Geology topics

Travis A. Courtney

Publications and source records attributed to Travis A. Courtney.

9 recordsLinked to original sources

USGS2026

CoralCache: A virtual coral core repository for transparent and reproducible annual growth rate analyses

As science fields enter the Big Data revolution, open-access repositories are essential for addressing larger-scale questions than are possible for single researchers by making data findable, accessible, interoperable, and reusable (FAIR). Furthermore, transparent data and code are increasingly important for reproducible research, especially for data types that inherently require subjective human interpretations. These ideas are applicable to coral sclerochronology, as the field has long been characterized by individual researchers collecting and analyzing coral skeletal cores from their study sites without substantial data sharing or archiving of the core images to meet FAIR principles. Here, we present CoralCache, a virtual coral core repository that not only archives image datasets (i.e., digitized X-rays and computed tomography scans), but also observer interpretations of the density banding patterns. CoralCache is linked to a graphical user interface, CoralCT, which together offer a way forward for coral growth rate analysis that is reproducible and collaborative. The data organization systems presented here could also be readily applied to related archives such as tree rings or bivalve shells.

Earth System Science Data↗

USGS2026

Scenarios and strategies for future-proofing ecosystem management under climatic novelty

Climate change is driving unprecedented declines in dominant, habitat-forming foundation species across marine and terrestrial ecosystems globally. As climatic novelty becomes the norm, ecosystem reassembly will become increasingly common. Predicting and understanding these transitions, and their implications for future ecosystem functioning, is essential for designing effective forward-looking management strategies. We explored 3 scenarios that describe a range of ecosystem reassembly trajectories following declines in previously dominant habitat-forming taxa: compensation, in which functionally similar subdominant or immigrating taxa maintain ecosystem structure and function; decline, in which no compensation occurs leading to loss of ecosystem structure and function; and transformation, in which the ecosystem present historically can no longer persist and shifts into a fundamentally different ecosystem type with distinct structure and function. This range of potential outcomes highlights the urgent need to assess the ecological feasibility and functional implications of potential management actions. Scientists and managers can work together to quantify local-scale climatic novelty and ecosystem resilience to better predict the most likely reassembly trajectories and identify management interventions that will optimize ecosystem function. This approach would allow for more proactive planning to support persistence of ecosystem structure and function, helping to future-proof ecosystem management in a rapidly changing world.

Conservation Biology↗

USGS2026

Persistence of coral reef structures into the twenty-first century

Coral reefs provide important socioecological services but are vulnerable to climate change, which shifts the balance between the production and erosion of calcium carbonate (CaCO 3 ). In this Review, we summarize understanding of reef accretion, describe the mechanisms of carbonate production and erosion, and consider the effects of future ocean warming and acidification on key reef-building and eroding taxa. The combined stressors of climate change substantially reduce net carbonate production, with a more pronounced effect on calcifying algae than corals. However, declining coral cover driven by marine heatwaves and mass bleaching will probably be the dominant determinant of future reef carbonate budgets, and thus only reefs with thermally adapted populations are predicted to maintain the ability to sustain positive CaCO 3 production under climate change, even if calcareous algal cover increases. As carbonate budgets become net negative in the future, the longevity of pre-existing reef frameworks remains unknown and understudied owing to the timescales required to meaningfully assess framework removal rates. Improving estimates of the rates of biologically driven framework loss and chemical dissolution will also be important in better predicting future reef persistence. Key knowledge gaps exist in understanding the effects of deoxygenation on coral reefs, as well as the influence of climate change on understudied sediment-producing taxa such as foraminifera and tropical molluscs.

Nature Reviews Earth & Environment↗

USGS2023

Stony coral tissue loss disease accelerated shifts in coral composition and declines in reef accretion potential in the Florida Keys

