Heat stress destabilizes symbiotic nutrient cycling in corals

Unraveling the differential tolerance mechanisms of Acropora formosa and Montipora digitata to Benzo[a]pyrene (BaP) exposure via 4D proteomics

Coral reefs are suffering from environmental pollution worldwide, implying unprecedented survival challenges. In this paper we investigate the effects of the Benzo[a]pyrene (BaP) on the survival status of coral and explore its potential tolerance mechanism. By applying advanced 4D proteomics techniques, we systematically compared the differences in the protein expression profiles of Acropora formosa (A. formosa) and Montipora digitata (M. digitata) under BaP exposure conditions (50 μg/L, 72 h and 120 h). Under the same BaP exposure conditions, the bleaching rate of A. formosa was faster, and the zooxanthellae density and chlorophyll content were lower. M. digitata showed higher BaP tolerance than A. formosa, may attributed to significantly enhanced protein synthesis, folding, and stability in its host cells, as well as a more efficient energy metabolism mechanism. While A. formosa coral hosts showed low protein stability and high ferritin expression, and iron metabolism imbalance was aggravated under BaP stress, which increased oxidative stress damage. Specifically, the zooxanthellae of M. digitata without exposed to BaP showed stronger photosynthetic efficiency and glucose metabolism, especially the activation of the pyruvate metabolic pathway. However, these advantages were rapidly diminished after exposure to BaP. In response to BaP exposure, A. formosa's zooxanthellae may activated longevity related pathways and hypoxia-inducing factor signaling pathways, significantly enhancing energy metabolism pathways. This study is helpful to reveal the complex adaptive mechanism of coral reef ecosystem to environmental pollution.

Nitrate enrichment exacerbates microbiome and metabolism disturbances of the coral holobiont under heat stress

Coral reef ecosystems are facing severe deterioration due to escalating global temperatures and human-induced activities. Combined nitrate and heat stress can exacerbate coral bleaching, however, the underlying mechanism is still unclear. In the present study, we assessed the bleaching status of Acropora hyacinthus, a reef-building coral species, under high temperature and nitrate stress conditions using chemostat cultivation. We observed nitrate enrichment (9 μM) induced a significant reduction in photosystem efficiency (Fv/Fm) of Symbiodiniaceae and an increased thermal bleaching of corals under high temperature (30 °C). Nitrate exposure promoted the proliferation of Enterobacteriaceae and Vibrionaceae, which are bacterial families, potentially augmenting the coral's susceptibility to disease while exerting negligible effects on the fungal community. Alterations were observed in the metabolic pathways of both the coral hosts and Symbiodiniaceae, including down-regulated folate biosynthesis and inflammatory mediator regulation of TRP channels. Our findings indicate that nitrate enrichment under heat stress disrupts the metabolism of coral holobionts through altering bacterial communities, ultimately leading to increased coral bleaching.

Physiology and metabolism of eukaryotic microalgae involved in aquatic photosymbioses

Symbiosis between eukaryotic microalgae and heterotrophic hosts is a widespread, phylogenetically convergent, and ecologically important phenomenon in aquatic ecosystems. Partners include taxonomically diverse microalgae interacting with multicellular or unicellular hosts in marine or freshwater environments. While progress has been made recently, there are still major knowledge gaps on the microenvironmental conditions of microalgae in hospite (e.g. nutrient and CO2 availability), the algal carbon metabolism (production and storage), and the cellular mechanisms of carbohydrate export to the host. This review aims to provide current knowledge on the physiology and metabolism of symbiotic microalgae, to highlight whether there are commonalities across different photosymbioses, and to identify new approaches and technologies for disentangling photosymbiotic interactions at relevant temporal and spatial scales.

Inhibiting inositol transport disrupts metabolite profiles and mimics heat stress in a model cnidarian-Symbiodiniaceae symbiosis

The nutrient exchange between corals and their symbiotic microalgae (Symbiodiniaceae) is vital for coral survival. Disruptions in this mutualistic relationship, often due to stress-induced dysbiosis, contribute significantly to coral mortality and reef decline globally. Dysbiosis is associated with substantial shifts in various metabolites, notably a rise in inositol, a sugar alcohol, though its role in coral-algae interactions remains unclear. Using a cnidarian model, we identify Symbiodiniaceae as the main source of inositol, with myo- and scyllo-inositol being the dominant forms under normal conditions. During heat stress, scyllo-inositol levels increase by 1.8 times in symbiotic hosts, and up to 26 times in cultured Symbiodiniaceae (Breviolum minutum). Meanwhile, myo-inositol decreases in host tissues but doubles within Symbiodiniaceae, indicating altered nutrient-sharing or stress signalling. In contrast, no changes are observed in aposymbiotic cnidarians (without Symbiodiniaceae). Additionally, inhibiting inositol production and transport in symbiotic tissues disrupts metabolite profiles, mimicking effects seen under heat stress, suggesting that inositol transport is crucial for maintaining metabolic balance and nutrient exchange. These findings reveal that disruptions in inositol dynamics play a critical role in stress responses, offering insights into dysbiosis mechanisms driving coral reef crises.

Physiological and molecular responses to urea environment in Cladocopium goreaui (Symbiodiniaceae)

Nitrogen is an essential nutrient for photosynthetic productivity, and its enrichment in coral reef ecosystems due to anthropogenic activities has raised concerns about ecological impacts. Urea is a readily available nitrogen source that can influence nitrogen dynamics in coral reef ecosystems, but the underlying mechanisms of its assimilation and utilization by coral symbionts remain unclear. This study investigates the physiological and molecular responses of Cladocopium goreaui to urea and nitrate, highlighting key differences in nitrogen assimilation. Although there was no significant difference in the expression of urease genes and proteins under urea and nitrate conditions, the form of nitrogen source did not affect urease activity; instead, nitrogen concentration was the primary factor influencing urease expression. Moreover, the regulation of C. goreaui gene expression by light intensity was more pronounced than the influence of nitrogen source type, suggesting that environmental light plays a more substantial role in gene regulation than the form of nitrogen available. In addition, transcriptomic analysis revealed that the response time of gene expression to nitrogen availability occurred approximately 2 h later than expected, emphasizing the delayed nature of the C. goreaui response. A total of 7786 differentially expressed genes (DEGs) were identified, including 2209 DEGs specific to urea treatment and 2675 DEGs specific to nitrate treatment. Proteomic analysis confirmed these findings, further detailing distinct nitrogen regulatory pathways, including stable metabolic responses to urea and dynamic shifts under nitrate treatment. Additionally, isotopic analyses showed that urea conditions resulted in higher δ13C and δ15N enrichment, indicating more efficient nitrogen and carbon assimilation. These results highlight the advantages of urea as an energetically favorable nitrogen source for C. goreaui, leading to stable metabolic responses and more efficient assimilation of both nitrogen and carbon. The findings underscore the metabolic flexibility of C. goreaui and its ability to adapt to varying nitrogen sources, with a greater impact from light conditions than nitrogen source type.

Environmental acclimatization of the relatively high latitude scleractinian coral Pavona decussata: integrative perspectives on seasonal subaerial exposure and temperature fluctuations

BACKGROUND

Coral reefs are being increasingly threatened due to global climate change. However, some coral species have shown strong tolerance despite living in marginal environments. The species Pavona decussata from Weizhou Island in the South China Sea experiences subaerial exposure in summer and winter due to extreme low tides, and their environmental acclimatization to this aerial exposure remains unexplored.

RESULTS

Here we aimed to explore the molecular mechanism of P. decussata under season or subaerial exposure background through physiological and multi-omics integrative analyses. Specifically, corals with a history of seasonal air exposure underwent comprehensive changes in energy metabolism and defense mechanisms compared to permanently submerged corals. In summer, corals experiencing subaerial exposure enhanced antioxidant defense by increasing the activities of the enzymes T-SOD and CAT, and the coral-associated bacterial community shifted toward the class Alphaproteobacteria that may have provided corals with resistance to environmental stresses. Moreover, the decrease in the transcript levels of the TCA cycle and the increase in metabolite content of ornithine suggested an alteration in energy metabolic pathways. Corals with an air-exposed background may have enhanced energy reserves in winter, as indicated by a higher content of Chl a and a rebound in coral-associated bacterial community toward the class Gammaproteobacteria. Furthermore, accumulation of the metabolite leukotriene D4 and activation of the TGF-beta signaling pathway suggested higher anti-inflammatory requirements and positive regulation by innate immunity.

