Search Results (207)

Coral reef ecosystems are declining rapidly due to climate change, disease, and anthropogenic stressors, driving the expansion of land-based coral propagation for reef restoration. A major bottleneck in these efforts is the manual measurement of coral recruit tissue area from microscopy images, which requires 2–7 min per image and limits scalability. We present a hierarchical deep learning pipeline that automates this measurement by integrating YOLO-based detection with Segment Anything Model (SAM) segmentation. YOLO localizes recruits and classifies them by developmental stage; stage-specific fine-tuned SAM models then segment live tissue using bounding box and background point prompts to suppress segmentation leakage and improve boundary precision. Surface area is computed directly from the segmented masks using pixel size extracted from image metadata. The pipeline reduces processing time to approximately 3–5 s per image—a 24–140× speedup over manual tracing. Evaluated on 3668 microscopy images from two national coral research facilities, the system achieves a mean IoU exceeding 95% and an auto-acceptance rate (AAR) of 71.51%, where predicted-to-ground-truth area ratios fall within a ±5% tolerance of expert annotation, substantially reducing manual workload while maintaining measurement reliability across species, developmental stages, and imaging conditions. This workflow addresses a critical bottleneck in restoration research and demonstrates the broader applicability of AI-based image analysis in marine ecology. Full article

The tomato hind (Cephalopholis sonnerati) is a marine aquaculture fish species with high economic value. Elucidating the mechanisms underlying its growth regulation is crucial for the development of the aquaculture industry. To analyze the biological mechanisms underlying growth differences, individuals with extreme body sizes at 8 months of age from the same batch were selected in this study. A combined experiment of “body size × feeding status” was constructed, and transcriptome sequencing and weighted gene co-expression network analysis (WGCNA) were performed on brain and muscle tissues. The results showed that 2553 differentially expressed genes (DEGs) were identified between individuals with distinct body sizes, which were significantly enriched in growth regulation pathways such as PI3K–Akt, MAPK, and FoxO. Feeding differences affected 4480 genes, which were significantly enriched in signaling pathways including the insulin signaling pathway. WGCNA further identified co-expression modules (brown4, blue, coral1) significantly correlated with growth, as well as hub genes including pik3r1 and eif4ebp2. Comprehensive analysis demonstrated that the growth regulation of C. sonnerati operates as a cascade network. Brain tissues perceive signals through neuroactive ligand–receptor interactions and integrate and transduce these signals via core pathways including Ras–MAPK and PI3K–Akt. Finally, growth processes are executed in muscle tissues by regulating glycogen metabolism, protein synthesis, and other processes, which are precisely regulated by terminal processes such as cellular senescence. Among them, pik3r1 and eif4ebp2, as key molecular switches, play a central role in integrating upstream signals and precisely regulating downstream growth programs. This study preliminarily clarifies the molecular mechanism network of growth differences in C. sonnerati, providing a theoretical basis and candidate genes for the genetic improvement of its growth traits. Full article

This study investigated the effects of Lycium barbarum polysaccharides (LBP) supplementation on various indicators in coral trout (Plectropomus leopardus), including growth performance, digestive enzyme activity, muscle and skin morphology, inflammatory immune gene expression, as well as immune and antioxidant responses. In the experiment, fish were fed diets supplemented with different concentrations of LBP (0%, 0.05%, 0.1%, 0.2%, 0.5%, and 1%) over a designated experimental period. The results showed that moderate supplementation of LBP significantly improved growth performance, with the optimal concentration being around 0.243%, achieving the highest specific growth rate. LBP supplementation also enhanced intestinal digestive enzyme activity, such as trypsin in the 0.1% and 1% groups, and α-amylase in the 0.5% group. Additionally, LBP improved the nutritional composition of muscle, with the 1% group showing higher crude protein content and the 0.2–1% groups having lower crude fat content. Moderate LBP supplementation improved skin color and pigmentation, increasing the brightness, redness, and yellowness of the dorsal skin, as well as boosting carotenoid and astaxanthin concentrations. It also enhanced the immune and antioxidant functions of the skin (e.g., SOD, CAT, GSH-Px, AKP, and LZ) and improved the immune functions of the mucus (e.g., C3, C4, IgM, IgT, AKP, and LZ). Furthermore, the expression of key pro-inflammatory genes, such as TNF-α and IL-1β, was reduced. These findings suggest that LBP can serve as a natural feed additive to enhance the overall quality and health of coral trout, contributing to sustainable aquaculture practices. Full article

