orbicella faveolata, and Pseudodiploria clivosa outplanted at six reef locations from the northern extent of the FCR through the lower Florida Keys over 24 months. We also compare SCTLD incidence rates among naturally occurring coral communities located within the experimental coral outplant sites with those at adjacent control reef locations to assess the effect of outplanting SCTLD-susceptible coral colonies on the wild coral communities.

2 Materials and methods

2.1 Experimental coral outplant design

Three species of coral, each susceptible to varying degrees to SCTLD, were used in the experimental outplanting study, Montastraea cavernosa, Pseudodiploria clivosa, and Orbicella faveolata. Montastraea cavernosa and O. faveolata are considered intermediately susceptible species, and P. clivosa is considered highly susceptible to SCTLD (FKNMS, 2018). The inclusion of these three species was driven by the goal of restoring reef building coral species in FCR and by their availability within various in-water coral nurseries and land-based coral facilities. Corals were sourced from the in-water nurseries managed by the FWC, Coral Restoration Foundation, and Reef Renewal, L.L.C. and from the land-based facilities of Mote Marine Laboratory and the University of Miami.

The coral outplanting effort spanned the FCR from Martin County in the north to the lower Florida Keys. The survey area was divided into six regions: The Martin and Palm Beach County region (Martin), the Broward county region (Broward), the Miami-Dade County region (Miami), the upper Florida Keys region (Upper Keys), the middle Florida Keys region (Middle Keys), and the lower Florida Keys (Lower Keys) (Figure 1).

Figure 1

At each of the six regions, four coral outplant sites were established. To the extent possible, these were stratified by reef type. Within the four southern regions (Miami, Upper Keys, Middle Keys, and Lower Keys), two sites were selected on offshore bank reef habitat and two on nearshore patch reef habitat. Because of differences in the reef tract off of the two most northern regions (Martin and Broward Counties), sites were established on the available suitable habitat, with two offshore and two inshore sites. Site locations are summarized in Table 1.

Each outplant site consisted of 48 total colonies comprising three SCTLD-susceptible coral species (Figure 2). Each colony unit was composed of five individual coral fragments from the same genet, and colonies were placed approximately 1 m apart from one another such that the completed site was an approximately an 8 x 6 m rectangle. Colony units were derived from 99 source colonies (25 M. cavernosa, 41 O. faveolata, 33 P. clivosa genets; Bell et al., 2025), ensuring multi-genet replication across all species and treatments.

Figure 2

Genet identity was assigned based on source nursery records maintained by participating restoration programs (FWC, Coral Restoration Foundation, Reef Renewal, Mote Marine Laboratory, and University of Miami), which included previously genotyped colonies and/or colonies with documented lineage histories tracked through nursery propagation. In cases where such records were unavailable, colonies were classified as having unknown genet identity (see Figure 2).

The project contracted Reef Cells L.L.C. to fabricate cement bases to hold five coral fragments each. These bases were designed to standardize outplant structure across regions, elevate corals off the substrate to increase survival, and decrease the time it takes for the corals to fuse into one colony (Figure 3). Each base was fitted with a nylon fastener with a unique numerical sheep ear identification tag. The bases were secured to flat reef substrate at least one week prior to coral outplanting using cement.

Figure 3

Corals were outplanted across the study area from May 4 through May 6, 2021. Coral fragments were distributed across the sites to maximize the representation of each species, source, and genotype across all regions. The species, source, and genotype, if known, for each coral cluster was carefully tracked, distributed, and attached to a specific base at each site. There were also additional coral fragments beyond those required by the experimental design available during distribution and some were outplanted at two of the regions. Six additional colonies were outplanted and surveyed in the Broward region, and seven additional colonies were outplanted and surveyed in the Lower Keys region in addition to the 1,152 dictated by the experimental design. In all, 1,165 colonies were outplanted. In total, 223 colonies of M. cavernosa, 652 of O. faveolata, and 290 of P. clivosa were distributed across FCR.

