Global species richness, whether estimated by taxon, habitat, or ecosystem, is a key biodiversity metric. Yet, despite the global importance of biodiversity and increasing threats to it (e.g., we are no better able to estimate global species richness now than we were six decades ago. Estimates of global species richness remain highly uncertain and are often logically inconsistent. They are also difficult to validate because estimation of global species richness requires extrapolation beyond the number of species known. Given that somewhere between 3% and >96% of species on Earth may remain undiscovered, depending on the methods used and the taxa considered, such extrapolations, especially from small percentages of known species, are likely to be highly uncertain. An alternative approach is to estimate all species, the known and unknown, directly. Using expert taxonomic knowledge of the species already described and named, those already discovered but not yet described and named, and those still awaiting discovery, we estimate there to be 830,000 (95% credible limits: 550,000-1,330,000) multi-cellular species on coral reefs worldwide, excluding fungi. Uncertainty surrounding this estimate and its components were often strongly skewed toward larger values, indicating that many more species on coral reefs is more plausible than many fewer. The uncertainties revealed here should guide future research toward achieving convergence in global species richness estimates for coral reefs and other ecosystems via adaptive learning protocols whereby such estimates can be tested and improved, and their uncertainties reduced, as new knowledge is acquired.Copyright © 2015 Elsevier Ltd. All rights reserved.

The genus Symbiochlorum, initially described from a single strain isolated from a coral in the South China Sea, was shown to be a sister lineage of Ignatius within the green algal order Ignatiales. Its significant phylogenetic divergence from Ignatius raises the possibility of its classification as a new family. To further investigate this hypothesis, we conducted a more elaborate analysis of sequence diversity within the Symbiochlorum clade. We aligned the 18S nuclear ribosomal DNA gene sequences of newly isolated Symbiochlorum culture strains from coral in the South China Sea and environmental sequences from the Great Barrier Reef. Strains isolated from Porites lutea coral colonies exhibited morphological similarities to typical S. hainanense (CCTCC M2018096). Analysis of the 18S nuclear ribosomal DNA gene revealed substantial diversity in both the V4 and V9 regions of the gene, with sequences clustering into two distinct lineages. Lineage 1 (L1), represented solely by environmental sequences from Great Barrier Reef sediment samples, displayed high levels of sequence divergence (2.2%-5.8%), suggesting it consists of multiple species. Lineage 2 (L2) included coral-derived strains and environmental sequences from the South China Sea and the Great Barrier Reef, as well as an ascidian-associated strain from Palau. The significant divergence between L1 and L2 (3.1%-9.1%) suggests they represent different genera. Based on these results, we propose the recognition of the new family Symbiochloraceae within the Ignatiales order.© 2025 The Author(s). Journal of Phycology published by Wiley Periodicals LLC on behalf of Phycological Society of America.

Many corals have formed mutualistic associations with dinoflagellate symbionts, which are thought to provide nutrients and other benefits. To examine the underlying genetics of this association, S. Lin et al. sequenced the genome of the endosymbiont dinoflagellate Symbiodinium kawagutii. The genome includes gene number expansions and encodes microRNAs that show complementarity to genes within the coral genome. Such microRNAs may be involved in regulating coral genes. Furthermore, coral and S. kawagutii appear to share homologs of genes encoding specific nutrient transporters. The findings shed light on how symbiosis is established and maintained between dinoflagellates and corals.\n

