Full in vivo characterization of carbonate chemistry at the site of calcification in corals

pH regulation in coral photosymbiosis and calcification: a compartmental perspective

The coral-dinoflagellate photosymbiosis and coral calcification underpin shallow water, coral reef ecosystems. This review examines the pivotal role of pH regulation in the cell physiology of these processes. Despite simple tissue organization, photosymbiotic corals maintain a complex internal microenvironment, with distinct compartments exhibiting contrasting pH levels. For example, the acidic 'symbiosome' surrounds the algal symbionts, while the alkaline 'extracellular calcifying medium' occurs at the growing front of the skeleton. We discuss how pH regulation of these compartments is crucial to the functioning of coral photosymbiosis and calcification, as well as mitigating the internal acid-base imbalances that these processes create. The role of pH regulation in the interplay between photosymbiosis and calcification is also discussed, focusing on the influence of symbiont photosynthesis on transepithelial gradients and the distribution of energy sources in the coral colony. Throughout this review, insights into pH regulation derived from previous research on ocean acidification are integrated to deepen understanding. Finally, we propose research priorities to advance knowledge of coral resilience under changing ocean conditions, such as investigating inorganic carbon concentration within coral compartments, species-specific differences and the impacts of thermal stress on pH regulation.

Impact of Mg2+ and pH on amorphous calcium carbonate nanoparticle formation: Implications for biomineralization and ocean acidification

Crystallization by amorphous calcium carbonate (ACC) particle attachment (CPA) is a prevalent biomineralization mechanism among calcifying organisms. A narrow, controlled size distribution of ACC nanoparticles is essential for macroscopic crystal formation via CPA. Using in situ synchrotron small-angle X-ray scattering, we demonstrate that synthetic magnesium-stabilized ACC (Mg-ACC) nanoparticles form with an exceptionally narrow size distribution near the spinodal line during liquid-liquid phase separation. We monitored ACC formation kinetics at pH 8.4 to 8.9 and Mg[Formula: see text] contents of 50 to 80%, observing a 2-order magnitude rise in nucleation kinetics for a 0.1 pH increase and a 6-order magnitude rise for a 10% Mg[Formula: see text] decrease. Within the binodal region, faster nucleation kinetics result in more monodisperse particles, narrowing the particle size distribution by factors of 2 for a pH increase of merely 0.1 and by a factor of 3 for a 10% Mg[Formula: see text] decrease. While the influence of Mg[Formula: see text] on calcite biomineralization is well studied, its effect on Mg-ACC formation and particle size distribution-an essential parameter in CPA-based biomineralization pathways-remained unexplored. These findings highlight the delicate interplay of pH and Mg[Formula: see text] in controlling the kinetics and thermodynamics of Mg-ACC formation, significantly impacting particle size distribution.

Internal hydrodynamics within the skeleton of Acropora pulchra coral

Many marine life forms, like Acropora coral, develop abiotic components to host and support the growth of living organisms. Using numerical models based on real coral samples reconstructed from micro-computed tomography (CT) scan images, we simulated internal flows inside the skeletons of Acropora pulchra coral under the influence of ambient ocean currents. The results showed that the coral's skeletal structure, with specially connected pore space, leads to the flow and material transport within and through the skeleton to assist the coral growth and stability. However, under intensified ocean acidification, the skeletal internal flow may induce the dissolution of aragonite inside the skeleton and weaken the whole coral structure.

Micro-CT analysis reveals porosity driven growth banding in Caribbean coral Siderastrea siderea

X-radiography of massive scleractinian coral skeletons reveal light and dark couplets termed "growth bands", which are commonly related to seasonal fluctuations in environmental parameters including insolation and sea surface temperature (SST). Massive corals grow by extension of skeletal structures followed by thickening within the surface tissue layer. Therefore, an understanding of the depth in which skeletal thickening occurs is important to aid the interpretation of seasonal banding patterns. In this study, two colonies of Caribbean coral Siderastrea siderea were sampled from the north-west coast of Barbados at water depths of 5 and 15 m. The three-dimensional skeletal structure of each sample was reconstructed at high spatial resolutions using micro-computed tomography (µCT) scanning. A pixel segmentation algorithm was developed to classify different microstructures within the skeleton and to quantify spatial variations in corallite and theca porosity at the micrometer scale. The porosity reconstructions of the deeper sample reveal clearer growth banding, with a more dominant signal originating from within the corallite. Skeletal thickening occurs within the top two-thirds of the total depth of soft tissues and the rate of thickening varies between microstructures. Seasonality in the shallower sample is less clear, although porosity variability with depth is more similar across microstructures. The difference in signal origin and clarity between the two samples is attributed to the varying stability of water depth-dependent variables (i.e., insolation and wave energy). This study provides a new, powerful method of reconstructing and understanding growth strategies in massive scleractinian corals.

Bioinformatic approach to explain how Mg from seawater may be incorporated into coral skeletons

Corals have been used as geochemical proxies since the 1970s, playing a prominent role in paleoceanography. However, it has not been well elucidated how aqueous ions sourced from seawater are transported and precipitated in coral skeletons. There are limited foundational methods to differentiate and quantify biogenic and abiogenic effects during skeletal formation. Especially, Mg in coral skeletons show individual variations suggesting large biogenic effects. Here, we evaluated biological complexity by investigating how coral genes evolved over geologic time scales. We focused on Mg transporter and analysed five species from genus Acropora and three species from genus Porites. Mg transporter of Acropora digitifera, Acropora hyacinthus, Acropora millepora and Porites australiensis showed higher similarity to Mg transporter of vertebrates and were reported to appear on Earth during the Pleistocene. On the other hand, Acropora palmata, Acropora tenuis and Porites astreoides showed lower or no similarity to vertebrates, and they were reported to appear on Earth before the Pleistocene. We suggest such evolutional records can be evidence to demonstrate biological complexity of Mg transport from seawater. This might explain that Mg transport is subject to evolution and why Mg incorporated in coral skeletons tends to show strong biogenic effects compared with other elements.

The Role of Polyamines in pH Regulation in the Extracellular Calcifying Medium of Scleractinian Coral Spats

This study aims to elucidate a novel mechanism for elevating the pH within the calicoblastic extracellular calcifying medium (pHECM) of corals and demonstrate the potential contribution of calcifying organisms to CO2 sequestration. Departing from traditional models that attribute the increase in pHECM primarily to H+ expulsion via Ca2+-ATPase, we emphasize the significant role of polyamines. These ubiquitous biogenic amines conveyed by calicoblastic cells through polyamine transporters demonstrate a remarkable affinity for CO2. Their ability to form stable carbamate complexes is pivotal in facilitating carbonate ion transport, which is crucial for pH regulation and skeletal structure formation. In this study, a polyamine transporter inhibitor and a polyamine biosynthesis inhibitor in conjunction with the pH-sensitive probe 8-hydroxypyrene-1,3,6-trisulfonic acid (HPTS) were employed to monitor pH variations. Furthermore, FM1-43FX dye was utilized to delineate the extracellular calcifying medium (ECM), whereas calcein was applied to visualize paracellular gaps and ECM. These methodologies provide profound insights into the intricate structural and functional dynamics of coral spats calcification. Findings suggest a potential reconsideration of established models of marine calcification and highlight the necessity to reassess the role of marine calcifying organisms in the carbon cycle, particularly their influence on CO2 fluxes.

