Coral Research Articles

Influence of reef habitat on coral microbial associations.

Corals have complex symbiotic associations that can be influenced by the environment. We compare symbiotic dinoflagellate (family: Symbiodiniaceae) associations and the microbiome of five scleractinian coral species from three different reef habitats in Palau, Micronesia. Although pH and temperature corresponded with specific host-Symbiodiniaceae associations common to the nearshore and offshore habitats, bacterial community dissimilarity analyses indicated minimal influence of these factors on microbial community membership for the corals Coelastrea aspera, Psammocora digitata, and Pachyseris rugosa. However, coral colonies sampled close to human development exhibited greater differences in microbial community diversity compared to the nearshore habitat for the coral species Coelastrea aspera, Montipora foliosa, and Pocillopora acuta, and the offshore habitat for Coelastrea aspera, while also showing less consistency in Symbiodiniaceae associations. These findings indicate the influence that habitat location has on the bacterial and Symbiodiniaceae communities comprising the coral holobiont and provide important considerations for the conservation of coral reef communities, especially for island nations with increasing human populations and development.

Exploring the potential of native sea urchins as ex situ coral propagation allies

Caribbean coral reefs face unprecedented decline due to anthropogenic and environmental stressors, necessitating active restoration efforts. Among the strategies to conserve and restore reef ecosystems, land‐based sexual propagation of corals is crucial for preserving genetic diversity and population resilience. This study explores the efficacy of utilizing native sea urchin herbivory to control benthic macroalgal proliferation and enhance coral growth in land‐based propagation systems. Three captive‐reared urchin species—Lytechinus variegatus, Tripneustes ventricosus, and Diadema antillarum—were evaluated for their influence on algal cover and growth of sexually propagated brain coral Pseudodiploria strigosa. Juveniles of each urchin species were co‐cultured with 6‐month‐old coral colonies over a 105‐day experiment. Results indicated that all urchin treatments effectively reduced algal cover compared to controls; however, only T. ventricosus significantly increased coral growth rate, while the other urchin species did not have a notable effect. Despite differences in growth, coral survival was consistently high across all treatments. Benthic community analysis revealed shifts in algal composition, with D. antillarum grazing associated with increased crustose coralline algae. However, overgrazing by D. antillarum may have resulted in mild peripheral tissue damage to some corals. Urchin survival remained high, suggesting potential for downstream utilization in restoration (e.g. urchin population enhancement). This study highlights the potential of native urchins as biocontrol agents in coral propagation, emphasizing the importance of species‐specific interactions in shaping benthic communities and promoting coral resilience.

Fish–Seascape Associations Within an Offshore Protected Area in the Arabian Gulf

ABSTRACTCoral reef ecosystems support high fish biodiversity through ecological interactions with structural complexity across multiple spatial scales including coral colony architecture and the surrounding seascape structure. In an era where the complexity of coral reef ecosystems is being diminished, understanding the importance of structural characteristics beyond single focal patches has the potential to better inform actions for protecting, restoring or creating habitat for reef‐associated species. A seascape ecology approach was applied to explore the associations between multiple scales of seascape structure and fish assemblage response variables within a small (49.6 km2) offshore no‐take MPA, Sir Bu Nair Island Protected Area, in Sharjah, United Arab Emirates. Fish–seascape associations were modelled with single regression trees. Both in situ and remote sensing–derived variables produced the best models with highest contributions from coral cover, amount of hard‐bottom habitat type and structural complexity of the seafloor terrain. Fish species richness was significantly higher where coral cover exceeded 35%. The hard‐bottom areas with coral supported diverse assemblages dominated by carnivorous and omnivorous fishes. The Sir Bu Nair Island Protected Area provides a critical refuge for threatened and regionally overexploited species including those with low resilience to fishing. The ecological success of this protected area is key to safeguarding regional marine biodiversity and recovering fish populations to enhance food security.