CONCLUSIONS

This study provides insights into the acclimatization of P. decussata to seasonal environmental fluctuations and demonstrates that relatively high-latitude corals possess the plasticity and acclimatory capacity to adapt to marginal environments.

Spatially restricted coral bleaching as an ecological manifestation of within-colony heterogeneity

Coral bleaching is a widespread stress response of reef-building corals to elevated sea temperatures, resulting in the loss of symbiotic algae and often leading to coral death and reef degradation. Although coral bleaching occurs globally, not all reefs, species, colonies, or polyps bleach equally. Understanding intra-colony bleaching heterogeneity is crucial to anticipate the extent of coral loss at 2°C warming and harness variability to inform restorative interventions. Partially bleached coral colonies are commonly documented yet rarely tracked to determine whether they reflect ecologically distinct heterogeneity (e.g., in thermal tolerance) or eventually bleach completely. Focusing on bleaching that appears restricted to certain areas within a coral colony, we examine its putative basis in the spatial variability of the holobiont. A coral's three-dimensional structure creates mosaics of microenvironments. Adaptations to these microenvironments are underpinned by intra-colony differences in Symbiodiniaceae association, microbiome assemblage, and nutritional status, giving rise to microhabitats. Genetic mosaicism and epigenetic changes further contribue to intra-colony phenotypic heterogeneity. We pinpoint methodologies to align spatially restricted bleaching to different forms of coral surface heterogeneity, examine the common assumption that coral fragments represent entire colonies, and illuminate implications for coral biology and restoration.

Ecologically expanding the One Health framework to unify the microbiome sciences

The One Health framework, traditionally focused on microbial threats, needs a bold expansion to include the full breadth of microbial diversity-from pathogenic to beneficial-within its ecological and evolutionary context. By shifting focus from disease surveillance to microbial stewardship, an integrative One Health microbiome science approach breaks down traditional silos in microbiome research, accelerating integrative and comparative science to uncover foundational insights into microbial community assembly, stability, and resilience. Ultimately, this will help unlock the full potential of microbiomes to enhance global health and sustainably manage ecosystems.

Herbicide prometryn aggravates the detrimental effects of heat stress on the potential for mutualism of Symbiodiniaceae

Ocean warming threatens the health of corals globally, and superimposed coastal environmental pollution can result in severe and irreversible coral bleaching. However, the responses of the coral symbiont Symbiodiniaceae to multiple stresses remain largely unknown. This study investigated the response of the coral symbiotic algae Cladocopium sp. to short-term exposure (4 days) to an environmentally relevant concentration (1 μg L-1) of the photosystem II (PSII) herbicide prometryn under heat stress (32 ℃) through physiological and omic analyses. These results showed that co-stress affected the photosynthetic efficiency of Cladocopium sp. negatively. Overproduction of reactive oxygen species and subsequent oxidative stress under co-stress activated distinct regulatory pathways in Cladocopium sp. Transcriptomic and proteomic analyses revealed that prometryn exacerbated heat stress-induced photosystem damage and reduced the regulatory capacity of Cladocopium sp. Moreover, co-stress disrupted energy metabolism, and further impaired nitrogen assimilation and nutrient transfer processes, potentially compromising the symbiotic potential between corals and Symbiodiniaceae. In summary, this study offers a valuable insight into understanding the molecular responses of Symbiodiniaceae to thermal and prometryn co-stress. It helps uncover the potential toxicity mechanisms induced by herbicide on coral symbionts in the context of climate change.

Coral-associated Symbiodiniaceae exhibit host specificity but lack phylosymbiosis, with Cladocopium and Durusdinium showing different cophylogenetic patterns

Altering the composition of the Symbiodiniaceae community to adapt to anomalous sea water warming represents a potential survival mechanism for scleractinian corals. However, the processes of Symbiodiniaceae assembly and long-standing evolution of coral-Symbiodiniaceae interactions remain unclear. Here, we utilized ITS2 (internal transcribed spacer 2) amplicon sequencing and the SymPortal framework to investigate the diversity and specificity of Symbiodiniaceae across 39 scleractinian coral species. Furthermore, we tested phylosymbiosis and cophylogeny between coral hosts and their Symbiodiniaceae. In our study, environmental samples exhibited the highest Symbiodiniaceae diversity. Cladocopium and Durusdinium dominated the Symbiodiniaceae communities, with significant β-diversity differences among coral species. Additionally, host specificity was widespread in Symbiodiniaceae, especially Durusdinium spp., yet lacked a phylosymbiotic pattern. Moreover, Cladocopium spp. showed cophylogenetic congruence with their hosts, while there was no evidence for Durusdinium spp. Furthermore, host switching was the predominant evolutionary event, implying its contribution to Cladocopium diversification. These findings suggest that Symbiodiniaceae assembly does not recapitulate host phylogeny, and host specificity alone does not drive phylosymbiosis or cophylogeny. As environmental reservoirs, free-living Symbiodiniaceae may influence symbiotic communities. Additionally, Durusdinium-coral associations lack cophylogenetic signals, indicating more flexible partnerships than Cladocopium. Overall, our results enhance understanding of Symbiodiniaceae assembly and coral-Symbiodiniaceae evolutionary interactions.

Exploring the function of key species in different composting stages for effective waste biotransformation

Composting is a microbial-driven process that plays a vital role in recycling waste and promoting sustainable production. To develop more effective bioaugmentation strategies, this study examined three successive stages in an aerobic composting system, focusing on microbial community adaptation to high-temperature stress (mode_2) and nutrient-poor conditions (mode_3). The results revealed a shift from an r-strategy (rapid growth) to a K-strategy (thriving under resource-limited conditions). Community succession was predominantly driven by deterministic processes (>90 %) and exhibited strong cooperative interactions. Using multiple statistical approaches, key species were identified for each condition. These species enhanced microbial network connectivity under environmental stresses, increasing network edges by 29 %-35 %. Under high-temperature stress, Bacillus and Ureibacillus maintained core functions, while Chelativorans and Aeribacillus contributed to key metabolic pathways, including amino acid metabolism. In nutrient-poor conditions, Saccharomonospora and Pseudoxanthomonas enhanced overall system functionality, and Novibacillus played a key role in carbon and nitrogen cycling, particularly nitrogen fixation. Predictive models for microbial community stability (R2 = 0.68-0.97) were developed based on these key species to enable rapid assessment of system stability. Overall, this study identifies essential microbes involved in composting across different environmental conditions and clarifies their functional roles, providing valuable insights for optimizing aerobic composting efficiency and advancing waste resource management.

Phototrophic bacteria as potential probiotics for corals

Coral-associated microorganisms provide crucial nutritional, protective, and developmental benefits, yet many functional traits remain unexplored. Phototrophic bacteria may enhance coral nutrition and reduce oxidative stress during bleaching via photosynthesis and antioxidant production. Despite this potential, their role in the holobiont's energy budget and heat stress resilience is understudied. This review explores the functional traits and potential of phototrophic bacteria to enhance coral health and resilience under environmental stress.

Metabolic Shifts and Muscle Remodeling as Pro-Survival and Energy Compensation Strategies in Photosymbiotic Giant Clams after Bleaching

Tropical photosymbiotic giant clams are increasingly threatened by climate change, leading to widespread bleaching. Decline in density of symbionts caused mortality events in symbiotic organisms; however, giant clams appear to exhibit prior survival capacity against these detrimental effects. It remains unclear whether giant clams can mitigate the adverse impacts of bleaching. Herein, we found that bleaching events after chronic heat stress induce remarkable changes and remodeling in symbiotic tissue of the giant clam Tridacna crocea. The density and structure of unique muscle fibers with high collagen content, observed in siphonal mantle of these animals, were negatively altered after heat stress. These changes were associated with a metabolic shift from carbohydrates and fatty acids to amino acids as the breakdown of collagen-rich muscle fibers can partially compensate for energy loss during bleaching. Such a shift was proposed to be regulated by AMP-activated protein kinase (AMPK) signaling and FoxO-atrogin pathways. Overall, our study highlights a pro-survival mechanism in giant clams through plastic regulation, which likely contributes to their relatively high environmental resilience during bleaching.