2.2 Experimental coral outplant survey methodology

Each site was surveyed twice during May 2021, then monthly thereafter through April 2023. During each survey, divers using SCUBA took photographs of each coral colony using a standardized camera mount with a ruler visible for scale. Using a standardized field data sheet, divers then recorded the general status (i.e., live, dead, missing) of each colony, as well as any external signs of SCTLD. SCTLD was defined as exhibiting small circular or irregular lesions of white, newly exposed skeleton indicative of rapid tissue mortality (FKNMS, 2018). If SCTLD was observed, divers recorded the percentage of the colony affected as a proportion of colony size. Divers also recorded the presence of bleaching on each colony and evidence of fish bites or the number of corallivorous snails. If detected, the percentage of damaged tissue was estimated as a proportion of the total colony. If any loose or detached fragments with live tissue were encountered and positively associated with the cluster from which it originated, they were epoxied back to the base.

2.3 Natural coral community survey methodology

During the coral outplant site set up and each subsequent outplant site survey, a roving diver survey of the natural coral community at the outplant site was conducted to establish a baseline for coral species diversity and abundance, size classes of live corals present, and disease prevalence. Two divers conducted a non-overlapping 10-minute roving diver survey to assess the presence of active SCTLD. Each diver noted the condition of the SCTLD-susceptible colonies they encountered (i.e., healthy, active diseased, dead). Using the same methodology, an additional survey was conducted quarterly at a site at least 500 m from the outplant site that mirrored its coral community. These surveys served as ‘control sites’ to assess the potential relationship between the outplanted corals and the prevalence of SCTLD within the community in the immediate vicinity of the outplant site and sites without outplanting activity.

2.4 Data analysis of outplanted coral

We evaluated the probability of coral colony survival, the probability of coral colonies exhibiting signs of SCTLD infection, and the probability of colonies exhibiting signs of finfish predation by fitting mixed effects generalized linear regression models to the coral outplant data. Due to the number of predictor variables and their interactions, we evaluated each coral species used in the outplant study separately to ensure the inclusion of interactions and convergence of logistic regression models. For each of the three species, we fitted a mixed effects logistic regression model to the binary survival (1 = alive; 0 = dead), SCTLD (1 = evidence of SCTLD present; 0 = no evidence of SCTLD) metrics (i.e., response variables) recorded for each colony during each of the 25 survey periods. Predictor variables were: 1) Region (i.e., a categorical variable representing the six geographic regions), 2) Reef Stratum (i.e., a categorical variable representing “Inshore Sites” and “Offshore Sites”), 3) Colony Source (i.e., a categorical variable representing corals from in-water nurseries sourced from FWC, Reef Renewal, U.S.A. L.L.C., and the Coral Restoration Foundation, and those from land-based facilities sourced from Mote Marine Laboratory and University of Miami), and 4) a continuous variable representing each of 25 survey periods (hereafter, monitoring intervals). To account for spatial and temporal dependence (e.g., instances of non-independence), we included a random intercept representing unique combinations of study site, species, geographic region, reef stratum, and monitoring intervals. We acknowledge that because individual colony identity was not included as a random effect, the models may not fully account for temporal autocorrelation associated with repeated measurements of the same colonies. However, the inclusion of site-by-time random effects captures shared environmental and disease-related variation at the relevant spatial and temporal scales.

We then fitted a suite of (up to) eight candidate logistic regression models, starting with the global model that included all predictor variables, including several interaction terms. The number of models fitted varied due to convergence issues owing to quasi- or complete separation (i.e., instances where all individuals in a group exhibited all, or almost all, 1 or 0 responses in the binary logistic regression). Each of the candidate models represented a unique combination of the predictors listed above, and all were subsets of the global model. We used Akaike’s Information Criterion corrected for small sample size (AICc; Hurvich and Tsai, 1989) to rank the relative support for each candidate model. We identified the best approximating logistic regression model as the one with the lowest AICc.

Following model fitting, we assessed goodness-of-fit for each species’ best approximating model using a simulation-based approach to residual analysis, implemented in the R package `DHARMa` (Hartig and Hartig, 2022), to detect any evidence of unexplained patterns in model residuals.

