We announce the U.S. Geological Survey (USGS) Rotating X-ray Computed Tomography (RXCT) Coral-Core Archive, a digital resource derived from similar to 360 coral reef cores curated at the USGS Pacific and St. Petersburg Coastal and Marine Science Centers. The archive delivers calibrated 3-dimensional image volumes that enable reproducible values of skeletal density, linear extension, and calcification from decadal- to centennial-scale records of coral growth and bioerosion. Cross-study comparability within the archive is supported by a unified RXCT workflow that minimizes imaging artifacts. This includes rejecting image-intensity-density calibrations with r(2) < 0.95, back-calculating standard densities to verify a +/- 10% target precision, and confirming that band-averaged density values fall within published species- and site-specific ranges. Our release of data under FAIR (Findable, Accessible, Interoperable, Reusable) principles is important given global coral reef decline and the rarity of physical coral archives. Calibrated imagery and scan metadata are distributed through CoralCache/CoralCT for analysis (DOI: 10.5194/essd-2025-598), while core locations and collection metadata are published through the USGS Geologic Core and Sample Database (DOI: 10.5066/F7319TR3) with links to CT imagery in a USGS ScienceBase repository (DOI: 10.5066/P139Y9H4). This archive provides a powerful dataset for evaluating environmental controls on coral growth, establishing restoration baselines, and improving coastal hazard assessments in the face of global coral reef declines.

The ecological significance of the reef-building elkhorn coral, Acropora palmata, is threatened by heat-stress-induced mortality. The intensity and duration of the ocean heatwave affecting Dry Tortugas National Park in the summer of 2023 was historically unprecedented in its early timing and maximum temperatures reached and resulted in 100

The ongoing global‐scale reassembly of modern coral reefs is unprecedented compared with the observed stability of most late Quaternary reef assemblages. One notable exception is the marine isotope stage (MIS) 5e ( ca 130–116 thousand years ago [ka]) reefs in the Florida Keys, where the ubiquitous shallow‐water coral, Acropora palmata , was near absent. Little is known, however, about reefs that grew during MIS5d–a ( ca 116–74 ka), between MIS5e and the Holocene. It is therefore unclear whether Florida's unique MIS5e coral assemblages represent a geologically brief anomaly or a more persistent departure from the western Atlantic coral‐reef archetype. We addressed that question by reconstructing the composition of MIS5d–a reefs within 29 coral‐reef cores collected throughout the Florida Keys. We then compared the relative composition of corals during MIS5d–a to existing datasets from MIS5e, Holocene and modern (1996 and 2022) reefs to evaluate how far today's reef assemblages have diverged from geological baselines. We show that although the proportion of reef frameworks built by corals was remarkably consistent ( ca 38%), species composition changed significantly through time. Acropora palmata was rare throughout MIS5, which we hypothesise was due to greater cold‐temperature stress in Florida's subtropical reefs compared with the more climatically stable tropics. In contrast, the massive reef‐building coral, Orbicella spp., was regionally dominant throughout the late Quaternary, but has become increasingly rare on modern reefs. By 2022, reefs in the Florida Keys were characterised by a truly novel coral assemblage dominated by Porites astreoides and Siderastrea siderea . In many ways, Florida's reefs defy the concept of a natural baseline; instead, their most persistent characteristic since the Late Pleistocene is their uniqueness. Yet, as reefs are increasingly subjected to unprecedented levels of environmental change, the exceptions to what was normal in the past could, paradoxically, provide the best geological analogues for the future.

Coral-reef degradation is disrupting the balance between reef accretion and erosion and threatening the persistence of essential coral-reef habitats. In south Florida, most reefs are already net eroding, and without intervention, valuable ecosystem services may be lost. Coral restoration holds the potential to reverse those trends; however, typical restoration monitoring does not adequately capture key geo-ecological functions. We addressed this knowledge gap using carbonate budgets and Structure-from-Motion models to evaluate the impact of coral restoration on reef-accretion potential and structural complexity at eight offshore and three inshore coral reefs in the Lower Florida Keys. Within 2–6 years following outplanting, restoration of rapidly growing A. cervicornis populations increased reef-accretion potential to 2.8 mm y− 1 and drove significant increases in structural complexity. There was no measurable impact of restoring slower-growing, massive corals on reef-accretion potential inshore; however, whereas the severe 2023 coral-bleaching event immediately following our study caused near-complete mortality of A. cervicornis, 59% of massive corals survived, highlighting potential trade-offs between coral growth and survival on future restoration efficacy. We conclude that although restoration can produce rapid, small-scale increases in reef-accretion potential, there remain important uncertainties about how and whether ecosystem-scale benefits of restoration on important geo-ecological reef functions can persist long term.