Ocean warming is a leading cause of increasing episodes of coral bleaching, the dissociation between coral hosts and their dinoflagellate algal symbionts in the family Symbiodiniaceae. While the diversity and flexibility of Symbiodiniaceae is presumably responsible for variations in coral response to physical stressors such as elevated temperature, there is little data directly comparing physiological performance that accounts for symbiont identity associated with the same coral host species. Here, using Pocillopora damicornis harboring genotypically distinct Symbiodiniaceae strains, we examined the physiological responses of the coral holobiont and the dynamics of symbiont community change under thermal stress in a laboratory-controlled experiment.We found that P. damicornis dominated with symbionts of metahaplotype D1-D4-D6 in the genus Durusdinium (i.e., PdD holobiont) was more robust to thermal stress than its counterpart with symbionts of metahaplotype C42-C1-C1b-C1c in the genus Cladocopium (i.e., PdC holobiont). Under ambient temperature, however, the thermally sensitive Cladocopium spp. exhibited higher photosynthetic efficiency and translocated more fixed carbon to the host, likely facilitating faster coral growth and calcification. Moreover, we observed a thermally induced increase in Durusdinium proportion in the PdC holobiont; however, this "symbiont shuffling" in the background was overwhelmed by the overall Cladocopium dominance, which coincided with faster coral bleaching and reduced calcification.These findings support that lineage-specific symbiont dominance is a driver of distinct coral responses to thermal stress. In addition, we found that "symbiont shuffling" may begin with stress-forced, subtle changes in the rare biosphere to eventually trade off growth for increased resilience. Furthermore, the flexibility in corals' association with thermally tolerant symbiont lineages to adapt or acclimatize to future warming oceans should be viewed with conservative optimism as the current rate of environmental changes may outpace the evolutionary capabilities of corals. Video Abstract.© 2023. BioMed Central Ltd., part of Springer Nature.

Coral exhibits diel rhythms in behavior and gene transcription. However, the influence of elevated temperature, a key factor causing coral bleaching, on these rhythms remains poorly understood. To address this, we examined physiological, metabolic, and gene transcription oscillations in the Acropora tenuis-Cladocopium sp. holobiont under constant darkness (DD), light-dark cycle (LD), and LD with elevated temperature (HLD). Under LD, the values of photosystem II efficiency, reactive oxygen species leakage, and lipid peroxidation exhibited significant diel oscillations. These oscillations were further amplified during coral bleaching under HLD. Gene transcription analysis identified 24-hour rhythms for specific genes in both coral and Symbiodiniaceae under LD. Notably, these rhythms were disrupted in coral and shifted in Symbiodiniaceae under HLD. Importantly, we identified over 20 clock or clock-controlled genes in this holobiont. Specifically, we suggested CIPC (CLOCK-interacting pacemaker-like) gene as a core clock gene in coral. We observed that the transcription of two abundant rhythmic genes encoding glycoside hydrolases (CBM21) and heme-binding protein (SOUL) were dysregulated by elevated temperature. These findings indicate that elevated temperatures disrupt diel gene transcription rhythms in the coral-Symbiodiniaceae holobiont, affecting essential symbiosis processes, such as carbohydrate utilization and redox homeostasis. These disruptions may contribute to the thermal bleaching of coral.© 2024. The Author(s).

Corals are exposed to organic ultraviolet (UV) filters and other personal care product (PCP) ingredients in the environment, but the toxicities of organic UV filters and their related PCP to corals are not well understood. In this study, 7-day exposures were conducted to evaluate the toxicities and bioaccumulation of two organic UV filters, ethylhexylmethoxy-cinnamate (EHMC; octinoxate) and octocrylene (OC) (single- and combined-chemical tests), and diluted sunscreen wash-off water containing both active ingredients to the adult life stage of two hard coral species, Seriatopora caliendrum and Pocillopora damicornis. In the single-chemical tests, death (33.3%) and bleaching (83.3%) were only observed in the 1000 μg/L EHMC treatment of S. caliendrum. In the sunscreen product exposures, 5% sunscreen water (containing 422.34 ± 37.34 μg/L of EHMC and 33.50 ± 7.60 μg/L of OC at Day 0) caused high mortality in S. caliendrum (66.7-83.3%) and P. damicornis (33.3-50%), and tissue concentrations were up to 10 times greater than in the single-chemical exposures; co-exposure to EHMC and OC at similar levels to those in the sunscreen product resulted in bioaccumulation similar to the single-chemical tests. These results confirm the bioaccumulation potential of EHMC and OC and show that other ingredients in sunscreen products may increase the bioavailability of active ingredients to corals and exacerbate the toxicity of sunscreen products. Future studies on the toxicities of PCPs to aquatic organisms should not only focus on the toxicities of active ingredients.Copyright © 2018 Elsevier Ltd. All rights reserved.