Proteomic insights into the environmental adaptation of the subtropical brain coral host Platygyra carnosa

Despite the rapid coral reef decline from climate change, the molecular dynamics underlying coral environmental responses remain elusive. Filling this gap is vital to reef conservation. Here, we investigated the seasonal proteomes of Platygyra carnosa, a stress-tolerant subtropical brain coral, using natural samples across wet and dry seasons with distinct environmental conditions. Over 5,000 coral host proteins were profiled, revealing co-regulated modules related to temperature, pH, dissolved oxygen, salinity, and turbidity. Importantly, these modules formed scale-free networks coordinated by hub proteins that are strongly correlated with environmental drivers, suggesting their key roles in environmental adaptation. Laboratory validation confirmed the temperature-responsive hub proteins, including HSP90B1 and HSPA5 that modulate stress response and protein homeostasis. Our study characterized the brain coral host proteome with unprecedented depth, revealing co-regulated modules underlying environmental adaptation. It sets the stage for proteome-based approaches in promoting coral resilience, leading to more informed conservation and restoration efforts.

A photophysiological model of coral bleaching under light and temperature stress: experimental assessment

Marine heatwaves occurring against the backdrop of rising global sea surface temperatures have triggered mass coral bleaching and mortality. Irradiance is critical to coral growth but is also an implicating factor in photodamage, leading to the expulsion of symbiotic algae under increased temperatures. Numerical modelling is a valuable tool that can provide insight into the state of the symbiont photochemistry during coral bleaching events. However, very few numerical physiological models combine the influence of light and temperature for simulating coral bleaching. The coral bleaching model used was derived from the coral bleaching representation in the eReefs configuration of the CSIRO Environmental Modelling Suite, with the most significant change being the equation for the rate of detoxification of reactive oxygen species. Simulated physiological bleaching outcomes from the model were compared to photochemical bleaching proxies measured during an ex situ moderate degree-heating week (up to 4.4) experiment. The bleaching response of Acropora divaricata was assessed in an unshaded and 30% shade treatment. The model-simulated timing for the onset of bleaching under elevated temperatures closely corresponded with an initial photochemical decline as observed in the experiment. Increased bleaching severity under elevated temperature and unshaded light was also simulated by the model, an outcome confirmed in the experiment. This is the first experimental validation of a temperature-mediated, light-driven model of coral bleaching from the perspective of the symbiont. When forced by realistic environmental conditions, process-based mechanistic modelling could improve accuracy in predicting heterogeneous bleaching outcomes during contemporary marine heatwave events and future climate change scenarios. Mechanistic modelling will be invaluable in evaluating management interventions for deployment in coral reef environments.

Stability of the cnidarian-dinoflagellate symbiosis is primarily determined by symbiont cell-cycle arrest

The cnidarian-dinoflagellate symbiosis relies on the regulation of resident symbiont populations to maintain biomass stability; however, the relative importance of host regulatory mechanisms [cell-cycle arrest (CC), apoptosis (AP), autophagy (AU), and expulsion (EX)] during symbiosis onset and maintenance is largely unknown. Here, we inoculated a symbiont-free (aposymbiotic) model cnidarian (Exaiptasia diaphana: "Aiptasia") with either its native symbiont Breviolum minutum or one of three non-native symbionts: Symbiodinium microadriaticum, Cladocopium goreaui, and Durusdinium trenchii. We then measured and compared host AP, host AU, symbiont EX, and symbiont cell-cycle phase for up to a year with these different symbionts and used these discrete measurements to inform comparative models of symbiont population regulation. Our models showed a general pattern, where regulation through AP and AU is reduced after onset, followed by an overshoot of the symbiont population that requires a strong regulatory response, dealt with by strong CC and increased EX. As colonization progresses into symbiosis maintenance, CC remains crucial for achieving steady-state symbiont populations, with our models estimating that CC regulates 10-fold more cells (60 to 90%) relative to the other mechanisms. Notably though, our models also revealed that D. trenchii is less tightly regulated than B. minutum, consistent with D. trenchii's reputation as a suboptimal partner for this cnidarian. Overall, our models suggest that single regulatory mechanisms do not accurately replicate observed symbiont colonization patterns, reflecting the importance of all mechanisms working concomitantly. This ultimately sheds light on the cell biology underpinning the stability of this ecologically significant symbiosis.

The Thermal Stress History of South Atlantic Reefs Reveals Increasing Intensity, Duration, Frequency, and Likely Undocumented Bleaching Episodes

The primary consequence of global warming for reefs is coral bleaching, often leading to extensive coral mortality. Although bleaching is well-documented globally, the thermal stress and bleaching experienced by the unique South Atlantic reefs remain largely unknown due to insufficient monitoring on both spatial and temporal scales. Therefore, this work aimed to reconstruct past thermal stress episodes across South Atlantic reefs, and assessed whether episodes are becoming more intense, longer-lasting, and more frequent. We retrieved daily 5 km-resolution Degree Heating Week (DHW) data from the U.S. National Oceanic and Atmospheric Administration Coral Reef Watch server for 33 reef sites spanning the last 40 years. For each thermal stress episode, we assessed the intensity (maximum DHW value), duration (number of continuous days under stress), and frequency (number of days between episodes). Generalized linear models were fitted to intensity, duration, and frequency data to evaluate the influence of latitude and the time x region interaction as predictors. We recorded multiple thermal stress episodes, increasing from 2010 onwards, ranging from 10 episodes between 1985-89 and 75 between 2020-24. Intensity and duration increased over time across the entire South Atlantic. Frequency also increased across the Southwestern Atlantic coast and oceanic islands, but not for Africa. Episodes at higher latitudes were more intense, prolonged, and frequent. The validity of the thermal stress history reconstruction was groundtruthed using information from the Abrolhos Bank, the only consistently monitored reef site in the South Atlantic-DHW data accurately matched the observed bleaching episodes at this site. With this, our dataset shows that multiple bleaching episodes likely occurred in the South Atlantic, but went undocumented in the field. Therefore, the information currently available for the South Atlantic likely underestimates the extent of bleaching occurring in the area, which is experiencing increases in intensity, duration, and frequency of thermal stress.

Moderate levels of dissolved iron stimulate cellular growth and increase lipid storage in Symbiodinium sp

Dinoflagellates in the family Symbiodiniaceae are fundamental in coral reef ecosystems and facilitate essential processes such as photosynthesis, nutrient cycling, and calcium carbonate production. Iron (Fe) is an essential element for the physiological processes of Symbiodiniaceae, yet its role remains poorly understood in the context of cellular development and metabolic health. Here, we investigated the effect of iron availability-0-100 nM Fe(III)-on Symbiodinium sp. ITS2 type A1 cultures and quantified cellular content using flow cytometry and holotomography. Moderate levels of dissolved Fe (50 nM) enhanced growth rates and cellular content development in Symbiodinium sp., including lipids and proteins. We observed distinct growth patterns, pigment concentrations, and cellular morphology under increasing Fe concentrations, indicating the influence of iron availability on cellular physiology. Nondestructive, label-free holotomographic microscopy enabled single-cell in vivo imaging, revealing higher intracellular lipid accumulation (+57%) in response to 50 nM Fe(III) enrichment. Our findings contribute to a deeper understanding of the relationship between iron availability and Symbiodinium sp. growth and cellular development, with potential implications for coral health and reef resilience in the face of environmental stressors.

Temperature-dependent responses of the hard corals Acropora sp. and Pocillopora verrucosa to molecular hydrogen

Coral reefs are increasingly threatened by mass bleaching events due to global ocean warming. Novel management strategies are urgently needed to support coral survival until global efforts can mitigate ocean warming. Given the strong antioxidant, anti-inflammatory and anti-apoptotic properties of molecular hydrogen, our study explores its potential to alleviate the negative effects of heat stress on corals. We investigated the ecophysiological responses of two common hard corals (Acropora sp. and Pocillopora verrucosa) from the Central Red Sea under ambient (26 °C) and elevated seawater temperatures (32 °C), with and without hydrogen addition ( ~ 150 µ M H2) over 48 h. Our results showed that at 32 °C without hydrogen addition, P. verrucosa exhibited high temperature tolerance, whereas Acropora sp. showed significant reductions in photosynthetic efficiency and maximum electron transport rate compared to the ambient condition (26 °C). The addition of hydrogen at 32 °C increased the maximum electron transport rate of Acropora sp. by 28%, maintaining it at levels compared to those at 26 °C. In contrast, the addition of hydrogen at 26 °C caused a significant decrease in the photophysiology of both Acropora sp. and P. verrucosa. This suggests that the short-term response of the coral holobiont to molecular hydrogen is temperature-dependent, potentially benefiting the coral holobiont under heat stress, while impairing the photophysiology under ambient temperatures. Our findings therefore provide the foundation for future long-term studies uncovering the mechanisms behind molecular hydrogen, potentially informing the development of new management strategies to enhance coral resilience to ocean warming.

