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.

Extreme Environmental Variability Induces Frontloading of Coral Biomineralisation Genes to Maintain Calcification Under pCO2 Variability

Corals residing in habitats that experience high-frequency seawater pCO2 variability may possess an enhanced capacity to cope with ocean acidification, yet we lack a clear understanding of the molecular toolkit enabling acclimatisation to environmental extremes or how life-long exposure to pCO2 variability influences biomineralisation. Here, we examined the gene expression responses and micro-skeletal characteristics of Pocillopora damicornis originating from the reef flat and reef slope of Heron Island, southern Great Barrier Reef. The reef flat and reef slope had similar mean seawater pCO2, but the reef flat experienced twice the mean daily pCO2 amplitude (range of 797 v. 399 μatm day-1, respectively). A controlled mesocosm experiment was conducted over 8 weeks, exposing P. damicornis from the reef slope and reef flat to stable (218 ± 9) or variable (911 ± 31) diel pCO2 fluctuations (μatm; mean ± SE). At the end of the exposure, P. damicornis originating from the reef flat demonstrated frontloading of 25% of the expressed genes regardless of treatment conditions, suggesting constitutive upregulation. This included higher expression of critical biomineralisation-related genes such as carbonic anhydrases, skeletal organic matrix proteins, and bicarbonate transporters. The observed frontloading corresponded with a 40% increase of the fastest deposited areas of the skeleton in reef flat corals grown under non-native, stable pCO2 conditions compared to reef slope conspecifics, suggesting a compensatory response that stems from acclimatisation to environmental extremes and/or relief from stressful pCO2 fluctuations. Under escalating ocean warming and acidification, corals acclimated to environmental variability warrant focused investigation and represent ideal candidates for active interventions to build reef resilience while societies adopt strict policies to limit climate change.

Sustainably cultured coral scaffold supports human bone marrow mesenchymal stromal cell osteogenesis

The current gold standard grafting material is autologous bone due to its osteoinductive and osteoconductive properties. Autograft harvesting results in donors site morbidity. Coral scaffolds offer a natural autograft alternative, sharing the density and porosity of human bone. This study investigated the biocompatibility and osteogenic potential of a novel, sustainably grown Pocillopora scaffold with human bone marrow-derived mesenchymal stromal cells (MSCs). The coral-derived scaffold displays a highly textured topography, with concavities of uniform size and a high calcium carbonate content. Large scaffold samples exhibit compressive and diametral tensile strengths in the range of trabecular bone, with strengths likely increasing for smaller particulate samples. Following the in vitro seeding of MSCs adjacent to the scaffold, the MSCs remained viable, continued proliferating and metabolising, demonstrating biocompatibility. The seeded MSCs densely covered the coral scaffold with organized, aligned cultures with a fibroblastic morphology. In vivo coral scaffolds with MSCs supported earlier bone and blood vessel formation as compared to control constructs containing TCP-HA and MSCs. This work characterized a novel, sustainably grown coral scaffold that was biocompatible with MSCs and supports their in vivo osteogenic differentiation, advancing the current repertoire of biomaterials for bone grafting.

Correlative geochemical imaging of Desmophyllum dianthus reveals biomineralisation strategy as a key coral vital effect

The chemical and isotopic composition of stony coral skeletons form an important archive of past climate. However, these reconstructions are largely based on empirical relationships often complicated by "vital effects" arising from uncertain physiological processes of the coral holobiont. The skeletons of deep-sea corals, such as Desmophyllum dianthus, are characterised by micron-scale or larger geochemical heterogeneity associated with: (1) centres of calcification (COCs) where nucleation of new skeleton begins, and (2) fibres that thicken the skeleton. These features are difficult to sample cleanly using traditional techniques, resulting in uncertainty surrounding both the causes of geochemical differences and their influence on environmental signals. Here we combine optical, and in-situ chemical and isotopic, imaging tools across a range of spatial resolutions (~ 100 nm to 10 s of μm) in a correlative multimodal imaging (CMI) approach to isolate the microstructural geochemistry of each component. This reveals COCs are characterised by higher organic content, Mg, Li and Sr and lower U, B and δ11B compared to fibres, reflecting the contrasting biomineralisation mechanisms employed to construct each feature. CMI is rarely applied in Environmental/Earth Sciences, but here we illustrate the power of this approach to unpick the "vital effects" in D. dianthus, and by extension, other scleractinian corals.

A novel in vivo system to study coral biomineralization in the starlet sea anemone, Nematostella vectensis

Coral conservation requires a mechanistic understanding of how environmental stresses disrupt biomineralization, but progress has been slow, primarily because corals are not easily amenable to laboratory research. Here, we highlight how the starlet sea anemone, Nematostella vectensis, can serve as a model to interrogate the cellular mechanisms of coral biomineralization. We have developed transgenic constructs using biomineralizing genes that can be injected into Nematostella zygotes and designed such that translated proteins may be purified for physicochemical characterization. Using fluorescent tags, we confirm the ectopic expression of the coral biomineralizing protein, SpCARP1, in Nematostella. We demonstrate via calcein staining that SpCARP1 concentrates calcium ions in Nematostella, likely initiating the formation of mineral precursors, consistent with its suspected role in corals. These results lay a fundamental groundwork for establishing Nematostella as an in vivo system to explore the evolutionary and cellular mechanisms of coral biomineralization, improve coral conservation efforts, and even develop novel biomaterials.

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.

Directing polymorph specific calcium carbonate formation with de novo protein templates

Biomolecules modulate inorganic crystallization to generate hierarchically structured biominerals, but the atomic structure of the organic-inorganic interfaces that regulate mineralization remain largely unknown. We hypothesized that heterogeneous nucleation of calcium carbonate could be achieved by a structured flat molecular template that pre-organizes calcium ions on its surface. To test this hypothesis, we design helical repeat proteins (DHRs) displaying regularly spaced carboxylate arrays on their surfaces and find that both protein monomers and protein-Ca2+ supramolecular assemblies directly nucleate nano-calcite with non-natural {110} or {202} faces while vaterite, which forms first in the absence of the proteins, is bypassed. These protein-stabilized nanocrystals then assemble by oriented attachment into calcite mesocrystals. We find further that nanocrystal size and polymorph can be tuned by varying the length and surface chemistry of the designed protein templates. Thus, bio-mineralization can be programmed using de novo protein design, providing a route to next-generation hybrid materials.