We announce the U.S. Geological Survey (USGS) Rotating X-ray Computed Tomography (RXCT) Coral-Core Archive, a digital resource derived from ~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 r² < 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. Full article

Symbiotic dinoflagellates from the family Symbiodiniaceae play a central role in coral reef ecosystems by forming mutualistic relationships with reef invertebrates, particularly stony corals. These relationships underpin reef productivity in nutrient-poor waters but are vulnerable to disruption from marine heatwaves and climate change. While laboratory culturing of symbionts has enabled controlled studies of thermal stress, prolonged culturing may lead to physiological changes that do not reflect in hospite conditions. Here, we examined the thermal stress responses of two axenic cultures of Symbiodinium A1, freshly isolated and long-term cultured (2.5 years), originally from the jellyfish Cassiopea andromeda in the Red Sea. Both cultures were exposed to a daily temperature increase of 1 °C, up to 37 °C. Freshly isolated symbionts consistently showed higher photochemical efficiency (0.515 ± 0.007) and growth rates (1.68 ± 0.60 µ day⁻¹) compared to long-term cultured cells (0.401 ± 0.007; −2.25 ± 0.38 µ day⁻¹), which collapsed at 37 °C. Heat stress also led to decreases in O₂ and increases in pCO₂ across treatments. Long-term cultured symbionts exhibited greater lipid body accumulation, suggesting a shift to anaerobic metabolism. These findings demonstrate that extended batch culturing alters symbiont physiology and stress responses, highlighting the need to consider culture history in experimental designs to avoid bias in interpreting holobiont resilience. Full article

The lateral line is a highly differentiated skin sensory organ in fish, but few studies have explored the relationship between stocking density and the physiological responses of the lateral line in different species. In this study, grass carp, turbot and leopard coral grouper were cultured at different stocking densities for 6, 8 or 10 weeks. The results indicate that high stocking densities reduced weight gain and feed efficiency, increased serum cortisol, malondialdehyde contents, and superoxide dismutase activity, and caused oxidative damage in juvenile grass carp (2.04 kg/m³) and turbot (12.61 kg/m³), but did not affect these indicators in juvenile leopard coral grouper (2.33 kg/m³). Meanwhile, high stocking densities did not affect the survival rate and feed intake of the fish, but decreased the viscerosomatic index in all three fish species. In the lateral line skin, high stocking densities upregulated the expression of genes related to glucocorticoid secretion, hypoxia, and oxidative stress in grass carp and turbot, and altered circadian rhythm-related gene expression in leopard coral grouper. The study shows that growth, cortisol level, and oxidative damage can serve as effective indicators for monitoring fish in high-density cultures, and demonstrates that optimal stocking density should be determined based on the farming system, fish species, and developmental stage. Full article

Coral body plans are constructed through repeated modular units, with polyps serving as the fundamental structural and functional units, yet the rules underlying tissue and polyp pattern formation remain poorly understood. This study investigated lateral, two-dimensional (2D) tissue and polyp expansion in the coral Stylophora pistillata under controlled laboratory conditions. Using the nubbin assay, we investigated the effects of colony, fragment origin (branch tips versus sub-apical fragments), and nubbin density on this 2D expansion assay. Nubbins from ten colonies (SC1–SC10) were grown on glass slides, and tissue expansion was quantified from digital images over six months. For three fast-growing colonies (SC1, SC2, and SC5), single-, double-, and triple-nubbin configurations were used to evaluate proximity effects. Across all colonies, lateral tissue area strongly correlated with polyp number (R² = 0.68), indicating a close relationship between surface expansion and polyp proliferation. Pronounced colony differences emerged: SC9 and SC1 exhibited the largest tissue areas, while SC5 developed compact, polyp-dense morphologies. Fragment origin did not influence 2D growth, suggesting the absence of apical dominance. Nubbin density influenced growth in a colony-specific manner; SC1 exhibited strong inhibition under crowded conditions, whereas SC2 and SC5 were largely unaffected. Collectively, these results suggest that intrinsic genetic factors and local spatial interactions, rather than a fragment’s position along a branch, are the primary drivers of 2D growth, highlighting the self-organizing nature of coral tissues and illustrating how controlled 2D systems can clarify the interplay between genetic regulation and local interactions in coral morphogenesis. Full article