Emblematic of global coral‐reef ecosystem decline, the coral ecosystem‐engineer Acropora palmata is now rare throughout much of the western Atlantic. Understanding when and where this foundation species occurred during the past can provide information about the environmental limits defining its distribution through space and time. In this paper, the present, historical and newly dated geological records of A. palmata are compared to reveal novel insights into the environmental constraints on its occurrence in Dry Tortugas National Park, a subtropical reef system at the south‐western terminus of the Florida reef tract. Although past geological investigation found little evidence of the species in the park, a single, moderately sized A. palmata reef existed throughout historical times (1881 Common Era [CE] to present day; ‘historical population’, termed herein). Over the last 140 years, repeated population declines occurred with little to no recovery, culminating in the extirpation of A. palmata from the area during the 2023–2024 CE global coral bleaching event. Reported here for the first time is a significant record of Late Holocene A. palmata populations that existed from ca 4500 to 375 years before present (‘Late Holocene population,’ termed herein) in three broadly distributed areas of the shallow Dry Tortugas platform. This discovery challenges previous assumptions regarding the species' limited contribution to reef development in the area by providing data that extend the known spatial and stratigraphic extent of Holocene populations in this location. It is posited that, although the Late Holocene climate largely suppressed regional reef development, the new records provide evidence for centennial‐scale periods of more favourable and stable climate that allowed for short‐term expansions of A. palmata populations in the Dry Tortugas. In conclusion, the species' prospects for future success in this and other subtropical locations is discussed given the observed global trends of increasing sea‐surface temperatures.

The ability of reefs to protect coastlines from storm-driven flooding hinges on their capacity to keep pace with sea-level rise. Here, we show how and whether coral restoration could achieve the often-cited goal of reversing the impacts of coral-reef degradation to preserve this essential function. We combined coral-growth measurements and carbonate-budget assessments of reef-accretion potential at Buck Island Reef, U.S. Virgin Islands, with hydrodynamic modeling to quantify future coastal flooding under various coral-restoration, sea-level rise, and storm scenarios. Our results provide guidance on how restoration of Acropora palmata, if successful, could mitigate the most extreme impacts of coastal flooding by reversing projected trajectories of reef erosion and allowing reefs to keep pace with the ~0.5 m of sea-level rise expected by 2100 with moderate carbon-emissions reductions. This highlights the potential long-term benefits of pursuing coral-reef restoration alongside climate-change mitigation to support the persistence of essential coral-reef ecosystem services.

The iconic and threatened Caribbean coral, Acropora palmata , is an essential reef-ecosystem engineer. Understanding the processes underpinning this coral’s survival and growth is essential to restoring this foundational species. Here, we compared replicate A. palmata colonies transplanted along 350 km of Florida’s offshore coral reef to determine holobiont and/or environmental variables that predict transplant success. We found a west-to-east gradient in coral physiology coupled with site-specific coral-associated microbiomes. Interestingly, no variables were linked to coral genet. Our results suggest that the unique oceanographic conditions with periodic upwelling events in the Dry Tortugas provide corals with greater opportunity for heterotrophy that in turn enhances coral growth and survivorship, and positively influences the microbiome. Our findings indicate that restoration efforts in the Dry Tortugas, and other places exhibiting higher food availability, could be most effective for A. palmata .

The Florida Keys reef tract (FKRT) has a unique geological history wherein Holocene sea-level rise and bathymetry interacted, resulting in a reef-building system with notable spatial differences in reef development. Overprinted on this geologic history, recent global and local stressors have led to degraded reefs dominated by fleshy algae, soft corals, and sponges. Here, we assessed how coral physiology (calcification rate, tissue thickness, reproduction, symbiosis, and bleaching) varies seasonally (winter vs. summer) and geographically using 40 colonies of the mustard hill coral Porites astreoides from four sites across 350 km along the FKRT from 2015 to 2017. The study coincided with a high-temperature event in late summer 2015 that caused heterogeneous levels of coral bleaching across sites. Bleaching severity differed by site, with bleaching response more aligned with heat stress retroactively calculated from local degree heating weeks than those predicted by satellites. Despite differences in temperature profiles and bleaching severity, all colonies hosted Symbiodiniaceae of the same genus (formerly Clade A and subtypes). Overall, P. astreoides at Dry Tortugas National Park, the consistently coolest site, had the highest calcification rates, symbiont cell densities, and reproductive potential (all colonies were reproductive, with most planula larvae per polyp). Corals at Dry Tortugas and Fowey Rocks Light demonstrated strong seasonality in net calcification (higher in summer) and did not express visual or partial-mortality responses from the bleaching event; in contrast, colonies in the middle and southern part of the upper keys, Sombrero Key and Crocker Reef, demonstrated similar reduced fitness from bleaching, but differential recovery trajectories following the heat stress. Identifying reefs, such as Dry Tortugas and possibly Fowey Rocks Light that may serve as heat-stress refugia, is important in selecting candidate sites for adaptive reef-management strategies, such as selective propagation and assisted gene flow, to increase coral-species adaptation to ocean warming.