Contrasting the Effects of Aspartic Acid and Glycine in Free Amino Acid and Peptide Forms on the Growth Rate, Morphology, Composition, and Structure of Synthetic Aragonites

Corals and mollusks produce aragonite skeletons and shells containing highly acidic proteins, rich in aspartic acid (Asp) and glycine (Gly). These biomolecules are pivotal in controlling biomineral formation. We explore the effects of l-Asp, Gly, and two peptides: glycyl-l-aspartic acid (Gly-Asp) and tetra-aspartic acid (Asp4) on the precipitation rate, crystal morphology, and CO3 group rotational disorder (inferred from Raman spectroscopy) in aragonite precipitated in vitro at the approximate pH, [Ca2+], and Ωar occurring in coral calcification media. All of the biomolecules, except Gly, inhibit aragonite precipitation. Biomolecules are incorporated into the aragonite and create CO3 group rotational disorder in the following order: Asp4 > Asp = Gly-Asp > Gly. Asp4 inhibits aragonite precipitation more than Asp at comparable solution concentrations, but Asp reduces aragonite precipitation more effectively than Asp4 for each Asp residue incorporated into the aragonite. At the highest solution concentration, the molar ratio of Asp4:CaCO3 in the aragonite is 1:690. We observe a significant inverse relationship between the aragonite precipitation rate and aragonite Raman spectrum ν1 peak fwhm across the entire data set. Tetra-aspartic acid inhibits aragonite precipitation at all concentrations, suggesting that the aspartic acid-rich domains of coral skeletal proteins influence biomineralization by suppressing mineral formation, thereby shaping skeletal morphology and preventing uncontrolled precipitation.

Genome of Halimeda opuntia reveals differentiation of subgenomes and molecular bases of multinucleation and calcification in algae

Algae mostly occur either as unicellular (microalgae) or multicellular (macroalgae) species, both being uninucleate. There are important exceptions, however, as some unicellular algae are multinucleate and macroscopic, some of which inhabit tropical seas and contribute to biocalcification and coral reef robustness. The evolutionary mechanisms and ecological significance of multinucleation and associated traits (e.g., rapid wound healing) are poorly understood. Here, we report the genome of Halimeda opuntia, a giant multinucleate unicellular chlorophyte characterized by interutricular calcification. We achieve a high-quality genome assembly that shows segregation into four subgenomes, with evidence for polyploidization concomitant with historical sea level and climate changes. We further find myosin VIII missing in H. opuntia and three other unicellular multinucleate chlorophytes, suggesting a potential mechanism that may underpin multinucleation. Genome analysis provides clues about how the unicellular alga could survive fragmentation and regenerate, as well as potential signatures for extracellular calcification and the coupling of calcification with photosynthesis. In addition, proteomic alkalinity shifts were found to potentially confer plasticity of H. opuntia to ocean acidification (OA). Our study provides crucial genetic information necessary for understanding multinucleation, cell regeneration, plasticity to OA, and different modes of calcification in algae and other organisms, which has important implications in reef conservation and bioengineering.

Spatial variability of and effect of light on the cœlenteron pH of a reef coral

Coral reefs, the largest bioconstruction on Earth, are formed by calcium carbonate skeletons of corals. Coral skeleton formation commonly referred to as calcification occurs in a specific compartment, the extracellular calcifying medium (ECM), located between the aboral ectoderm and the skeleton. Calcification models often assume a direct link between the surrounding seawater and the ECM. However, the ECM is separated from the seawater by several tissue layers and the cœlenteron, which contains the cœlenteric fluid found in both polyps and cœnosarc (tissue connecting the polyps). Symbiotic dinoflagellate-containing cells line the cœlenteron and their photosynthetic activity contributes to changes in the chemistry of the cœlenteric fluid, particularly with respect to pH. The aim of our study is to compare cœlenteron pH between the cœnosarc and polyps and to compare areas of high or low dinoflagellate density based on tissue coloration. To achieve this, we use liquid ion exchange (LIX) pH microsensors to profile pH in the cœlenteron of polyps and the cœnosarc in different regions of the coral colony in light and darkness. We interpret our results in terms of what light and dark exposure means for proton gradients between the ECM and the coelenteron, and how this could affect calcification.

Myriad Mapping of nanoscale minerals reveals calcium carbonate hemihydrate in forming nacre and coral biominerals

Calcium carbonate (CaCO3) is abundant on Earth, is a major component of marine biominerals and thus of sedimentary and metamorphic rocks and it plays a major role in the global carbon cycle by storing atmospheric CO2 into solid biominerals. Six crystalline polymorphs of CaCO3 are known-3 anhydrous: calcite, aragonite, vaterite, and 3 hydrated: ikaite (CaCO3·6H2O), monohydrocalcite (CaCO3·1H2O, MHC), and calcium carbonate hemihydrate (CaCO3·½H2O, CCHH). CCHH was recently discovered and characterized, but exclusively as a synthetic material, not as a naturally occurring mineral. Here, analyzing 200 million spectra with Myriad Mapping (MM) of nanoscale mineral phases, we find CCHH and MHC, along with amorphous precursors, on freshly deposited coral skeleton and nacre surfaces, but not on sea urchin spines. Thus, biomineralization pathways are more complex and diverse than previously understood, opening new questions on isotopes and climate. Crystalline precursors are more accessible than amorphous ones to other spectroscopies and diffraction, in natural and bio-inspired materials.

Porites' coral calcifying fluid chemistry regulation under normal- and low-pH seawater conditions in Palau Archipelago: Impacts on growth properties

Ongoing ocean acidification is known to be a major threat to tropical coral reefs. To date, only few studies have evaluated the impacts of natural long-term exposure to low-pH seawater on the chemical regulation and growth of reef-building corals. This work investigated the different responses of the massive Porites coral living at normal (pHsw ~ 8.03) and naturally low-pH (pHsw ~ 7.85) seawater conditions at Palau over the last decades. Our results show that both Porites colonies maintained similar carbonate properties (pHcf, [CO32-]cf, DICcf, and Ωcf) within their calcifying fluid since 1972. However, the Porites skeleton of the more acidified conditions revealed a significantly lower density (~ 1.21 ± 0.09 g·cm-3) than the skeleton from the open-ocean site (~ 1.41 ± 0.07 g·cm-3). Overall, both Porites colonies exerted a strong biological control to maintain stable calcifying fluid carbonate chemistry that favored the calcification process, especially under low-pH conditions. However, the decline in skeletal density observed at low pH provides critical insights into Porites vulnerability to future global change.

Molecular and mineral responses of corals grown under artificial Calcite Sea conditions

The formation of skeletal structures composed of different calcium carbonate polymorphs (e.g. aragonite and calcite) appears to be both biologically and environmentally regulated. Among environmental factors influencing aragonite and calcite precipitation, changes in seawater conditions-primarily in the molar ratio of magnesium and calcium during so-called 'Calcite' (mMg:mCa below 2) or 'Aragonite' seas (mMg:mCa above 2)-have had profound impacts on the distribution and performance of marine calcifiers throughout Earth's history. Nonetheless, the fossil record shows that some species appear to have counteracted such changes and kept their skeleton polymorph unaltered. Here, the aragonitic octocoral Heliopora coerulea and the aragonitic scleractinian Montipora digitata were exposed to Calcite Sea-like mMg:mCa with various levels of magnesium and calcium concentration, and changes in both the mineralogy (i.e. CaCO3 polymorph) and gene expression were monitored. Both species maintained aragonite deposition at lower mMg:mCa ratios, while concurrent calcite presence was only detected in M. digitata. Despite a strong variability between independent experimental replicates for both species, the expression for a set of putative calcification-related genes, including known components of the M. digitata skeleton organic matrix (SkOM), was found to consistently change at lower mMg:mCa. These results support the previously proposed involvements of the SkOM in counteracting decreases in seawater mMg:mCa. Although no consistent expression changes in calcium and magnesium transporters were observed, down-regulation calcium channels in H. coerulea in one experimental replicate and at an mMg:mCa of 2.5, pointing to a possible active calcium uptake regulation by the corals under altered mMg:mCa.

