A vacuole-like compartment concentrates a disordered calcium phase in a key coccolithophorid alga

The synergistic effect of multiple organic macromolecules on the formation of calcium oxalate raphides of Musa spp

Needle-like calcium oxalate crystals called raphides are unique structures in the plant kingdom. Multiple biomacromolecules work together in the regulatory and transportation pathways to form raphides; however, the mechanism by which this occurs remains unknown. Using banana (Musa spp.), this study combined in vivo methods including confocal microscopy, transmission electron microscopy, and Q Exactive mass spectrometry to identify the main biomolecules, such as vesicles, together with the compositions of lipids and proteins in the crystal chamber, which is the membrane compartment that surrounds each raphide during its formation. Simulations of the vesicle transportation process and the synthesis of elongated calcium oxalate crystals in vitro were then conducted, and the results suggested that the vesicles carrying amorphous calcium oxalate and proteins embedded in raphides are transported along actin filaments. These vesicles subsequently fuse with the crystal chamber, utilizing the proteins embedded in the raphides as a template for the final formation of the structure. Our findings contribute to the fundamental understanding of the regulation of the diverse biomacromolecules that are crucial for raphide formation. Moreover, the implications of these findings extend to other fields such as materials science, and particularly the synthesis of functionalized materials.

Gephyrocapsa huxleyi (Emiliania huxleyi) as a model system for coccolithophore biology

Coccolithophores are the most abundant calcifying organisms in modern oceans and are important primary producers in many marine ecosystems. Their ability to generate a cellular covering of calcium carbonate plates (coccoliths) plays a major role in marine biogeochemistry and the global carbon cycle. Coccolithophores also play an important role in sulfur cycling through the production of the climate-active gas dimethyl sulfide. The primary model organism for coccolithophore research is Emiliania huxleyi, now named Gephyrocapsa huxleyi. G. huxleyi has a cosmopolitan distribution, occupying coastal and oceanic environments across the globe, and is the most abundant coccolithophore in modern oceans. Research in G. huxleyi has identified many aspects of coccolithophore biology, from cell biology to ecological interactions. In this perspective, we summarize the key advances made using G. huxleyi and examine the emerging tools for research in this model organism. We discuss the key steps that need to be taken by the research community to advance G. huxleyi as a model organism and the suitability of other species as models for specific aspects of coccolithophore biology.

Soft X-ray Microscopy in Cell Biology: Current Status, Contributions and Prospects

The recent advances achieved in microscopy technology have led to a significant breakthrough in biological research. Super-resolution fluorescent microscopy now allows us to visualize subcellular structures down to the pin-pointing of the single molecules in them, while modern electron microscopy has opened new possibilities in the study of protein complexes in their native, intracellular environment at near-atomic resolution. Nonetheless, both fluorescent and electron microscopy have remained beset by their principal shortcomings: the reliance on labeling procedures and severe sample volume limitations, respectively. Soft X-ray microscopy is a candidate method that can compensate for the shortcomings of both technologies by making possible observation of the entirety of the cellular interior without chemical fixation and labeling with an isotropic resolution of 40-70 nm. This will thus bridge the resolution gap between light and electron microscopy (although this gap is being narrowed, it still exists) and resolve the issue of compatibility with the former, and possibly in the near future, the latter methods. This review aims to assess the current state of soft X-ray microscopy and its impact on our understanding of the subcellular organization. It also attempts to look into the future of X-ray microscopy, particularly as relates to its seamless integration into the cell biology toolkit.