2.5 Coral community monitoring

Because individual colonies were not uniquely identified during roving diver surveys, we analyzed SCTLD prevalence using generalized linear mixed models (GLMMs) with a beta-binomial distribution to account for overdispersion common in proportion data with excess zeros. The full model included the three-way interaction of Region, Reef Stratum, Site Type (control vs. outplant) as fixed effects. To account for spatial and temporal dependence (e.g., instances of non-independence), we included a random intercept representing unique combinations of survey site, geographic region, reef stratum, and monitoring interval. We used the beta-binomial family rather than binomial due to greater variance in the data than expected under the binomial distribution. Model fit was assessed using DHARMa residual diagnostics, including tests for dispersion, outliers, and quantile deviations. We note that although the outplanted colonies consisted of species considered to be moderately or highly susceptible to SCTLD, we included all species considered susceptible to SCTLD, regardless of perceived susceptibility to comprehensively assess disease impacts across the entire natural coral community.

3 Results

3.1 Summary of coral outplant monitoring

Of the potential 600 surveys of the outplant sites scheduled from May 2021 through April 2023, 596 were completed. Because of weather and logistical considerations, four sites were not visited at all time-points.

By the final surveys conducted during April 2023 (2 years post-outplant), 901 colonies (77.3%) were classified as alive (i.e., live tissue present), while 260 (22.3%) were classified as dead (i.e., living tissue was absent and the skeleton was exposed or had been colonized by algae or biofilm) or had been recorded as missing and presumed dead (Figure 4). The status of the remaining four colonies (0.3%) was not recorded. The proportion of living coral colonies (mean ± SE) with signs of SCTLD infection across all sites during the study period ranged from 0% (May 2021) to 4.2% (July 2022) (1.14 ± 0.20%) (Figure 5). A total of 192 colonies were recorded as exhibiting SCTLD (Figure 6). Of the 223 M. cavernosa colonies outplanted, 32 (14.0%) were recorded as exhibiting SCTLD during at least one monitoring interval over the 24-month study. Of the 652 O. faveolata, 118 (18.1%) were recorded as exhibiting SCTLD, and SCTLD was recorded for 42 (14.4%) of the 290 P. clivosa colonies. The whole-colony mortality rates among SCTLD affected colonies were 25.0%, 35.6%, and 59.5% among M. cavernosa, O. faveolata, and P. clivosa, respectively. Of those colonies that died, 26 (34.7%) were dead by the next survey period after initially being observed with SCTLD, and a total of 45 colonies (60.0%) were dead by two survey periods after the initial observation.

Figure 4

Figure 5

Figure 6

3.2 Summary of the roving diver surveys of the natural coral communities

During the monthly roving diver surveys within the outplant areas, divers recorded a total of 20,320 (mean ± SE = 3,511.5 ± 98.4) colonies of SCTLD-susceptible species per survey event across all sites, based on paired 10-minute non-overlapping roving diver surveys. Colonies observed during different survey periods were not assumed to represent unique individuals, and counts were used solely to estimate disease prevalence during each survey. The monthly prevalence of those colonies that were observed with active SCTLD across the surveys ranged from 0.3% to 1.4% (0.33 ± 0.07%). During the quarterly roving diver surveys within the control area, divers observed a total of 8,184 (mean of 3,224.0 ± 167.5) colonies of SCTLD-susceptible coral species. The prevalence of colonies that were observed with active SCTLD during the quarterly surveys ranged from 0.1% to 2.1% (0.66 ± 0.20%). As with the surveys of the natural areas, these surveys did not identify individual colonies, and thus colonies may have been observed during multiple survey periods. Counts therefore represent the number of colonies encountered during each survey event and were used only to estimate disease prevalence at the time of the survey.

3.3 Probability of SCTLD infection—outplanted colonies

The GLMM indicated that the probability of M. cavernosa exhibiting SCTLD at any monitoring interval was < ~1% across all regions, reef strata, and colony sources (Figure 7A). Neither monitoring interval (OR: 0.94, p = 0.740) nor reef stratum (OR: 1.55, p = 0.501) significantly affected SCTLD infection (Table 2; Supplementary Table 1). However, a significant effect of coral colony source was detected. UM-sourced colonies exhibited 55% lower odds of SCTLD infection compared to FWC-sourced colonies (OR: 0.45, p = 0.029) (Table 1). The intraclass correlation coefficient (ICC) indicated substantial clustering of SCTLD occurrence within site-region-species-monitoring interval combinations (ICC = 0.89), and the marginal R² (0.020) indicated that the fixed effects (region, stratum, source, time) explained little of the observed variation in SCTLD incidence.