The response of coral skeletal nano structure and hardness to ocean acidification conditions

Ocean acidification typically reduces coral calcification rates and can fundamentally alter skeletal morphology. We use atomic force microscopy (AFM) and microindentation to determine how seawater pCO2 affects skeletal structure and Vickers hardness in a Porites lutea coral. At 400 µatm, the skeletal fasciculi are composed of tightly packed bundles of acicular crystals composed of quadrilateral nanograins, approximately 80-300 nm in dimensions. We interpret high adhesion at the nanograin edges as an organic coating. At 750 µatm the crystals are less regular in width and orientation and composed of either smaller/more rounded nanograins than observed at 400 µatm or of larger areas with little variation in adhesion. Coral aragonite may form via ion-by-ion attachment to the existing skeleton or via conversion of amorphous calcium carbonate precursors. Changes in nanoparticle morphology could reflect variations in the sizes of nanoparticles produced by each crystallization pathway or in the contributions of each pathway to biomineralization. We observe no significant variation in Vickers hardness between skeletons cultured at different seawater pCO2. Either the nanograin size does not affect skeletal hardness or the effect is offset by other changes in the skeleton, e.g. increases in skeletal organic material as reported in previous studies.

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.

Coral growth anomalies, neoplasms, and tumors in the Anthropocene

One of the most widespread coral diseases linked to anthropogenic activities and recorded on reefs worldwide is characterized by anomalous growth formations in stony corals, referred to as coral growth anomalies (GAs). The biological functions of GA tissue include limited reproduction, reduced access to resources, and weakened ability to defend against predators. Transcriptomic analyses have revealed that, in some cases, disease progression can involve host genes related to oncogenesis, suggesting that the GA tissues may be malignant neoplasms such as those developed by vertebrates. The number of studies reporting the presence of GAs in common reef-forming species highlights the urgency of a thorough understanding of the pathology and causative factors of this disease and its parallels to higher organism malignant tissue growth. Here, we review the current state of knowledge on the etiology and holobiont features of GAs in reef-building corals.

Amorphous Calcium Carbonate Cluster Nanospheres in Water-Deficient Organic Solvents

As the key intermediate phase of crystalline calcium carbonate biominerals, amorphous calcium carbonate (ACC) remains mysterious in its structures because of its long-range disorder and instability. We herein report the synthesis of ACC nanospheres in a water-deficient organic solvent system. The obtained ACC nanospheres are very stable under dry conditions. Cryo-TEM reveals that each nanospheres consists of smaller nanosized clusters. We further demonstrate that these clusters can precipitate on other substrates to form an ultrathin ACC coating, which should be an ACC cluster monolayer. The results demonstrate that the presence of small ACC clusters as the subunits of larger aggregates is inherent to ACC synthesized in water-alcohol system but not induced by polymer additives.

Utilizing an artificial intelligence system to build the digital structural proteome of reef-building corals

BACKGROUND

Reef-building corals play an important role in the marine ecosystem, and analyzing their proteomes from a structural perspective will exert positive effects on exploring their biology. Here we integrated mass spectrometry with newly published ColabFold to obtain digital structural proteomes of dominant reef-building corals.

RESULTS

Of the 8,382 homologous proteins in Acropora muricata, Montipora foliosa, and Pocillopora verrucosa identified, 8,166 received predicted structures after about 4,060 GPU hours of computation. The resulting dataset covers 83.6% of residues with a confident prediction, while 25.9% have very high confidence.

CONCLUSIONS

Our work provides insight-worthy predictions for coral research, confirms the reliability of ColabFold in practice, and is expected to be a reference case in the impending high-throughput era of structural proteomics.

Global change differentially modulates Caribbean coral physiology

Global change driven by anthropogenic carbon emissions is altering ecosystems at unprecedented rates, especially coral reefs, whose symbiosis with algal symbionts is particularly vulnerable to increasing ocean temperatures and altered carbonate chemistry. Here, we assess the physiological responses of three Caribbean coral (animal host + algal symbiont) species from an inshore and offshore reef environment after exposure to simulated ocean warming (28, 31°C), acidification (300–3290 μatm), and the combination of stressors for 93 days. We used multidimensional analyses to assess how a variety of coral physiological parameters respond to ocean acidification and warming. Our results demonstrate reductions in coral health in Siderastrea siderea and Porites astreoides in response to projected ocean acidification, while future warming elicited severe declines in Pseudodiploria strigosa. Offshore S. siderea fragments exhibited higher physiological plasticity than inshore counterparts, suggesting that this offshore population was more susceptible to changing conditions. There were no plasticity differences in P. strigosa and P. astreoides between natal reef environments, however, temperature evoked stronger responses in both species. Interestingly, while each species exhibited unique physiological responses to ocean acidification and warming, when data from all three species are modelled together, convergent stress responses to these conditions are observed, highlighting the overall sensitivities of tropical corals to these stressors. Our results demonstrate that while ocean warming is a severe acute stressor that will have dire consequences for coral reefs globally, chronic exposure to acidification may also impact coral physiology to a greater extent in some species than previously assumed. Further, our study identifies S. siderea and P. astreoides as potential ‘winners’ on future Caribbean coral reefs due to their resilience under projected global change stressors, while P. strigosa will likely be a ‘loser’ due to their sensitivity to thermal stress events. Together, these species-specific responses to global change we observe will likely manifest in altered Caribbean reef assemblages in the future.