Outbreaks of coral disease have been a dominant force shaping western Atlantic coral-reef assemblages since the late 1970s. Stony coral tissue loss disease (SCTLD) is nonetheless having an unprecedented impact in the region. Whereas numerous studies over the last decade have worked to characterize this novel pathogen and its impacts on coral populations, few have quantified its functional effects on reef ecosystems. Of particular importance is how SCTLD may be impacting the essential reef-accretion process and the myriad ecosystem services it supports. Here, we evaluated the impact of SCTLD on reef-accretion potential by estimating carbonate budgets and taxon-level carbonate production at 43 sites throughout the Florida Keys from 2016−2022. Average regional reef-accretion potential declined from an already low, but positive rate of 0.30 ± 0.16 mm y -1 (mean ± standard error) in 2016 before the disease was first observed, to a state of accretionary stasis (0.08 ± 0.12 mm y -1 ) by 2022. This 70% relative decline in reef-accretion potential was driven by the loss of reef-building corals, with significant decreases in carbonate production by massive taxa including Colpophyllia natans , Montastraea cavernosa , Pseudodiploria strigosa , Orbicella spp., and Siderastrea siderea , and increasing contributions from less susceptible, weedy taxa including Millepora spp., Agaricia spp., and Porites astreoides . In general, changes in taxon-level carbonate production following the SCTLD outbreak mirror long-term shifts in reef assemblages in response to previous stressors. One striking exception, however, is S. siderea , which had become increasingly dominant in recent decades, but declined significantly in response to SCTLD. Overall, by further decimating the already depauperate reef-building coral populations in the Florida Keys, SCTLD has caused a functionally significant shift in the composition of Florida’s coral-reef assemblages and accelerated the loss of regional reef-building capacity. The dire impacts of the disease in south Florida may serve as an early warning that the persistence of the invaluable ecological and socioeconomic functions coral reefs provide will be increasingly threatened throughout the western Atlantic in the aftermath of SCTLD.

Florida↗

USGS2023

Increasing hypoxia on global coral reefs under ocean warming

Ocean deoxygenation is predicted to threaten marine ecosystems globally. However, current and future oxygen concentrations and the occurrence of hypoxic events on coral reefs remain underexplored. Here, using autonomous sensor data to explore oxygen variability and hypoxia exposure at 32 representative reef sites, we reveal that hypoxia is already pervasive on many reefs. Eighty-four percent of reefs experienced weak to moderate (≤153 µmol O 2 kg −1 to ≤92 µmol O 2 kg −1 ) hypoxia and 13% experienced severe (≤61 µmol O 2 kg −1 ) hypoxia. Under different climate change scenarios based on four Shared Socioeconomic Pathways (SSPs), we show that projected ocean warming and deoxygenation will increase the duration, intensity and severity of hypoxia, with more than 94% and 31% of reefs experiencing weak to moderate and severe hypoxia, respectively, by 2100 under SSP5-8.5. This projected oxygen loss could have negative consequences for coral reef taxa due to the key role of oxygen in organism functioning and fitness.

Nature Climate Change↗

USGS2022

The past, present, and future of coral reef growth in the Florida Keys

Coral-reef degradation is driving global-scale reductions in reef-building capacity and the ecological, geological, and socioeconomic functions it supports. The persistence of those essential functions will depend on whether coral-reef management is able to rebalance the competing processes of reef accretion and erosion. Here, we reconstructed census-based carbonate budgets of 46 reefs throughout the Florida Keys from 1996 to 2019. We evaluated the environmental and ecological drivers of changing budget states and compared historical trends in reef-accretion potential to millennial-scale baselines of accretion from reef cores and future projections with coral restoration. We found that historically, most reefs had positive carbonate budgets, and many had reef-accretion potential comparable to the ~3 mm year −1 average accretion rate during the peak of regional reef building ~7000 years ago; however, declines in reef-building Acropora palmata and Orbicella spp. corals following a series of thermal stress events and coral disease outbreaks resulted in a shift from positive to negative budgets for most reefs in the region. By 2019, only ~15% of reefs had positive net carbonate production. Most of those reefs were in inshore, Lower Keys patch-reef habitats with low water clarity, supporting the hypothesis that environments with naturally low irradiance may provide a refugia from thermal stress. We caution that our estimated carbonate budgets are likely overly optimistic; comparison of reef-accretion potential to measured accretion from reef cores suggests that, by not accounting for the role of nonbiological physical and chemical erosion, census-based carbonate budgets may underestimate total erosion by ~1 mm year −1 (−1.15 kg CaCO 3 m −2 year −1 ). Although the present state of Florida's reefs is dire, we demonstrate that the restoration of reef-building corals has the potential to help mitigate declines in reef accretion in some locations, which could allow some key ecosystem functions to be maintained until the threat of global climate change is addressed.