Figure 7

The GLMM for O. faveolata revealed greater variability in the probability of SCTLD infection than M. cavernosa (Table 2; Supplementary Table 2), yet mean infection probabilities at any survey period did not exceed approximately 2% across treatment levels (Figure 7B). Monitoring interval (OR: 0.96, p = 0.386) and reef stratum (OR: 0.96, p = 0.872) did not significantly affect SCTLD infection probability. Coral colony source showed significant differences, as FWC-sourced colonies exhibited twice the odds of SCTLD infection compared to CRF-sourced colonies (OR: 2.09, p = 0.017) (Table 2). Additionally, a significant interaction between region and monitoring interval was detected in the Upper Keys, where SCTLD infection probability increased over the survey period (OR: 1.16, p = 0.033), but the absolute infection probability was < 2% across all sources and regions.

Finally, the GLMM for P. clivosa indicated SCTLD infection rates at any monitoring interval approximated 1% across the survey period (Figure 7C). Survey monitoring interval (OR: 0.97, p = 0.688) and reef stratum (OR: 1.79, p = 0.145) did not significantly affect SCTLD infection probability (Table 2; Supplementary Table 3). However, colony source showed significant effects. Both UM-sourced (OR: 0.43, p = 0.033) and MML-sourced (OR: 0.33, p = 0.047) colonies exhibited 57% and 67% lower odds of SCTLD infection, respectively, compared to CRF-sourced colonies (Table 1). But again, as with the other two species, SCTLD occurrence was uniformly ~ 1%. The ICC (0.63) indicated considerable clustering of SCTLD occurrence within site, region, reef stratum, and monitoring interval combinations.

3.4 Prevalence of SCTLD of the natural coral communities

The beta-binomial mixed-effects GLMM explained 60.3% of total variance in SCTLD prevalence (conditional R²) (Supplementary Table 4). Fixed effects (region, reef stratum, outplant site/control site, and interactions) accounted for 21.2% of variance, while site-level random effects contributed an additional 39.1%. The model detected no significant differences in SCTLD prevalence between the diver surveys conducted within the outplant sites and at control sites (OR = 1; p = 0.997), and none of the two-way or three-way interactions that included outplant site and controls sites were significant (Supplementary Table 4). The random effect variable indicated substantial natural variation in SCTLD prevalence between site groupings (ICC = 0.271), indicating that 27.1% of total variance was attributable to spatial clustering within unique site, region, reef stratum, and monitoring interval combinations.

3.5 Probability of colony survival–outplanted colonies

The GLMM for M. cavernosa survival indicated strong effects of both time and reef stratum (Figure 8A). Survival probability declined significantly over the survey period, with a 10% decrease in odds of survival per monitoring interval (OR: 0.90; p < 0.001) (Table 3; Supplementary Table 5). Reef stratum had a pronounced effect, with offshore sites exhibiting 77% lower odds of survival compared to inshore sites (OR: 0.23; p < 0.001). Colony source also significantly affected survival. The UM-sourced colonies had 62% lower odds of survival compared to FWC-sourced colonies (OR: 0.38; p < 0.001). A significant interaction between region and monitoring interval was detected in the Middle Keys, where survival declined more slowly than other regions over the monitoring period. The moderate intraclass correlation coefficient (ICC = 0.11) indicated some clustering of survival outcomes within site-region-species-monitoring interval combinations. The marginal R² (0.40) indicates that fixed effects explained 40% of the variation in survival, with the conditional R² (0.47) showing that the full model including random effects explained 47% of total variation.

