Coral reefs are one of the most valuable ecological resources in nature. Coral reefs’ unique ocean-land-atmosphere three-dimensional structure provides an excellent foundation for constructing multidisciplinary marine sciences, and can form a complete and independent system—Coral Reef Systems Science. Over the past decade, the discipline of coral reef science in China has developed rapidly, making significant progress in almost all aspects, including macro- and micro-ecology, ecological disaster monitoring and early warning, coral sexual and asexual reproduction, carbon and nitrogen cycling in coral reef areas, emerging contaminants in coral reef areas, coral reef geomorphology and geology, high-resolution environmental records from corals, and coral reef engineering applications, among others. By briefly reviewing the research progress on coral reefs in China over the past decade, this paper expounds the fundamental connotations of Coral Reef Systems Science. And it calls for the establishment and improvement of this discipline to fully and sustainably utilize coral reef resources in service of the building of a strong marine nation.

Coral reef ecosystems possess significant ecological and socioeconomic value; however, their risk of degradation has continued to intensify under the combined pressures of global climate change and anthropogenic disturbances. Owing to its advantages of extensive spatial coverage, high temporal efficiency, and relatively low cost, optical remote sensing has become an important technological approach for monitoring coral reef ecosystems. Focusing on key indicators including shallow-water depth, benthic substrates, water environmental conditions, and ecological status, this review systematically summarizes recent advances in the remote sensing monitoring of coral reef ecosystems in optically shallow waters. Particular emphasis is placed on the underlying theoretical foundations, model evolution, and application progress, thereby clarifying the developmental trajectory and methodological framework from innovations in physical mechanisms to the dual-driven paradigm integrating physical principles and data-driven approaches. Building on this review, we further summarize the key challenges currently faced in multi-parameter synergistic retrieval, cross-regional generalization, and long-term dynamic monitoring, and discuss future directions involving physical mechanism constraints, artificial intelligence integration, and multi-source observational synergy. This review provides a reference for the future development of intelligent remote sensing monitoring and ecological conservation of coral reef ecosystems.

The South China Sea is one of the most important coral reef regions in China and also represents a high-risk area for the input and accumulation of emerging contaminants (ECs). In recent years, numerous studies have reported the widespread occurrence of ECs, including persistent organic pollutants, endocrine-disrupting chemicals, antibiotics, and microplastics, in the South China Sea and its adjacent coastal waters, posing potential threats to coral reef ecosystems. However, a comprehensive understanding of how ECs alter coral holobiont carbon cycling functions through their effects on key physiological processes remains limited. This review systematically summarizes the current status of ECs pollution in the South China Sea and critically evaluates their impacts on key carbon cycling processes in coral holobionts, including photosynthesis, respiration, calcification, and microbially mediated processes. Available evidence indicates that ECs can suppress photosynthetic carbon fixation by symbiotic dinoflagellates, enhance heterotrophic respiration, disrupt calcification, and alter microbial community structure and metabolic functions, thereby weakening the carbon sink capacity of coral holobionts and under certain conditions, promoting a shift from a carbon sink to a carbon source. Overall, the impacts of ECs on carbon metabolism in coral holobionts exhibit process coupling and cumulative functional effects, which may compromise the long-term stability of coral reef carbon sink functions and their potential relevance in the blue carbon framework. Based on the synthesis of current knowledge, this review further highlights critical research priorities, such as the long-term consequences of ECs exposure, multi-process coupling mechanisms, and their integrated impacts on coral reef carbon sink functions, providing a scientific basis for coral reef conservation, carbon sink assessment, and related marine management in the South China Sea.