Crystal orientation mapping and microindentation reveal anisotropy in Porites skeletons

Structures made by scleractinian corals support diverse ocean ecosystems. Despite the importance of coral skeletons and their predicted vulnerability to climate change, few studies have examined the mechanical and crystallographic properties of coral skeletons at the micro- and nano-scales. Here, we investigated the interplay of crystallographic and microarchitectural organization with mechanical anisotropy within Porites skeletons by measuring Young's modulus and hardness along surfaces transverse and longitudinal to the primary coral growth direction. We observed micro-scale anisotropy, where the transverse surface had greater Young's modulus and hardness by ∼ 6 GPa and 0.2 GPa, respectively. Electron backscatter diffraction (EBSD) revealed that this surface also had a higher percentage of crystals oriented with the a-axis between ± 30-60^∘, relative to the longitudinal surface, and a broader grain size distribution. Within a region containing a sharp microscale gradient in Young's modulus, nanoscale indentation mapping, energy dispersive spectroscopy (EDS), EBSD, and Raman crystallography were performed. A correlative trend showed higher Young's modulus and hardness in regions with individual crystal bases (c-axis) facing upward, and in crystal fibers relative to centers of calcification. These relationships highlight the difference in mechanical properties between scales (i.e. crystals, crystal bundles, grains). Observations of crystal orientation and mechanical properties suggest that anisotropy is driven by microscale organization and crystal packing, rather than intrinsic crystal anisotropy. In comparison with previous observations of nanoscale isotropy in corals, our results illustrate the role of hierarchical architecture in coral skeletons and the influence of biotic and abiotic factors on mechanical properties at different scales. STATEMENT OF SIGNIFICANCE: Coral biomineralization and the ability of corals' skeletal structure to withstand biotic and abiotic forces underpins the success of reef ecosystems. At the microscale, we show increased skeletal stiffness and hardness perpendicular to the coral growth direction. By comparing nano- and micro-scale indentation results, we also reveal an effect of hierarchical architecture on the mechanical properties of coral skeletons and hypothesize that crystal packing and orientation result in microscale anisotropy. In contrast to previous findings, we demonstrate that mechanical and crystallographic properties of coral skeletons can vary between surface planes, within surface planes, and at different analytical scales. These results improve our understanding of biomineralization and the effects of scale and direction on how biomineral structures respond to environmental stimuli.

Crystal Nucleation and Growth of Inorganic Ionic Materials from Aqueous Solution: Selected Recent Developments, and Implications

In this review article, selected, latest theoretical, and experimental developments in the field of nucleation and crystal growth of inorganic materials from aqueous solution are highlighted, with a focus on literature after 2015 and on non-classical pathways. A key point is to emphasize the so far underappreciated role of water and solvent entropy in crystallization at all stages from solution speciation through to the final crystal. While drawing on examples from current inorganic materials where non-classical behavior has been proposed, the potential of these approaches to be adapted to a wide-range of systems is also discussed, while considering the broader implications of the current re-assessment of pathways for crystallization. Various techniques that are suitable for the exploration of crystallization pathways in aqueous solution, from nucleation to crystal growth are summarized, and a flow chart for the assignment of specific theories based on experimental observations is proposed.

Molecular characterization, immunofluorescent localization, and expression levels of two bicarbonate anion transporters in the whitish mantle of the giant clam, Tridacna squamosa, and the implications for light-enhanced shell formation

Giant clams conduct light-enhanced shell formation, which requires the increased transport of Ca²⁺ and inorganic carbon (C_i) from the hemolymph through the shell-facing epithelium of the whitish inner mantle to the extrapallial fluid where CaCO₃ deposition occurs. The major form of C_i in the hemolymph is HCO₃^-, but the mechanisms of HCO₃^- transport through the basolateral and apical membranes of the shell-facing epithelial cells remain unknown. This study aimed to clone from the inner mantle of Tridacna squamosa the complete coding cDNA sequences of electrogenic Na⁺-HCO₃^-cotransporter 1 homolog (NBCe1-like-b) and electrogenic Na⁺-HCO₃^-cotransporter 2 homolog (NBCe2-like). NBCe1-like-b comprised 3360 bp, encoding a 125.7 kDa protein with 1119 amino acids. NBCe1-like-b was slightly different from NBCe1-like-a of the ctenidium reported elsewhere, as it had a serine residue (Ser¹⁰²⁵), which might undergo phosphorylation leading to the transport of Na⁺: HCO₃^- at a ratio of 1: 2 into the cell. NBCe1-like-b was localized at the basolateral membrane of the shell-facing epithelial cells, and its gene and protein expression levels increased significantly in the inner mantle during illumination, indicating a role in the light-enhanced uptake of HCO₃^- from the hemolymph. The sequence of NBCe2-like obtained from the inner mantle was identical to that reported previously for the outer mantle. In the inner mantle, NBCe2-like had an apical localization in the shell-facing epithelial cells, and its protein abundance was upregulated during illumination. Hence, NBCe2-like might take part in the light-enhanced transport of HCO₃^- through the apical membrane of these cells into the extrapallial fluid.

Multiscale mechanical consequences of ocean acidification for cold-water corals

Ocean acidification is a threat to deep-sea corals and could lead to dramatic and rapid loss of the reef framework habitat they build. Weakening of structurally critical parts of the coral reef framework can lead to physical habitat collapse on an ecosystem scale, reducing the potential for biodiversity support. The mechanism underpinning crumbling and collapse of corals can be described via a combination of laboratory-scale experiments and mathematical and computational models. We synthesise data from electron back-scatter diffraction, micro-computed tomography, and micromechanical experiments, supplemented by molecular dynamics and continuum micromechanics simulations to predict failure of coral structures under increasing porosity and dissolution. Results reveal remarkable mechanical properties of the building material of cold-water coral skeletons of 462 MPa compressive strength and 45-67 GPa stiffness. This is 10 times stronger than concrete, twice as strong as ultrahigh performance fibre reinforced concrete, or nacre. Contrary to what would be expected, CWCs retain the strength of their skeletal building material despite a loss of its stiffness even when synthesised under future oceanic conditions. As this is on the material length-scale, it is independent of increasing porosity from exposure to corrosive water or bioerosion. Our models then illustrate how small increases in porosity lead to significantly increased risk of crumbling coral habitat. This new understanding, combined with projections of how seawater chemistry will change over the coming decades, will help support future conservation and management efforts of these vulnerable marine ecosystems by identifying which ecosystems are at risk and when they will be at risk, allowing assessment of the impact upon associated biodiversity.

Two decades of seawater acidification experiments on tropical scleractinian corals: Overview, meta-analysis and perspectives

Ocean acidification has emerged as a major concern in the last fifteen years and studies on the impacts of seawater acidification on marine organisms have multiplied accordingly. This review aimed at synthesizing the literature on the effects of seawater acidification on tropical scleractinians under laboratory-controlled conditions. We identified 141 articles (published between 1999 and 2021) and separated endpoints into 22 biological categories to identify global trends for mitigation and gaps in knowledge and research priorities for future investigators. The relative number of affected endpoints increased with pH intensity (particularly for endpoints associated to calcification and reproduction). When exposed to pH 7.6-7.8 (compared to higher pH), 49% of endpoints were affected. The diversity in experimental designs prevented deciphering the modulating role of coral life stages, genera or duration of exposure. Finally, important bias in research efforts included most experiments on adult corals (68.5%), in 27 out of 150 (18%) coral ecoregions and exclusively from shallow-waters.