Shallow water depth measurements using multispectral images are crucial for marine surveying and mapping. At present, relevant studies either depend on the use of other auxiliary data (such as field water depths or water column data) or contain too many unknown variables, thus making these studies suitable only for images that contain enough visible wavebands. To solve this problem, a Quasi-Analytical Algorithm (QAA) approach is proposed in this paper for estimating the water depths around Weizhou Island by developing a QAA to estimate the diffuse attenuation coefficients and simplifying the parameterization of the bathymetric model. The approach contains an initialization sub-approach and a novel global adjustment sub-approach. It is not only independent of other auxiliary data but also greatly reduces the number of unknowns. Experimental results finally demonstrated that the Root Mean Square Errors (RMSEs) were 1.01 m and 0.77 m for the ZY-3 image and the WorldView-3 (WV-3) image, respectively, so the approach is competitive to other QAA bathymetric methods. Besides, the global adjustment sub-approach was also seen to be superior to common smoothing filters: if the Signal-to-Noise Ratio (SNR) is as low as 42, i.e., ZY-3, it can smooth the water depths and improve the accuracies, otherwise can avoid the over-smoothing of water depths.

Coral reefs are vital to marine biodiversity but are increasingly threatened by global climate change and human activities, leading to significant declines in live coral cover (LCC). Monitoring LCC is crucial for assessing the health of coral reef ecosystems and understanding their degradation and recovery. Traditional methods for estimating LCC, such as the manual interpretation of underwater survey videos, are labor-intensive and time-consuming, limiting their scalability for large-scale ecological monitoring. To overcome these challenges, this study introduces an innovative deep learning-based approach that utilizes semantic segmentation to automatically interpret LCC from underwater videos. That is, we enhanced PSPNet for live coral segmentation by incorporating channel and spatial attention mechanisms, along with pixel shuffle modules. Experimental results demonstrated that the proposed model achieved a mean Intersection over Union (mIoU) of 89.51% and a mean Pixel Accuracy (mPA) of 94.47%, showcasing superior accuracy in estimating LCC compared to traditional methods. Moreover, comparisons indicated that the proposed model aligns more closely with manual interpretations than other models, with an mean absolute error of 4.17%, compared to 5.89% for the original PSPNet, 6.03% for Deeplab v3+, 7.12% for U-Net, and 6.45% for HRNet, suggesting higher precision in LCC estimation. By automating the estimation of LCC, this deep learning-based approach can greatly enhance efficiency, thereby contributing significantly to global conservation efforts by enabling more scalable and efficient monitoring and management of coral reef ecosystems.

With the rapid rise in pollution-associated nitrogen inputs to the western Pacific, it has been suggested that even the open ocean has been affected. In a coral core from Dongsha Atoll, a remote coral reef ecosystem, we observe a decline in the N/N of coral skeleton-bound organic matter, which signals increased deposition of anthropogenic atmospheric N on the open ocean and its incorporation into plankton and, in turn, the atoll corals. The first clear change occurred just before 2000 CE, decades later than predicted by other work. The amplitude of change suggests that, by 2010, anthropogenic atmospheric N deposition represented 20 ± 5% of the annual N input to the surface ocean in this region, which appears to be at the lower end of other estimates.Copyright © 2017, American Association for the Advancement of Science.

The South China Sea throughflow (SCSTF) serves as a heat and freshwater conveyor, playing a pivotal role in regulating physical processes and biogeochemical cycles in the SCS. Because of limited observations, the long-term changes of the SCSTF under a warming climate and underlying dynamics remain unclear. In this study, we reconstructed centennial-scale variability of the SCSTF (1894–2022) using coral oxygen isotope (δ 18 O) and satellite observations. Besides prominent interannual and decadal variabilities, there exists a marked long-term decreasing trend at −0.14 ± 0.02 Sv (1 Sv = 10 6 m 3 s −1 ) per decade for the total SCSTF volume transport. Consequently, the SCSTF transport decreased by 35 ± 5% over the past 129 years in comparison with the mean value of 5.15 Sv. Using the Time-dependent Island Rule theory, we further reveal that the intensified trade wind in the tropical western Pacific drives the SCSTF slowdown. The findings substantially contribute to investigating the physical, ecological, and biogeochemical changes in the SCS and the Indo-Pacific Oceans.\n