Coral reef ecosystems represent one of the most biodiverse and productive marine habitats, yet they are increasingly threatened by a range of anthropogenic stressors. Among these, emerging contaminants including pharmaceutical and personal care products (PPCPs) have started to feature as contaminants of concern due to their persistence, bioaccumulation potential, and complex interactions within reef environments. This review synthesizes current research on the occurrence, transport pathways, and ecological impacts of emerging contaminants, specifically focusing on PPCPs on coral reef systems. Evidence indicates that compounds such as UV filters, antibiotics, and endocrine-disrupting chemicals can impair coral physiology, disrupt symbiotic relationships with zooxanthellae, and contribute to bleaching events. The review further highlights the variability in coral species’ sensitivity to these contaminants, with documented effects ranging from oxidative stress to reduced growth and reproductive capacity. Despite advances in detection and risk assessment, significant knowledge gaps remain regarding long-term exposure, mixture effects, and the influence of local environmental conditions on contaminant toxicity. By consolidating recent findings, this review underscores the urgent need for targeted research and policy action to mitigate the threat of emerging contaminants to coral reef ecosystems. Full article

This study presents updated biological and stock assessment information for two coral groupers, Plectropomus areolatus and Plectropomus marisrubri, in the Eastern Red Sea. A large sample collected from nine landing sites provided new estimates of growth, maturity, mortality, and exploitation, derived from otolith ageing, length–weight relationships, and yield-per-recruit and spawning potential ratio analyses. The two species showed distinct life-history patterns, with P. areolatus maturing earlier and exhibiting faster growth. Both species were found to be overexploited under current fishing pressure, with spawning biomass reduced well below commonly used sustainability thresholds. These results indicate that reductions in fishing mortality are required to rebuild reproductive capacity, particularly for P. areolatus. Management actions, such as increasing hook selectivity and enforcing minimum landing sizes, are supported by the observed maturity schedules. Seasonal protection of spawning periods is consistent with the low spawning potential ratios. This study provides the first recent age-based assessment for these two species in the region, offering a biological basis for species-specific management planning in the Eastern Red Sea. Full article

As an important marginal sea in the western Pacific, sea-level changes in the South China Sea not only respond to global warming but are also regulated by regional ocean dynamics and climate modes, exerting profound impacts on the socioeconomic development and engineering safety of coastal regions. To address the widespread issues of low accuracy and robustness in existing sea-level prediction models when handling nonlinear, multi-scale sequences, as well as the complexity of sea-level change mechanisms in the South China Sea, this study constructs a hybrid model combining Singular Spectrum Analysis and Long Short-Term Memory neural networks (SSA-LSTM). The coral skeletal oxygen isotope ratio (δ¹⁸O) used in this study is a key indicator for characterizing the marine environment, defined as the per mille difference in the ¹⁸O/¹⁶O ratio of a sample relative to a standard. Based on coral δ¹⁸O data from the South China Sea, the sea level from 1850 to 2015 is reconstructed. SSA is then applied to decompose the sea-level data into trend and periodic components. The trend component, accounting for 37.03%, and components 2 to 11, containing major periodic information, are extracted to reconstruct the sea-level series. The reconstructed series retains 95.89% of the original information. The trend component is modeled through curve fitting, while the periodic components are modeled using an LSTM neural network. Optimal hyperparameters for the LSTM are determined through parameter sensitivity analysis. An integrated SSA-LSTM model is constructed to predict sea level in the South China Sea, and its predictions are compared with those from a Singular Spectrum Analysis-Autoregressive Integrated Moving Average (SSA-ARIMA) model. The results indicate that from 1850 to 2015, sea level in the South China Sea exhibits periodic fluctuations with a significant overall upward trend. Specifically, the growth rate from 1921 to 1940 reaches 5.49 mm/yr. Predictions from the SSA-LSTM model are significantly higher than those from the SSA-ARIMA model. The SSA-LSTM model projects that from 2016 to 2035, sea level in the South China Sea will continue to rise at a fluctuating rate of 0.75 mm/yr, with a cumulative rise of approximately 15 mm. This study provides a novel methodology for investigating the mechanisms of sea-level change in the South China Sea and offers a scientific basis for coastal risk management. Full article