Figure 8

The GLMM for O. faveolata revealed the strongest temporal decline among the three species, with survival probability decreasing 21% per monitoring interval (OR: 0.79; p < 0.001) (Table 3; Supplementary Table 6; Figure 8B). Unlike the other two species, reef stratum did not show a significant main effect (OR: 0.49; p = 0.347), though significant region × stratum interactions were detected in the Upper Keys and Lower Keys, where offshore sites showed lower survival than expected. Colony source had a pronounced effect. RR-sourced colonies exhibited six times the odds of survival compared to CRF-sourced colonies (OR: 6.00; p < 0.001). Additionally, multiple significant interactions between region and monitoring interval were detected (Broward, Upper Keys, Lower Keys), indicating that temporal decline of survival rates varied geographically, with these regions showing slower declines than others. The model also detected multiple three-way interactions, suggesting complex relationships among region, reef stratum, and time that varied across the study area. The ICC (0.02) indicated minimal clustering at the site level, with most variation explained by the measured fixed effects. The fixed effects explained 45% of variation in survival (marginal R² = 0.45). The virtually identical conditional R² (0.46) confirmed that there was minimal contribution of random effects to the model.

The GLMM for P. clivosa indicated a moderate temporal decline, as the probability of survival decreased 14% per monitoring interval (OR: 0.86; p = 0.036) (Table 3; Supplementary Table 7; Figure 8C). This species exhibited the most extreme reef stratum effect, as offshore sites exhibited 99% lower probability of survival compared to inshore sites (OR: 0.01; p < 0.001). Colony source also significantly affected survival. The MML-sourced colonies exhibited 92% lower odds of survival compared to FWC-sourced colonies (OR: 0.08; p = 0.002). No significant interactions between region and monitoring interval were detected. However, significant interactions between region and reef stratum were detected in all five regions where offshore sites were present, indicating that whereas the survival of corals at the offshore sites was uniformly lower compared to inshore sites, the magnitude of this effect varied geographically. The model also detected multiple three-way interactions among region, reef stratum, and other predictors. The marginal R² (0.73) indicated that fixed effects explained 73% of variation in survival, indicating that the measured predictors captured most of the systematic variation in P. clivosa survival, while the conditional R² (0.74) and ICC (0.05) indicated minimal additional contribution from random effects.

4 Discussion

The probability of SCTLD infection in outplanted corals ranged from < 1-2% across all three species, regions, reef strata, and colony sources throughout the study period. Similarly, SCTLD prevalence in the natural coral communities at outplant sites approximated 1% and was statistically indistinguishable from control sites, indicating that outplanting activities did not function as disease vectors. These infection rates are substantially lower than those observed along FCR from 2014–2018 during the epizootic phase of SCTLD (Precht et al., 2016; Walton et al., 2018; Sharp et al., 2020). Consequently, compared to overall colony survival rates, SCTLD infection was not the primary driver of colony mortality during this study.

Although statistically significant differences in SCTLD susceptibility were detected among colony sources, these differences occurred within a narrow range of infection probabilities, with all sources exhibiting infection rates near or below 1%. Similarly, the only temporal trend detected was a modest increase in SCTLD infection probability in O. faveolata outplants in the Upper Keys region, but absolute infection rates remained below 2% throughout the monitoring period. Moreover, the study found no support for the hypothesis that host genetic lineages predicted SCTLD susceptibility among the outplanted colonies (Bell et al., 2025).

The intraclass correlation coefficients across all three species indicate that most variation in SCTLD occurrence was attributable to site-level random effects rather than the measured fixed effects, indicating that site selection and local environmental conditions were more important determinants of SCTLD risk than the broad regional or reef strata classifications defined in this study. We note, however, that individual colony identity was not included as a random effect, which may not fully account for repeated measurements of the same colonies. Despite this limitation, SCTLD infection and mortality were markedly reduced from epizootic levels, indicating that restoration activities are unlikely to be constrained by concerns about SCTLD prevalence under current enzootic conditions.

These results contribute to our understanding of coral restoration in disease-affected systems, particularly whether outplanting increases disease risk through host density or transmission (Bruno and Selig, 2007; Weil et al., 2006), or whether restored populations can persist under chronic disease exposure (Papke et al., 2024; Hein et al., 2020). Contrary to expectations, coral survival was more strongly shaped by site, species, and propagation source than by SCTLD prevalence.

It is clear that during epizootic phases, SCTLD constrains restoration through acute disease mortality and transmission risk (e.g., Sharp et al., 2020). In contrast, our results suggest that under enzootic conditions, restoration outcomes become increasingly structured by habitat suitability, propagation practices, and other local ecological drivers. This shift in the relative importance of disease versus environmental and operational factors has important implications for how restoration strategies are prioritized and evaluated in chronically disease-affected reef systems.