As climate change intensifies and coral reef ecosystems continue to degrade, epigenetic regulation is increasingly recognized as playing a critical role in the rapid response and adaptation of scleractinian corals to environmental stressors. Epigenetic mechanisms are critical for screening stress-tolerant “super coral” strains, informing restoration efforts, and evaluating the stability and evolutionary trends of reef ecosystems. In this article, domestic and international research on epigenetics in scleractinian corals were reviewed, which included: 1) The characteristics and functions of major epigenetic modifications in scleractinian corals; 2) Research methods and technical approaches in epigenetics of scleractinian corals (WGBS and RNA-seq); 3) Epigenetic regulation of scleractinian corals in response to environmental stresses (heat, acidification, nutrient enrichment, and bacterial infection) and their potential for transgenerational inheritance. Accordingly, despite low global DNA methylation levels, scleractinian corals can modulate their phenotypes and adaptability by modifying and reprogramming key functional genes implicated in energy transport, signaling, tissue growth, biomineralization, symbiont transport, and immune regulation. Thus, DNA methylation serves as a crucial molecular regulatory mechanism in coral responses to global change and possesses the potential to drive “intragenerational-intergenerational-transgenerational” epigenetic adaptation in coral populations. Although scleractinian corals exhibit diverse histone variants and histone post-translational modifications, the epigenetic regulatory mechanisms of these modifications, along with noncoding RNAs and chromatin accessibility, during coral responses to environmental stress remain to be thoroughly investigated. Herein, based on these research advances and considering the molecular ecological context of scleractinian corals in the South China Sea, the following research directions are proposed: 1) The multi-species, multi-generation, multi-temporal, multi-habitat, and multi-stress epigenetic regulation studies in scleractinian corals of the South China Sea; 2) To explore the ecological roles of RNA modifications and chromatin threedimensional structures in the environmental phenotypic plasticity of scleractinian corals of the South China Sea; 3) The identification of superior epigenetic modification traits in environmentally stressresistant scleractinian corals of the South China Sea and their application in breeding.

Coral bleaching driven by climate warming is a major driving factor causing mass coral mortality and reef degradation globally. Understanding coral thermal adaptation is crucial for predicting the responses of coral reef ecosystem to future climate change. While adult corals often exhibit enhanced heat tolerance after short-term heat acclimation, it remains unclear whether similarly positive effects occur during the vulnerable and sensitive planktonic larval stage. This study investigated the impact of heat acclimation (32 ℃ for four days) on survival and respiration rate of planula larvae of the broadcast-spawning reef coral Acropora digitifera, and further analyzed the effect of heat acclimation on larval high-temperature tolerance through reciprocal transplant experiments. The results showed that heat acclimation did not significantly affect larval survival but significantly reduced their respiration rate. Upon exposure to a second thermal stress (34 ℃), survival rates significantly decreased in both acclimated and non-acclimated larvae, with no significant difference between the two groups. Moreover, acclimated larvae exhibited significantly lower respiration rates than non-acclimated larvae under both ambient and high temperatures, indicating a metabolic suppression effect induced by acclimation. In conclusion, heat acclimation during the coral larval stage did not enhance high-temperature tolerance in Acropora digitifera, instead inducing metabolic suppression that might negatively impact subsequent high-energy-demanding processes like settlement and metamorphosis. These findings provide an important scientific basis for objectively assessing the high-temperature acclimation adaptation potential of corals during their early life history stages.

Acropora muricata, characterized by branching morphology and fast growth, enhances the structural complexity of reef habitats and is considered a key candidate species for coral reef restoration. However, this species is relatively sensitive to heat stress and prone to bleaching and even mortality during extreme high-temperature events such as marine heatwaves, limiting the stability and sustainability of its application in restoration. In this study, A.muricata colonies collected from subtidal habitats were subjected to a 14-day acclimation in natural fluctuating environments within intertidal rock pools; subsequently, a controlled indoor heat-stress experiment was conducted to compare phenotypic traits and physiological and biochemical responses between the acclimated and non-acclimated groups. Results showed that both groups exhibited similar response patterns to heat stress, including bleaching, declines in Symbiodiniaceae density and chlorophyll a content, increases in antioxidant enzyme activities, and elevated malondialdehyde (MDA) content. Under heat stress, the acclimated group displayed superior physiological condition and stronger antioxidant capacity: Symbiodiniaceae density, chlorophyll a content, catalase (CAT) activity, and superoxide dismutase (SOD) activity were 21.48%, 37.20%, 45.09%and 60.26%higher, respectively, than those in the non-acclimated group. In summary, acclimation in naturally fluctuating environments can improve the stability of the A.muricata-Symbiodiniaceae symbiosis, enhance coral antioxidant capacity, alleviate heat-stress-induced physiological damage, and thereby increase the heat tolerance of this species.