Anion elements incorporation into corals skeletons: Experimental approach for biomineralization and paleo-proxies

The elemental composition of coral skeletons provides important information for palaeoceanographic reconstructions and coral biomineralization. Partition of anions and their stable isotopes in coral skeleton enables the reconstruction of past seawater carbonate chemistry, paleo-CO2, and past climates. Here, we investigated the partition of B, S, As, Br, I, and Mo into the skeletons of two corals, Acropora cervicornis and Pocillopora damicornis, as a function of calcium and carbonate concentrations.* Anion-to-calcium ratio in the corals (An/CaCoral) were correlated with the equivalent ratios in the culturing seawater (An/CO32-SW). Negative intercepts of these relationships suggest a higher CO32- concentration in the coral extracellular calcifying fluid (ECF) relative to seawater, from which the skeleton precipitates. The enrichment factor of CO32- at the ECF was 2.5 for A. cervicornis and 1.9 for P. damicornis, consistent with their relative calcification rates. The CO32-ECF concentrations thus calculated are similar to those proposed by previous studies based on B/Ca coupled with δ11B, as well as by direct measurements using microsensors and fluorescent dyes. Rayleigh fractionation modeling demonstrates a uniform Ca utilization at various CaSW concentrations, providing further evidence that coral calcification occurs directly from a semiclosed seawater reservoir as reported previously. The partition coefficients reported in this study for B, S, As, Br, I, and Mo open up wide possibilities for past ocean chemistry reconstructions based on Br having long residence time (~160 Ma) in the ocean. Other elements like S, Mo, B, as well as pCO2 may also be calculated based on these elements in fossil coral.

Differences in carbonate chemistry up-regulation of long-lived reef-building corals

With climate projections questioning the future survival of stony corals and their dominance as tropical reef builders, it is critical to understand the adaptive capacity of corals to ongoing climate change. Biological mediation of the carbonate chemistry of the coral calcifying fluid is a fundamental component for assessing the response of corals to global threats. The Tara Pacific expedition (2016-2018) provided an opportunity to investigate calcification patterns in extant corals throughout the Pacific Ocean. Cores from colonies of the massive Porites and Diploastrea genera were collected from different environments to assess calcification parameters of long-lived reef-building corals. At the basin scale of the Pacific Ocean, we show that both genera systematically up-regulate their calcifying fluid pH and dissolved inorganic carbon to achieve efficient skeletal precipitation. However, while Porites corals increase the aragonite saturation state of the calcifying fluid (Ω_cf) at higher temperatures to enhance their calcification capacity, Diploastrea show a steady homeostatic Ω_cf across the Pacific temperature gradient. Thus, the extent to which Diploastrea responds to ocean warming and/or acidification is unclear, and it deserves further attention whether this is beneficial or detrimental to future survival of this coral genus.

Role of the bicarbonate transporter SLC4γ in stony-coral skeleton formation and evolution

Coral reefs are highly diverse ecosystems of immense ecological, economic, and aesthetic importance built on the calcium-carbonate-based skeletons of stony corals. The formation of these skeletons is threatened by increasing ocean temperatures and acidification, and a deeper understanding of the molecular mechanisms involved may assist efforts to mitigate the effects of such anthropogenic stressors. In this study, we focused on the role of the predicted bicarbonate transporter SLC4γ, which was suggested in previous studies to be a product of gene duplication and to have a role in coral-skeleton formation. Our comparative-genomics study using 30 coral species and 15 outgroups indicates that SLC4γ is present throughout the stony corals, but not in their non-skeleton-forming relatives, and apparently arose by gene duplication at the onset of stony-coral evolution. Our expression studies show that SLC4γ, but not the closely related and apparently ancestral SLC4β, is highly upregulated during coral development coincident with the onset of skeleton deposition. Moreover, we show that juvenile coral polyps carrying CRISPR/Cas9-induced mutations in SLC4γ are defective in skeleton formation, with the severity of the defect in individual animals correlated with their frequencies of SLC4γ mutations. Taken together, the results suggest that the evolution of the stony corals involved the neofunctionalization of the newly arisen SLC4γ for a unique role in the provision of concentrated bicarbonate for calcium-carbonate deposition. The results also demonstrate the feasibility of reverse-genetic studies of ecologically important traits in adult corals.

Testing hypotheses on the calcification in scleractinian corals using a spatio-temporal model that shows a high degree of robustness

Calcification in photosynthetic scleractinian corals is a complicated process that involves many different biological, chemical, and physical sub-processes that happen within and around the coral tissue. Identifying and quantifying the role of separate processes in vivo or in vitro is difficult or not possible. A computational model can facilitate this research by simulating the sub-processes independently. This study presents a spatio-temporal model of the calcification physiology, which is based on processes that are considered essential for calcification: respiration, photosynthesis, Ca^2＋-ATPase, carbonic anhydrase. The model is used to test different hypotheses considering ion transport across the calicoblastic cells and Light Enhanced Calcification (LEC). It is also used to quantify the effect of ocean acidification (OA) on the Extracellular Calcifying Medium (ECM) and ATP-consumption of Ca^2＋-ATPase. It was able to reproduce the experimental data of three separate studies and finds that paracellular transport plays a minor role compared to transcellular transport. In the model, LEC results from increased Ca^2＋-ATPase activity in combination with increased metabolism. Implementing OA increases the concentration of CO₂ throughout the entire tissue, thereby increasing the availability of CO₃^- in the ECM. As a result, the model finds that calcification becomes more energy-demanding and the calcification rate increases.

Soluble adenylyl cyclase coordinates intracellular pH homeostasis and biomineralization in calcifying cells of a marine animal

Biomineralizing cells concentrate dissolved inorganic carbon (DIC) and remove protons from the site of mineral precipitation. However, the molecular regulatory mechanisms that orchestrate pH homeostasis and biomineralization of calcifying cells are poorly understood. Here, we report that the acid-base sensing enzyme soluble adenylyl cyclase (sAC) coordinates intracellular pH (pH_i) regulation in the calcifying primary mesenchyme cells (PMCs) of sea urchin larvae. Single-cell transcriptomics, in situ hybridization, and immunocytochemistry elucidated the spatiotemporal expression of sAC during skeletogenesis. Live pH_i imaging of PMCs revealed that the downregulation of sAC activity with two structurally unrelated small molecules inhibited pH_i regulation of PMCs, an effect that was rescued by the addition of cell-permeable cAMP. Pharmacological sAC inhibition also significantly reduced normal spicule growth and spicule regeneration, establishing a link between PMC pH_i regulation and biomineralization. Finally, increased expression of sAC mRNA was detected during skeleton remineralization and exposure to CO₂-induced acidification. These findings suggest that transcriptional regulation of sAC is required to promote remineralization and to compensate for acidic stress. This work highlights the central role of sAC in coordinating acid-base regulation and biomineralization in calcifying cells of a marine animal.

Optimising a method for aragonite precipitation in simulated biogenic calcification media

Resolving how factors such as temperature, pH, biomolecules and mineral growth rate influence the geochemistry and structure of biogenic CaCO3, is essential to the effective development of palaeoproxies. Here we optimise a method to precipitate the CaCO3 polymorph aragonite from seawater, under tightly controlled conditions that simulate the saturation state (Ω) of coral calcification fluids. We then use the method to explore the influence of aspartic acid (one of the most abundant amino acids in coral skeletons) on aragonite structure and morphology. Using ≥200 mg of aragonite seed (surface area 0.84 m2), to provide a surface for mineral growth, in a 330 mL seawater volume, generates reproducible estimates of precipitation rate over Ωaragonite = 6.9-19.2. However, unseeded precipitations are highly variable in duration and do not provide consistent estimates of precipitation rate. Low concentrations of aspartic acid (1-10 μM) promote aragonite formation, but high concentrations (≥ 1 mM) inhibit precipitation. The Raman spectra of aragonite precipitated in vitro can be separated from the signature of the starting seed by ensuring that at least 60% of the analysed aragonite is precipitated in vitro (equivalent to using a seed of 200 mg and precipitating 300 mg aragonite in vitro). Aspartic acid concentrations ≥ 1mM caused a significant increase in the full width half maxima of the Raman aragonite v1 peak, reflective of increased rotational disorder in the aragonite structure. Changes in the organic content of coral skeletons can drive variations in the FWHM of the Raman aragonite ν1 peak, and if not accounted for, may confuse the interpretation of calcification fluid saturation state from this parameter.