Florida↗

USGS2022

Scale dependence of coral reef oases and their environmental correlates

Identifying relatively intact areas within ecosystems and determining the conditions favoring their existence is necessary for effective management in the context of widespread environmental degradation. In this study, we used 3766 surveys of randomly selected sites in the United States and U.S. Territories to identify the correlates of sites categorized as “oases” (defined as sites with relatively high total coral cover). We used occupancy models to evaluate the influence of 10 environmental predictors on the probability that an area (21.2-km 2 cell) would harbor coral oases defined at four spatial extents: cross-basin, basin, region, and subregion. Across all four spatial extents, oases were more likely to occur in habitats with high light attenuation. The influence of the other environmental predictors on the probability of oasis occurrence were less consistent and varied with the scale of observation. Oases were most likely in areas of low human population density, but this effect was evident only at the cross-basin and subregional extents. At the regional and subregional extents oases were more likely where sea-surface temperature was more variable, whereas at the larger spatial extents the opposite was true. By identifying the correlates of oasis occurrence, the model can inform the prioritization of reef areas for management. Areas with biophysical conditions that confer corals with physiological resilience, as well as limited human impacts, likely support coral reef oases across spatial extents. Our approach is widely applicable to the development of conservation strategies to protect biodiversity and ecosystems in an era of magnified human disturbance.

Ecological Applications↗

USGS2020

Disturbances drive changes in coral community assemblages and coral calcification capacity

Anthropogenic environmental change has increased coral reef disturbance regimes in recent decades, altering the structure and function of many coral reefs globally. In this study, we used coral community survey data collected from 1996 to 2015 to evaluate coral calcification capacity (CCC) dynamics with respect to recorded pulse disturbances for 121 reef sites in the Main Hawaiian Islands and Mo'orea (French Polynesia) in the Pacific and the Florida Keys Reef Tract and St. John (U.S. Virgin Islands) in the Western Atlantic. CCC remained relatively high in the Main Hawaiian Islands in the absence of recorded widespread disturbances; declined and subsequently recovered in Mo'orea following a crown-of-thorns sea star outbreak, coral bleaching, and major cyclone; decreased and remained low following coral bleaching in the Florida Keys Reef Tract; and decreased following coral bleaching and disease in St. John. Coral taxa have diverse calcification rates and susceptibility to disturbances characterized by their life history strategies. As a result, changes in CCC over the time series in this study were driven by a combination of shifts in both overall coral cover and in the contributions of calcification by the dominant calcifying coral taxa to CCC. Analysis of coral life history strategies showed that ‘weedy’ corals increased their contributions to CCC over time while ‘competitive’ corals decreased. Conversely, shifts in contributions by ‘stress-tolerant’ and ‘generalist’ corals to CCC varied by taxa across the regions. The increasing frequency and intensity of disturbances under 21st century global change is therefore predicted to affect CCC for many coral reefs with potentially lower and more variable CCC sustained under increased disturbance regimes by the increasing dominance of ‘weedy’ and some ‘stress-tolerant’ corals.

Ecosphere↗

USGS2018

A framework for identifying and characterising coral reef “oases” against a backdrop of degradation

Human activities have led to widespread ecological decline; however, the severity of degradation is spatially heterogeneous due to some locations resisting, escaping, or rebounding from disturbances. We developed a framework for identifying oases within coral reef regions using long‐term monitoring data. We calculated standardised estimates of coral cover ( z ‐scores) to distinguish sites that deviated positively from regional means. We also used the coefficient of variation (CV) of coral cover to quantify how oases varied temporally, and to distinguish among types of oases. We estimated “coral calcification capacity” (CCC), a measure of the coral community's ability to produce calcium carbonate structures and tested for an association between this metric and z ‐scores of coral cover. We illustrated our z ‐score approach within a modelling framework by extracting z ‐scores and CVs from simulated data based on four generalized trajectories of coral cover. We then applied the approach to time‐series data from long‐term reef monitoring programmes in four focal regions in the Pacific (the main Hawaiian Islands and Mo'orea, French Polynesia) and western Atlantic (the Florida Keys and St. John, US Virgin Islands). Among the 123 sites analysed, 38 had positive z ‐scores for median coral cover and were categorised as oases. Synthesis and applications . Our framework provides ecosystem managers with a valuable tool for conservation by identifying “oases” within degraded areas. By evaluating trajectories of change in state (e.g., coral cover) among oases, our approach may help in identifying the mechanisms responsible for spatial variability in ecosystem condition. Increased mechanistic understanding can guide whether management of a particular location should emphasise protection, mitigation or restoration. Analysis of the empirical data suggest that the majority of our coral reef oases originated by either escaping or resisting disturbances, although some sites showed a high capacity for recovery, while others were candidates for restoration. Finally, our measure of reef condition (i.e., median z ‐scores of coral cover) correlated positively with coral calcification capacity suggesting that our approach identified oases that are also exceptional for one critical component of ecological function.

Florida, Hawaii↗