Oulastrea crispata is a widely distributed reef-building coral with strong adaptability to various environmental stressors. However, existing studies lack systematic genetic background analysis of this species as a host organism to elucidate its underlying adaptive mechanisms. In this study, coral bleaching was induced by high-temperature treatment to obtain coral tissues with low symbiotic algal background. Transcriptome sequencing and bioinformatics analysis were then performed based on the Illumina HiSeq^TM high-throughput sequencing platform. Following data quality assessment, EST-SSR loci were systematically identified, and EST-SSR molecular markers were developed. The results showed that the percentage of bases with Q30 scores (96.32%) of all samples met the high-quality sequencing standard. A total of 594 447 unigenes were assembled, with a transcript N50 length of 1 699 bp, indicating good transcriptome data quality. A total of 101 034 EST-SSR loci were identified from 87 979 unigenes, among which mono- and tri-nucleotide repeats were the dominant motif types, and the EST-SSR repeat number showed a decreasing trend with increasing motif length. Multi-database joint functional annotation revealed significant enrichment of EST-SSR loci in functional genes involved in environmental information processing, suggesting that EST-SSR marker-associated genes were closely linked to the core physiological mechanisms underlying coral environmental stress response. The EST-SSR marker system constructed in this study can serve as a high-quality candidate genetic marker library, provide not only important molecular tools for deciphering the environmental adaptation potential and evolutionary mechanisms of Oulastrea crispata populations, but also scientific references for coral population genetic analysis, cross-latitude adaptability research, and coral reef resource conservation and restoration.

Environmental DNA (eDNA) metabarcoding has been widely applied in marine biodiversity monitoring and research. However, its effectiveness in coral diversity monitoring requires further evaluation due to limitations in primer specificity and the accuracy of coral molecular databases. In this study, three primer pairs—CoralITS2, CoralITS2_acro, and 12S—were used to conduct eDNA metabarcoding detection in a coral aquaculture system with a well-defined genus composition, aiming to investigate the differences in detection and application effectiveness of individual primers and their combinations on the genus-level taxonomic diversity of scleractinian corals. The results showed that both CoralITS2 and 12S primers detected 19 coral genera belonging to the order Scleractinia, whereas CoralITS2-acro detected only 11 genera, indicating clear complementarity among the primers. The combined amplification using multiple primers detected a total of 27 scleractinian coral genera, representing 87.5% of the total coral genera known to be present in the system. Compared with single-primer detection, the multi-primer combination effectively narrowed detection blind spots and significantly improved the detection rate of scleractinian coral genus-level taxa. The multi-primer strategy can effectively optimize the eDNA monitoring protocol for scleractinian coral communities and serves as an effective means to enhance the completeness and accuracy of coral community surveys. Meanwhile, we also found that the eDNA sequencing annotation results identified six coral genera that were not actually distributed in the study system, indicating a certain risk of false positives in this technology. Future improvements in the precision and reliability of eDNA metabarcoding in coral diversity monitoring could be pursued by refining local reference sequence databases for scleractinian corals and establishing a standardized multi-primer combined amplification and analysis pipeline.

Coral skeletal carbon isotope composition (δ¹³C_s) is an important proxy for reconstructing past environmental changes and has been widely applied in paleoclimate and paleoenvironmental studies across various temporal scales. However, the factors controlling skeletal δ¹³C_s remain controversial, particularly the roles of seasonal variations in coral nutritional strategy and the relative intensities of photosynthesis and respiration. In this study, Porites lutea samples collected from Weizhou Island, Guangxi, China, in October 2023 (autumn) and April 2024 (spring) were analyzed using isotopic geochemical proxies in combination with physiological and environmental parameters. Compared with spring, corals collected in autumn exhibited lower zooxanthellae density (ZD), chlorophyll a (Chl a) content, zooxanthellae carbon isotope composition (δ¹³C_z), gross photosynthesis-to-gross respiration ratio (P/R), host tissue carbon isotope composition (δ¹³C_h), and the isotopic difference between host tissue and zooxanthellae (Δ¹³C_h-z). These results indicate that autumn corals experienced reduced zooxanthellae density and photosynthetic activity, accompanied by an increased contribution of heterotrophy, whereas enhanced zooxanthellae density and photosynthesis in spring resulted in a lower relative contribution of heterotrophy. Coral skeletal δ¹³C_s was positively correlated with both ZD and δ¹³C_z, while its seasonal variation was consistent with changes in Δ¹³C_h-z and P/R, suggesting that shifts in the autotrophic/heterotrophic balance and metabolic activity contribute to seasonal variations in skeletal δ¹³C_s. Therefore, variations in the photosynthetic and respiratory activities of the coral holobiont should be taken into account when interpreting coral skeletal δ¹³C_s records for paleoenvironmental reconstructions.