The nano- and meso-scale structure of amorphous calcium carbonate

Understanding the underlying processes of biomineralization is crucial to a range of disciplines allowing us to quantify the effects of climate change on marine organisms, decipher the details of paleoclimate records and advance the development of biomimetic materials. Many biological minerals form via intermediate amorphous phases, which are hard to characterize due to their transient nature and a lack of long-range order. Here, using Monte Carlo simulations constrained by X-ray and neutron scattering data together with model building, we demonstrate a method for determining the structure of these intermediates with a study of amorphous calcium carbonate (ACC) which is a precursor in the bio-formation of crystalline calcium carbonates. We find that ACC consists of highly ordered anhydrous nano-domains of approx. 2 nm that can be described as nanocrystalline. These nano-domains are held together by an interstitial net-like matrix of water molecules which generate, on the mesoscale, a heterogeneous and gel-like structure of ACC. We probed the structural stability and dynamics of our model on the nanosecond timescale by molecular dynamics simulations. These simulations revealed a gel-like and glassy nature of ACC due to the water molecules and carbonate ions in the interstitial matrix featuring pronounced orientational and translational flexibility. This allows for viscous mobility with diffusion constants four to five orders of magnitude lower than those observed in solutions. Small and ultra-small angle neutron scattering indicates a hierarchically-ordered organization of ACC across length scales that allow us, based on our nano-domain model, to build a comprehensive picture of ACC formation by cluster assembly from solution. This contribution provides a new atomic-scale understanding of ACC and provides a framework for the general exploration of biomineralization and biomimetic processes.

Desert dust deposition supplies essential bioelements to Red Sea corals

Climate change-related increase in seawater temperature has become a leading cause of coral bleaching and mortality. However, corals from the northern Red Sea show high thermal tolerance and no recorded massive bleaching event. This specific region is frequently subjected to intense dust storms, coming from the surrounding arid deserts, which are expected to increase in frequency and intensity in the future. The aerial dust deposition supplies essential bioelements to the water column. Here, we investigated the effect of dust deposition on the physiology of a Red Sea coral, Stylophora pistillata. We measured the modifications in coral and Symbiodiniaceae metallome (cellular metal content), as well as the changes in photosynthesis and oxidative stress status of colonies exposed during few weeks to dust deposition. Our results show that 1 mg L^-1 of dust supplied nanomolar amounts of nitrate and other essential bioelements, such as iron, manganese, zinc and copper, rapidly assimilated by the symbionts. At 25°C, metal bioaccumulation enhanced the chlorophyll concentration and photosynthesis of dust-exposed corals compared to control corals. These results suggest that primary production was limited by metal availability in seawater. A 5°C increase in seawater temperature enhanced iron assimilation in both control and dust-enriched corals. Temperature rise increased the photosynthesis of control corals only, dust-exposed ones having already reached maximal photosynthesis rates at 25°C. Finally, we observed a combined effect of temperature and bioelement concentration on the assimilation of molybdenum, cadmium, manganese and copper, which were in higher concentrations in symbionts of dust-exposed corals maintained at 30°C. All together these observations highlight the importance of dust deposition in the supply of essential bioelements, such as iron, to corals and its role in sustaining coral productivity in Red Sea reefs.

Designed nanostructures created via physicochemical switching of the growth mode between single crystals and mesocrystals

Most biominerals are composed of mesocrystals, in which individual nanoparticle building units have a defined long-range order on the atomic scale in at least one direction. Although the crystal size and orientation of the mesostructures are spatially designed in biological architectures, it has been difficult to achieve adequate control of the crystal growth to produce modulated mesostructures in artificial aqueous systems. Here, we propose a simple physicochemical approach for the spatial design of nanostructures using an aqueous solution system. The ordered arrays of oriented fluorapatite (FA) rods similar to tooth enamel are produced on a polymer substrate in a supersaturated solution. We succeeded in reversible switching of the growth mode of FA between single-crystalline rods and mesocrystalline grains through the disturbance of the solution. The primary crystal size was tuned between micrometric rods ∼0.5 μm wide and >5 μm long and nanoscale grains ∼10 nm wide and 50 nm long without a drastic change in the c direction. Hierarchical architectures consisting of iso-oriented FA microrods and nanograins were constructed via temporal control of the crystal growth mode by switching a physicochemical parameter, such as the degree of supersaturation at the growth front.

Artificial Intelligence as a Tool to Study the 3D Skeletal Architecture in Newly Settled Coral Recruits: Insights into the Effects of Ocean Acidification on Coral Biomineralization

Understanding the formation of the coral skeleton has been a common subject uniting various marine and materials study fields. Two main regions dominate coral skeleton growth: Rapid Accretion Deposits (RADs) and Thickening Deposits (TDs). These have been extensively characterized at the 2D level, but their 3D characteristics are still poorly described. Here, we present an innovative approach to combine synchrotron phase contrast-enhanced microCT (PCE-CT) with artificial intelligence (AI) to explore the 3D architecture of RADs and TDs within the coral skeleton. As a reference study system, we used recruits of the stony coral Stylophora pistillata from the Red Sea, grown under both natural and simulated ocean acidification conditions. We thus studied the recruit’s skeleton under both regular and morphologically-altered acidic conditions. By imaging the corals with PCE-CT, we revealed the interwoven morphologies of RADs and TDs. Deep-learning neural networks were invoked to explore AI segmentation of these regions, to overcome limitations of common segmentation techniques. This analysis yielded highly-detailed 3D information about the RAD’s and TD’s architecture. Our results demonstrate how AI can be used as a powerful tool to obtain 3D data essential for studying coral biomineralization and for exploring the effects of environmental change on coral growth.