Morphosedimentary evolution of the Belgica Mound Drift: Controls on contourite depositional system development in association with cold-water coral mounds

Small-scale contourite drift is an important component of continental margins that can record information about complex oceanographic processes. The Belgica Mound Drift is one example of a small-scale contourite drift. It is formed under the influence of cold-water coral (CWC) mounds and represents one of the most distal contouritic expressions influenced by the Mediterranean Outflow Water (MOW) in the NE Atlantic Ocean. Three distinct evolutionary stages have been identified from new high-resolution pseudo-3D reflection seismic data, each associated with a significant change in paleoceanography, affecting both bottom-current intensity and sediment input. The pre-drift stage (Pliocene–Early Pleistocene) corresponds to the regional RD1 erosive event, which was caused by the reintroduction of the MOW in the Porcupine Seabight, creating a distinct paleotopography that will influence all ensuing sedimentary processes. The second stage (Early Pleistocene–Middle Pleistocene) is the contourite drift inception in two distinct centres of growth, strongly steered by topographic obstacles such as the CWC mounds. During the third and final stage (Middle Pleistocene–present day), the contourite drift is developed under a more stable but less dynamic environment, characterised by more continuous and mounded aggradational stratification. The final stage of the contourite drift is related to the Middle Pleistocene Transition, with a spatially variable reduction in the MOW-related bottom currents and sediment input. The spatial and temporal evolution of this drift shows that its present-day morphology is controlled by the location of initial growth. Evolving moat morphology indicates that the intensity of the bottom currents generally increases during the drift evolution.This research presents a crucial paradigm for advancing our knowledge of elucidating the complexities of smaller-sized contourite systems in diverse oceanic environments.

Microplastics alter crystal growth in coral skeleton structures

Microplastics alter crystal growth in coral skeleton structures

Dancing Towards the End—Ecological Oscillations in Mediterranean Coral Reefs Prior to the Messinian Salinity Crisis (Calcare di Rosignano Formation, Acquabona, Tuscany, Italy)

The lower Messinian Calcare di Rosignano Formation (Tuscany, Italy, 43° N) preserves one of the youngest and northernmost examples of coral reefs in the Mediterranean. The outcropping succession of the Acquabona quarry consists of four main facies, namely, in ascending stratigraphic order: (1) coral boundstone, (2) coralline algal rudstone, (3) serpulid floatstone to packstone, and (4) peloidal packstone to grainstone. The succession displays a trend toward increasingly more shallow conditions and progressively more restricted water circulation. The coral reef displays a limited coral biodiversity and a remarkable abundance of heterotrophs, similar to modern coral reefs developed at the edges of the ecological niche of symbiont-bearing colonial corals. The widespread presence of coral colonies pervasively encrusted by coralline algae and benthic foraminifera suggests that short-term environmental perturbations caused temporary shutdowns of the coral-dominated carbonate factory. Moving upwards, there are fewer corals and more highly adaptable carbonate producers like coralline algae and serpulids. This suggests that the decline of corals had been caused by the conditions in the basin becoming more stressful, up to the collapse of the coral community. The overall succession indicates that coral-dominated ecosystems located at the edges of the coral zone are very sensitive; they can be affected even by minor perturbations and easily collapse if negative conditions persist.

Coral Sr/Ca-SST calibration: SST records from Kenyan corals

To better understand the seasonal variability in SST in Kenyan coral reef ecosystems, Sr/Ca ratios have been measured in Kenyan coral skeletons as proxies of SST, and a new Sr/Ca = f(SST) calibration was established: Sr/Ca = − 0.053 (± 0.006) *SST + 10.43 (± 0.16). The slope was within the margins of − 0.04 and − 0.08 mmolmol−1 °C of previously published Sr/Ca-SST calibration equations. A reliability test revealed that the present calibration equation reproduces a previously published calibration equation developed for Kenyan corals. This calibration was applied to corals collected in reef ecosystems under different natural and anthropogenic influences: Tana Delta Ziwayu Island, Watamu National Marine Park, and Shimon Mupunguti Marine Reserve. Using the developed Sr/Ca-thermometry, the reconstructed Sr/Ca-SST revealed that reefs from the southern basin of the Kenyan Indian Ocean are exposed to warmer SSTs than reefs in the northern Basin are. Additionally, the results revealed that the seasonal variability on SST increased moving toward the southern basin of the Kenyan Indian Ocean. We use the local instrument SST as an SST reference, which is aligned against the Sr/Ca seasonal signals recorded in SMR3-18 (the nearest coral site), and the intensity of the third global coral bleaching (April and May 2016) is affirmed.