The stable carbon and oxygen isotopes of the calcitic skeleton of cold-water bamboo corals can be used as a paleo-thermometer, but the imcomplete the understanding of their fractionation mechanisms limits the accuracy and range of its application in paleo-environmental reconstruction. We analyzed the stable carbon and oxygen isotope compositions of the calcitic skeleton of bamboo corals from the South China Sea, and found that their δ¹⁸O-δ¹³C slopes were similar to those of bamboo corals from the Pacific Ocean. Adapting a published kinetic calcification model of aragonitic cold-water scleractinian corals, we found that the carbonic anhydrase (CA) activity in calcitic bamboo corals was significantly lower than that in aragonitic cold-water scleractinian corals, and varied considerably throughout their entire lifespans. Based on the isotopic fractionation flux balance model, we found that the carbon and oxygen isotopes of bamboo coral skeletons were mainly affected by kinetic fractionations during aqueous CO₂ hydration and hydroxylation, while equilibrium fractionation due to transcellular aqueous CO₂ flux contributed no more than 50%. This result is helpful to correct for isotopic vital effects when reconstructing paleo-temperature.

Coral reef constitute important habitats for sea turtles, providing essential refuge and foraging grounds. However, global coral reef ecosystems are experiencing severe degradation due to the combined pressures of anthropogenic activities and natural stressors. In this study, we conducted a survey of scleractinian coral communities around Guangdong Huidong Sea Turtle National Nature Reserve, China, establishing 33 monitoring stations to analyze species composition, spatial distribution, and community structure. The survey recorded 32 species of scleractinian corals (4 unidentified), representing 8 families and 14 genera, with a mean coverage of 15.94%. Coral assemblages were dominated by stress-tolerant massive species, such as Porites lutea and Plesiastrea versipora. The Xiaoxingshan-Shenggao Island area was identified as the core distribution zone, with an average coverage of 22.53%and 27 species recorded. In comparison, coral communities in Pinghai Bay and Honghai Bay were disturbed by multiple human interferences including coastal sewage discharge, mariculture and tourism, leading to simplified community structures. Consequently, we recommend enhanced protection for coral communities in Xiaoxingshan and Shenggao Island, stringent regulation of peripheral aquaculture and tourism developments, and the implementation of differentiated conservation strategies based on ecological functional zoning, so as to achieve synergistic conservation and sustainable management of both sea turtle habitats and coral reef ecosystems.

The deleterious effects of turf algae overgrowth on coral performance have intensified across coral reef ecosystems; nevertheless, the microbial pathways mediating coral health deterioration driven by competitive turf algae interactions remain poorly characterized. Using 16S rRNA gene high-throughput amplicon sequencing, the present work explored how physical contact with turf algae alters the bacterial community diversity, taxonomic composition, and functional gene profiles of Porites lutea colonies at Weizhou Island coral reefs. Our findings showed that turf algae-associated bacterial communities exhibited substantially higher α-diversity than those colonizing healthy corals. Physical turf algae exposure significantly boosted the α-diversity of coral microbiomes and triggered taxonomic convergence between coral bacterial assemblages and turf algae microbiotas. Differential abundance testing illustrated that relative abundances of core coral symbiotic genera—including Pseudoalteromonas, Endozoicomonas, Ruegeria, and Ralstonia—were markedly depleted in coral tissues exposed to turf algae relative to healthy counterparts. In contrast, the putative pathogen Woeseia, alongside multiple uncharacterized bacterial taxa with undetermined pathogenic potential, underwent dramatic enrichment. Additionally, PICRUSt2-based functional prediction at the KEGG secondary pathway tier revealed that turf algae contact triggered significant upregulation of genes linked to energy metabolism and concurrent downregulation of lipid metabolism within coral bacterial consortia. Synthesizing these observations, physical turf algae contact remodels coral microbiomes to resemble turf algae-associated microbial assemblages: this contact suppresses populations of coral symbiotic beneficial taxa while enriching opportunistic pathogens, elevates overall bacterial energy metabolic capacity, and reduces lipid pools serving as key energy substrates. Such community and functional reorganizations may constitute the core microbial mechanisms through which turf algae competition compromises coral physiological fitness.

