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Abstract We present CoralCT, a software application for analysis of annual extension, density, and calcification in coral skeletal cores. CoralCT can be used to analyze computed tomography (CT) scans or X‐ray images of skeletal cores through a process in which observers interact with images of a core to define the locations of annual density bands. The application streamlines this process by organizing the observer‐defined banding patterns and automatically measuring growth parameters. Analyses can be conducted in two or three dimensions, and observers have the option to utilize an automatic band‐detection feature. CoralCT is linked to a server that stores the raw CT and X‐ray image data, as well as output growth rate data for hundreds of cores. Overall, this server‐based system enables broad collaborations on coral core analysis with standardized methods and—crucially—creates a pathway for implementing multiobserver analysis. We assess the method by comparing multiple techniques for measuring annual extension and density, including a corallite‐tracing approach, medical imaging software, two‐dimensional vs. three‐dimensional analyses, and between multiple observers. We recommend that CoralCT be used not only as a measurement tool but also as a platform for data archiving and conducting open, collaborative science. 

Climate change is imposing multiple stressors on marine life, leading to a restructuring of ecological communities as species exhibit differential sensitivities to these stressors. With the ocean warming and wind patterns shifting, processes that drive thermal variations in coastal regions, such as marine heatwaves and upwelling events, can change in frequency, timing, duration, and severity. These changes in environmental parameters can physiologically impact organisms residing in these habitats. Here, we investigate the synchrony of coral and reef fish responses to environmental disturbance in the Red Sea, including an unprecedented combination of heat stress and upwelling that led to mass coral bleaching in 2015. We developed cross-dated growth chronologies from otoliths of 156 individuals of two planktivorous damselfish species,Pomacentrus sulfureusandAmblyglyphidodon flavilatus, and from skeletal cores of 48Poritesspp. coral colonies. During and immediately after the 2015 upwelling and bleaching event, damselfishes exhibited a positive growth anomaly but corals displayed reduced growth. Yet, after 2015–2016, these patterns were reversed with damselfishes showing a decline in growth and corals rebounding to pre-disturbance growth rates. Our results reveal an asynchronous response between corals and reef fish, with corals succumbing to the direct effects of heat stress, and then quickly recovering when the heat stress subsided—at least, for those corals that survived the bleaching event. Conversely, damselfish growth temporarily benefited from the events of 2015, potentially due to the increased metabolic demand from increased temperature and increased food supply from the upwelling event, before declining over four years, possibly related to indirect effects associated with habitat degradation following coral mortality. Overall, our study highlights the increasingly complex, often asynchronous, ecological ramifications of climate extremes on the diverse species assemblages of coral reefs. 

Abstract As mass bleaching events decimate stony coral populations, production of calcium carbonate is diminished on reefs, dampening their capacity to keep pace with rising sea levels. However, perturbations to the calcification process of surviving wild corals during bleaching are poorly constrained, owing to the lack of suitable techniques to retroactively extract this information from coral skeletons at sufficient resolution. Here, we use novel Raman spectrometry techniques to test the biogeochemical response of long‐lived corals before, during, and after bleaching. Maintenance of high aragonite saturation state (Ω_Ar) in the coral calcifying fluid is key to driving rapid skeletal growth but would be expected to decrease when corals become energetically depleted without their symbionts. Contrary to this expectation, our results demonstrate that corals upregulate calcifying fluid Ω_Arduring bleaching and for at least 2 yr after recovery. This indicates that the calcification process of coral‐bleaching survivors is unexpectedly resilient. 

Abstract Corals nucleate and grow aragonite crystals, organizing them into intricate skeletal structures that ultimately build the world’s coral reefs. Crystallography and chemistry have profound influence on the material properties of these skeletal building blocks, yet gaps remain in our knowledge about coral aragonite on the atomic scale. Across a broad diversity of shallow-water and deep-sea scleractinian corals from vastly different environments, coral aragonites are remarkably similar to one another, confirming that corals exert control on the carbonate chemistry of the calcifying space relative to the surrounding seawater. Nuances in coral aragonite structures relate most closely to trace element chemistry and aragonite saturation state, suggesting the primary controls on aragonite structure are ionic strength and trace element chemistry, with growth rate playing a secondary role. We also show how coral aragonites are crystallographically indistinguishable from synthetic abiogenic aragonite analogs precipitated from seawater under conditions mimicking coral calcifying fluid. In contrast, coral aragonites are distinct from geologically formed aragonites, a synthetic aragonite precipitated from a freshwater solution, and mollusk aragonites. Crystallographic signatures have future applications in understanding the material properties of coral aragonite and predicting the persistence of coral reefs in a rapidly changing ocean. 