Cold-water coral mortality under ocean warming is associated with pathogenic bacteria

Cold-water corals form vast reefs that are highly valuable habitats for diverse deep-sea communities. However, as the deep ocean is warming, it is essential to assess the resilience of cold-water corals to future conditions. The effects of elevated temperatures on the cold-water coral Lophelia pertusa (now named Desmophyllum pertusum) from the north-east Atlantic Ocean were experimentally investigated at the holobiont level, the coral host, and its microbiome. We show that at temperature increases of + 3 and + 5 °C, L. pertusa exhibits significant mortality concomitant with changes in its microbiome composition. In addition, a metagenomic approach revealed the presence of gene markers for bacterial virulence factors suggesting that coral death was due to infection by pathogenic bacteria. Interestingly, different coral colonies had different survival rates and, colony-specific microbiome signatures, indicating strong colony-specific variability in their response to warming waters. These results suggest that L. pertusa can only survive a long-term temperature increase of < 3 °C. Therefore, regional variations in deep-sea temperature increase should be considered in future estimates of the global distribution of cold-water corals.

Spatial variability of sedimentary assemblages reflects variations in bioerosion pressure of adjacent coral reefs.

The composition of coral-reef sediments is highly variable across space and time, and differences in the life histories of the dominant calcifying organisms on reefs contribute to the heterogeneity of reef sediments. Previous studies have suggested that variations in coral-reef bioerosion can influence spatial and temporal variations of sedimentary assemblages: elevated erosion rates of dead coral skeletons can trigger a pulse of coral-derived sediments and cause a shift in the dominance of sedimentary grains from coralline algae, such as Halimeda, to coral. We assessed the variability of the sedimentary composition and bioerosion rates of reefs at different spatial scales to determine the association between these two variables. We surveyed the benthic assemblages on reefs exhibiting different ecological states and collected samples of the associated sediments. We calculated the carbonate budget for each site and compared their variability at different hierarchical levels to the variability of their respective sedimentary assemblages. At the scale of sites (1-10 km), Halimeda cover was a significant predictor of the relative abundance of Halimeda grains. Both the relative abundance of coral grains and reef bioerosion rates varied significantly at the scale of locality (tens to hundreds of km), with high abundances of coral grains in the sediments coinciding with high rates of bioerosion. The main drivers of bioerosion at our localities were parrotfish assemblages dominated by large size classes of excavating species such as Sparisoma viride. Reef sediments may reflect the gross degree of bioerosion pressure that reefs experience, and historical changes in bioerosion rates could potentially be assessed by examining the sediments across temporal scales.

Coral carbonate production across depth: homogenisation after bleaching?

AbstractRecurrent climate-driven warming events, which can induce severe coral bleaching and mortality on tropical reefs, are predicted to cause homogenisation of coral communities and loss of ecosystem functions in shallow reef systems (&lt; 30 m). However, data documenting the variation in coral carbonate production across depth are limited. Here we explore differences in coral cover, community composition, coral colony size structure and carbonate production rates between two depths (10 m and 17.5 m) across four atolls in the remote Chagos Archipelago. We show higher coral carbonate production rates at 10 m (4.82 ± 0.27 G, where G = kg CaCO3 m−2 yr−1) compared to sites at 17.5 m (3.1 ± 0.18 G). The main carbonate producers at 10 m consisted of fast-growing branching and tabular corals (mainly Acroporids) and massive corals (mainly Porites), with high abundances of medium- and large-sized colonies. In contrast, coral carbonate production at 17.5 m was driven by slow-growing encrusting and foliose morphotypes and small colony sizes. Utilising a dataset following 6–7 years of recovery after the 2015–2017 bleaching event, our results show that depth-homogenisation of coral communities was temporary and carbonate production rates at 10 m depth recovered quicker at 3 of 4 studied atolls. The exception is Great Chagos Bank where slower recovery of branching and tabular corals at 10 m has led to a longer-lasting depth-homogenisation of carbonate production rates. The latter example cautions that more frequent bleaching events may drive increasing homogenisation of carbonate production rates across depth gradients, with implications for vital reef geo-ecological functions.

Incorporating parrotfish bioerosion into the herbivory paradigm of coral reef resilience

AbstractPromoting resilience is highly relevant to preserving biodiversity and ecosystem functioning. For coral reefs, parrotfish protection emerged as a mainstream action for reversing the degradation experienced by these systems. The rationale is that restoring their populations will increase grazing activity and reinforce control of fast‐growing macroalgae, facilitating coral cover recovery. A lack of a link between parrotfish trends and macroalgae and coral cover trends at a large scale has, however, often been the case. Suggesting more complex underlying dynamics that should be reexamined. In this review, we discuss how lumping parrotfish species as if they were functionally redundant may obscure trends. And how a lack of appreciation of other functions around the parrotfish paradigm, specifically bioerosion, may have unforeseen and potentially adverse effects on degraded reefs. We show that bioerosion responded more directly and quickly to spatial and temporal changes in parrotfish assemblages than macroalgae consumption, arguably due to the varying vulnerability among Caribbean parrotfishes to fisheries and habitat loss. For highly degraded reefs, positive changes in parrotfish populations could hence compromise the remaining coral skeleton structures and the reef framework, further accentuating reef degradation, where increases in macroalgae consumption could not necessarily compensate for higher rates of bioerosion.