Genetic analyses reveal wildfire particulates as environmental pollutants rather than nutrient sources for corals

Heterotrophic nutrients are crucial for coral growth and recovery from bleaching events. Although wildfire emissions are a potential source of these nutrients, their impact on corals was minimally investigated. In this microcosm experiment, Acropora formosa corals exhibited rapid tissue detachment upon exposure to wildfire fine particulate matter (PM2.5). Physiological and genetic analyses revealed mechanisms associated with oxidation-reduction homeostasis and nutrient metabolism. Excessive hydrogen peroxide was generated as corals activated cytochrome P450 enzymes and the respiratory burst in phagocytic cells to metabolize PM2.5, leading to oxidative damage, mitochondrial dysfunction, and cell apoptosis due to reduced superoxide dismutase activity and compromised glutathione antioxidant function. Subsequently, corals upregulated the transcriptions of genes which are related to tyrosine receptor proteins to regulate multicellular development for self-repair, increasing energy consumption. However, Symbiodiniaceae upregulated their metabolism and retained photosynthates, reducing nutrient supply to the coral host. Therefore, the host temporarily utilized lipid reserves via the glyoxylate cycle, but excessive consumption disrupted lipid and carbohydrate metabolism, ultimately weakening cell adhesion and causing coral tissue detachment. Additionally, the downregulation of HSP70 expression, potentially linked to decreased sacsin and mitochondrial apoptosis, accelerated coral heat bleaching. This study elucidates the mechanisms by which wildfire PM2.5 at environmental concentrations poses risks to corals, particularly in a warming climate.

Nitrogen source type modulates heat stress response in coral symbiont (Cladocopium goreaui)

Ocean warming due to climate change endangers coral reefs, and regional nitrogen overloading exacerbates the vulnerability of reef-building corals as the dual stress disrupts coral-Symbiodiniaceae mutualism. Different forms of nitrogen may create different interactive effects with thermal stress, but the underlying mechanisms remain elusive. To address the gap, we measured and compared the physiological and transcriptional responses of the Symbiodiniaceae Cladocopium goreaui to heat stress (31°C) when supplied with different types of nitrogen (nitrate, ammonium, or urea). Under heat stress (HS), cell proliferation and photosynthesis of C. goreaui declined, while cell size, lipid storage, and total antioxidant capacity increased, both to varied extents depending on the nitrogen type. Nitrate-cultured cells exhibited the most robust acclimation to HS, as evidenced by the fewest differentially expressed genes (DEGs) and less ROS accumulation, possibly due to activated nitrate reduction and enhanced ascorbate biogenesis. Ammonium-grown cultures exhibited higher algal proliferation and ROS scavenging capacity due to enhanced carotenoid and ascorbate quenching, but potentially reduced host recognizability due to the downregulation of N-glycan biosynthesis genes. Urea utilization led to the greatest ROS accumulation as genes involved in photorespiration, plant respiratory burst oxidase (RBOH), and protein refolding were markedly upregulated, but the greatest cutdown in photosynthate potentially available to corals as evidenced by photoinhibition and selfish lipid storage, indicating detrimental effects of urea overloading. The differential warming nitrogen-type interactive effects documented here has significant implication in coral-Symbiodiniaceae mutualism, which requires further research.IMPORTANCERegional nitrogen pollution exacerbates coral vulnerability to globally rising sea-surface temperature, with different nitrogen types exerting different interactive effects. How this occurs is poorly understood and understudied. This study explored the underlying mechanism by comparing physiological and transcriptional responses of a coral symbiont to heat stress under different nitrogen supplies (nitrate, ammonium, and urea). The results showed some common, significant responses to heat stress as well as some unique, N-source dependent responses. These findings underscore that nitrogen eutrophication is not all the same, the form of nitrogen pollution should be considered in coral conservation, and special attention should be given to urea pollution.

Microbiome Stability Is Linked to Acropora Coral Thermotolerance in Northwestern Philippines

Corals associate with a diverse community of prokaryotic symbionts that provide nutrition, antioxidants and other protective compounds to their host. However, the influence of microbes on coral thermotolerance remains understudied. Here, we examined the prokaryotic microbial communities associated with colonies of Acropora cf. tenuis that exhibit high or low thermotolerance upon exposure to 33°C (heated) relative to 29°C (control). Using 16S rRNA sequencing, we show that the microbial community structure of all A. cf. tenuis colonies was similar to each other at control temperature. Thermotolerant colonies, however, had relatively greater abundance of Endozoicomonas, Arcobacter, Bifidobacterium and Lactobacillus. At elevated temperature, only thermosensitive colonies showed a distinct shift in their microbiome, with an increase in Flavobacteriales, Rhodobacteraceae and Vibrio, accompanying a marked bleaching response. Functional prediction indicated that prokaryotic communities associated with thermotolerant corals were enriched for genes related to metabolism, while microbiomes of thermosensitive colonies were enriched for cell motility and antibiotic compound synthesis. These differences may contribute to the variable performance of thermotolerant and thermosensitive corals under thermal stress. Identification of microbial taxa correlated with thermotolerance provides insights into beneficial bacterial groups that could be used for microbiome engineering to support reef health in a changing climate.

Destabilization of mutualistic interactions shapes the early heat stress response of the coral holobiont

BACKGROUND

The stability of the symbiotic relationship between coral and their dinoflagellate algae (Symbiodiniaceae) is disrupted by ocean warming. Although the coral thermal response depends on the complex interactions between host, Symbiodiniaceae and prokaryotes, the mechanisms underlying the initial destabilization of these symbioses are poorly understood.

RESULTS

In a 2-month manipulative experiment, we exposed the coral Porites lutea to gradually increasing temperatures corresponding to 0-8 degree heating weeks (DHW) and assessed the response of the coral holobiont using coral and Symbiodiniaceae transcriptomics, microbial 16S rRNA gene sequencing and physiological measurements. From early stages of heat stress (< 1 DHW), the increase in metabolic turnover shifted the holobiont to a net heterotrophic state in which algal-derived nutrients were insufficient to meet host energy demands, resulting in reduced holobiont performance at 1 DHW. We postulate the altered nutrient cycling also affected the coral-associated microbial community, with the relative abundance of Endozoicomonas bacteria declining under increasing heat stress. Integration of holobiont stress responses correlated this decline to an increase in expression of a host ADP-ribosylation factor, suggesting that Symbiodiniaceae and Endozoicomonas may underlie similar endosymbiotic regulatory processes.

CONCLUSIONS

The thermotolerance of coral holobionts therefore is influenced by the nutritional status of its members and their interactions, and this identified metabolic interdependency highlights the importance of applying an integrative approach to guide coral reef conservation efforts. Video Abstract.

Coral probiotics induce tissue-specific and putative beneficial microbiome restructuring in a coral-dwelling fish

The ongoing fourth mass global coral bleaching event reinforces the need for active solutions to support corals through this major crisis. The use of beneficial microorganisms for corals (BMCs) offers a promising nature-based solution to rehabilitate coral's dysbiotic microbiomes. While the benefits to corals are increasingly recognized, the impacts on associated reef organisms, such as fish, remain unexplored. This study investigated the effects of BMCs on the tissue-associated microbiomes of Dascyllus abudafur (Pomacentridae), a damselfish that lives closely associated with coral colonies. Over three months, we applied BMCs three times per week to healthy Pocillopora verrucosa colonies in the central Red Sea and analyzed the resultant changes in the inhabiting fish's microbiomes. Our findings reveal significant, tissue-specific shifts in bacterial communities, particularly skin and gut, with moderate changes observed in gills. Notably, putative fish beneficial bacteria such as Mitsuokella spp. were enriched in the skin, while various Firmicutes taxa increased in the gut. There was also a marked decrease in potential fish pathogens. This study highlights the potential extended benefits of BMCs on coral reef fish and sets a foundation for understanding the broader ecological interactions between BMCs and reef-associated organisms.