Climate plays a central role in coral-reef development, especially in marginal environments. The high-latitude reefs of southeast Florida are currently non-accreting, relict systems with low coral cover. This region also did not support the extensive Late Pleistocene reef development observed in many other locations around the world; however, there is evidence of significant reef building in southeast Florida during the Holocene. Using 146 radiometric ages from reefs extending ~ 120 km along Florida’s southeast coast, we test the hypothesis that the latitudinal extent of Holocene reef development in this region was modulated by climatic variability. We demonstrate that although sea-level changes impacted rates of reef accretion and allowed reefs to backstep inshore as new habitats were flooded, sea level was not the ultimate cause of reef demise. Instead, we conclude that climate was the primary driver of the expansion and contraction of Florida’s reefs during the Holocene. Reefs grew to 26.7° N in southeast Florida during the relatively warm, stable climate at the beginning of the Holocene Thermal Maximum (HTM) ~ 10,000 years ago, but subsequent cooling and increased frequency of winter cold fronts were associated with the equatorward contraction of reef building. By ~ 7800 years ago, actively accreting reefs only extended to 26.1° N. Reefs further contracted to 25.8° N after 5800 years ago, and by 3000 years ago reef development had terminated throughout southern Florida (24.5–26.7° N). Modern warming is unlikely to simply reverse this trend, however, because the climate of the Anthropocene will be fundamentally different from the HTM. By increasing the frequency and intensity of both warm and cold extreme-weather events, contemporary climate change will instead amplify conditions inimical to reef development in marginal reef environments such as southern Florida, making them more likely to continue to deteriorate than to resume accretion in the future.

Recovery of the elkhorn coral Acropora palmata is critical to reversing coral reef ecosystem collapse in the western Atlantic, but the species is severely threatened. To gauge potential for the species’ restoration in Florida, USA, we conducted an assisted migration experiment where 50 coral fragments of 5 nursery-raised genetic strains (genets) from the upper Florida Keys were moved to 5 sites across 350 km of the offshore reef. Additionally, 4 fragments from the 1 remaining colony of A. palmata in Dry Tortugas National Park (DRTO) were added to the 2 DRTO experimental sites to test for local adaptation. To measure coral performance, we tracked coral survival, calcification, growth, and condition from May 2018 to October 2019. All 24 corals relocated to the DRTO sites survived and calcified ~85% faster than the fewer surviving corals transplanted to the 2 upper Keys sites. While coral survival across the entire experiment did not depend on genet, there was a weak but statistically significant genetic effect on calcification rate among the corals relocated to DRTO. The DRTO native genet was among the fastest growing genets, but it was not the fastest, suggesting a lack of local adaptation at this scale. Our results indicate that DRTO, a remote reef system inhabited by the species during the Holocene and located at the nexus of major ocean currents, may be a prime location for reestablishing A. palmata. Assisted migration of A. palmata to DRTO could restore a sexually reproducing population in <10 yr, thereby promoting the species’ regional recovery.

The coral reefs and mangrove habitats of the south Florida region have long been used in sea-level studies for the western Atlantic because of their broad geographic extent and composition of sea-level tracking biota. The data from this region have been used to support several very different Holocene sea-level reconstructions (SLRs) over the years. However, many of these SLRs did not incorporate all available coral-based data, in part because detailed characterizations necessary for inclusion into sea-level databases were lacking. Here, we present an updated database comprised of 303 coral samples from published sources that we extensively characterized for the first time. The data were carefully screened by evaluating and ranking the visual taphonomic characteristics of every dated sample within the database, which resulted in the identification of 134 high-quality coral samples for consideration as suitable sea-level indicators. We show that our database largely agrees with the most recent SLR for south Florida over the last ∼7,000 years; however, the early Holocene remains poorly characterized because there are few high-quality data spanning this period. Suggestions to refine future Holocene SLRs in the region are provided including filling spatial and temporal data gaps of coral samples, particularly from the early Holocene, as well as constructing a more robust peat database to better constrain sea-level variability during the middle to late Holocene. Our database and taphonomic-ranking protocol provide a framework for researchers to evaluate data-selection criteria depending on the robustness of their sea-level models.