Coral reefs are declining worldwide primarily because of bleaching and subsequent mortality resulting from thermal stress. Currently, extensive efforts to engage in more holistic research and restoration endeavors have considerably expanded the techniques applied to examine coral samples. Despite such advances, coral bleaching and restoration studies are often conducted within a specific disciplinary focus, where specimens are collected, preserved, and archived in ways that are not always conducive to further downstream analyses by specialists in other disciplines. This approach may prevent the full utilization of unexpended specimens, leading to siloed research, duplicative efforts, unnecessary loss of additional corals to research endeavors, and overall increased costs. A recent US National Science Foundation-sponsored workshop set out to consolidate our collective knowledge across the disciplines of Omics, Physiology, and Microscopy and Imaging regarding the methods used for coral sample collection, preservation, and archiving. Here, we highlight knowledge gaps and propose some simple steps for collecting, preserving, and archiving coral-bleaching specimens that can increase the impact of individual coral bleaching and restoration studies, as well as foster additional analyses and future discoveries through collaboration. Rapid freezing of samples in liquid nitrogen or placing at −80 °C to −20 °C is optimal for most Omics and Physiology studies with a few exceptions; however, freezing samples removes the potential for many Microscopy and Imaging-based analyses due to the alteration of tissue integrity during freezing. For Microscopy and Imaging, samples are best stored in aldehydes. The use of sterile gloves and receptacles during collection supports the downstream analysis of host-associated bacterial and viral communities which are particularly germane to disease and restoration efforts. Across all disciplines, the use of aseptic techniques during collection, preservation, and archiving maximizes the research potential of coral specimens and allows for the greatest number of possible downstream analyses. 

Abstract Internal waves strongly influence the physical and chemical environment of coastal ecosystems worldwide. We report novel observations from a distributed temperature sensing (DTS) system that tracked the transformation of internal waves from the shelf break to the surf zone over a narrow shelf slope region in the South China Sea. The spatially continuous view of temperature fields provides a perspective of physical processes commonly available only in laboratory settings or numerical models, including internal wave reflection off a natural slope, shoreward transport of dense fluid within trapped cores, and observations of internal rundown (near‐bed, offshore‐directed jets of water preceding a breaking internal wave). Analysis shows that the fate of internal waves on this shelf—whether transmitted into shallow waters or reflected back offshore—is mediated by local water column density structure and background currents set by the previous shoaling internal waves, highlighting the importance of wave‐wave interactions in nearshore internal wave dynamics. 

Abstract Internal waves can influence water properties in coastal ecosystems through the shoreward transport and mixing of subthermocline water into the nearshore region. In June 2014, a field experiment was conducted at Dongsha Atoll in the northern South China Sea to study the impact of internal waves on a coral reef. Instrumentation included a distributed temperature sensing system, which resolved spatially and temporally continuous temperature measurements over a 4‐km cross‐reef section from the lagoon to 50‐m depth on the fore reef. Our observations show that during summer, internal waves shoaling on the shallow atoll regularly transport cold, nutrient‐rich water shoreward, altering near‐surface water properties on the fore reef. This water is transported shoreward of the reef crest by tides, breaking surface waves and wind‐driven flow, where it significantly alters the water temperature and nutrient concentrations on the reef flat. We find that without internal wave forcing on the fore reef, temperatures on the reef flat could be up to 2.0°C ± 0.2°C warmer. Additionally, we estimate a change in degree heating weeks of 0.7°C‐weeks warmer without internal waves, which significantly increases the probability of a more severe bleaching event occurring at Dongsha Atoll. Furthermore, using nutrient samples collected on the fore reef during the study, we estimated that instantaneous onshore nitrate flux is about four‐fold higher with internal waves than without internal waves. This work highlights the importance of internal waves as a physical mechanism shaping the nearshore environment, and likely supporting resilience of the reef. 

Abstract The global impacts of climate change are evident in every marine ecosystem. On coral reefs, mass coral bleaching and mortality have emerged as ubiquitous responses to ocean warming, yet one of the greatest challenges of this epiphenomenon is linking information across scientific disciplines and spatial and temporal scales. Here we review some of the seminal and recent coral‐bleaching discoveries from an ecological, physiological, and molecular perspective. We also evaluate which data and processes can improve predictive models and provide a conceptual framework that integrates measurements across biological scales. Taking an integrative approach across biological and spatial scales, using for example hierarchical models to estimate major coral‐reef processes, will not only rapidly advance coral‐reef science but will also provide necessary information to guide decision‐making and conservation efforts. To conserve reefs, we encourage implementing mesoscale sanctuaries (thousands of km²) that transcend national boundaries. Such networks of protected reefs will provide reef connectivity, through larval dispersal that transverse thermal environments, and genotypic repositories that may become essential units of selection for environmentally diverse locations. Together, multinational networks may be the best chance corals have to persist through climate change, while humanity struggles to reduce emissions of greenhouse gases to net zero.