Cellular adaptations leading to coral fragment attachment on artificial substrates in Acropora millepora (Am-CAM)

Reproductive propagation by asexual fragmentation in the reef-building coral Acropora millepora depends on (1) successful attachment to the reef substrate through modification of soft tissues and (2) a permanent bond with skeletal encrustation. Despite decades of research examining asexual propagation in corals, the initial response, cellular reorganisation, and development leading to fragment substrate attachment via a newly formed skeleton has not been documented in its entirety. Here, we establish the first "coral attachment model" for this species ("Am-CAM") by developing novel methods that allow correlation of fluorescence and electron microscopy image data with in vivo microscopic time-lapse imagery. This multi-scale imaging approach identified three distinct phases involved in asexual propagation: (1) the contact response of the coral fragment when contact with the substrate, followed by (2) fragment stabilisation through anchoring by the soft tissue, and (3) formation of a "lappet-like appendage" structure leading to substrate bonding of the tissue for encrustation through the onset of skeletal calcification. In developing Am-CAM, we provide new biological insights that can enable reef researchers, managers and coral restoration practitioners to begin evaluating attachment effectiveness, which is needed to optimise species-substrate compatibility and achieve effective outplanting.

Environmental memory gained from exposure to extreme pCO2 variability promotes coral cellular acid-base homeostasis

Ocean acidification is a growing threat to coral growth and the accretion of coral reef ecosystems. Corals inhabiting environments that already endure extreme diel pCO₂ fluctuations, however, may represent acidification-resilient populations capable of persisting on future reefs. Here, we examined the impact of pCO₂ variability on the reef-building coral Pocillopora damicornis originating from reefs with contrasting environmental histories (variable reef flat versus stable reef slope) following reciprocal exposure to stable (218 ± 9) or variable (911 ± 31) diel pCO₂ amplitude (μtam) in aquaria over eight weeks. Endosymbiont density, photosynthesis and net calcification rates differed between origins but not treatment, whereas primary calcification (extension) was affected by both origin and acclimatization to novel pCO₂ conditions. At the cellular level, corals from the variable reef flat exhibited less intracellular pH (pHi) acidosis and faster pHi recovery rates in response to experimental acidification stress (pH 7.40) than corals originating from the stable reef slope, suggesting environmental memory gained from lifelong exposure to pCO₂ variability led to an improved ability to regulate acid–base homeostasis. These results highlight the role of cellular processes in maintaining acidification resilience and suggest that prior exposure to pCO₂ variability may promote more acidification-resilient coral populations in a changing climate.

Disentangling compartment functions in sessile marine invertebrates

Sessile invertebrates are frequently sampled and processed whole for downstream analyses. However, their apparent structural simplicity is deceptive as these organisms often harbour discrete compartments. These compartments have physicochemical conditions that differ markedly from neighbouring tissues, and that have likely evolved to support specific functions. Here, we argue that such compartments should be specifically targeted when characterising sessile invertebrate biology and we use the coral gastrovascular cavity to support our argument. This complex compartment displays steep and dynamic chemical gradients, harbours distinct microorganisms, and presumably plays a key role in coral biology. Disentangling the functions played by (and amongst) compartments will likely provide transformative insight into the biology of sessile invertebrates and their future under environmental change.

The combined effects of ocean acidification and copper on the physiological responses of the tropical coral Stylophora pistillata

A decrease in ocean pH of 0.3 units will likely double the proportion of dissolved copper (Cu) present as the free metal ion, Cu²⁺, the most bioavailable form of Cu, and one of the most common marine pollutants. We assess the impact of ocean acidification and Cu, separately and in combination, on calcification, photosynthesis and respiration of sub-colonies of a single tropical Stylophora pistillata colony. After 15 days of treatment, total calcification rates were significantly decreased in corals exposed to high seawater pCO₂ (∼1000-μatm, 2100 scenario) and at both ambient (1.6-1.9 nmols) and high (2.5-3.6 nmols) dissolved Cu concentrations compared to controls. The effect was increased when both stressors were combined. Coral respiration rates were significantly reduced by the combined stressors after 2 weeks of exposure, indicating the importance of experiment duration. It is therefore likely rising atmospheric CO₂ will exacerbate the negative effects of Cu pollution to S. pistillata.

pH variability at volcanic CO2 seeps regulates coral calcifying fluid chemistry

Coral reefs are iconic ecosystems with immense ecological, economic and cultural value, but globally their carbonate-based skeletal construction is threatened by ocean acidification (OA). Identifying coral species that have specialised mechanisms to maintain high rates of calcification in the face of declining seawater pH is of paramount importance in predicting future species composition, and growth of coral reefs. Here, we studied multiple coral species from two distinct volcanic CO₂ seeps in Papua New Guinea to assess their capacity to control their calcifying fluid (CF) chemistry. Several coral species living under conditions of low mean seawater pH, but with either low or high variability in seawater pH, were examined and compared with those living in 'normal' (non-seep) ambient seawater pH. We show that when mean seawater pH is low but highly variable, corals have a greater ability to maintain constant pH_cf in their CF, but this characteristic was not linked with changes in abundance. Within less variable low pH seawater, corals with limited reductions in pH_cf at the seep sites compared with controls tended to be more abundant at the seep site than at the control site. However, this finding was strongly influenced by a single species (Montipora foliosa), which was able to maintain complete pH_cf homeostasis. Overall, although our findings indicate that there might be an association between ecological success and greater pH_cf homeostasis, further research with additional species and at more sites with differing seawater pH regimes is required to solidify inferences regarding coral ecological success under future OA.

Distinct fine-scale variations in calcification control revealed by high-resolution 2D boron laser images in the cold-water coral Lophelia pertusa

Coral calcification is a complex biologically controlled process of hard skeleton formation, and it is influenced by environmental conditions. The chemical composition of coral skeletons responds to calcification conditions and can be used to gain insights into both the control asserted by the organism and the environment. Boron and its isotopic composition have been of particular interest because of links to carbon chemistry and pH. In this study, we acquired high-resolution boron images (concentration and isotopes) in a skeleton sample of the azooxanthellate cold-water coral Lophelia pertusa. We observed high boron variability at a small spatial scale related to skeletal structure. This implies differences in calcification control during different stages of skeleton formation. Our data point to bicarbonate active transport as a critical pathway during early skeletal growth, and the variable activity rates explain the majority of the observed boron systematic.

Biomineralization: Integrating mechanism and evolutionary history

Calcium carbonate (CaCO₃) biomineralizing organisms have played major roles in the history of life and the global carbon cycle during the past 541 Ma. Both marine diversification and mass extinctions reflect physiological responses to environmental changes through time. An integrated understanding of carbonate biomineralization is necessary to illuminate this evolutionary record and to understand how modern organisms will respond to 21st century global change. Biomineralization evolved independently but convergently across phyla, suggesting a unity of mechanism that transcends biological differences. In this review, we combine CaCO₃ skeleton formation mechanisms with constraints from evolutionary history, omics, and a meta-analysis of isotopic data to develop a plausible model for CaCO₃ biomineralization applicable to all phyla. The model provides a framework for understanding the environmental sensitivity of marine calcifiers, past mass extinctions, and resilience in 21st century acidifying oceans. Thus, it frames questions about the past, present, and future of CaCO₃ biomineralizing organisms.