Uncovering the Effects of Symbiosis and Temperature on Coral Calcification

AbstractWe tested the impact of temperature and symbiont state on calcification in corals, using the facultatively symbiotic coral Astrangia poculata as a model system. Symbiotic and aposymbiotic colonies of A. poculata were reared in 15, 20, and 27 °C conditions. We used scanning electron microscopy to quantify how these physiological and environmental conditions impact skeletal structure. Buoyant weight data over time revealed that temperature significantly affects calcification rates. Scanning electron microscopy of A. poculata skeletons showed that aposymbiotic colonies appear to have a lower density of calcium carbonate in actively growing septal spines. We describe a novel approach to analyze the roughness and texture of scanning electron microscopy images. Quantitative analysis of the roughness of septal spines revealed that aposymbiotic colonies have a rougher surface than symbiotic colonies in tropical conditions (27 °C). This trend reversed at 15 °C, a temperature at which the symbionts of A. poculata may exhibit parasitic properties. Analysis of surface texture patterns showed that temperature impacts the spatial variance of crystals on the spine surface. Few published studies have examined the skeleton of A. poculata by using scanning electron microscopy. Our approach provides a way to study detailed changes in skeletal microstructure in response to environmental parameters and can serve as a proxy for more expensive and time-consuming analyses. Utilizing a facultatively symbiotic coral that is native to both temperate and tropical regions provides new insights into the impact of both symbiosis and temperature on calcification in corals.

Natural Biomaterials from Biodiversity for Healthcare Applications

Natural biomaterials originating during the growth cycles of all living organisms have been used for many applications. They span from bioinert to bioactive materials including bioinspired ones. As they exhibit an increasing degree of sophistication, natural biomaterials have proven suitable to address the needs of the healthcare sector. Here the different natural healthcare biomaterials, their biodiversity sources, properties, and promising healthcare applications are reviewed. The variability of their properties as a result of considered species and their habitat is also discussed. Finally, some limitations of natural biomaterials are discussed and possible future developments are provided as more natural biomaterials are yet to be discovered and studied.

Demonstrated gradual evolution of disorder in crystalline structures between single crystal and polycrystal via chemical and physicochemical approaches

Single-crystal fluorapatite rods elongated in the c direction are switched to iso-oriented nanorods by adding a specific carboxy compound (chemical approach) and to roughly arranged nanograins by increasing the supersaturation at the growth front (physicochemical approach).

Intracellular nanoscale architecture as a master regulator of calcium carbonate crystallization in marine microalgae

Unicellular marine microalgae are responsible for one of the largest carbon sinks on Earth. This is in part due to intracellular formation of calcium carbonate scales termed coccoliths. Traditionally, the influence of changing environmental conditions on this process has been estimated using poorly constrained analogies to crystallization mechanisms in bulk solution, yielding ambiguous predictions. Here, we elucidated the intracellular nanoscale environment of coccolith formation in the model species Pleurochrysis carterae using cryoelectron tomography. By visualizing cells at various stages of the crystallization process, we reconstructed a timeline of coccolith development. The three-dimensional data portray the native-state structural details of coccolith formation, uncovering the crystallization mechanism, and how it is spatially and temporally controlled. Most strikingly, the developing crystals are only tens of nanometers away from delimiting membranes, resulting in a highly confined volume for crystal growth. We calculate that the number of soluble ions that can be found in such a minute volume at any given time point is less than the number needed to allow the growth of a single atomic layer of the crystal and that the uptake of single protons can markedly affect nominal pH values. In such extreme confinement, the crystallization process is expected to depend primarily on the regulation of ion fluxes by the living cell, and nominal ion concentrations, such as pH, become the result, rather than a driver, of the crystallization process. These findings call for a new perspective on coccolith formation that does not rely exclusively on solution chemistry.

Sclerites of the soft coral Ovabunda macrospiculata (Xeniidae) are predominantly the metastable CaCO3 polymorph vaterite

Soft corals (Cnidaria, Anthozoa, Octocorallia, Alcyonacea) produce internal sclerites of calcium carbonate previously shown to be composed of calcite, the most stable calcium carbonate polymorph. Here we apply multiple imaging and physical chemistry analyses to extracted and in-vivo sclerites of the abundant Red Sea soft coral, Ovabunda macrospiculata, to detail their mineralogy. We show that this species' sclerites are comprised predominantly of the less stable calcium carbonate polymorph vaterite (> 95%), with much smaller components of aragonite and calcite. Use of this mineral, which is typically considered to be metastable, by these soft corals has implications for how it is formed as well as how it will persist during the anticipated anthropogenic climate change in the coming decades. This first documentation of vaterite dominating the mineral composition of O. macrospiculata sclerites is likely just the beginning of establishing its presence in other soft corals. STATEMENT OF SIGNIFICANCE: Vaterite is typically considered to be a metastable polymorph of calcium carbonate. While calcium carbonate structures formed within the tissues of octocorals (phylum Cnidaria), have previously been reported to be composed of the more stable polymorphs aragonite and calcite, we observed that vaterite dominates the mineralogy of sclerites of Ovabunda macrospiculata from the Red Sea. Based on electron microscopy, Raman spectroscopy, and X-ray diffraction analysis, vaterite appears to be the dominant polymorph in sclerites both in the tissue and after extraction and preservation. Although this is the first documentation of vaterite in soft coral sclerites, it likely will be found in sclerites of other related taxa as well.

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.

The Evolution of Calcification in Reef-Building Corals

Corals build the structural foundation of coral reefs, one of the most diverse and productive ecosystems on our planet. Although the process of coral calcification that allows corals to build these immense structures has been extensively investigated, we still know little about the evolutionary processes that allowed the soft-bodied ancestor of corals to become the ecosystem builders they are today. Using a combination of phylogenomics, proteomics, and immunohistochemistry, we show that scleractinian corals likely acquired the ability to calcify sometime between ∼308 and ∼265 Ma through a combination of lineage-specific gene duplications and the co-option of existing genes to the calcification process. Our results suggest that coral calcification did not require extensive evolutionary changes, but rather few coral-specific gene duplications and a series of small, gradual optimizations of ancestral proteins and their co-option to the calcification process.