The genus Pavona includes massive to submassive hermatypic corals and represents one of the main reef builders of the coral reefs in the Eastern Tropical Pacific (ETP). However, its development and specific ecological role, particularly on offshore reefs (e.g., oceanic Atolls), remain poorly understood. This study aims to determine the sclerochronological characteristics of the four Pavona species (Pavona duerdeni, Pavona clavus, Pavona maldivensis, and Pavona varians) in Clipperton Atoll, and their contributions to reef maintenance. Using the optical densitometry technique, Pavona annual growth parameters were obtained, showing that skeletal density (1.26 ± 0.23 g cm⁻³), extension rate (0.94 ± 0.31 cm year⁻¹), and calcification rate (1.17 ± 0.36 g cm⁻² year⁻¹) were consistent with previous data from the ETP. However, differences at the species level showed that P. duerdeni, P. varians, and P. maldivensis invested their calcification resources into building denser skeletons, demonstrating the morphological plasticity of the genus, likely driven by local factors, such as strong hydrodynamics and depth, rather than regional conditions (e.g., El Niño-Southern Oscillation events). Pavona’s growth strategies contribute to the preservation potential on a geological timescale of Clipperton Atoll, highlighting their importance as one of the main reef builders at a massive coral-dominated reef. Full article

The Caribbean Coastal Marine Productivity (CARICOMP) program was conceptualized in 1985 to monitor coral reefs, seagrass beds, and mangrove forests at multiple sites across the wider Caribbean. Mangrove monitoring was focused on the dominant Caribbean species, red mangrove (Rhizophora mangle). Forest structure and productivity were monitored at 21 sites (18 countries) across different geomorphological settings, from tropical to subtropical mainland and island systems. Here, we provide the key findings from the CARICOMP mangrove data collected, mostly from 1992 to 2013, to assess spatial and temporal variability across the region. Red mangrove above-ground biomass averaged 190 t ha⁻¹ (far higher than previously reported) but ranged widely across sites from 33 to 590 t ha⁻¹, equating to an average above-ground ‘blue carbon’ of 84 t ha⁻¹ (range 15–260 t ha⁻¹). Tree density averaged 3237 trees ha⁻¹, tree basal area averaged 19.7 m² ha⁻¹, tree height averaged 6.1 ± 2.8 m, and seedling density varied from 1.2 to 74 seedlings m⁻² across the sites. Among the environmental factors that influence mangroves, local temperature and rainfall explained 48% of the variability in measured tree structure parameters. Annual litterfall, as a proxy for productivity, measured on average 1.24 ± 0.70 kg m⁻² yr⁻¹, with 60% of the total litterfall composed of leaves. Litterfall varied seasonally by 42%. No relationship was apparent between litterfall and seasonal ocean–atmosphere climate indices (ONI and AMM). With exception of the three most southwesterly CARICOMP sites, hurricanes and tropical storms impacted the mangrove sites repeatedly, resulting in considerable damage. A direct strike by a category-4 hurricane in 1998 in Dominican Republic killed 67% of the red mangrove trees, lowered above-ground biomass by 91%, basal area by 89%, litterfall by 63%, and resulted in the subsequent growth of many tall and thin saplings, totally changing the structure of the forest ecosystem in the first few years after the hurricane. In comparing mangrove systems, major differences may be explained by time elapsed since the last destructive event (hurricane) affecting each site. This highlights the fact that despite an increasing focus on preserving these valuable ecosystems, they are still highly vulnerable to natural hazards and likely to face a poor outcome under ongoing climate change. Full article