Faster Crystallization during Coral Skeleton Formation Correlates with Resilience to Ocean Acidification

The mature skeletons of hard corals, termed stony or scleractinian corals, are made of aragonite (CaCO3). During their formation, particles attaching to the skeleton's growing surface are calcium carbonate, transiently amorphous. Here we show that amorphous particles are observed frequently and reproducibly just outside the skeleton, where a calicoblastic cell layer envelops and deposits the forming skeleton. The observation of particles in these locations, therefore, is consistent with nucleation and growth of particles in intracellular vesicles. The observed extraskeletal particles range in size between 0.2 and 1.0 μm and contain more of the amorphous precursor phases than the skeleton surface or bulk, where they gradually crystallize to aragonite. This observation was repeated in three diverse genera of corals, Acropora sp., Stylophora pistillata─differently sensitive to ocean acidification (OA)─and Turbinaria peltata, demonstrating that intracellular particles are a major source of material during the additive manufacturing of coral skeletons. Thus, particles are formed away from seawater, in a presumed intracellular calcifying fluid (ICF) in closed vesicles and not, as previously assumed, in the extracellular calcifying fluid (ECF), which, unlike ICF, is partly open to seawater. After particle attachment, the growing skeleton surface remains exposed to ECF, and, remarkably, its crystallization rate varies significantly across genera. The skeleton surface layers containing amorphous pixels vary in thickness across genera: ∼2.1 μm in Acropora, 1.1 μm in Stylophora, and 0.9 μm in Turbinaria. Thus, the slow-crystallizing Acropora skeleton surface remains amorphous and soluble longer, including overnight, when the pH in the ECF drops. Increased skeleton surface solubility is consistent with Acropora's vulnerability to OA, whereas the Stylophora skeleton surface layer crystallizes faster, consistent with Stylophora's resilience to OA. Turbinaria, whose response to OA has not yet been tested, is expected to be even more resilient than Stylophora, based on the present data.

Genetic basis of stony coral biomineralization: History, trends and future prospects

Despite their simple body plan, stony corals (order Scleractinia, phylum Cnidaria) can produce massive and complex exoskeletal structures in shallow, tropical and subtropical regions of Earth's oceans. The species-specific macromorphologies of their aragonite skeletons suggest a highly coordinated biomineralization process that is rooted in their genomes, and which has persisted across major climatic shifts over the past 400 + million years. The mechanisms by which stony corals produce their skeletons has been the subject of interest for at least the last 160 years, and the pace of understanding the process has increased dramatically in the past decade since the sequencing of the first coral genome in 2011. In this review, we detail what is known to date about the genetic basis of the stony coral biomineralization process, with a focus on advances in the last several years as well as ways that physical and chemical tools can be combined with genetics, and then propose next steps forward for the coming decade.

The calcifying interface in a stony coral primary polyp: An interplay between seawater and an extracellular calcifying space

Stony coral exoskeletons build the foundation for the most biologically diverse marine ecosystems on Earth, coral reefs, which face major threats due to many anthropogenic-related stressors. Therefore, understanding coral biomineralization mechanisms is crucial for coral reef management in the coming decades and for using coral skeletons in geochemical studies. This study combines in-vivo imaging with cryo-electron microscopy and cryo-elemental mapping to gain novel insights into the biological microenvironment and the ion pathways that facilitate biomineralization in primary polyps of the stony coral Stylophora pistillata. We document increased tissue permeability in the primary polyp and a highly dispersed cell packing in the tissue directly responsible for producing the coral skeleton. This tissue arrangement may facilitate the intimate involvement of seawater at the mineralization site, also documented here. We further observe an extensive filopodial network containing carbon-rich vesicles extruding from some of the calicoblastic cells. Single-cell RNA-Sequencing data interrogation supports these morphological observations by showing higher expression of genes involved in filopodia and vesicle structure and function in the calicoblastic cells. These observations provide a new conceptual framework for resolving the ion pathway from the external seawater to the tissue-mineral interface in stony coral biomineralization processes.

Total Dissolved Inorganic Carbon Sensor Based on Amperometric CO2 Microsensor and Local Acidification

We present a dipping probe total dissolved inorganic carbon (DIC) microsensor based on a localized acidic microenvironment in front of an amperometric CO₂ microsensor. The acidic milieu facilitates conversion of bicarbonate and carbonate to CO₂, which in turn is reduced at a silver cathode. Interfering oxygen is removed by an acidic CrCl₂ oxygen trap. Theoretical simulations of microsensor functioning were performed to find a suitable compromise between response time and near-complete conversion of bicarbonate to CO₂. The sensor exhibited a linear response over a wide range of 0-8 mM DIC, with a calculated LOD of 5 μM and a 90% response time of 150 s. The sensor was successfully tested in measuring DIC in bottled mineral water and seawater. This DIC microsensor holds the potential to become an important tool in environmental sensing and beyond for measurements of DIC at high spatial and temporal resolution.

Applying model approaches in non-model systems: A review and case study on coral cell culture

Model systems approaches search for commonality in patterns underlying biological diversity and complexity led by common evolutionary paths. The success of the approach does not rest on the species chosen but on the scalability of the model and methods used to develop the model and engage research. Fine-tuning approaches to improve coral cell cultures will provide a robust platform for studying symbiosis breakdown, the calcification mechanism and its disruption, protein interactions, micronutrient transport/exchange, and the toxicity of nanoparticles, among other key biological aspects, with the added advantage of minimizing the ethical conundrum of repeated testing on ecologically threatened organisms. The work presented here aimed to lay the foundation towards development of effective methods to sort and culture reef-building coral cells with the ultimate goal of obtaining immortal cell lines for the study of bleaching, disease and toxicity at the cellular and polyp levels. To achieve this objective, the team conducted a thorough review and tested the available methods (i.e. cell dissociation, isolation, sorting, attachment and proliferation). The most effective and reproducible techniques were combined to consolidate culture methods and generate uncontaminated coral cell cultures for ~7 days (10 days maximum). The tests were conducted on scleractinian corals Pocillopora acuta of the same genotype to harmonize results and reduce variation linked to genetic diversity. The development of cell separation and identification methods in conjunction with further investigations into coral cell-type specific metabolic requirements will allow us to tailor growth media for optimized monocultures as a tool for studying essential reef-building coral traits such as symbiosis, wound healing and calcification at multiple scales.

The Biology and Evolution of Calcite and Aragonite Mineralization in Octocorallia

Octocorallia (class Anthozoa, phylum Cnidaria) is a group of calcifying corals displaying a wide diversity of mineral skeletons. This includes skeletal structures composed of different calcium carbonate polymorphs (aragonite and calcite). This represents a unique feature among anthozoans, as scleractinian corals (subclass Hexacorallia), main reef builders and focus of biomineralization research, are all characterized by an aragonite exoskeleton. From an evolutionary perspective, the presence of aragonitic skeletons in Octocorallia is puzzling as it is observed in very few species and has apparently originated during a Calcite sea (i.e., time interval characterized by calcite-inducing seawater conditions). Despite this, octocorals have been systematically overlooked in biomineralization studies. Here we review what is known about octocoral biomineralization, focusing on the evolutionary and biological processes that underlie calcite and aragonite formation. Although differences in research focus between octocorals and scleractinians are often mentioned, we highlight how strong variability also exists between different octocoral groups. Different main aspects of octocoral biomineralization have been in fact studied in a small set of species, including the (calcitic) gorgonian Leptogorgia virgulata and/or the precious coral Corallium rubrum. These include descriptions of calcifying cells (scleroblasts), calcium transport and chemistry of the calcification fluids. With the exception of few histological observations, no information on these features is available for aragonitic octocorals. Availability of sequencing data is also heterogeneous between groups, with no transcriptome or genome available, for instance, for the clade Calcaxonia. Although calcite represents by far the most common polymorph deposited by octocorals, we argue that studying aragonite-forming could provide insight on octocoral, and more generally anthozoan, biomineralization. First and foremost it would allow to compare calcification processes between octocoral groups, highlighting homologies and differences. Secondly, similarities (exoskeleton) between Heliopora and scleractinian skeletons, would provide further insight on which biomineralization features are driven by skeleton characteristics (shared by scleractinians and aragonitic octocorals) and those driven by taxonomy (shared by octocorals regardless of skeleton polymorph). Including the diversity of anthozoan mineralization strategies into biomineralization studies remains thus essential to comprehensively study how skeletons form and evolved within this ecologically important group of marine animals.