Comparative Proteomics of Octocoral and Scleractinian Skeletomes and the Evolution of Coral Calcification

Corals are the ecosystem engineers of coral reefs, one of the most biodiverse marine ecosystems. The ability of corals to form reefs depends on the precipitation of calcium carbonate (CaCO₃) under biological control. However, several mechanisms underlying coral biomineralization remain elusive, for example, whether corals employ different molecular machineries to deposit different CaCO₃ polymorphs (i.e., aragonite or calcite). Here, we used tandem mass spectrometry (MS/MS) to compare the proteins occluded in the skeleton of three octocoral and one scleractinian species: Tubipora musica and Sinularia cf. cruciata (calcite sclerites), the blue coral Heliopora coerulea (aragonitic skeleton), and the scleractinian aragonitic Montipora digitata. Reciprocal Blast analysis revealed extremely low overlap between aragonitic and calcitic species, while a core set of proteins is shared between octocorals producing calcite sclerites. However, the carbonic anhydrase CruCA4 is present in the skeletons of both polymorphs. Phylogenetic analysis highlighted several possible instances of protein co-option in octocorals. These include acidic proteins and scleritin, which appear to have been secondarily recruited for calcification and likely derive from proteins playing different functions. Similarities between octocorals and scleractinians included presence of a galaxin-related protein, carbonic anhydrases, and one hephaestin-like protein. Although the first two appear to have been independently recruited, the third appear to share a common origin. This work represents the first attempt to identify and compare proteins associated with coral skeleton polymorph diversity, providing several new research targets and enabling both future functional and evolutionary studies aimed at elucidating the origin and evolution of coral biomineralization.

Genes encoding putative bicarbonate transporters as a missing molecular link between molt and mineralization in crustaceans

During their life, crustaceans undergo several molts, which if theoretically compared to the human body would be equivalent to replacing all bones at a single event. Such a dramatic repetitive event is coupled to unique molecular mechanisms of mineralization so far mostly unknown. Unlike human bone mineralized with calcium phosphate, the crustacean exoskeleton is mineralized mainly by calcium carbonate. Crustacean growth thus necessitates well-timed mobilization of bicarbonate to specific extracellular sites of biomineralization at distinct molt cycle stages. Here, by looking at the crayfish Cherax quadricarinatus at different molting stages, we suggest that the mechanisms of bicarbonate ion transport for mineralization in crustaceans involve the SLC4 family of transporters and that these proteins play a key role in the tight coupling between molt cycle events and mineral deposition. This discovery of putative bicarbonate transporters in a pancrustacean with functional genomic evidence from genes encoding the SLC4 family-mostly known for their role in pH control-is discussed in the context of the evolution of calcium carbonate biomineralization.

Gas assisted in situ biomimetic mineralization of bacterial cellulose/calcium carbonate bio composites by bacterial

Biomineralization inspired process to produce polymer of desired need is a promising approach in the field of research. In the present work, the bacterial cellulose (BC) based nanocomposites with a 3D network were synthesized via a biological route by choosing the calcium salt of primary metabolites (calcium gluconate) as the carbon source. The BC based composites were characterized by employing with Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM). During the preparation of nanocomposites, the calcium ions embedded on the cellulose fibrils were served as the nucleation center and calcium carbonate was deposited into BC network in the assistance of CO₂. The uniform distribution of embedded objects on the cellulose nanofibers between internal and external was achieved. The exploitation of organisms for inorganic growth, shape and self-assembling explores new opportunities to the design of original nanostructures.

Patterns of Element Incorporation in Calcium Carbonate Biominerals Recapitulate Phylogeny for a Diverse Range of Marine Calcifiers

Elemental ratios in biogenic marine calcium carbonates are widely used in geobiology, environmental science, and paleoenvironmental reconstructions. It is generally accepted that the elemental abundance of biogenic marine carbonates reflects a combination of the abundance of that ion in seawater, the physical properties of seawater, the mineralogy of the biomineral, and the pathways and mechanisms of biomineralization. Here we report measurements of a suite of nine elemental ratios (Li/Ca, B/Ca, Na/Ca, Mg/Ca, Zn/Ca, Sr/Ca, Cd/Ca, Ba/Ca, and U/Ca) in 18 species of benthic marine invertebrates spanning a range of biogenic carbonate polymorph mineralogies (low-Mg calcite, high-Mg calcite, aragonite, mixed mineralogy) and of phyla (including Mollusca, Echinodermata, Arthropoda, Annelida, Cnidaria, Chlorophyta, and Rhodophyta) cultured at a single temperature (25°C) and a range of pCO₂ treatments (ca. 409, 606, 903, and 2856 ppm). This dataset was used to explore various controls over elemental partitioning in biogenic marine carbonates, including species-level and biomineralization-pathway-level controls, the influence of internal pH regulation compared to external pH changes, and biocalcification responses to changes in seawater carbonate chemistry. The dataset also enables exploration of broad scale phylogenetic patterns of elemental partitioning across calcifying species, exhibiting high phylogenetic signals estimated from both uni- and multivariate analyses of the elemental ratio data (univariate: λ = 0-0.889; multivariate: λ = 0.895-0.99). Comparing partial R ² values returned from non-phylogenetic and phylogenetic regression analyses echo the importance of and show that phylogeny explains the elemental ratio data 1.4-59 times better than mineralogy in five out of nine of the elements analyzed. Therefore, the strong associations between biomineral elemental chemistry and species relatedness suggests mechanistic controls over element incorporation rooted in the evolution of biomineralization mechanisms.

The spatial network of skeletal proteins in a stony coral

Coral skeletons are materials composed of inorganic aragonitic fibres and organic molecules including proteins, sugars and lipids that are highly organized to form a solid biomaterial upon which the animals live. The skeleton contains tens of proteins, all of which are encoded in the animal genome and secreted during the biomineralization process. While recent advances are revealing the functions and evolutionary history of some of these proteins, how they are spatially arranged in the skeleton is unknown. Using a combination of chemical cross-linking and high-resolution tandem mass spectrometry, we identify, for the first time, the spatial interactions of the proteins embedded within the skeleton of the stony coral Stylophora pistillata. Our subsequent network analysis revealed that several coral acid-rich proteins are invariably associated with carbonic anhydrase(s), alpha-collagen, cadherins and other calcium-binding proteins. These spatial arrangements clearly show that protein-protein interactions in coral skeletons are highly coordinated and are key to understanding the formation and persistence of coral skeletons through time.

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.

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.

Morphological study of fibrous aragonite in the skeletal framework of a stony coral

The overall calcareous skeletons, including a low-crystalline core and surrounding fibrous crystals, of juvenile stony corals were characterized to clarify the entire calcic architecture and the contribution of abiotic processes.

