Untangling the molecular basis of coral response to sedimentation

Potential drivers of pocilloporid coral extirpations in Singapore

The reason why four out of five historically recorded pocilloporid species in Singapore went extinct remains unclear. However, potential causes include urbanization-related stressors such as sedimentation and low light. In this study, we conducted two ex-situ experiments to examine the effects of light limitation and sediment load on the survival and health of two extirpated (Stylophora pistillata, and Seriatopora hystrix), one extant (Pocillopora acuta), and one regional (Pocillopora meandrina) pocilloporid species. All were able to photoacclimate to high sedimentation and low light conditions. However, P. acuta and Se. hystrix exhibited reduced growth under low light, and mortality was significantly higher under increased sedimentation, especially for St. pistillata. While our results indicate that sedimentation and low light characteristic in Singapore's urban reefs are unlikely to be the sole drivers of pocilloporid extirpations, these variables probably contributed to the overall stress burden, pushing already uncommon species into functional, and then actual, extinction.

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.

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.

Transcriptomic and physiological analyses reveal the toxic effects of inorganic filters (nZnO and nTiO2) on scleractinian coral Galaxea fascicularis

The effects of sunscreen on scleractinian corals have garnered widespread attention; however, the toxic effects and mechanisms remain unclear. This study investigated the toxicological effects of two common inorganic filters used in sunscreens, nano zinc oxide and titanium dioxide (nZnO and nTiO₂), on the reef-building coral Galaxea fascicularis, focusing on the phenotypic, physiological, and transcriptomic responses. The results showed that after exposure to 0.8 mg/L of nZnO and 30 mg/L of nTiO₂ for 48 h, all coral polyps exhibited retraction. Zn and Ti ions were detected in coral tissues at concentrations of 67.18 and 24.87 μg/g, respectively, indicating the accumulation of nZnO and nTiO2 in coral tissues. The zooxanthellae density, Fv/Fm, and chlorophyll-a content decreased significantly. The activity of antioxidant enzymes showed an increasing trend. Meanwhile, glutamine synthetase and glutamate dehydrogenase activities exhibited a decreasing trend. The health status of corals was impacted as a result of nZnO and nTiO2 stress. Transcriptomic analysis showed that the toxicity mechanisms of nZnO and nTiO2 differed in corals. Following exposure to nZnO, differentially expressed genes (DEGs) in corals were mainly enriched in signaling pathways related to immune response. The genes related to innate immunity, such as MASP1, MUC5AC, TLRs, and C2, were significantly upregulated, indicating that nZnO exposure induces an innate immune response in corals. Meanwhile, following nTiO2 exposure, the upregulated DEGs were mainly enriched in signaling pathways related to transporter activity. In contrast, the downregulated DEGs were mainly enriched in energy metabolism pathways, indicating that nTiO2 disrupted the energy supply of corals, thereby leading to an increased demand for nutrient transport. This study reveals the toxic effects of nZnO and nTiO2, and their mechanisms of action on scleractinian corals, providing a reference for further assessing the toxicity of sunscreen on corals.

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.

Transcriptomic signatures across a critical sedimentation threshold in a major reef-building coral

Sedimentation is a major cause of global near-shore coral reef decline. Although the negative impacts of sedimentation on coral reef community composition have been well-documented, the effects of sedimentation on coral metabolism in situ have received comparatively little attention. Using transcriptomics, we identified gene expression patterns changing across a previously defined sedimentation threshold that was deemed critical due to changes in coral cover and community composition. We identified genes, pathways, and molecular processes associated with this transition that may allow corals, such as Porites lobata, to tolerate chronic, severe sedimentation and persist in turbid environments. Alternative energy generation pathways may help P. lobata maintain a persistent stress response to survive when the availability of light and oxygen is diminished. We found evidence for the expression of genes linked to increased environmental sensing and cellular communication that likely allow P. lobata to efficiently respond to sedimentation stress and associated pathogen challenges. Cell damage increases under stress; consequently, we found apoptosis pathways over-represented under severe sedimentation, a likely consequence of damaged cell removal to maintain colony integrity. The results presented here provide a framework for the response of P. lobata to sedimentation stress under field conditions. Testing this framework and its related hypotheses using multi-omics approaches can deepen our understanding of the metabolic plasticity and acclimation potential of corals to sedimentation and their resilience in turbid reef systems.

Multiomics data integration, limitations, and prospects to reveal the metabolic activity of the coral holobiont

Since their radiation in the Middle Triassic period ∼240 million years ago, stony corals have survived past climate fluctuations and five mass extinctions. Their long-term survival underscores the inherent resilience of corals, particularly when considering the nutrient-poor marine environments in which they have thrived. However, coral bleaching has emerged as a global threat to coral survival, requiring rapid advancements in coral research to understand holobiont stress responses and allow for interventions before extensive bleaching occurs. This review encompasses the potential, as well as the limits, of multiomics data applications when applied to the coral holobiont. Synopses for how different omics tools have been applied to date and their current restrictions are discussed, in addition to ways these restrictions may be overcome, such as recruiting new technology to studies, utilizing novel bioinformatics approaches, and generally integrating omics data. Lastly, this review presents considerations for the design of holobiont multiomics studies to support lab-to-field advancements of coral stress marker monitoring systems. Although much of the bleaching mechanism has eluded investigation to date, multiomic studies have already produced key findings regarding the holobiont's stress response, and have the potential to advance the field further.

Characterizing transcriptomic responses to sediment stress across location and morphology in reef-building corals

Anthropogenic activities increase sediment suspended in the water column and deposition on reefs can be largely dependent on colony morphology. Massive and plating corals have a high capacity to trap sediments, and active removal mechanisms can be energetically costly. Branching corals trap less sediment but are more susceptible to light limitation caused by suspended sediment. Despite deleterious effects of sediments on corals, few studies have examined the molecular response of corals with different morphological characteristics to sediment stress. To address this knowledge gap, this study assessed the transcriptomic responses of branching and massive corals in Florida and Hawai'i to varying levels of sediment exposure. Gene expression analysis revealed a molecular responsiveness to sediments across species and sites. Differential Gene Expression followed by Gene Ontology (GO) enrichment analysis identified that branching corals had the largest transcriptomic response to sediments, in developmental processes and metabolism, while significantly enriched GO terms were highly variable between massive corals, despite similar morphologies. Comparison of DEGs within orthogroups revealed that while all corals had DEGs in response to sediment, there was not a concerted gene set response by morphology or location. These findings illuminate the species specificity and genetic basis underlying coral susceptibility to sediments.

Vulnerability of six cold-water corals to sediment resuspension from bottom trawling fishing

Bottom trawling can significantly affect benthic communities, directly through immediate removal of sessile organisms and indirectly through sediment resuspension. Submarine canyons, often surrounded by fishing grounds, are important habitats for cold-water corals (CWC). Vulnerability of CWCs to increased suspended sediment concentration (SSC) is key to understanding the severity of bottom trawling effects on those communities. Here we show survival, growth, and physiological response of six CWCs from a Mediterranean submarine canyon (Dendrophyllia cornigera, Desmophyllum dianthus, Desmophyllum pertusum, Madrepora oculata, Leiopathes glaberrima and Muriceides lepida), exposed to a long-term, aquarium-based sedimentary disturbance experiment. Compared to cup coral and octocoral, which did not exhibit symptoms of distress, our data indicate that colonial scleractinian corals and black coral, which experienced substantial polyp mortality in enhanced SSC treatments, are more vulnerable. Indirect impact of bottom trawling could thus contribute to structural simplification of CWC communities posing an additional stressor alongside with global climate change.