Crystal nucleation and growth of spherulites demonstrated by coral skeletons and phase-field simulations

Spherulites are radial distributions of acicular crystals, common in biogenic, geologic, and synthetic systems, yet exactly how spherulitic crystals nucleate and grow is still poorly understood. To investigate these processes in more detail, we chose scleractinian corals as a model system, because they are well known to form their skeletons from aragonite (CaCO3) spherulites, and because a comparative study of crystal structures across coral species has not been performed previously. We observed that all 12 diverse coral species analyzed here exhibit plumose spherulites in their skeletons, with well-defined centers of calcification (CoCs), and crystalline fibers radiating from them. In 7 of the 12 species, we observed a skeletal structural motif not observed previously: randomly oriented, equant crystals, which we termed "sprinkles". In Acropora pharaonis, these sprinkles are localized at the CoCs, while in 6 other species, sprinkles are either layered at the growth front (GF) of the spherulites, or randomly distributed. At the nano- and micro-scale, coral skeletons fill space as much as single crystals of aragonite. Based on these observations, we tentatively propose a spherulite formation mechanism in which growth front nucleation (GFN) of randomly oriented sprinkles, competition for space, and coarsening produce spherulites, rather than the previously assumed slightly misoriented nucleations termed "non-crystallographic branching". Phase-field simulations support this mechanism, and, using a minimal set of thermodynamic parameters, are able to reproduce all of the microstructural variation observed experimentally in all of the investigated coral skeletons. Beyond coral skeletons, other spherulitic systems, from aspirin to semicrystalline polymers and chocolate, may also form according to the mechanism for spherulite formation proposed here. STATEMENT OF SIGNIFICANCE: Understanding the fundamental mechanisms of spherulite nucleation and growth has broad ranging applications in the fields of metallurgy, polymers, food science, and pharmaceutical production. Using the skeletons of reef-building corals as a model system for investigating these processes, we propose a new spherulite growth mechanism that can not only explain the micro-structural diversity observed in distantly related coral species, but may point to a universal growth mechanism in a wide range of biologically and technologically relevant spherulitic materials systems.

Mapping coral calcification strategies from in situ boron isotope and trace element measurements of the tropical coral Siderastrea siderea

Boron isotopic and elemental analysis of coral aragonite can give important insights into the calcification strategies employed in coral skeletal construction. Traditional methods of analysis have limited spatial (and thus temporal) resolution, hindering attempts to unravel skeletal heterogeneity. Laser ablation mass spectrometry allows a much more refined view, and here we employ these techniques to explore boron isotope and co-varying elemental ratios in the tropical coral Siderastrea siderea. We generate two-dimensional maps of the carbonate parameters within the calcification medium that deposited the skeleton, which reveal large heterogeneities in carbonate chemistry across the macro-structure of a coral polyp. These differences have the potential to bias proxy interpretations, and indicate that different processes facilitated precipitation of different parts of the coral skeleton: the low-density columella being precipitated from a fluid with a carbonate composition closer to seawater, compared to the high-density inter-polyp walls where aragonite saturation was ~ 5 times that of external seawater. Therefore, the skeleton does not precipitate from a spatially homogeneous fluid and its different parts may thus have varying sensitivity to environmental stress. This offers new insights into the mechanisms behind the response of the S. siderea skeletal phenotype to ocean acidification.

Thermal stress reduces pocilloporid coral resilience to ocean acidification by impairing control over calcifying fluid chemistry

The combination of thermal stress and ocean acidification (OA) can more negatively affect coral calcification than an individual stressors, but the mechanism behind this interaction is unknown. We used two independent methods (microelectrode and boron geochemistry) to measure calcifying fluid pH (pH_cf) and carbonate chemistry of the corals Pocillopora damicornis and Stylophora pistillata grown under various temperature and pCO₂ conditions. Although these approaches demonstrate that they record pH_cf over different time scales, they reveal that both species can cope with OA under optimal temperatures (28°C) by elevating pH_cf and aragonite saturation state (Ω_cf) in support of calcification. At 31°C, neither species elevated these parameters as they did at 28°C and, likewise, could not maintain substantially positive calcification rates under any pH treatment. These results reveal a previously uncharacterized influence of temperature on coral pH_cf regulation-the apparent mechanism behind the negative interaction between thermal stress and OA on coral calcification.

A role for primary cilia in coral calcification?

Cilia are evolutionarily conserved organelles that extend from the surface of cells and are found in diverse organisms from protozoans to multicellular organisms. Motile cilia play various biological functions by their beating motion, including mixing fluids and transporting food particles. Non-motile cilia act as sensors that signal cells about their microenvironment. In corals, cilia have been described in some of the cell layers but never in the calcifying epithelium, which is responsible for skeleton formation. In the present study, we used scanning electron microscopy and immunolabelling to investigate the cellular ciliature of the different tissue layers of the coral Stylophora pistillata, with a focus on the calcifying calicoblastic ectoderm. We show that the cilium of the calcifying cells is different from the cilium of the other cell layers. It is much shorter, and more importantly, its base is structurally distinct from the base observed in cilia of the other tissue layers. Based on these structural observations, we conclude that the cilium of the calcifying cells is a primary cilium. From what is known in other organisms, primary cilia are sensors that signal cells about their microenvironment. We discuss the implications of the presence of a primary cilium in the calcifying epithelium for our understanding of the cellular physiology driving coral calcification and its environmental sensitivity.

From particle attachment to space-filling coral skeletons

Reef-building corals and their aragonite (CaCO3) skeletons support entire reef ecosystems, yet their formation mechanism is poorly understood. Here we used synchrotron spectromicroscopy to observe the nanoscale mineralogy of fresh, forming skeletons from six species spanning all reef-forming coral morphologies: Branching, encrusting, massive, and table. In all species, hydrated and anhydrous amorphous calcium carbonate nanoparticles were precursors for skeletal growth, as previously observed in a single species. The amorphous precursors here were observed in tissue, between tissue and skeleton, and at growth fronts of the skeleton, within a low-density nano- or microporous layer varying in thickness from 7 to 20 µm. Brunauer-Emmett-Teller measurements, however, indicated that the mature skeletons at the microscale were space-filling, comparable to single crystals of geologic aragonite. Nanoparticles alone can never fill space completely, thus ion-by-ion filling must be invoked to fill interstitial pores. Such ion-by-ion diffusion and attachment may occur from the supersaturated calcifying fluid known to exist in corals, or from a dense liquid precursor, observed in synthetic systems but never in biogenic ones. Concomitant particle attachment and ion-by-ion filling was previously observed in synthetic calcite rhombohedra, but never in aragonite pseudohexagonal prisms, synthetic or biogenic, as observed here. Models for biomineral growth, isotope incorporation, and coral skeletons' resilience to ocean warming and acidification must take into account the dual formation mechanism, including particle attachment and ion-by-ion space filling.