A modern scleractinian coral with a two-component calcite-aragonite skeleton

Until now, all of the ca. 1,800 known modern scleractinian coral species were thought to produce skeletons exclusively of aragonite. Asymbiotic Paraconotrochus antarcticus living in the Southern Ocean is the first example of an extant scleractinian that forms a two-component carbonate skeleton, with an inner structure made of high-Mg calcite and an outer structure composed of aragonite. This discovery adds support to the notion that the coral skeletal formation process is strongly biologically controlled. Mitophylogenomic analysis shows that P. antarcticus represents an ancient scleractinian clade, suggesting that skeletal mineralogy/polymorph of a taxon, once established, is a trait conserved throughout the evolution of that clade.

One of the most conserved traits in the evolution of biomineralizing organisms is the taxon-specific selection of skeletal minerals. All modern scleractinian corals are thought to produce skeletons exclusively of the calcium-carbonate polymorph aragonite. Despite strong fluctuations in ocean chemistry (notably the Mg/Ca ratio), this feature is believed to be conserved throughout the coral fossil record, spanning more than 240 million years. Only one example, the Cretaceous scleractinian coral Coelosmilia (ca. 70 to 65 Ma), is thought to have produced a calcitic skeleton. Here, we report that the modern asymbiotic scleractinian coral Paraconotrochus antarcticus living in the Southern Ocean forms a two-component carbonate skeleton, with an inner structure made of high-Mg calcite and an outer structure composed of aragonite. P. antarcticus and Cretaceous Coelosmilia skeletons share a unique microstructure indicating a close phylogenetic relationship, consistent with the early divergence of P. antarcticus within the Vacatina (i.e., Robusta) clade, estimated to have occurred in the Mesozoic (ca. 116 Mya). Scleractinian corals thus join the group of marine organisms capable of forming bimineralic structures, which requires a highly controlled biomineralization mechanism; this capability dates back at least 100 My. Due to its relatively prolonged isolation, the Southern Ocean stands out as a repository for extant marine organisms with ancient traits.

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.

Aragonite-Polylysine: Neuro-Regenerative Scaffolds with Diverse Effects on Astrogliosis

Biomaterials, especially when coated with adhesive polymers, are a key tool for restorative medicine, being biocompatible and supportive for cell adherence, growth, and function. Aragonite skeletons of corals are biomaterials that support survival and growth of a range of cell types, including neurons and glia. However, it is not known if this scaffold affects neural cell migration or elongation of neuronal and astrocytic processes, prerequisites for initiating repair of damage in the nervous system. To address this, hippocampal cells were aggregated into neurospheres and cultivated on aragonite skeleton of the coral Trachyphyllia geoffroyi (Coral Skeleton (CS)), on naturally occurring aragonite (Geological Aragonite (GA)), and on glass, all pre-coated with the oligomer poly-D-lysine (PDL). The two aragonite matrices promoted equally strong cell migration (4.8 and 4.3-fold above glass-PDL, respectively) and axonal sprouting (1.96 and 1.95-fold above glass-PDL, respectively). However, CS-PDL had a stronger effect than GA-PDL on the promotion of astrocytic processes elongation (1.7 vs. 1.2-fold above glass-PDL, respectively) and expression of the glial fibrillary acidic protein (3.8 vs. and 1.8-fold above glass-PDL, respectively). These differences are likely to emerge from a reaction of astrocytes to the degree of roughness of the surface of the scaffold, which is higher on CS than on GA. Hence, CS-PDL and GA-PDL are scaffolds of strong capacity to derive neural cell movements and growth required for regeneration, while controlling the extent of astrocytic involvement. As such, implants of PDL-aragonites have significant potential as tools for damage repair and the reduction of scar formation in the brain following trauma or disease.

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.

Illumination enhances the protein abundance of sarcoplasmic reticulum Ca2+-ATPases-like transporter in the ctenidium and whitish inner mantle of the giant clam, Tridacna squamosa, to augment exogenous Ca2+ uptake and shell formation, respectively

The fluted giant clam, Tridacna squamosa, can perform light-enhanced shell formation, aided by its symbiotic dinoflagellates (Symbiodinium, Cladocopium, Durusdinium), which are able to donate organic nutrients to the host. During light-enhanced shell formation, increased Ca²⁺ transport from the hemolymph through the shell-facing epithelium of the inner mantle to the extrapallial fluid, where calcification occurs, is necessary. Additionally, there must be increased absorption of exogenous Ca²⁺ from the surrounding seawater, across the epithelial cells of the ctenidium (gill) into the hemolymph, to supply sufficient Ca²⁺ for light-enhanced shell formation. When Ca²⁺ moves across these epithelial cells, the low intracellular Ca²⁺ concentration must be maintained. Sarco(endo)plasmic reticulum Ca²⁺-ATPase (SERCA) regulates the intracellular Ca²⁺ concentration by pumping Ca²⁺ into the sarcoplasmic/endoplasmic reticulum (SR/ER) and Golgi apparatus. Indeed, the ctenidium and inner mantle of T. squamosa, expressed a homolog of SERCA (SERCA-like transporter) that consists of 3009 bp, encoding 1002 amino acids of 110.6 kDa. SERCA-like-immunolabeling was non-uniform in the cytoplasm of epithelial cells of ctenidial filaments, and that of the shell-facing epithelial cells of the inner mantle. Importantly, the protein abundance of SERCA-like increased significantly in the ctenidium and the inner mantle of T. squamosa after 12 h and 6 h, respectively, of light exposure. This would increase the capacity of pumping Ca²⁺ into the endoplasmic reticulum and avert a possible surge in the cytosolic Ca²⁺ concentration in epithelial cells of the ctenidial filaments during light-enhanced Ca²⁺ absorption, and in cells of the shell-facing epithelium of the inner mantle during light-enhanced shell formation.

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.

Caribbean reefs of the Anthropocene: Variance in ecosystem metrics indicates bright spots on coral depauperate reefs

Dramatic coral loss has significantly altered many Caribbean reefs, with potentially important consequences for the ecological functions and ecosystem services provided by reef systems. Many studies examine coral loss and its causes-and often presume a universal decline of ecosystem services with coral loss-rather than evaluating the range of possible outcomes for a diversity of ecosystem functions and services at reefs varying in coral cover. We evaluate 10 key ecosystem metrics, relating to a variety of different reef ecosystem functions and services, on 328 Caribbean reefs varying in coral cover. We focus on the range and variability of these metrics rather than on mean responses. In contrast to a prevailing paradigm, we document high variability for a variety of metrics, and for many the range of outcomes is not related to coral cover. We find numerous "bright spots," where herbivorous fish biomass, density of large fishes, fishery value, and/or fish species richness are high, despite low coral cover. Although it remains critical to protect and restore corals, understanding variability in ecosystem metrics among low-coral reefs can facilitate the maintenance of reefs with sustained functions and services as we work to restore degraded systems. This framework can be applied to other ecosystems in the Anthropocene to better understand variance in ecosystem service outcomes and identify where and why bright spots exist.