Correlating cryo-super resolution radial fluctuations and dual-axis cryo-scanning transmission electron tomography to bridge the light-electron resolution gap

Visualization of organelles and their interactions with other features in the native cell remains a challenge in modern biology. We have introduced cryo-scanning transmission electron tomography (CSTET), which can access 3D volumes on the scale of 1 micron with a resolution of nanometers, making it ideal for this task. Here we introduce two relevant advances: (a) we demonstrate the utility of multi-color super-resolution radial fluctuation light microscopy under cryogenic conditions (cryo-SRRF), and (b) we extend the use of deconvolution processing for dual-axis CSTET data. We show that cryo-SRRF nanoscopy is able to reach resolutions in the range of 100 nm, using commonly available fluorophores and a conventional widefield microscope for cryo-correlative light-electron microscopy. Such resolution aids in precisely identifying regions of interest before tomographic acquisition and enhances precision in localizing features of interest within the 3D reconstruction. Dual-axis CSTET tilt series data and application of entropy regularized deconvolution during post-processing results in close-to-isotropic resolution in the reconstruction without averaging. The integration of cryo-SRRF with deconvolved dual-axis CSTET provides a versatile workflow for studying unique objects in a cell.

Locating cellular contents during cryoFIB milling using cellular secondary-electron imaging

Cryo-electron tomography (cryoET) is a powerful technology that allows in-situ observation of the molecular structure of tissues and cells. Cryo-focused ion beam (cryoFIB) milling plays an important role in the preparation of high-quality thin lamellar samples for cryoET studies, thus, promoting the rapid development of cryoET in recent years. However, locating the regions of interest in a large cell or tissue during cryoFIB milling remains a major challenge limiting cryoET applications on arbitrary biological samples. Here, we report an on-the-fly localization method based on cellular secondary electron imaging (CSEI), which is derived from a basic imaging function of the cryoFIB instruments and enables high-contrast imaging of the cellular contents of frozen-hydrated biological samples. Moreover, CSEI does not require fluorescent labels and additional devices. The present study discusses the imaging principles and settings for optimizing CSEI. Tests on several commercially available cryoFIB instruments demonstrated that CSEI was feasible on mainstream instruments to observe all types of cellular contents and reliable under different milling conditions. We established a simple milling-localization workflow and tested it using the basal body of Chlamydomonas reinhardtii.

Formation of Amorphous Iron-Calcium Phosphate with High Stability

Amorphous iron-calcium phosphate (Fe-ACP) plays a vital role in the mechanical properties of teeth of some rodents, which are very hard, but its formation process and synthetic route remain unknown. Here, the synthesis and characterization of an iron-bearing amorphous calcium phosphate in the presence of ammonium iron citrate (AIC) are reported. The iron is distributed homogeneously on the nanometer scale in the resulting particles. The prepared Fe-ACP particles can be highly stable in aqueous media, including water, simulated body fluid, and acetate buffer solution (pH 4). In vitro study demonstrates that these particles have good biocompatibility and osteogenic properties. Subsequently, Spark Plasma Sintering (SPS) is utilized to consolidate the initial Fe-ACP powders. The results show that the hardness of the ceramics increases with the increase of iron content, but an excess of iron leads to a rapid decline in hardness. Calcium iron phosphate ceramics with a hardness of 4 GPa can be achieved, which is higher than that of human enamel. Furthermore, the ceramics composed of iron-calcium phosphates show enhanced acid resistance. This study provides a novel route to prepare Fe-ACP, and presents the potential role of Fe-ACP in biomineralization and as starting material to fabricate acid-resistant high-performance bioceramics.

A joint proteomic and genomic investigation provides insights into the mechanism of calcification in coccolithophores

Coccolithophores are globally abundant, calcifying microalgae that have profound effects on marine biogeochemical cycles, the climate, and life in the oceans. They are characterized by a cell wall of CaCO3 scales called coccoliths, which may contribute to their ecological success. The intricate morphologies of coccoliths are of interest for biomimetic materials synthesis. Despite the global impact of coccolithophore calcification, we know little about the molecular machinery underpinning coccolithophore biology. Working on the model Emiliania huxleyi, a globally distributed bloom-former, we deploy a range of proteomic strategies to identify coccolithogenesis-related proteins. These analyses are supported by a new genome, with gene models derived from long-read transcriptome sequencing, which revealed many novel proteins specific to the calcifying haptophytes. Our experiments provide insights into proteins involved in various aspects of coccolithogenesis. Our improved genome, complemented with transcriptomic and proteomic data, constitutes a new resource for investigating fundamental aspects of coccolithophore biology.