Cell-tailored calcium carbonate particles with different crystal forms from nanoparticle to nano/microsphere

Inspired by biomineralization, the first synthesis of size-tunable calcium carbonates from nanoparticles (YC-CaCO3 NPs) to nano/microspheres (YC-CaCO3 N/MSs) with a porous structure was accomplished using a facile method under the mediation of the secretion from yeast cells (YCs). The biomolecules derived from the secretion of YCs were used as conditioning and stabilizing agents to control the biosynthesis of the YC-CaCO3 materials. The morphology and crystal forms of YC-CaCO3 materials can be affected by the biomolecules from the secretion of YCs. With increasing concentrations of biomolecules, the morphologies of the obtained CaCO3 materials changed from nanoparticles to nano/microspheres with a porous structure, while the crystal forms transformed from amorphous to calcite. Functional investigations showed that YC-CaCO3 NSs with a porous structure effectively acted as anticancer drug carriers with accurate and selective drug release in tumor tissue, which suggests that they have great potential to function as a therapeutic delivery system. These application features are mainly attributed to the satisfactory biocompatibility and biodegradability, high drug-loading capacity, and pH-dependent sustained drug release performance of the porous YC-CaCO3 NSs. The biomimetic synthesis strategy of YC-CaCO3 materials mediated by YC secretion not only helps to shed light on the biomineralization mechanism in organisms, but may also lead to a new means of biosynthesizing organic-inorganic nanocomposites.

First sequencing of ancient coral skeletal proteins

Here we report the first recovery, sequencing, and identification of fossil biomineral proteins from a Pleistocene fossil invertebrate, the stony coral Orbicella annularis. This fossil retains total hydrolysable amino acids of a roughly similar composition to extracts from modern O. annularis skeletons, with the amino acid data rich in Asx (Asp + Asn) and Glx (Glu + Gln) typical of invertebrate skeletal proteins. It also retains several proteins, including a highly acidic protein, also known from modern coral skeletal proteomes that we sequenced by LC-MS/MS over multiple trials in the best-preserved fossil coral specimen. A combination of degradation or amino acid racemization inhibition of trypsin digestion appears to limit greater recovery. Nevertheless, our workflow determines optimal samples for effective sequencing of fossil coral proteins, allowing comparison of modern and fossil invertebrate protein sequences, and will likely lead to further improvements of the methods. Sequencing of endogenous organic molecules in fossil invertebrate biominerals provides an ancient record of composition, potentially clarifying evolutionary changes and biotic responses to paleoenvironments.

Paracellular transport to the coral calcifying medium: effects of environmental parameters

Coral calcification relies on the transport of ions and molecules to the extracellular calcifying medium (ECM). Little is known about paracellular transport (via intercellular junctions) in corals and other marine calcifiers. Here, we investigated whether the permeability of the paracellular pathway varied in different environmental conditions in the coral Stylophora pistillata Using the fluorescent dye calcein, we characterised the dynamics of calcein influx from seawater to the ECM and showed that increases in paracellular permeability (leakiness) induced by hyperosmotic treatment could be detected by changes in calcein influx rates. We then used the calcein-imaging approach to investigate the effects of two environmental stressors on paracellular permeability: seawater acidification and temperature change. Under conditions of seawater acidification (pH 7.2) known to depress pH in the ECM and the calcifying cells of S. pistillata, we observed a decrease in half-times of calcein influx, indicating increased paracellular permeability. By contrast, high temperature (31°C) had no effect, whereas low temperature (20°C) caused decreases in paracellular permeability. Overall, our study establishes an approach to conduct further in vivo investigation of paracellular transport and suggests that changes in paracellular permeability could form an uncharacterised aspect of the physiological response of S. pistillata to seawater acidification.

The role of aspartic acid in reducing coral calcification under ocean acidification conditions

Biomolecules play key roles in regulating the precipitation of CaCO₃ biominerals but their response to ocean acidification is poorly understood. We analysed the skeletal intracrystalline amino acids of massive, tropical Porites spp. corals cultured over different seawater pCO₂. We find that concentrations of total amino acids, aspartic acid/asparagine (Asx), glutamic acid/glutamine and alanine are positively correlated with seawater pCO₂ and inversely correlated with seawater pH. Almost all variance in calcification rates between corals can be explained by changes in the skeletal total amino acid, Asx, serine and alanine concentrations combined with the calcification media pH (a likely indicator of the dissolved inorganic carbon available to support calcification). We show that aspartic acid inhibits aragonite precipitation from seawater in vitro, at the pH, saturation state and approximate aspartic acid concentrations inferred to occur at the coral calcification site. Reducing seawater saturation state and increasing [aspartic acid], as occurs in some corals at high pCO₂, both serve to increase the degree of inhibition, indicating that biomolecules may contribute to reduced coral calcification rates under ocean acidification.

Regulation of coral calcification by the acid-base sensing enzyme soluble adenylyl cyclase

Coral calcification is intricately linked to the chemical composition of the fluid in the extracellular calcifying medium (ECM), which is situated between the calcifying cells and the skeleton. Here we demonstrate that the acid-base sensing enzyme soluble adenylyl cyclase (sAC) is expressed in calcifying cells of the coral Stylophora pistillata. Furthermore, pharmacological inhibition of sAC in coral microcolonies resulted in acidification of the ECM as estimated by the pH-sensitive ratiometric indicator SNARF, and decreased calcification rates, as estimated by calcein labeling of crystal growth. These results indicate that sAC activity modulates some of the molecular machinery involved in producing the coral skeleton, which could include ion-transporting proteins and vesicular transport. To our knowledge this is the first study to directly demonstrate biological regulation of the alkaline pH of the coral ECM and its correlation with calcification.

Ubiquitous macropinocytosis in anthozoans

Transport of fluids, molecules, nutrients or nanoparticles through coral tissues are poorly documented. Here, we followed the flow of various tracers from the external seawater to within the cells of all tissues in living animals. After entering the general coelenteric cavity, we show that nanoparticles disperse throughout the tissues via the paracellular pathway. Then, the ubiquitous entry gate to within the cells' cytoplasm is macropinocytosis. Most cells form large vesicles of 350-600 nm in diameter at their apical side, continuously internalizing their surrounding medium. Macropinocytosis was confirmed using specific inhibitors of PI3K and actin polymerization. Nanoparticle internalization dynamics is size dependent and differs between tissues. Furthermore, we reveal that macropinocytosis is likely a major endocytic pathway in other anthozoan species. The fact that nearly all cells of an animal are continuously soaking in the environment challenges many aspects of the classical physiology viewpoints acquired from the study of bilaterians.

Ocean Acidification and Coastal Marine Invertebrates: Tracking CO2 Effects from Seawater to the Cell

In the last few decades, numerous studies have investigated the impacts of simulated ocean acidification on marine species and communities, particularly those inhabiting dynamic coastal systems. Despite these research efforts, there are many gaps in our understanding, particularly with respect to physiological mechanisms that lead to pathologies. In this review, we trace how carbonate system disturbances propagate from the coastal environment into marine invertebrates and highlight mechanistic links between these disturbances and organism function. We also point toward several processes related to basic invertebrate biology that are severely understudied and prevent an accurate understanding of how carbonate system dynamics influence organismic homeostasis and fitness-related traits. We recommend that significant research effort be directed to studying cellular phenotypes of invertebrates acclimated or adapted to elevated seawater pCO₂ using biochemical and physiological methods.

How corals made rocks through the ages

Hard, or stony, corals make rocks that can, on geological time scales, lead to the formation of massive reefs in shallow tropical and subtropical seas. In both historical and contemporary oceans, reef-building corals retain information about the marine environment in their skeletons, which is an organic-inorganic composite material. The elemental and isotopic composition of their skeletons is frequently used to reconstruct the environmental history of Earth's oceans over time, including temperature, pH, and salinity. Interpretation of this information requires knowledge of how the organisms formed their skeletons. The basic mechanism of formation of calcium carbonate skeleton in stony corals has been studied for decades. While some researchers consider coral skeletons as mainly passive recorders of ocean conditions, it has become increasingly clear that biological processes play key roles in the biomineralization mechanism. Understanding the role of the animal in living stony coral biomineralization and how it evolved has profound implications for interpreting environmental signatures in fossil corals to understand past ocean conditions. Here we review historical hypotheses and discuss the present understanding of how corals evolved and how their skeletons changed over geological time. We specifically explain how biological processes, particularly those occurring at the subcellular level, critically control the formation of calcium carbonate structures. We examine the different models that address the current debate including the tissue-skeleton interface, skeletal organic matrix, and biomineralization pathways. Finally, we consider how understanding the biological control of coral biomineralization is critical to informing future models of coral vulnerability to inevitable global change, particularly increasing ocean acidification.