Heat-Evolved Microalgae (Symbiodiniaceae) Are Stable Symbionts and Influence Thermal Tolerance of the Sea Anemone Exaiptasia diaphana

Symbiotic cnidarians, such as sea anemones and corals, rely on their mutualistic microalgal partners (Symbiodiniaceae) for survival. Marine heatwaves can disrupt this partnership, and it has been proposed that introducing experimentally evolved, heat-tolerant algal symbionts could enhance host thermotolerance. To test this hypothesis, the sea anemone Exaiptasia diaphana (a coral model) was inoculated with either the heterologous wild type or heat-evolved algal symbiont, Cladocopium proliferum, and homologous wild-type Breviolum minutum. The novel symbioses persisted for 1.5 years and determined holobiont thermotolerance during a simulated summer heatwave. Anemones hosting SS8, one of the six heat-evolved strains tested, exhibited the highest thermotolerance. Notably, anemones hosting the wild-type C. proliferum (WT10) were the second most thermally tolerant group, whereas anemones hosting the heat-evolved SS5 or SS9 strains were among the most thermosensitive. Elevated temperatures led to an increase in the levels of many amino acids and a decrease in tricarboxylic acid (TCA) metabolites in all anemone hosts, potentially indicating an increase in autophagy and a reduction in energy and storage production. Some consistent differences were observed in changes in metabolite levels between anemone groups in response to elevated temperature, suggesting that the algal symbiont influenced host metabolome and nutritional budget.

Standardized Methods to Assess the Impacts of Thermal Stress on Coral Reef Marine Life

The Earth's oceans have absorbed more than 90% of the excess, climate change-induced atmospheric heat. The resulting rise in oceanic temperatures affects all species and can lead to the collapse of marine ecosystems, including coral reefs. Here, we review the range of methods used to measure thermal stress impacts on reef-building corals, highlighting current standardization practices and necessary refinements to fast-track discoveries and improve interstudy comparisons. We also present technological developments that will undoubtedly enhance our ability to record and analyze standardized data. Although we use corals as an example, the methods described are widely employed in marine sciences, and our recommendations therefore apply to all species and ecosystems. Enhancing collaborative data collection efforts, implementing field-wide standardized protocols, and ensuring data availability through dedicated, openly accessible databases will enable large-scale analysis and monitoring of ecosystem changes, improving our predictive capacities and informing active intervention to mitigate climate change effects on marine life.

Seasonal changes in coral thermal threshold suggest species-specific strategies for coping with temperature variations

Coral thermotolerance research has focused on the ability of coral holobionts to maximize withstanding thermal stress exposure. Yet, it's unclear whether thermal thresholds adjust across seasons or remain constant for a given species and location. Here, we assessed the thermal tolerance thresholds over time spanning the annual temperature variation in the Red Sea for Pocillopora verrucosa and Acropora spp. colonies. Utilizing  the Coral Bleaching Automated Stress System (CBASS), we conducted standardized acute thermal assays by exposing corals to a range of temperatures (30 to 39 °C) and measuring their photosynthetic efficiency (Fv/Fm). Our results reveal species-specific thermal tolerance patterns. P. verrucosa exhibited significant seasonal changes in their thermal thresholds of around 3 °C, while Acropora spp. remained rather stable, showing changes of around 1 °C between seasons. Our work shows that thermal thresholds can vary with seasonal temperature fluctuations, suggesting that coral species may acclimate to these natural temperature hanges over short periods in a species-specific manner.

Potential adaptation of scleractinian coral Pocillopora damicornis during hypo-salinity stress caused by extreme pre-flood rainfall over south China

Global warming intensifies the water cycle, resulting in significant increases in precipitation and river runoff, which brings severe hypo-salinity stress to nearshore coral reefs. Ecological investigations have found that some corals exhibit remarkable adaptability to hypo-salinity stress during mass-bleaching events. However, the exact cause of this phenomenon remains unclear. To elucidate the potential molecular mechanism leading to high tolerance to hypo-salinity stress, Pocillopora damicornis was used as a research object in this study. We compared the differences in transcriptional responses and symbiotic microbiomes between bleaching and unbleaching P. damicornis during hypo-salinity stress caused by extreme pre-flood rainfall over South China in 2022. The results showed that: (1) Under hypo-salinity stress, the coral genes related to immune defense and cellular stress were significantly upregulated in bleaching corals, indicating more severe immune damage and stress, and the Symbiodiniaceae had no significant gene enrichment. Conversely, metabolic genes related to glycolysis/gluconeogenesis were significantly downregulated in unbleaching corals, whereas Symbiodiniaceae genes related to oxidative phosphorylation were significantly upregulated to meet the energy requirements of coral holobiont; (2) C1d was the dominant Symbiodiniaceae subclade in all samples, with no significant difference between the two groups; (3) The symbiotic bacterial community structure was reorganized under hypo-salinity stress. The abundance of opportunistic bacteria increased significantly in bleaching coral, whereas the relative abundance of probiotics was higher in unbleaching coral. This may be due to severe immune damage, making the coral more susceptible to opportunistic infection and bleaching. These results suggest that long-term hypo-salinity acclimation in the Pearl River Estuary enhances the tolerance of some corals to hypo-salinity stress. Corals with higher tolerance may reduce energy consumption by slowing down their metabolism, improve the energy metabolism of Symbiodiniaceae to meet the energy requirements of the coral holobiont, and alter the structure of symbiotic bacterial communities to avoid bleaching.

A draft genome assembly of the reef-building coral Acropora hemprichii from the central Red Sea

Coral reef ecosystems are under threat from climate change. Thus, active interventions to spur coral conservation/restoration are critical to support reef survival, greatly informed by a molecular understanding of resilience. The genus Acropora is a species-rich and globally prevalent reef builder that has experienced dramatic declines in the Caribbean. Here we generated a draft genome of the common coral Acropora hemprichii from the central Red Sea, one of the warmest water bodies in the world. We assembled the genome using 10x Chromium sequencing with subsequent scaffolding using a reference genome and Illumina short-read sequencing contigs. The A. hemprichii genome has an assembly size of 495.6 Mb confirmed using physical size estimation, of which 247.8 Mb (50%) are repeats. The scaffold N50 is 1.38 Mb with 99.6% of BUSCO genes identified (93.7% complete, 5.9% fragmented), providing a set of 26,865 protein-coding genes. The Red Sea A. hemprichii reference genome provides a valuable resource for studies aiming to decode the genomic architecture of resilience, e.g. through comparative analyses with other Acropora genomes.

Symbiodiniaceae algal symbionts of Pocillopora damicornis larvae provide more carbon to their coral host under elevated levels of acidification and temperature

Climate change destabilizes the symbiosis between corals and Symbiodiniaceae. The effects of ocean acidification and warming on critical aspects of coral survical such as symbiotic interactions (i.e., carbon and nitrogen assimilation and exchange) during the planula larval stage remain understudied. By combining physiological and stable isotope techniques, here we show that photosynthesis and carbon and nitrogen assimilation (H13CO3- and 15NH4+) in Pocillopora damicornis coral larvae is enhanced under acidification (1000 µatm) and elevated temperature (32 °C). Larvae maintain high survival and settlement rates under these treatment conditions with no observed decline in symbiont densities or signs of bleaching. Acidification and elevated temperature both enhance the net and gross photosynthesis of Symbiodiniaceae. This enhances light respiration and elevates C:N ratios within the holobiont. The increased carbon availability is primarily reflected in the 13C enrichment of the host, indicating a greater contribution of the algal symbionts to the host metabolism. We propose that this enhanced mutualistic symbiotic nutrient cycling may bolster coral larvae's resistance to future ocean conditions. This research broadens our understanding of the early life stages of corals by emphasizing the significance of symbiotic interactions beyond those of adult corals.

Not only for corals: exploring the uptake of beneficial microorganisms for corals by sponges

Microbiome restoration using beneficial microorganisms for corals (BMCs) comprise a promising strategy to help corals cope with anthropogenic stressors. However, there is limited knowledge on the uptake of BMCs by nontarget animals, especially sponges. This study explores whether sponges can acquire BMCs upon direct application and whether inoculations affect sponge health. A 4-week field experiment applying BMCs to Stylissa carteri and Callyspongia crassa assessed three conditions: no inoculation, and BMCs inoculation once and thrice a week. BMC-related strains were naturally present in the seawater and the microbiome of S. carteri. These strains were enriched in response to the inoculation only in the S. carteri microbiome. Microbiomes of both sponges were restructured; sponges were visually healthy and efficiently pumped water at the end of the experiment. These results suggest that sponges can be enriched with BMC-related strains, and that BMC application on nearby corals is unlikely to negatively affect sponge health.