Recruitment is a crucial process for the recovery of coral populations after large-scale disturbances causing mass mortality events such as coral bleaching. This study examined the juvenile coral community of the remote Huvadhoo Atoll (southern Maldives, Indian Ocean) 11 years apart (2009 and 2020). Coral recruits (≤5 cm) and juveniles (5–15 cm) were surveyed at eight reef sites located in both lagoon- and ocean-facing environments, under the hypothesis that density and survival of recruits differ with respect to exposure. The total mean number of recruits differed slightly between years, with densities of 25 individuals·m⁻² in 2009 and 30 individuals·m⁻² in 2020. However, Acropora populations, which represented 60% of juvenile corals in 2009, halved in 2020, particularly in ocean reefs. The decrease in Acropora recruits seems to have favoured other corals: Pocillopora doubled compared to 2009, and species with massive growth morphologies became dominant. In all, the juvenile coral community structure underwent substantial changes between the two surveys. The comparison between the number of recruits and that of juvenile corals suggested higher survival of the species with massive growth morphologies. Whether branching corals will also have the ability to adapt to increasingly frequent climatic disturbances deserves attention in the future. Full article

Coral reefs are crucial ecosystems for marine biodiversity but are increasingly threatened by anthropogenic pressures and climate anomalies. The 2016 global bleaching event resulted in widespread coral mortality, altering reef structure and benthic communities. Here, we examine the evolution of Maldivian reefs from 2015 to 2023 using long-term monitoring data to assess post-disturbance dynamics. Analyses of 26 benthic descriptors revealed severe impacts from thermal stress, with heterogeneous recovery patterns. Reef-building capacity, which reflects the reef’s accretion potential and is mainly sustained by primary (e.g., Acropora branching corals) and secondary constructors (e.g., Tridacna spp.), rebounded substantially, while binders (e.g., coralline algae) and bafflers (e.g., erect sponges) remained depleted. Among growth forms, fast-growing branching and digitate corals, despite substantial declines, drove rapid recovery. Massive corals were less affected and continued growing, while encrusting corals declined steadily over the period. Post-bleaching community composition shifted markedly toward increased abiotic cover and reduced coral dominance, with partial reversion by 2023. Despite the 2016 collapse in constructional capacity, most reefs exhibited notable recovery within seven years. These findings underscore the moderate yet promising resilience of Maldivian reefs, exceeding previous bleaching events, and emphasize the importance of long-term monitoring to understand ecosystem responses under accelerating climate stress. Full article

Reef restoration is the major way to compensate the loss of scleractinian corals, which requires huge amounts of transplantation donors. Previous study revealed that some species of corals can conduct polyp bailout and reattachment under environmental stress, which contributes to the living of coral communities and offer a novel way to produce numerous coral colonies for reef restoration. In the present study, physiological and transcriptomic approaches were conducted to illustrate the effects and molecular mechanisms of brine shrimp feeding on the newly attached polyps of coral Poccillopora damicornis. It was observed that brine shrimp feeding significantly prompted the growth of reattached polyps by elevating polyp diameter, number of new polyps, weight of the calcified skeleton, symbiont density, chlorophyll a + c₂ content and Ea values. Transcriptomic analysis also inferred that signaling pathways responsive for energy metabolism, cell growth and biomineralization were dramatically activated. Furthermore, brine shrimp feeding enhanced the immunity of the reattached polyps by suppressing caspase-3 activation level and elevating antioxidant capacity. These results collectively reveals the influence and detailed molecular mechanisms of brine shrimp feeding on the growth of newly reattached coral polyps, which shed light on the potential application of such methods in the cultivation of coral transplantation donors. Full article