The decline in living coral since the 1970s has conspicuously slowed reef construction on a global scale, but the related process of reef erosion is less visible and not often quantified. Here, we present new data on the constructional and deconstructional sides of the carbonate-budget equation in the Florida Keys, U.S.A. We documented Orbicella spp. calcification rates at four offshore reefs and quantified decadal-scale rates of Orbicella-reef erosion at a mid-shore patch reef. Using Orbicella coral heads fitted with permanent markers in 1998, we measured reef-elevation loss at 28 stations over 17.3 yr to estimate a mean erosion rate of -5.5 (+/- 3.2, SD) mm yr(-1). This loss equates to an erosion rate of -8.2 (+/- 4.8, SD) kg m(-2) yr(-1) on dead Orbicella colonies, or -6.6 kg m(-2) yr(-1) when adjusted reef-wide. Calculating net carbonate production using a census-based approach on the same patch reef in 2017, we estimated a reef-wide bioerosion rate of -1.9 (+/- 2.0, SD) kg m(-2) yr(-1), and a net carbonate production rate of 0.5 (+/- 0.3, SD) kg m(-2) yr(-1). Substituting the erosion rate we estimated with the markers would suggest that net carbonate production at this patch reef was lower and negative, -4.2 kg m(-2) yr(-1). This divergence could be a function of high erosion rates measured on the tops of Orbicella colonies, which may be preferentially targeted by parrotfish. Nonetheless, our study suggests the need for new field data to improve estimates of reef-structure persistence as coral reefs continue to degrade.

Abstract Over the last half century, climate change, coral disease, and other anthropogenic disturbances have restructured coral‐reef ecosystems on a global scale. The disproportionate loss of once‐dominant, reef‐building taxa has facilitated relative increases in the abundance of “weedy” or stress‐tolerant coral species. Although the recent transformation of coral‐reef assemblages is unprecedented on ecological timescales, determining whether modern coral reefs have truly reached a novel ecosystem state requires evaluating the dynamics of reef composition over much longer periods of time. Here, we provide a geologic perspective on the shifting composition of Florida's reefs by reconstructing the millennial‐scale spatial and temporal variability in reef assemblages using 59 Holocene reef cores collected throughout the Florida Keys Reef Tract (FKRT). We then compare the relative abundances of reef‐building species in the Holocene reef framework to data from contemporary reef surveys to determine how much Florida's modern reef assemblages have diverged from long‐term baselines. We show that the composition of Florida's reefs was, until recently, remarkably stable over the last 8000 yr. The same corals that have dominated shallow‐water reefs throughout the western Atlantic for hundreds of thousands of years, Acropora palmata, Orbicella spp., and other massive coral taxa, accounted for nearly 90% of Florida's Holocene reef framework. In contrast, the species that now have the highest relative abundances on the FKRT, primarily Porites astreoides and Siderastrea siderea, were rare in the reef framework, suggesting that recent shifts in species assemblages are unprecedented over millennial timescales. Although it may not be possible to return coral reefs to pre‐Anthropocene states, our results suggest that coral‐reef management focused on the conservation and restoration of the reef‐building species of the past, will optimize efforts to preserve coral reefs, and the valuable ecosystem services they provide into the future.

The global‐scale degradation of coral reefs has reached a critical threshold wherein further declines threaten both ecological functionality and the persistence of reef structure. Geological records can provide valuable insights into the long‐term controls on reef development that may be key to solving the modern coral‐reef crisis. Our analyses of new and existing coral‐reef cores from throughout the Florida Keys reef tract (FKRT) revealed significant spatial and temporal variability in reef development during the Holocene. Whereas maximum Holocene reef thickness in the Dry Tortugas was comparable to elsewhere in the western Atlantic, most of Florida's reefs had relatively thin accumulations of Holocene reef framework. During periods of active reef development, average reef accretion rates were similar throughout the FKRT at ~3 m/ky. The spatial variability in reef thickness was instead driven by differences in the duration of reef development. Reef accretion declined significantly from ~6,000 years ago to present, and by ~3,000 years ago, the majority of the FKRT was geologically senescent. Although sea level influenced the development of Florida's reefs, it was not the ultimate driver of reef demise. Instead, we demonstrate that the timing of reef senescence was modulated by subregional hydrographic variability, and hypothesize that climatic cooling was the ultimate cause of reef shutdown. The senescence of the FKRT left the ecosystem balanced at a delicate tipping point at which a veneer of living coral was the only barrier to reef erosion. Modern climate change and other anthropogenic disturbances have now pushed many reefs past that critical threshold and into a novel ecosystem state, in which reef structures built over millennia could soon be lost. The dominant role of climate in the development of the FKRT over timescales of decades to millennia highlights the potential vulnerability of both geological and ecological reef processes to anthropogenic climate change.