Regime shift of skeletal δ13C after 1997/1998 El Nino event in Porites coral from Green Island, Taiwan

The 1997/1998 El Niño event caused mass coral bleaching and mortality in many tropical and subtropical regions, including corals on Green Island, Taiwan, in the northwestern Pacific Ocean. This study analyzed coral carbon isotope ratios (δ13C), oxygen isotope ratios (δ18O), and Sr/Ca ratios for 29 years, including the 1997/1998 El Niño period, to examine how high water temperature events are recorded in coral geochemical indicators. Sr/Ca ratios in coral skeletons from Green Island show the lowest peak, means the highest temperature during the 1997/1998 El Niño period. However, we couldn’t observe high-temperature events on δ18O. Furthermore, a negative δ13C shift was observed after El Niño events. The regime shift of δ13C might have been caused by temporal bleaching and/or a decrease in symbiotic algae due to high water temperature stress under the continuous decrease in δ13C in DIC due to the Suess effect.

2D geochemical imaging of biogenic marine carbonates using LA-TOF-ICP-MS at 1 and 2 μm pixel resolution

Many applications at the forefront of the study of the chemical composition of marine carbonates require in-situ micro-scale geochemical imaging. Such analyses are, however, challenging, requiring analytical techniques that are either expensive with limited accessibility (e.g. synchrotron X-Ray spectroscopy and secondary ion mass spectrometry), or time-consuming and able to only analyse a limited range of elements (e.g. electron microprobe). Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) as a tool for generating 2D images has grown in popularity, yet many analytical issues remain when generating high-spatial resolution geochemical images using this approach. Here we employ the imageGEO193 (ESL) fast wash-out laser ablation system coupled to the Nu Instruments Vitesse Time-of-Flight (TOF) ICP mass spectrometer, with its near-full mass spectra capabilities, to generate 2D geochemical images of a range of biogenic carbonates at ≤2 μm pixel resolution (pixel widths of either 1 or 2 μm) and at an unprecedented speed (200 pixels/s). We demonstrate sensitivity of ∼100 cps/μg g−1 at low mass rising to ∼1000 cps/μg g−1 at high mass based on analyses of reference materials JCp-1 (carbonate) and NIST SRM612 (silicate) with 1 μm wide square laser beams, and accuracy of ±7 % for elements present at concentrations >0.5 μg g−1 based on analyses of carbonate reference material JCt-1. By applying our quantitative method to a range of biogenic carbonates (coral skeletons, coralline algae, foraminifera), we demonstrate that considerable but coherent micron-scale compositional variability is the norm for nearly all quantified elements, including: Mg, Sr, Ba and U. This approach therefore has great potential to provide valuable insights into biomineralisation mechanisms and “vital effects”, ultimately facilitating more robust reconstructions of past environments.

Structural and hydrodynamic modelling of the probability of breakage of branching and plate coral colonies

Climate change is amplifying the intensity of severe weather events, with coastal regions such as coral reefs facing heightened vulnerability to cyclonic wave forces. Structural models to predict bending stress and breakage of corals have been developed for coral colonies to enhance comprehension and prediction of the effects of hydrodynamic disturbances on coral reefs. However, there is scope for improving these predictions by evolving the methodology for quantifying complicated and variable coral morphologies. This study aims to predict breakage thresholds for two of the most prevalent coral morphologies: branching and plate corals (using Acropora muricata and Acropora hyacinthus as study species). Laboratory and field measurements were taken to assess coral morphologies and material characteristics. Morphological features of 47 branching colonies and 100 plate colonies were surveyed at the study site (Heron Reef, southern GBR) and the tensile strength of 80 coral samples was obtained by in situ and laboratory testing. Three-dimensional structural models of branching and plate coral colonies were developed, encompassing multiple coral colonies with varying morphological patterns from relatively shallow (5-7 m) to deep (9-12 m) zones. Model results were calibrated and verified with existing data, revealing that velocity thresholds of 1.7 m/s and 5.0 m/s would destroy 90% of the simulated branching coral structures growing in the deep and shallow parts of the forereef zone, respectively. In contrast, the plate corals have sufficient margins of safety even in extreme flow conditions (7 m/s). Additionally, skeletal strength and structural performance were adjusted based on varying degrees of bioerosion inside the coral skeleton. A higher probability of breakage was observed as the extent of bioerosion increased. The laboratory experiments of hydrodynamic loads on coral colony show that the sheltering effect due to one or two neighbouring colonies in the upwave direction is negligible. These models can be easily adjusted to provide predictions for other coral species, shapes, levels of bioerosion, and locations (e.g., sheltered or exposed areas). Comprehensive predictions about the level of expected damage and rubble generation in different areas can be used in reef management planning and restoration prioritization.