A conventional fixation volume electron microscopy protocol for plants

Volume electron microscopy techniques play an important role in plant research from understanding organelles and unicellular forms to developmental studies, environmental effects and microbial interactions with large plant structures, to name a few. Due to large air voids central vacuole, cell wall and waxy cuticle, many plant tissues pose challenges when trying to achieve high quality morphology, metal staining and adequate conductivity for high-resolution volume EM studies. Here, we applied a robust conventional chemical fixation strategy to address the special challenges of plant samples and suitable for, but not limited to, serial block-face and focused ion beam scanning electron microscopy. The chemistry of this protocol was modified from an approach developed for improved and uniform staining of large brain volumes. Briefly, primary fixation was in paraformaldehyde and glutaraldehyde with malachite green followed by secondary fixation with osmium tetroxide, potassium ferrocyanide, thiocarbohydrazide, osmium tetroxide and finally uranyl acetate and lead aspartate staining. Samples were then dehydrated in acetone with a propylene oxide transition and embedded in a hard formulation Quetol 651 resin. The samples were trimmed and mounted with silver epoxy, metal coated and imaged via serial block-face scanning electron microscopy and focal charge compensation for charge suppression. High-contrast plant tobacco and duckweed leaf cellular structures were readily visible including mitochondria, Golgi, endoplasmic reticulum and nuclear envelope membranes, as well as prominent chloroplast thylakoid membranes and individual lamella in grana stacks. This sample preparation protocol serves as a reliable starting point for routine plant volume electron microscopy.

Direct Visualization and Restoration of Metallic Ion-Induced Subcellular Ultrastructural Remodeling

Analysis of cellular ultrastructure dynamics and metal ions' fate can provide insights into the interaction between living organisms and metal ions. Here, we directly visualize the distribution of biogenic metallic aggregates, ion-induced subcellular reorganization, and the corresponding regulation effect in yeast by the near-native 3D imaging approach, cryo-soft X-ray tomography (cryo-SXT). By comparative 3D morphometric assessment, we observe the gold ions disrupting cellular organelle homeostasis, resulting in noticeable distortion and folding of vacuoles, apparent fragmentation of mitochondria, extreme swelling of lipid droplets, and formation of vesicles. The reconstructed 3D architecture of treated yeast demonstrates ∼65% of Au-rich sites in the periplasm, a comprehensive quantitative assessment unobtained by TEM. We also observe some AuNPs in rarely identified subcellular sites, namely, mitochondria and vesicles. Interestingly, the amount of gold deposition is positively correlated with the volume of lipid droplets. Shifting the external starting pH to near-neutral results in the reversion of changes in organelle architectures, boosting the amount of biogenic Au nanoparticles, and increasing cell viability. This study provides a strategy to analyze the metal ions-living organism interaction from subcellular architecture and spatial localization perspectives.

A. Fernandes T, G. Pascutti P, de Souza W, Miranda K. A spatially resolved elemental nanodomain organization within acidocalcisomes in Trypanosoma cruzi

How are ions distributed in the three-dimensional (3D) volume confined in a nanoscale compartment? Regulation of ionic flow in the intracellular milieu has been explained by different theoretical models and experimentally demonstrated for several compartments with microscale dimensions. Most of these models predict a homogeneous distribution of ions seconds or milliseconds after an initial diffusion step formed at the ion translocation site, leaving open questions when it comes to ion/element distribution in spaces/compartments with nanoscale dimensions. Due to the influence of compartment size on the regulation of ionic flow, theoretical variations of classical models have been proposed, suggesting heterogeneous distributions of ions/elements within nanoscale compartments. Nonetheless, such assumptions have not been fully proven for the 3D volume of an organelle. In this work, we used a combination of cutting-edge electron microscopy techniques to map the 3D distribution of diffusible elements within the whole volume of acidocalcisomes in trypanosomes. Cryofixed cells were analyzed by scanning transmission electron microscopy tomography combined with elemental mapping using a high-performance setup of X-ray detectors. Results showed the existence of elemental nanodomains within the acidocalcisomes, where cationic elements display a self-excluding pattern. These were validated by Pearson correlation analysis and in silico molecular dynamic simulations. Formation of element domains within the 3D space of an organelle is demonstrated. Distribution patterns that support the electrodiffusion theory proposed for nanophysiology models have been found. The experimental pipeline shown here can be applied to a variety of models where ion mobilization plays a crucial role in physiological processes.