Phestilla fuscostriata is a nudibranch mollusk that exclusively preys on Pavona decussata. This study investigated the early developmental characteristics of P.fuscostriata and explored effective control methods through microscopic observation and physiological-biochemical analysis. The results showed that the embryonic development of P.fuscostriata progresses from fertilized eggs through the cleavage stage, blastula stage, gastrula stage, encapsulated trochophore stage, and encapsulated veliger stage, completing hatching at 168 hours post-fertilization under a water temperature of 26 ℃. Subsequent control experiments revealed that allicin exhibited strong killing efficacy and licorice extract showed good removal efficacy, and that both were safe for P.decussata with no toxic side effects. Therefore, they are recommended as effective agents for controlling P.fuscostriata. The findings of this study provide fundamental data for research on the reproductive biology of P.fuscostriata and offer valuable insights for developing green and efficient control strategies against coral-eating nudibranchs.

The crown-of-thorns starfish (Acanthaster solaris) preys on corals, and its population outbreaks directly reduce live coral coverage, severely impacting the stability of coral reef ecosystems. Heavy metal accumulation by marine organisms is an important indicator of anthropogenic impacts on marine ecology; however, studies on heavy metal bioaccumulation characteristics and spatial variations in A.solaris remain limited. Based on a comparative analysis of heavy metal content in different tissues of A.solaris from coral reefs in the Xisha and Nansha Islands in the South China Sea, this study revealed that heavy metal content in A.solaris collected from the Xisha Islands were generally higher than those from the Nansha Islands, with regional differences in vanadium (V) and cadmium (Cd) being most significant (p<0.05). V and Cd content in samples from the Xisha Islands were 1.73-4.79 and 1.33-3.64 times those of the Nansha Islands, respectively. It was also found that the weight, body size and arm length of A.solaris collected from the Xisha Islands were significantly higher than those from the Nansha Islands (p<0.001). In addition, heavy metal accumulation characteristics exhibited similarities across different tissues of A.solaris, and cluster analysis classified them into two groups: one included skeletons, body walls and spines, and the other included of stomachs, pyloric caeca and gonads. Finally, content of V and Mo in different tissues showed significant negative correlations with weight and body size (p<0.01), while Pb in skeletons showed a significant positive correlation with weight (p<0.05). The regional variations in heavy metal accumulation in A.solaris consistent with the “high nearshore, low offshore” spatial distribution pattern of heavy metals in seawater, reflecting differences in marine environmental background and anthropogenic disturbance intensity, and offering insights into the environmental indicator significance of A.solaris in the coral reef areas of the South China Sea.

Coral reef lagoon sediments serve as ideal archives for reconstructing past storm activity. In this study, we investigated sediment core HYDS1 (255 cm in length) collected from the lagoon of Huangyan Island in the South China Sea. A chronological framework was established using AMS¹⁴C dating of foraminifera from seven discrete horizons, while a high-resolution continuous grain-size sequence was obtained from 510 sediment samples. Peaks in the coarse fraction (grain-size≥2 mm) content and the presence of coral branches and shell gravels were employed as proxy indicators for identifying intense storm events, based on which the paleostorm activity sequence recorded in the Huangyan Island lagoon was reconstructed. Results indicated that the base of core HYDS1 dated back to 966 CE (before 1950 CE), preserving a sedimentary record spanning approximately the last millennium. Based on the vertical variations in coarse-fraction content, a total of 12 intense storm events were identified, including five super storms that occurred during 1189-1199 CE, 1538-1547 CE, 1760-1769 CE, 1851-1859 CE, and 1988-1996 CE. The period 1511-2015 CE corresponded to a phase of heightened storm activity, and over the past millennium, regional storm activity exhibited an overall increasing trend.

Deep coral reef limestone, as the primary load-bearing medium in island-reef engineering, contains multi-scale pores whose internal development is a key factor causing strength degradation and making the failure characteristics of damaged zones difficult to predict. Based on high-resolution CT scanning and digital image analysis techniques, this study conducted three-dimensional structural reconstruction and parametric analysis of four typical structural types of deep coral reef limestone, namely framework, boulder, gravel, and calcarenite. The results show that pore volume, surface area, shape factor, and major axis length all exhibit right-skewed distributions, indicating a high frequency of small-sized pores, whereas meso- to macro-scale pores occur less frequently but exert a significant mechanical influence. The lengths of the three principal pore axes are highly positively correlated, suggesting that diagenetic processes such as erosion and dissolution shape pores through proportional enlargement or reduction. Based on the superposition criterion of pore-perturbed stress fields, a complex network model was established that simultaneously considers stress attenuation and pore size effects. Weighted degree and betweenness centrality were then used to identify the key pores controlling the mechanical properties, providing insights into the mechanism of mechanical deterioration in deep coral reef limestone.