Delineation of outbreak stages of the coral-killing sponge Terpios hoshinota

Outbreaks of the cyanobacteriosponge Terpios hoshinota are one of the many issues contributing to coral reef decline in the Indo-Pacific. This species occasionally undergoes local outbreaks, becoming an aggressive space competitor and overgrowing and killing zooxanthellate corals. Large outbreaks have been observed in Taiwan and the Ryukyu Islands in southern Japan. Many questions regarding the characteristics and chronology of T. hoshinota outbreaks remain unsolved. Therefore, the aim of this research was to identify outbreak stages at an outbreak site (Ogimi) on the west coast of northern Okinawa Island, Japan. We developed a novel approach to understand the chronology of outbreaks. Distinct outbreak stages were defined based on observations, in which Terpios: 1) starts overgrowing coral colonies, 2) covers a whole coral colony, 3) in the case of branching corals, causes the coral colony to collapse, and 4) the sponge is eventually overgrown by other organisms including turf algae and other sponges. Analyses were done based on photographic transects and the relative proportions of each stage were calculated. Results showed Ogimi is likely in final outbreak stages as overgrown Terpios had the highest share of all stages (57.9% and 44.9% at two outbreak sites), while smaller patches of Terpios, marking the starting point of the successional process, made up less than 1.5% of all observations. We suggest collecting such stage information during Terpios monitoring as it can allow identification of outbreaks at early stages, and potentially identify global patterns.

Ecological shifts underlie parallels between ontogenetic and evolutionary allometries in parrotfishes.

During ontogeny, animals often undergo significant shape and size changes, coinciding with ecological shifts. This is evident in parrotfishes (Eupercaria: Labridae), which experience notable ecological shifts during development, transitioning from carnivorous diets as larvae and juveniles to herbivorous and omnivorous diets as adults, using robust beaks and skulls for feeding on coral skeletons and other hard substrates. These ontogenetic shifts mirror their evolutionary history, as parrotfishes are known to have evolved from carnivorous wrasse ancestors. Parallel shifts at ontogenetic and phylogenetic levels may have resulted in similar evolutionary and ontogenetic allometric trajectories within parrotfishes. To test this hypothesis, using micro-computed tomography (μCT) scanning and three-dimensional geometric morphometrics, we analyse the effects of size on the skull shape of the striped parrotfish Scarus iseri and compare its ontogenetic allometry to the evolutionary allometries of 57 parrotfishes and 162 non-parrotfish wrasses. The young S. iseri have skull shapes resembling non-parrotfish wrasses and grow towards typical adult parrotfish forms as they mature. There was a significant relationship between size and skull shapes and strong evidence for parallel ontogenetic and evolutionary slopes in parrotfishes. Our findings suggest that morphological changes associated with the ecological shift characterizing interspecific parrotfish evolution are conserved in their intraspecific ontogenies.

How do animals understand the physical world?

The natural world is full of examples of animals interacting with their physical environment in surprising ways: capuchin monkeys crack open nuts with rocks; dolphins use sponges as 'gloves' on their rostra when searching for prey on the sea floor; and New Caledonian crows manufacture stick tools to pull grubs from logs (Figure 1). Deeper into the phylogenetic tree we continue to see interesting examples of behaviors of this kind, such as octopuses using coconut shells for protection, tuskfish breaking open cockles by hitting them against coral heads, and bees learning to pull string to gain out-of-reach food. These sophisticated behavioral interactions with their physical environment suggest that animals might have a deep understanding of their physical world at a cognitive level. In this primer, we review the performances of a variety of species when faced with tasks that probe their understanding of their physical world.