Microbial-induced calcium carbonate precipitation: Influencing factors, nucleation pathways, and application in waste water remediation

Microbial-induced calcium carbonate precipitation (MICP) is a technique that uses the metabolic action of microorganisms to produce CO₃^2- which combines with free Ca²⁺ to form CaCO₃ precipitation. It has gained widespread attention in water treatment, aimed with the advantages of simultaneous removal of multiple pollutants, environmental protection, and ecological sustainability. This article reviewed the mechanism of MICP at both intra- and extra-cellular levels. It summarized the parameters affecting the MICP process in terms of bacterial concentration, ambient temperature, etc. The current status of MICP application in practical engineering is discussed. Based on this, the current technical difficulties faced in the use of MICP technology were outlined, and future research directions for MICP technology were highlighted. This review helps to improve the design of existing water treatment facilities for the simultaneous removal of multiple pollutants using the MICP and provides theoretical reference and innovative thinking for related research.

Elemental compositions of sea urchin larval cell vesicles evaluated by cryo-STEM-EDS and cryo-SEM-EDS

During spicule formation in sea urchin larvae, calcium ions translocate within the primary mesenchymal cells (PMCs) from endocytosed seawater vacuoles to various organelles and vesicles where they accumulate, and subsequently precipitate. During this process, calcium ions are concentrated by more than three orders of magnitude, while other abundant ions (Na, Mg) must be removed. To obtain information about the overall ion composition in the vesicles, we used quantitative cryo-SEM-EDS and cryo-STEM-EDS analyzes. For cryo-STEM-EDS, thin (500 nm) frozen hydrated lamellae of PMCs were fabricated using cryo-focused ion beam-SEM. The lamellae were then loaded into a cryo-TEM, imaged and the ion composition of electron dense bodies was measured. Analyzes performed on 18 Ca-rich particles/particle clusters from 6 cells contained Ca, Na, Mg, S and P in different ratios. Surprisingly, all the Ca-rich particles contained P in amounts up to almost 1:1 of Ca. These cryo-STEM-EDS results were qualitatively confirmed by cryo-SEM-EDS analyzes of 310 vesicles, performed on high pressure frozen and cryo-planed samples. We discuss the advantages and limitations of the two techniques, and their potential applicability, especially to study ion transport pathways and ion trafficking in cells involved in mineralization. STATEMENT OF SIGNIFICANCE: The 'inorganic side of life', encompassing ion trafficking and ion storage in soft tissues of organisms, is a generally overlooked problem. Addressing such a problem becomes possible through the application of innovative techniques, performed in cryogenic conditions, which preserve the tissues in quasi-physiological state. We developed here a set of analytical tools, cryo-SEM-EDS, and cryo-STEM-EDS, which allow reconstructing the ion composition inside vesicles in sea urchin larval cells, on their way to deposit mineral in the skeletons. The techniques are complex, and we evaluate here the advantages and disadvantages of each technique. The methodologies that we are developing here can be applied to other cells and other pathways as well, eventually leading to quantitative elemental analyzes of tissues under cryogenic conditions.