Optimization of skeletal protein preparation for LC-MS/MS sequencing yields additional coral skeletal proteins in Stylophora pistillata

Stony corals generate their calcium carbonate exoskeleton in a highly controlled biomineralization process mediated by a variety of macromolecules including proteins. Fully identifying and classifying these proteins is crucial to understanding their role in exoskeleton formation, yet no optimal method to purify and characterize the full suite of extracted coral skeletal proteins has been established and hence their complete composition remains obscure. Here, we tested four skeletal protein purification protocols using acetone precipitation and ultrafiltration dialysis filters to present a comprehensive scleractinian coral skeletal proteome. We identified a total of 60 proteins in the coral skeleton, 44 of which were not present in previously published stony coral skeletal proteomes. Extracted protein purification protocols carried out in this study revealed that no one method captures all proteins and each protocol revealed a unique set of method-exclusive proteins. To better understand the general mechanism of skeletal protein transportation, we further examined the proteins’ gene ontology, transmembrane domains, and signal peptides. We found that transmembrane domain proteins and signal peptide secretion pathways, by themselves, could not explain the transportation of proteins to the skeleton. We therefore propose that some proteins are transported to the skeleton via non-traditional secretion pathways.

A Sub-Micron Spherical Atomic Force Microscopic Tip for Surface Measurements

We report a novel methodology for fabricating a sub-micron spherical atomic force microscope (AFM) tip controllably-a silicon sub-micron sphere atop microcantilevers, which is desired for precise nanoscale tribology measurements, biological studies, and colloid science. Silicon sub-micron spheres are fabricated through swelling of single-crystal silicon with proper high-energy helium ion dosing, a traditionally undesired phenomenon known in helium ion microscopy. Silicon sub-micron spheres with diameters from 100 nm to 1 μm are demonstrated, and the placement of silicon sub-micron spheres can be as accurate as 10 nm or even below. This AFM tip demonstrates robust measurements during friction tests on graphene/silicon oxide substrates for more than 10 000 cycles. This AFM tip overcomes a critical challenge of reducing the size of spherical AFM tips from the micrometer scale to the sub-micron scale and is promising in cross-scale mechanics studies, nanotribology, colloid science, and biology.

Solid-State Phase Transformation and Self-Assembly of Amorphous Nanoparticles into Higher-Order Mineral Structures

Materials science has been informed by nonclassical pathways to crystallization, based on biological processes, about the fabrication of damage-tolerant composite materials. Various biomineralizing taxa, such as stony corals, deposit metastable, magnesium-rich, amorphous calcium carbonate nanoparticles that further assemble and transform into higher-order mineral structures. Here, we examine a similar process in abiogenic conditions using synthetic, amorphous calcium magnesium carbonate nanoparticles. Applying a combination of high-resolution imaging and in situ solid-state nuclear magnetic resonance spectroscopy, we reveal the underlying mechanism of the solid-state phase transformation of these amorphous nanoparticles into crystals under aqueous conditions. These amorphous nanoparticles are covered by a hydration shell of bound water molecules. Fast chemical exchanges occur: the hydrogens present within the nanoparticles exchange with the hydrogens from the surface-bound H₂O molecules which, in turn, exchange with the hydrogens of the free H₂O molecule of the surrounding aqueous medium. This cascade of chemical exchanges is associated with an enhanced mobility of the ions/molecules that compose the nanoparticles which, in turn, allow for their rearrangement into crystalline domains via solid-state transformation. Concurrently, the starting amorphous nanoparticles aggregate and form ordered mineral structures through crystal growth by particle attachment. Sphere-like aggregates and spindle-shaped structures were, respectively, formed from relatively high or low weights per volume of the same starting amorphous nanoparticles. These results offer promising prospects for exerting control over such a nonclassical pathway to crystallization to design mineral structures that could not be achieved through classical ion-by-ion growth.

Common Caribbean corals exhibit highly variable responses to future acidification and warming

We conducted a 93-day experiment investigating the independent and combined effects of acidification (280-3300 µatm pCO₂) and warming (28°C and 31°C) on calcification and linear extension rates of four key Caribbean coral species ( Siderastrea siderea, Pseudodiploria strigosa, Porites astreoides, Undaria tenuifolia) from inshore and offshore reefs on the Belize Mesoamerican Barrier Reef System. All species exhibited nonlinear declines in calcification rate with increasing pCO₂. Warming only reduced calcification in Ps. strigosa. Of the species tested, only S. siderea maintained positive calcification in the aragonite-undersaturated treatment . Temperature and pCO₂ had no effect on the linear extension of S. siderea and Po. astreoides, and natal reef environment did not impact any parameter examined. Results suggest that S. siderea is the most resilient of these corals to warming and acidification owing to its ability to maintain positive calcification in all treatments, Ps. strigosa and U. tenuifolia are the least resilient, and Po. astreoides falls in the middle. These results highlight the diversity of calcification responses of Caribbean corals to projected global change.

In Situ Investigation of Dynamic Silver Crystallization Driven by Chemical Reaction and Diffusion

Rational synthesis of materials is a long-term challenging issue due to the poor understanding on the formation mechanism of material structure and the limited capability in controlling nanoscale crystallization. The emergent in situ electron microscope provides an insight to this issue. By employing an in situ scanning electron microscope, silver crystallization is investigated in real time, in which a reversible crystallization is observed. To disclose this reversible crystallization, the radicals generated by the irradiation of electron beam are calculated. It is found that the concentrations of radicals are spatiotemporally variable in the liquid cell due to the diffusion and reaction of radicals. The fluctuation of the reductive hydrated electrons and the oxidative hydroxyl radicals in the cell leads to the alternative dominance of the reduction and oxidation reactions. The reduction leads to the growth of silver crystals while the oxidation leads to their dissolution, which results in the reversible silver crystallization. A regulation of radical distribution by electron dose rates leads to the formation of diverse silver structures, confirming the dominant role of local chemical concentration in the structure evolution of materials.