Endolithic Algae (Ostreobium) Diversity in Porites Corals at the Western Atlantic and Tropical Eastern Pacific

ABSTRACTOstreobium comprises endolithic algae commonly seen in conjunction with scleractinian corals. In the past, it was solely recognized as a coral skeleton bioeroder. Their relationship with corals is critical because they give photosynthetic byproducts and help the coral when it loses its primary symbionts due to stress. The variety of these algae in coral species of the genus Porites in the Tropical Eastern Pacific and western Atlantic was investigated. Ostreobium samples from seven Porites species including two from the Tropical Eastern Pacific (TEP) (P. panamensis and P. lobata) and five from the Caribbean (P. furcata, P. porites, P. colonensis, P. branneri, and P. astreoides) were extracted. Published rbcL sequences from algae found within various coral species from other parts of the world were also compared. A biogeographic analysis and two methodologies, PTP (Poisson tree process) and GMYC (general mixed Yule‐coalescent), were used to delineate the different species. The findings revealed a significant degree of genetic diversity within Ostreobium, with more than 15 groups of not more than three individuals and 40 individual lineages. Its origins date back to the Ordovician, 500 Ma, and it does not appear to preserve host specificity. The sampled locations still have a wide variety of Ostreobium. Biogeographically patterns were also confirmed, making it impossible to pinpoint the precise origins of most clades. The ancestry analyses revealed convergent events for not only the emergence of Ostreobium in a few genera of local corals, but also the phenomenon occurred in genera from far‐off places.

In Vivo Lifetime Imaging of the Internal O2 Dynamics in Corals with near-Infrared-Emitting Sensor Nanoparticles.

Mapping of O2 with luminescent sensors within intact animals is challenging due to attenuation of excitation and emission light caused by tissue absorption and scattering as well as interfering background fluorescence. Here we show the application of luminescent O2 sensor nanoparticles (∼50-70 nm) composed of the O2 indicator platinum(II) tetra(4-fluoro)phenyltetrabenzoporphyrin (PtTPTBPF) immobilized in poly(methyl methacrylate-co-methacrylic acid) (PMMA-MA). We injected the sensor nanoparticles into the gastrovascular system of intact colony fractions of reef-building tropical corals that harbor photosynthetic microalgae in their tissues. The sensor nanoparticles are excited by red LED light (617 nm) and emit in the near-infrared (780 nm), which enhances the transmission of excitation and emission light through biological materials. This enabled us to map the internal O2 concentration via time-domain luminescence lifetime imaging through the outer tissue layers across several coral polyps in flowing seawater. After injection, nanoparticles dispersed within the coral tissue for several hours. While luminescence intensity imaging showed some local aggregation of sensor particles, lifetime imaging showed a more homogeneous O2 distribution across a larger area of the coral colony. Local stimulation of symbiont photosynthesis in corals induced oxygenation of illuminated tissue areas and formation of lateral O2 gradients toward surrounding respiring tissues, which were dissipated rapidly after the onset of darkness. Such measurements are key to improving our understanding of how corals regulate their internal chemical microenvironment and metabolic activity, and how they are affected by environmental stress such as ocean warming, acidification, and deoxygenation. Our experimental approach can also be adapted for in vivo O2 imaging in other natural systems such as biofilms, plant and animal tissues, as well as in organoids and other cell constructs, where imaging internal O2 conditions are relevant and challenging due to high optical density and background fluorescence.

Quantifying attributes of boring bivalve populations in corals using micro-computed tomography

Bioerosion plays a crucial factor in shaping the structure and function of coral reef ecosystems, with bioeroders actively altering both the physical and ecological dynamics of coral substrates. Despite their importance, studying internal bioeroders in corals presents significant challenges owing to their cryptic nature within the skeletal structures. Additionally, invasive methods are often required to reveal the subtle and microscopic bioerosive alterations they induce in calcium carbonate substrates. Here, we demonstrate the effectiveness of high-resolution micro-computed tomography (μCT) in quantifying the abundance, size, distribution, and growth directions of coral bioeroders such as cryptic calcareous bivalves in the northern Red Sea. We scanned three coral species inhabited by bioeroders, followed by the utilization of three-dimensional image analysis software to identify, count, and measure each bivalve within the coral skeleton, along with quantifying boring cavity volumes. We revealed that μCT captures small boring cavities (&amp;lt; 1mm), providing more accurate abundance estimates of live and dead boring bivalves than the skeleton decalcification technique, with the added benefits of being rapid and non-destructive in contrast to traditional methods. Furthermore, measurements of empty cavity volumes enabled the estimations of the contribution of bioeroders to the overall coral skeletal porosity. Overall, our study highlights μCT as a practical and effective tool for studying cryptic coral bioeroders, providing novel ecological insights into bioeroder population ecology and coral-bioeroder interactions.