Reef stratum was the dominant factor affecting survival for both M. cavernosa and, in particular, P. clivosa. The higher offshore mortality documented in P. clivosa could have been anticipated given this species’ typical confinement to shallower habitats as compared to either M. cavernosa or O. faveolata (Bak, 1977). Nonetheless, P. clivosa was included in this project because it was the only highly SCTLD-susceptible species (FKNMS, 2018) available in sufficient numbers from coral propagation facilities to accommodate the experimental design. Montastraea cavernosa also exhibited substantially lower offshore survival. This is consistent with broader patterns of higher coral abundance on inshore reefs across FCR (Aguilar et al., 2024; Jones et al., 2022; Manzello, 2015). The environmental conditions that favor natural coral populations at inshore sites appear to similarly benefit M. cavernosa outplant survival. In contrast, the absence of a detectable stratum effect for O. faveolata is consistent with its comparatively broader depth and habitat distribution (Lirman and Fong, 2007). However, the significant interaction between regions and reef stratum detected in the Upper and Lower Keys suggested that the survival rates of O. faveolata varied geographically, perhaps mediated by local environmental conditions rather than representing a species-wide pattern. We did not directly quantify environmental covariates such as temperature, turbidity, nutrients, or hydrodynamics; therefore, the specific abiotic mechanisms underlying observed site-level differences remain unresolved. Given that offshore reef habitats represent conservation priorities for restoration along the FCR, identifying the ecological drivers affecting the survival of corals at offshore locations and developing outplanting strategies better suited to these conditions should be prioritized.

Yet the most striking differences in survival of M. cavernosa and P. clivosa were associated with the source of the corals. Corals sourced from the land-based facilities (UM, MML) exhibited 62% and 92% lower odds of survival, respectively, compared to in-water nursery corals (FWC, RR, CRF). Moreover, the absence of significant interactions between coral source and reef stratum indicates that these differences were consistent across both inshore and offshore sites. However, we note that corals sourced from the different research parter represents composite variable that includes propagation environment (i.e., land-based vs. in-water nurseries), husbandry practices, handling and transport history, and potentially unmeasured differences among propagated stocks. Accordingly, source effects cannot be attributed solely to propagation system.

It is possible that corals from in-water nurseries benefit from general preconditioning to reef conditions such as natural water flow regimes, temperature fluctuations, and microbial exposures that land-based systems cannot fully replicate. Such broad physiological hardening may contribute to the higher predicted survival rates we observed in this study, though we cannot separate the effects of nursery environment from inherent differences among coral sources. However, it has been shown that targeted conditioning of corals maintained in land-based facilities confers certain advantages to them compared to corals maintained within in-water nurseries. Ladd et al. (2024) demonstrated that Diploria labyrinthiformis maintained in land-based facilities and provided with supplemental feeding increased their growth rates, resulting in larger sized corals at the time of outplanting, and continued to exhibit higher growth rates, which decreased their probability of being removed by predators compared to conspecifics maintained within in-water nurseries prior to outplanting. Although we acknowledge that nursery duration and husbandry conditions differed between studies, this contrast between our findings suggests that differences in coral performance between land-based and in-water sources may reflect differences in specific husbandry practices rather than inherent limitations of either propagation system. Future work should identify which conditioning protocols most effectively improve post-outplant resilience and whether these can be replicated or enhanced in land-based systems.

Beyond the source-related differences in baseline survival, predation by corallivorous fishes emerged as an additional mortality factor, consistent with earlier outplanting efforts (Smith et al., 2021). Predation was particularly intensive during the first month post-outplant across all three species before declining (Sharp et al., 2024). Sites off Miami-Dade and Broward Counties experienced the highest predation intensity. As colonies grow in size over time, this temporal pattern—concentrated early predation on smaller recently outplanted colonies—aligns with Ladd et al.’s (2024) finding that larger colony size at deployment reduces predation risk, suggesting that size at outplanting may be a critical factor mediating survival. Developing strategies to mitigate early post-deployment predation, whether through increased colony size, protective structures, or site selection criteria, represents an important area for methodological refinement.