Coral larvae increase nitrogen assimilation to stabilize algal symbiosis and combat bleaching under increased temperature

Rising sea surface temperatures are increasingly causing breakdown in the nutritional relationship between corals and algal endosymbionts (Symbiodiniaceae), threatening the basis of coral reef ecosystems and highlighting the critical role of coral reproduction in reef maintenance. The effects of thermal stress on metabolic exchange (i.e., transfer of fixed carbon photosynthates from symbiont to host) during sensitive early life stages, however, remains understudied. We exposed symbiotic Montipora capitata coral larvae in Hawai'i to high temperature (+2.5°C for 3 days), assessed rates of photosynthesis and respiration, and used stable isotope tracing (4 mM 13C sodium bicarbonate; 4.5 h) to quantify metabolite exchange. While larvae did not show any signs of bleaching and did not experience declines in survival and settlement, metabolic depression was significant under high temperature, indicated by a 19% reduction in respiration rates, but with no change in photosynthesis. Larvae exposed to high temperature showed evidence for maintained translocation of a major photosynthate, glucose, from the symbiont, but there was reduced metabolism of glucose through central carbon metabolism (i.e., glycolysis). The larval host invested in nitrogen cycling by increasing ammonium assimilation, urea metabolism, and sequestration of nitrogen into dipeptides, a mechanism that may support the maintenance of glucose translocation under thermal stress. Host nitrogen assimilation via dipeptide synthesis appears to be used for nitrogen limitation to the Symbiodiniaceae, and we hypothesize that nitrogen limitation contributes to retention of fixed carbon by favoring photosynthate translocation to the host. Collectively, our findings indicate that although these larvae are susceptible to metabolic stress under high temperature, diverting energy to nitrogen assimilation to maintain symbiont population density, photosynthesis, and carbon translocation may allow larvae to avoid bleaching and highlights potential life stage specific metabolic responses to stress.

Effects of thermal and UV stress on the polar and non-polar metabolome of photosymbiotic jellyfish and sea anemones

Recently, the impacts of climate change, notably ocean warming and solar ultraviolet radiation, have led to significant stress and mortality in cnidarians. The objective of this study is to decode the metabolic responses of sea anemones Entacmaea quadricolor and upside-down jellyfish Cassiopea andromeda upon exposure to thermal and ultraviolet stress. Gas chromatography-mass spectrometry and ultraperformance liquid chromatography coupled with high-resolution mass spectrometry targeting polar and non-polar metabolites were applied. In total, 72 polar and 242 lipophilic metabolites were detected in jellyfish and sea anemones, respectively. Amino acids are the major metabolite class in jellyfish, and triacylglycerides are the predominant lipids in jellyfish and anemones. Exposure to stressors led to metabolic alterations, marked by elevated amino acids in jellyfish and increased amino acids and sugar alcohols in sea anemones at 34 °C and after four days of ultraviolet radiation. Non-polar metabolome analysis indicated distinct responses to ultraviolet radiation and thermal stress in both species.

Trade-offs in a reef-building coral after six years of thermal acclimation

There is growing evidence that reef-building corals can acclimate to novel and challenging thermal conditions. However, potential trade-offs that accompany acclimation remain largely unexplored. We investigated physiological trade-offs in colonies of a globally abundant coral species (Pocillopora acuta) that were acclimated ex situ to an elevated temperature of 31 °C (i.e., 1 °C above their bleaching threshold) for six years. By comparing them to conspecifics maintained at a cooler temperature, we found that the energy storage of corals was prioritized over skeletal growth at the elevated temperature. This was associated with the formation of higher density skeletons, lower calcification rates and consequently lower skeletal extension rates, which entails ramifications for future reef-building processes, structural complexity and reef community composition. Furthermore, symbionts were physiologically compromised at 31 °C and had overall lower energy reserves, likely due to increased exploitation by their host, resulting in an overall lower stress resilience of the holobiont. Our study shows how biological trade-offs of thermal acclimation unfold, helping to refine our picture of future coral reef trajectories. Importantly, our observations in this six-year study do not align with observations of short-term studies, where elevated temperatures were often associated with the depletion of energy reserves, highlighting the importance of studying acclimation of organisms at relevant biological scales.

Heat stress and bleaching in corals: a bioenergetic model

The coral-dinoflagellate endosymbiosis is based on nutrient exchanges that impact holobiont energetics. Of particular concern is the breakdown or dysbiosis of this partnership that is seen in response to elevated temperatures, where loss of symbionts through coral bleaching can lead to starvation and mortality. Here we extend a dynamic bioenergetic model of coral symbioses to explore the mechanisms by which temperature impacts various processes in the symbiosis and to enable simulational analysis of thermal bleaching. Our model tests the effects of two distinct mechanisms for how increased temperature impacts the symbiosis: 1) accelerated metabolic rates due to thermodynamics and 2) damage to the photosynthetic machinery of the symbiont caused by heat stress. Model simulations show that the model can capture key biological responses to different levels of increased temperatures. Moderately increased temperatures increase metabolic rates and slightly decrease photosynthesis. The slightly decreased photosynthesis rates cause the host to receive less carbon and share more nitrogen with the symbiont. This results in temporarily increased symbiont growth and a higher symbiont/host ratio. In contrast, higher temperatures cause a breakdown of the symbiosis due to escalating feedback that involves further reduction in photosynthesis and insufficient energy supply for CO 2 concentration by the host. This leads to the accumulation of excess light energy and the generation of reactive oxygen species, eventually triggering symbiont expulsion and coral bleaching. Importantly, bleaching does not result from accelerated metabolic rates alone; it only occurs as a result of the photodamage mechanism due to its effect on nutrient cycling. Both higher light intensities and higher levels of DIN render corals more susceptible to heat stress. Conversely, heterotrophic feeding can increase the maximal temperature that can be tolerated by the coral. Collectively these results show that a bioenergetics model can capture many observed patterns of heat stress in corals, such as higher metabolic rates and higher symbiont/host ratios at moderately increased temperatures and symbiont expulsion at strongly increased temperatures.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00338-024-02561-1.

Phosphorus limitation intensifies heat-stress effects on the potential mutualistic capacity in the coral-derived Symbiodinium

Coral reef ecosystems have been severely ravaged by global warming and eutrophication. Eutrophication often originates from nitrogen (N) overloading that creates stoichiometric phosphorus (P) limitation, which can be aggravated by sea surface temperature rises that enhances stratification. However, how P-limitation interacts with thermal stress to impact coral-Symbiodiniaceae mutualism is poorly understood and underexplored. Here, we investigated the effect of P-limitation (P-depleted vs. P-replete) superimposed on heat stress (31 °C vs. 25 °C) on a Symbiodinium strain newly isolated from the coral host by a 14-day incubation experiment. The heat and P-limitation co-stress induced an increase in alkaline phosphatase activity and reppressed cell division, photosynthetic efficiency, and expression of N uptake and assimilation genes. Moreover, P limitation intensified downregulation of carbon fixation (light and dark reaction) and metabolism (glycolysis) pathways in heat stressed Symbiodinium. Notably, co-stress elicited a marked transcriptional downregulation of genes encoding photosynthates transporters and microbe-associated molecular patterns, potentially undermining the mutualism potential. This work sheds light on the interactive effects of P-limitation and heat stress on coral symbionts, indicating that nutrient imbalance in the coral reef ecosystem can intensify heat-stress effects on the mutualistic capacity of Symbiodiniaceae.

Evidence for phosphate-dependent control of symbiont cell division in the model anemone Exaiptasia diaphana

Reef-building corals depend on symbiosis with photosynthetic algae that reside within their cells. As important as this relationship is for maintaining healthy reefs, it is strikingly delicate. When ocean temperatures briefly exceed the average summer maximum, corals can bleach, losing their endosymbionts. Although the mechanisms governing bleaching are unknown, studies implicate uncoupling of coral and algal cell divisions at high temperatures. Still, little is known regarding the coordination of host and algal cell divisions. Control of nutrient exchange is one likely mechanism. Both nitrogen and phosphate are necessary for dividing cells, and although nitrogen enrichment is known to increase symbiont density in the host, the consequences of phosphate enrichment are poorly understood. Here, we examined the effects of phosphate depletion on symbiont growth in culture and compared the physiology of phosphate-starved symbionts in culture to symbionts that were freshly isolated from a host. We found that available phosphate is as low in freshly isolated symbionts as it is in phosphate-starved cultures. Furthermore, RNAseq revealed that phosphate-limited and freshly isolated symbionts have similar patterns of gene expression for phosphate-dependent genes, most notably upregulation of phosphatases, which is consistent with phosphate recycling. Similarly, lipid profiling revealed a substantial decrease in phospholipid abundance in both phosphate-starved cultures and freshly isolated symbionts. These findings are important because they suggest that limited access to phosphate controls algal cell divisions within a host.