Numerical Analysis of the Light Modulation by the Frustule of Gomphonema parvulum: The Role of Integrated Optical Components

Siliceous diatom frustules present a huge variety of shapes and nanometric pore patterns. A better understanding of the light modulation by these frustules is required to determine whether or not they might have photobiological roles besides their possible utilization as building blocks in photonic applications. In this study, we propose a novel approach for analyzing the near-field light modulation by small pennate diatom frustules, utilizing the frustule of Gomphonema parvulum as a model. Numerical analysis was carried out for the wave propagation across selected 2D cross-sections in a statistically representative 3D model for the valve based on the finite element frequency domain method. The influences of light wavelength (vacuum wavelengths from 300 to 800 nm) and refractive index changes, as well as structural parameters, on the light modulation were investigated and compared to theoretical predictions when possible. The results showed complex interference patterns resulting from the overlay of different optical phenomena, which can be explained by the presence of a few integrated optical components in the valve. Moreover, studies on the complete frustule in an aqueous medium allow the discussion of its possible photobiological relevance. Furthermore, our results may enable the simple screening of unstudied pennate frustules for photonic applications.

Inorganic phosphate in growing calcium carbonate abalone shell suggests a shared mineral ancestral precursor

The presence of phosphate from different origins (inorganic, bioorganic) is found more and more in calcium carbonate-based biominerals. Phosphate is often described as being responsible for the stabilization of the transient amorphous calcium carbonate phase. In order to specify the composition of the mineral phase deposited at the onset of carbonated shell formation, the present study investigates, down to the nanoscale, the growing shell from the European abalone Haliotis tuberculata, using a combination of solid state nuclear magnetic resonance, scanning transmission electron microscope and spatially-resolved electron energy loss spectroscopy techniques. We show the co-occurrence of inorganic phosphate with calcium and carbonate throughout the early stages of abalone shell formation. One possible hypothesis is that this first-formed mixed mineral phase represents the vestige of a shared ancestral mineral precursor that appeared early during Evolution. In addition, our findings strengthen the idea that the final crystalline phase (calcium carbonate or phosphate) depends strongly on the nature of the mineral-associated proteins in vivo.

Phosphate involvement in calcium carbonate biominerals raises questions on biomineralisation pathways. Here, the authors explore the presence of phosphate in the growing shell of the European abalone and suggest a shared mixed mineral ancestral precursor with final crystal phase being selected by mineral-associated proteins.

Mantle tissue in the pearl oyster Pinctada fucata secretes immune components via vesicle transportation

Molluscan bivalves secrete shell matrices into the extrapallial space (EPS) to guide the precipitation of rigid shells. Meanwhile, immune components are present in the EPS and shell matrices, which are pivotal in resistant to invaded pathogens, thus ensuring the shell formation process. However, the origin of these components remains unclear. In this study, we revealed numerous vesicles were secreted from the outer mantle epithelial cells by using light and electron microscopes. The secreted vesicles were isolated by gradient centrifugation and confirmed by transmission electron microscopy. Proteomics analysis showed that the secreted vesicles were composed of cytoplasmic and immune components, most of which do not have signal peptides, indicating that they were secreted by a non-classical pathway. Moreover, real-time PCR revealed that some immune components were highly expressed in the mantle tissue, compared to the hemocytes. FTIR analysis verified the presence of lipids in the shell matrices, indicating that the vesicles have integrated into the shell layers. Taken together, our results suggested that mantle epithelial cells secreted some important immune components into the EPS via secreted vesicle transportation, thus cooperating with the hemocytes to play a vital role in immunity during shell formation.

Microfluidic Synthesis and Analysis of Bioinspired Structures Based on CaCO3 for Potential Applications as Drug Delivery Carriers

Naturally inspired biomaterials such as calcium carbonate, produced in biological systems under specific conditions, exhibit superior properties that are difficult to reproduce in a laboratory. The emergence of microfluidic technologies provides an effective approach for the synthesis of such materials, which increases the interest of researchers in the creation and investigation of crystallization processes. Besides accurate tuning of the synthesis parameters, microfluidic technologies also enable an analysis of the process in situ with a range of methods. Understanding the mechanisms behind the microfluidic biomineralization processes could open a venue for new strategies in the development of advanced materials. In this review, we summarize recent advances in microfluidic synthesis and analysis of CaCO₃-based bioinspired nano- and microparticles as well as core-shell structures on its basis. Particular attention is given to the application of calcium carbonate particles for drug delivery.