The interaction between source and geographic effects on survival, combined with Bell et al.’s (2025) finding that neither host genetic lineages nor pre-deployment algal symbiont types predicted SCTLD susceptibility, has important implications for a large-scale coral restoration strategy. Although specific genotypes did not confer resistance to SCTLD, the strong source and regional effects on survival suggest that coral performance is mediated by complex interactions between propagation conditions, local environmental factors, and potentially unmeasured genetic traits. This uncertainty reinforces the need for a restoration strategy that prioritizes genetically diverse coral assemblages rather than attempting to select for specific ‘superior’ genotypes based on single stressor responses. Genotyping should be prioritized within nurseries and before outplanting to verify species, maximize genetic variation, and enhance population-level resilience to the multiple, interacting stressors threatening Florida’s coral reefs. Yet the reliance on asexual propagation, which is the predominant method used in this study and across most current restoration efforts, ultimately limits the genetic diversity available for outplanting (Bell et al., 2025). Given the complex interactions among propagation source, local environmental conditions, and geographic region documented in this study, maximizing genetic variation through sexual propagation will be essential for achieving resilient restoration outcomes across the spatially heterogeneous FCR. The SCTLD rescue effort, which removed genetically diverse coral colonies from the reef ahead of the disease front and relocated them to land-based facilities for spawning (seeWilliamson et al., 2022), provides a critical pathway for this transition. These facilities have begun producing sexually derived offspring with substantially greater genetic diversity than asexual fragments. As these progeny reach outplanting size, they offer an opportunity to test whether sexually produced corals with diverse genotypes exhibit enhanced resilience compared to clonal lineages. Expanding sexual propagation efforts, particularly through continued spawning of rescued genotypes and integration of their offspring into restoration programs, should be prioritized as restoration activities scale within disease-enzootic zones where environmental unpredictability and multiple stressors demand broad adaptive capacity. Among these emerging frameworks, Florida’s Ecological Restoration Strategy (Florida's Coral Reef Resilience Program, 2024) and NOAA’s Manager’s Guide to Coral Reef Restoration Planning and Design (Shaver et al., 2020) provide complementary guidance that incorporates empirical findings like those documented here. Both emphasize adaptive management, strategic site selection based on survivorship potential, and continuous monitoring. These principles are directly supported by our documentation of substantial site-specific and source-specific survival differences. Our species-specific and site-specific performance findings provide baseline information essential for implementing the adaptive management approaches both documents outline.

Our study demonstrates that coral restoration can proceed within SCTLD-enzootic zones along Florida’s Coral Reef. Disease prevalence remained consistently ~1% among outplanted colonies throughout the 2-year monitoring period, and critically, outplanting activities did not increase SCTLD prevalence in adjacent natural coral communities. Moreover, targeted disease interventions using antibiotic treatments have proven effective at reducing SCTLD prevalence in enzootic areas when applied strategically (Toth et al., 2024), providing an additional tool for protecting both natural and outplanted populations. However, restoration success will ultimately depend on addressing the suite of factors that did drive mortality in this study. The pronounced offshore-inshore gradient in survival, particularly for M. cavernosa and P. clivosa, underscores the need for species-habitat matching and the development of outplanting strategies better suited to offshore reef environments that represent conservation priorities. The substantial performance differences between propagation sources highlight the importance of optimizing husbandry protocols across propagation systems to ensure corals are adequately conditioned for reef deployment. Early post-outplant predation by corallivorous fishes, particularly intensive in certain regions, represents one of several interacting biotic and abiotic factors contributing to early mortality, alongside habitat suitability and local environmental conditions, and may warrant mitigation strategies to protect newly deployed colonies during their most vulnerable period. Adaptive management approaches integrating site selection, propagation optimization, genetic diversity, and targeted intervention strategies will be essential for resilient restoration outcomes across the FCR. Although SCTLD has transitioned from an acute epizootic event to a chronic stressor, successful large-scale restoration in this transformed reef ecosystem will require continued refinement of coral restoration methods that address the multiple interacting factors determining longer-term coral survival.

Whether outplanted coral populations can achieve sustained recovery and contribute meaningfully to reef-scale population replenishment under continued chronic disease pressure remains an important question, and one that only long-term monitoring of restored reefs will resolve.

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