Ion transporter gene expression is linked to the thermal sensitivity of calcification in the reef coral Stylophora pistillata

Coral calcification underpins biodiverse reef ecosystems, but the physiology underlying the thermal sensitivity of corals to changing seawater temperatures remains unclear. Furthermore, light is also a key factor in modulating calcification rates, but a mechanistic understanding of how light interacts with temperature to affect coral calcification is lacking. Here, we characterized the thermal performance curve (TPC) of calcification of the wide-spread, model coral species Stylophora pistillata, and used gene expression analysis to investigate the role of ion transport mechanisms in thermally-driven declines in day and nighttime calcification. Focusing on genes linked to transport of dissolved inorganic carbon (DIC), calcium and H+, our study reveals a high degree of coherence between physiological responses (e.g. calcification and respiration) with distinct gene expression patterns to the different temperatures in day and night conditions. At low temperatures, calcification and gene expression linked to DIC transport processes were downregulated, but showed little response to light. By contrast, at elevated temperature, light had a positive effect on calcification and stimulated a more functionally diverse gene expression response of ion transporters. Overall, our findings highlight the role of mechanisms linked to DIC, calcium and H+ transport in the thermal sensitivity of coral calcification and how this sensitivity is influenced by light.

New Non-Bilaterian Transcriptomes Provide Novel Insights into the Evolution of Coral Skeletomes

A general trend observed in animal skeletomes-the proteins occluded in animal skeletons-is the copresence of taxonomically widespread and lineage-specific proteins that actively regulate the biomineralization process. Among cnidarians, the skeletomes of scleractinian corals have been shown to follow this trend. However, distributions and phylogenetic analyses of biomineralization-related genes are often based on only a few species, with other anthozoan calcifiers such as octocorals (soft corals), not being fully considered. We de novo assembled the transcriptomes of four soft-coral species characterized by different calcification strategies (aragonite skeleton vs. calcitic sclerites) and data-mined published nonbilaterian transcriptome resources to construct a taxonomically comprehensive sequence database to map the distribution of scleractinian and octocoral skeletome components. Cnidaria shared no skeletome proteins with Placozoa or Ctenophora, but did share some skeletome proteins with Porifera, such as galaxin-related proteins. Within Scleractinia and Octocorallia, we expanded the distribution for several taxonomically restricted genes such as secreted acidic proteins, scleritin, and carbonic anhydrases, and propose an early, single biomineralization-recruitment event for galaxin sensu stricto. Additionally, we show that the enrichment of acidic residues within skeletogenic proteins did not occur at the Corallimorpharia-Scleractinia transition, but appears to be associated with protein secretion into the organic matrix. Finally, the distribution of octocoral calcification-related proteins appears independent of skeleton mineralogy (i.e., aragonite/calcite) with no differences in the proportion of shared skeletogenic proteins between scleractinians and aragonitic or calcitic octocorals. This points to skeletome homogeneity within but not between groups of calcifying cnidarians, although some proteins such as galaxins and SCRiP-3a could represent instances of commonality.

Mineral formation in the primary polyps of pocilloporoid corals

In reef-building corals, larval settlement and its rapid calcification provides a unique opportunity to study the bio-calcium carbonate formation mechanism involving skeleton morphological changes. Here we investigate the mineral formation of primary polyps, just after settlement, in two species of the pocilloporoid corals: Stylophora pistillata (Esper, 1797) and Pocillopora acuta (Lamarck, 1816). We show that the initial mineral phase is nascent Mg-Calcite, with rod-like morphology in P. acuta, and dumbbell morphology in S. pistillata. These structures constitute the first layer of the basal plate which is comparable to Rapid Accretion Deposits (Centers of Calcification, CoC) in adult coral skeleton. We found also that the rod-like/dumbbell Mg-Calcite structures in subsequent growth step will merge into larger aggregates by deposition of aragonite needles. Our results suggest that a biologically controlled mineralization of initial skeletal deposits occurs in three steps: first, vesicles filled with divalent ions are formed intracellularly. These vesicles are then transferred to the calcification site, forming nascent Mg-Calcite rod/pristine dumbbell structures. During the third step, aragonite crystals develop between these structures forming spherulite-like aggregates. STATEMENT OF SIGNIFICANCE: Coral settlement and recruitment periods are highly sensitive to environmental conditions. Successful mineralization during these periods is vital and influences the coral's chances of survival. Therefore, understanding the exact mechanism underlying carbonate precipitation is highly important. Here, we used in vivo microscopy, spectroscopy and molecular methods to provide new insights into mineral development. We show that the primary polyp's mineral arsenal consists of two types of minerals: Mg-Calcite and aragonite. In addition, we provide new insights into the ion pathway by showing that divalent ions are concentrated in intracellular vesicles and are eventually deposited at the calcification site.

Investigating marine bio-calcification mechanisms in a changing ocean with in vivo and high-resolution ex vivo Raman spectroscopy

Ocean acidification poses a serious threat to marine calcifying organisms, yet experimental and field studies have found highly diverse responses among species and environments. Our understanding of the underlying drivers of differential responses to ocean acidification is currently limited by difficulties in directly observing and quantifying the mechanisms of bio-calcification. Here, we present Raman spectroscopy techniques for characterizing the skeletal mineralogy and calcifying fluid chemistry of marine calcifying organisms such as corals, coralline algae, foraminifera, and fish (carbonate otoliths). First, our in vivo Raman technique is the ideal tool for investigating non-classical mineralization pathways. This includes calcification by amorphous particle attachment, which has recently been controversially suggested as a mechanism by which corals resist the negative effects of ocean acidification. Second, high-resolution ex vivo Raman mapping reveals complex banding structures in the mineralogy of marine calcifiers, and provides a tool to quantify calcification responses to environmental variability on various timescales from days to years. We describe the new insights into marine bio-calcification that our techniques have already uncovered, and we consider the wide range of questions regarding calcifier responses to global change that can now be proposed and addressed with these new Raman spectroscopy tools.

Effects of light and darkness on pH regulation in three coral species exposed to seawater acidification

The resilience of corals to ocean acidification has been proposed to rely on regulation of extracellular calcifying medium pH (pH_ECM), but few studies have compared the capacity of coral species to control this parameter at elevated pCO₂. Furthermore, exposure to light and darkness influences both pH regulation and calcification in corals, but little is known about its effect under conditions of seawater acidification. Here we investigated the effect of acidification in light and darkness on pH_ECM, calcifying cell intracellular pH (pH_I), calcification, photosynthesis and respiration in three coral species: Stylophora pistillata, Pocillopora damicornis and Acropora hyacinthus. We show that S. pistillata was able to maintain pH_ECM under acidification in light and darkness, but pH_ECM decreased in P. damicornis and A. hyacinthus to a much greater extent in darkness than in the light. Acidification depressed calcifying cell pH_I in all three species, but we identified an unexpected positive effect of light on pH_I. Calcification rate and pH_ECM decreased together under acidification, but there are inconsistencies in their relationship indicating that other physiological parameters are likely to shape how coral calcification responds to acidification. Overall our study reveals interspecies differences in coral regulation of pH_ECM and pH_I when exposed to acidification, influenced by exposure to light and darkness.