Staghorn coral, Acropora cervicornis , is a threatened species and the primary focus of western Atlantic reef restoration efforts to date. We compared linear extension, calcification rate, and skeletal density of nursery-raised A. cervicornis branches reared for 6 months either on blocks attached to substratum or hanging from PVC trees in the water column. We demonstrate that branches grown on the substratum had significantly higher skeletal density, measured using computerized tomography, and lower linear extension rates compared to water-column fragments. Calcification rates determined with buoyant weighing were not statistically different between the two grow-out methods, but did vary among coral genotypes. Whereas skeletal density and extension rates were plastic traits that depended on grow-out method, calcification rate was conserved. Our results show that the two rearing methods generate the same amount of calcium carbonate skeleton but produce colonies with different skeletal characteristics and suggest that there is genetically based variability in coral calcification performance.

First posted July 21, 2016 For additional information, contact: Director, St. Petersburg Coastal and Marine Science Center U.S. Geological Survey 6000 4th Street South St. Petersburg, FL 33701 (727) 502-8068 http://coastal.er.usgs.gov/ The Florida Keys reef tract (FKRT) is the largest coral-reef ecosystem in the continental United States. The modern FKRT extends for 362 kilometers along the coast of South Florida from Dry Tortugas National Park in the southwest, through the Florida Keys National Marine Sanctuary (FKNMS), to Fowey Rocks reef in Biscayne National Park in the northeast. Most reefs along the FKRT are sheltered by the exposed islands of the Florida Keys; however, large channels are located between the islands of the Middle Keys. These openings allow for tidal transport of water from Florida Bay onto reefs in the area. The characteristics of the water masses coming from Florida Bay, which can experience broad swings in temperature, salinity, nutrients, and turbidity over short periods of time, are generally unfavorable or “inimical” to coral growth and reef development.Although reef habitats are ubiquitous throughout most of the Upper and Lower Keys, relatively few modern reefs exist in the Middle Keys most likely because of the impacts of inimical waters from Florida Bay. The reefs that are present in the Middle Keys generally are poorly developed compared with reefs elsewhere in the region. For example, Acropora palmata has been the dominant coral on shallow-water reefs in the Caribbean over the last 1.5 million years until populations of the coral declined throughout the region in recent decades. Although A. palmata was historically abundant in the Florida Keys, it was conspicuously absent from reefs in the Middle Keys. Instead, contemporary reefs in the Middle Keys have been dominated by occasional massive (that is, boulder or head) corals and, more often, small, non-reef-building corals.Holocene reef cores have been collected from many locations along the FKRT; however, despite the potential importance of the history of reefs in the Middle Florida Keys to our understanding of the environmental controls on reef development throughout the FKRT, there are currently no published records of the Holocene history of reefs in the region. The objectives of the present study were to (1) provide general descriptions of unpublished core records from Alligator Reef and (2) collect and describe new Holocene reef cores from two additional locations in the Middle Keys: Sombrero and Tennessee Reefs.

Sixteen new coral reef cores were collected to better understand the accretion history and composition of submerged relict reefs offshore of continental southeast (SE) Florida. Coral radiometric ages from three sites on the shallow inner reef indicate accretion initiated by 8,050 Cal BP and terminated by 5,640 Cal BP. The reef accreted up to 3.75 m of vertical framework with accretion rates that averaged 2.53 m kyr−1. The reef was composed of a nearly even mixture of Acropora palmata and massive corals. In many cases, cores show an upward transition from massives to A. palmata and may indicate local dominance by this species prior to reef demise. Quantitative macroscopic analyses of reef clasts for various taphonomic and diagenetic features did not correlate well with depth/environmental-related trends established in other studies. The mixed coral framestone reef lacks a classical Caribbean reef zonation and is best described as an immature reef and/or a series of fused patch reefs; a pattern that is evident in both cores and reef morphology. This is in stark contrast to the older and deeper outer reef of the SE Florida continental reef tract. Accretion of the outer reef lasted from 10,695–8,000 Cal BP and resulted in a larger and better developed structure that achieved a distinct reef zonation. The discrepancies in overall reef morphology and size as well as the causes of reef terminations remain elusive without further study, yet they likely point to different climatic/environmental conditions during their respective accretion histories.