IMPORTANCE

The corals responsible for building tropical reefs are disappearing at an alarming rate as elevated sea temperatures cause them to bleach and lose the algal symbionts they rely on. Without these symbionts, corals are unable to harvest energy from sunlight and, therefore, struggle to thrive or even survive in the nutrient-poor waters of the tropics. To devise solutions to address the threat to coral reefs, it is necessary to understand the cellular events underpinning the bleaching process. One model for bleaching proposes that heat stress impairs algal photosynthesis and transfer of sugar to the host. Consequently, the host's demands for nitrogen decrease, increasing nitrogen availability to the symbionts, which leads to an increase in algal proliferation that overwhelms the host. Our work suggests that phosphate may play a similar role to nitrogen in this feedback loop.

Not-so-mutually beneficial coral symbiosis

The partnership between corals and their intracellular algal symbionts has long been a textbook example of a mutually beneficial association. Here I argue that this view has been made obsolete by a steady accumulation of evidence over the past three decades. The coral-algal relationship is perhaps better viewed as one of domestication - think of it like a cattle farm, in which the coral is the farmer and the algae are the cows. I synthesize old and new evidence in support of this updated view and highlight remaining knowledge gaps, the largest of which continues to be the natural history of algal symbionts.

The coral microbiome in sickness, in health and in a changing world

Stony corals, the engines and engineers of reef ecosystems, face unprecedented threats from anthropogenic environmental change. Corals are holobionts that comprise the cnidarian animal host and a diverse community of bacteria, archaea, viruses and eukaryotic microorganisms. Recent research shows that the bacterial microbiome has a pivotal role in coral biology. A healthy bacterial assemblage contributes to nutrient cycling and stress resilience, but pollution, overfishing and climate change can break down these symbiotic relationships, which results in disease, bleaching and, ultimately, coral death. Although progress has been made in characterizing the spatial-temporal diversity of bacteria, we are only beginning to appreciate their functional contribution. In this Review, we summarize the ecological and metabolic interactions between bacteria and other holobiont members, highlight the biotic and abiotic factors influencing the structure of bacterial communities and discuss the impact of climate change on these communities and their coral hosts. We emphasize how microbiome-based interventions can help to decipher key mechanisms underpinning coral health and promote reef resilience. Finally, we explore how recent technological developments may be harnessed to address some of the most pressing challenges in coral microbiology, providing a road map for future research in this field.

Whole-genome duplication in an algal symbiont bolsters coral heat tolerance

The algal endosymbiont Durusdinium trenchii enhances the resilience of coral reefs under thermal stress. D. trenchii can live freely or in endosymbiosis, and the analysis of genetic markers suggests that this species has undergone whole-genome duplication (WGD). However, the evolutionary mechanisms that underpin the thermotolerance of this species are largely unknown. Here, we present genome assemblies for two D. trenchii isolates, confirm WGD in these taxa, and examine how selection has shaped the duplicated genome regions using gene expression data. We assess how the free-living versus endosymbiotic lifestyles have contributed to the retention and divergence of duplicated genes, and how these processes have enhanced the thermotolerance of D. trenchii. Our combined results suggest that lifestyle is the driver of post-WGD evolution in D. trenchii, with the free-living phase being the most important, followed by endosymbiosis. Adaptations to both lifestyles likely enabled D. trenchii to provide enhanced thermal stress protection to the host coral.

Diel transcriptional responses of coral-Symbiodiniaceae holobiont to elevated temperature

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.

Photosymbiosis reduces the environmental stress response under a heat challenge in a facultatively symbiotic coral

The symbiosis between corals and dinoflagellates of the family Symbiodiniaceae is sensitive to environmental stress. The oxidative bleaching hypothesis posits that extreme temperatures lead to accumulation of photobiont-derived reactive oxygen species ROS, which exacerbates the coral environmental stress response (ESR). To understand how photosymbiosis modulates coral ESRs, these responses must be explored in hosts in and out of symbiosis. We leveraged the facultatively symbiotic coral Astrangia poculata, which offers an opportunity to uncouple the ESR across its two symbiotic phenotypes (brown, white). Colonies of both symbiotic phenotypes were exposed to three temperature treatments for 15 days: (i) control (static 18 °C), (ii) heat challenge (increasing from 18 to 30 °C), and (iii) cold challenge (decreasing from 18 to 4 °C) after which host gene expression was profiled. Cold challenged corals elicited widespread differential expression, however, there were no differences between symbiotic phenotypes. In contrast, brown colonies exhibited greater gene expression plasticity under heat challenge, including enrichment of cell cycle pathways involved in controlling photobiont growth. While this plasticity was greater, the genes driving this plasticity were not associated with an amplified environmental stress response (ESR) and instead showed patterns of a dampened ESR under heat challenge. This provides nuance to the oxidative bleaching hypothesis and suggests that, at least during the early onset of bleaching, photobionts reduce the host's ESR under elevated temperatures in A. poculata.

Biodiversity, Distribution and Functional Differences of Fungi in Four Species of Corals from the South China Sea, Elucidated by High-Throughput Sequencing Technology

Recent studies have predominantly spotlighted bacterial diversity within coral microbiomes, leaving coral-associated fungi in the shadows of scientific inquiry. This study endeavors to fill this knowledge gap by delving into the biodiversity, distribution and functional differences of fungi associated with soft corals Cladiella krempfi and Sarcophyton tortuosum, gorgonian coral Dichotella gemmacea and stony coral Favia speciosa from the South China Sea. Leveraging high-throughput sequencing of fungal internal transcribed spacer-1 (ITS1) region of the rRNA gene, a total of 431 fungal amplicon sequence variants (ASVs) were identified in this study, which indicated that a large number of fungal communities were harbored in the South China Sea corals. Noteworthy among our findings is that 10 fungal genera are reported for the first time in corals, with Candolleomyces, Exophiala, Fomitopsis, Inaequalispora, Kneiffiella, Paraphaeosphaeria, and Yamadazyma belonging to the Ascomycota, and Cystobasidium, Psathyrella, and Solicoccozyma to the Basidiomycota. Moreover, significant differences (p < 0.05) of fungal communities were observed among the various coral species. In particular, the gorgonian coral D. gemmacea emerged as a veritable haven for fungal diversity, boasting 307 unique ASVs. Contrastingly, soft corals S. tortuosum and C. krempfi exhibited modest fungal diversity, with 36 and 21 unique ASVs, respectively, while the stony coral F. speciosa hosted a comparatively sparse fungal community, with merely 10 unique ASVs in total. These findings not only provide basic data on fungal diversity and function in the South China Sea corals, but also underscore the imperative of nuanced conservation and management strategies for coral reef ecosystems worldwide.

Unlocking the genomic potential of Red Sea coral probiotics

The application of beneficial microorganisms for corals (BMC) decreases the bleaching susceptibility and mortality rate of corals. BMC selection is typically performed via molecular and biochemical assays, followed by genomic screening for BMC traits. Herein, we present a comprehensive in silico framework to explore a set of six putative BMC strains. We extracted high-quality DNA from coral samples collected from the Red Sea and performed PacBio sequencing. We identified BMC traits and mechanisms associated with each strain as well as proposed new traits and mechanisms, such as chemotaxis and the presence of phages and bioactive secondary metabolites. The presence of prophages in two of the six studied BMC strains suggests their possible distribution within beneficial bacteria. We also detected various secondary metabolites, such as terpenes, ectoines, lanthipeptides, and lasso peptides. These metabolites possess antimicrobial, antifungal, antiviral, anti-inflammatory, and antioxidant activities and play key roles in coral health by reducing the effects of heat stress, high salinity, reactive oxygen species, and radiation. Corals are currently facing unprecedented challenges, and our revised framework can help select more efficient BMC for use in studies on coral microbiome rehabilitation, coral resilience, and coral restoration.

Symbionts out of sync: Decoupled physiological responses are widespread and ecologically important in lichen associations

A core vulnerability in symbioses is the need for coordination between the symbiotic partners, which are often assumed to be closely physiologically integrated. We critically re-examine this assumed integration between symbionts in lichen symbioses, recovering a long overlooked yet fundamental physiological asymmetry in carbon balance. We examine the physiological, ecological, and transcriptional basis of this asymmetry in the lichen Evernia mesomorpha. This carbon balance asymmetry depends on hydration source and aligns with climatic range limits. Differences in gene expression across the E. mesomorpha symbiosis suggest that the physiologies of the primary lichen symbionts are decoupled. Furthermore, we use gas exchange data to show that asymmetries in carbon balance are widespread and common across evolutionarily disparate lichen associations. Using carbon balance asymmetry as an example, we provide evidence for the wide-ranging importance of physiological asymmetries in symbioses.

Metabolic signatures of two scleractinian corals from the northern South China sea in response to extreme high temperature events

Coral bleaching events are becoming increasingly common worldwide, causing widespread coral mortality. However, not all colonies within the same coral taxa show sensitivity to bleaching events, and the current understanding of the metabolic mechanisms underlying thermal bleaching in corals remains limited. We used untargeted metabolomics to analyze the biochemical processes involved in the survival of two bleaching phenotypes of the common corals Pavona decussata and Acropora pruinosa, during a severe bleaching event in the northern South China Sea in 2020. During thermal bleaching, P. decussata and A. pruinosa significantly accumulated energy products such as succinate and EPA, antioxidants and inflammatory markers, and reduced energy storage substances like glutamate and thymidine. KEGG analysis revealed enrichment of energy production pathways such as ABC transporters, nucleotide metabolism and lipid metabolism, suggesting the occurrence of oxidative stress and energy metabolism disorders in bleached corals. Notably, heat stress exerted distinct effects on metabolic pathways in the two coral species, e.g., P. decussata activating carbohydrate metabolism pathways like glycolysis and the TCA cycle, along with amino acid metabolism pathways, whereas A. pruinosa significantly altered the content of multiple small peptides affected amino acid metabolism. Furthermore, the osmoregulatory potential of corals correlates with their ability to survive in heat-stress environments in the wild. This study provides valuable insights into the metabolic mechanisms linked to thermal tolerance in reef-building corals, contributes to the understanding of corals' adaptive potential to heat stress induced by global warming and lays the foundation for developing targeted conservation strategies in the future.

The bioenergetics response of the coral Pocillopora damicornis to temperature changes during its reproduction stage

Sexual reproduction of reef-building corals is vital for coral reef ecosystem recovery. Corals allocate limited energy to growth and reproduction, when being under environmental disturbance, which ultimately shapes the community population dynamics. In the present study, energetic and physiological parameters of both parental colonies and larvae of the coral Pocillopora damicornis were measured during their reproduction stage under four temperatures; 28 °C (low-temperature acclimation, LA), 29 °C (control temperature, CT), 31 °C (high-temperature acclimation, HA), and 32 °C (heat stress, HS). The results showed temperature changes altered the larvae release timing and fecundity in P. damicornis. Parental colonies exposed to the LA treatment exhibited reduced investment in reproduction and released fewer larvae, while retaining more energy for their development. However, each larva acquired higher energy and symbiont densities enabling survival through longer planktonic periods before settlement. In contrast, parental colonies exposed to the HA treatment had increased investment for reproduction and larvae output, while per larva gained less energy to mitigate the threat of higher temperature. Furthermore, the energy allocation processes restructured fatty acids concentration and composition in both parental colonies and larvae as indicated by shifts in membrane fluidity under adaptable temperature changes. Notably, parental colonies from the HS treatment expended more energy in response to heat stress, resulting in adverse effects, especially after larval release. Our study expands the current knowledge on the energy allocation strategies of P. damicornis and how it is impacted by temperature. Parental colonies employed different energy allocation strategies under distinct temperature regimes to optimize their development and offspring success, but under heat stress, both were compromised. Lipid metabolism is essential for the success of coral reproduction and further understanding their response to heat stress can improve intervention strategies for coral reef conservation in warmer future oceans.

Triggers, cascades, and endpoints: connecting the dots of coral bleaching mechanisms

The intracellular coral-dinoflagellate symbiosis is the engine that underpins the success of coral reefs, one of the most diverse ecosystems on the planet. However, the breakdown of the symbiosis and the loss of the microalgal symbiont (i.e. coral bleaching) due to environmental changes are resulting in the rapid degradation of coral reefs globally. There is an urgent need to understand the cellular physiology of coral bleaching at the mechanistic level to help develop solutions to mitigate the coral reef crisis. Here, at an unprecedented scope, we present novel models that integrate putative mechanisms of coral bleaching within a common framework according to the triggers (initiators of bleaching, e.g. heat, cold, light stress, hypoxia, hyposalinity), cascades (cellular pathways, e.g. photoinhibition, unfolded protein response, nitric oxide), and endpoints (mechanisms of symbiont loss, e.g. apoptosis, necrosis, exocytosis/vomocytosis). The models are supported by direct evidence from cnidarian systems, and indirectly through comparative evolutionary analyses from non-cnidarian systems. With this approach, new putative mechanisms have been established within and between cascades initiated by different bleaching triggers. In particular, the models provide new insights into the poorly understood connections between bleaching cascades and endpoints and highlight the role of a new mechanism of symbiont loss, i.e. 'symbiolysosomal digestion', which is different from symbiophagy. This review also increases the approachability of bleaching physiology for specialists and non-specialists by mapping the vast landscape of bleaching mechanisms in an atlas of comprehensible and detailed mechanistic models. We then discuss major knowledge gaps and how future research may improve the understanding of the connections between the diverse cascade of cellular pathways and the mechanisms of symbiont loss (endpoints).

Bacteria undergo significant shifts while archaea maintain stability in Pocillopora damicornis under sustained heat stress

Global warming reportedly poses a critical risk to coral reef ecosystems. Bacteria and archaea are crucial components of the coral holobiont. The response of archaea associated with warming is less well understood than that of the bacterial community in corals. Also, there have been few studies on the dynamics of the microbial community in the coral holobiont under long-term heat stress. In order to track the dynamic alternations in the microbial communities within the heat-stressed coral holobiont, three-week heat-stress monitoring was carried out on the coral Pocillopora damicornis. The findings demonstrate that the corals were stressed at 32 °C, and showed a gradual decrease in Symbiodiniaceae density with increasing duration of heat stress. The archaeal community in the coral holobiont remained relatively unaltered by the increasing temperature, whereas the bacterial community was considerably altered. Sustained heat stress exacerbated the dissimilarities among parallel samples of the bacterial community, confirming the Anna Karenina Principle in animal microbiomes. Heat stress leads to more complex and unstable microbial networks, characterized by an increased average degree and decreased modularity, respectively. With the extension of heat stress duration, the relative abundances of the gene (nifH) and genus (Tistlia) associated with nitrogen fixation increased in coral samples, as well as the potential pathogenic bacteria (Flavobacteriales) and opportunistic bacteria (Bacteroides). Hence, our findings suggest that coral hosts might recruit nitrogen-fixing bacteria during the initial stages of suffering heat stress. An environment that is conducive to the colonization and development of opportunistic and pathogenic bacteria when the coral host becomes more susceptible as heat stress duration increases.

Localization and symbiotic status of probiotics in the coral holobiont

Corals establish symbiotic relationships with microorganisms, especially endosymbiotic photosynthetic algae. Although other microbes have been commonly detected in coral tissues, their identity and beneficial functions for their host are unclear. Here, we confirm the beneficial outcomes of the inoculation of bacteria selected as probiotics and use fluorescence in situ hybridization (FISH) to define their localization in the coral Pocillopora damicornis. Our results show the first evidence of the inherent presence of Halomonas sp. and Cobetia sp. in native coral tissues, even before their inoculation. Furthermore, the relative enrichment of these coral tissue-associated bacteria through their inoculation in corals correlates with health improvements, such as increases in photosynthetic potential, and productivity. Our study suggests the symbiotic status of Halomonas sp. and Cobetia sp. in corals by indicating their localization within coral gastrodermis and epidermis and correlating their increased relative abundance through active inoculation with beneficial outcomes for the holobiont. This knowledge is crucial to facilitate the screening and application of probiotics that may not be transient members of the coral microbiome.

IMPORTANCE

Despite the promising results indicating the beneficial outcomes associated with the application of probiotics in corals and some scarce knowledge regarding the identity of bacterial cells found within the coral tissue, the correlation between these two aspects is still missing. This gap limits our understanding of the actual diversity of coral-associated bacteria and whether these symbionts are beneficial. Some researchers, for example, have been suggesting that probiotic screening should only focus on the very few known tissue-associated bacteria, such as Endozoicomonas sp., assuming that the currently tested probiotics are not tissue-associated. Here, we provide specific FISH probes for Halomonas sp. and Cobetia sp., expand our knowledge of the identity of coral-associated bacteria and confirm the probiotic status of the tested probiotics. The presence of these beneficial microorganisms for corals (BMCs) inside host tissues and gastric cavities also supports the notion that direct interactions with the host may underpin their probiotic role. This is a new breakthrough; these results argue against the possibility that the positive effects of BMCs are due to factors that are not related to a direct symbiotic interaction, for example, that the host simply feeds on inoculated bacteria or that the bacteria change the water quality.