Ion Pathways in Biomineralization: Perspectives on Uptake, Transport, and Deposition of Calcium, Carbonate, and Phosphate

Minerals are formed by organisms in all of the kingdoms of life. Mineral formation pathways all involve uptake of ions from the environment, transport of ions by cells, sometimes temporary storage, and ultimately deposition in or outside of the cells. Even though the details of how all this is achieved vary enormously, all pathways need to respect both the chemical limitations of ion manipulation, as well as the many "housekeeping" roles of ions in cell functioning. Here we provide a chemical perspective on the biological pathways of biomineralization. Our approach is to compare and contrast the ion pathways involving calcium, phosphate, and carbonate in three very different organisms: the enormously abundant unicellular marine coccolithophores, the well investigated sea urchin larval model for single crystal formation, and the complex pathways used by vertebrates to form their bones. The comparison highlights both common and unique processes. Significantly, phosphate is involved in regulating calcium carbonate deposition and carbonate is involved in regulating calcium phosphate deposition. One often overlooked commonality is that, from uptake to deposition, the solutions involved are usually supersaturated. This therefore requires not only avoiding mineral deposition where it is not needed but also exploiting this saturated state to produce unstable mineral precursors that can be conveniently stored, redissolved, and manipulated into diverse shapes and upon deposition transformed into more ordered and hence often functional final deposits.

Applications of Cryogenic Electron Microscopy in Biomineralization Research

Biological mineralization is a natural process manifested by living organisms in which inorganic minerals crystallize under the scrupulous control of biomolecules, producing hierarchical organic-inorganic composite structures with physical properties and design that galvanize even the most ardent structural engineer and architect. Understanding the mechanisms that control the formation of biominerals is challenging in the biomimetic engineering of hard tissues. In this regard, the contribution of cryogenic electron microscopy (cryo-EM) has been nothing short of phenomenal. By preserving materials in their native hydrated status and reducing damage caused by ion beam radiation, cryo-EM outperforms conventional transmission electron microscopy in its ability to directly observe the morphologic evolution of mineral precursor phases at different stages of biomineralization with nanoscale spatial resolution and subsecond temporal resolution in 2 or 3 dimensions. In the present review, the development and applications of cryo-EM are discussed to support the use of this powerful technique in dental research. Because of the rapid development of cryogenic sample preparation techniques, direct electron detection, and image-processing algorithms, the last decade has witnessed an exponential increase in the use of cryo-EM in structural biology and materials research. By amalgamating with other analytic techniques, cryo-EM may be used for qualitative and quantitative analyses of the kinetics and thermodynamic mechanisms in which organic macromolecules participate in the transformation of mineral precursors from their original liquid state to amorphous and ultimately crystalline phases. The present review concentrates on the biomineralization of calcium phosphate mineral phases, while that of calcium carbonate, silica, and magnetite is only briefly mentioned. Bioinspired organic matrix-mediated inorganic crystallization strategies are discussed from the perspective of tissue regeneration engineering.

Dense intracellular ion pools in unicellular organisms

Uptake and concentration of inorganic ions are part of the complex cellular processes required for cell homeostasis, as well as for mineral formation by organisms. These ion transport mechanisms include distinct cellular compartments and chemical phases that play various roles in the physiology of organisms. Here, the prominent cases of dense ion pools in unicellular organisms are briefly reviewed. The specific observations that were reported for different organisms are consolidated into a wide perspective that emphasizes general traits. It is suggested that the intracellular ion pools can be divided into three types: a high cytoplasmic concentration, a labile storage compartment that hosts dense ion-rich phases, and a mineral-forming compartment in which a stable long-lived structure is formed. Recently, many labile pools were identified in various organisms using advanced techniques, bringing many new questions about their possible roles in the formation of the stable mineralized structures.

Toward Compositional Contrast by Cryo-STEM

Electron microscopy (EM) is the most versatile tool for the study of matter at scales ranging from subatomic to visible. The high vacuum environment and the charged irradiation require careful stabilization of many specimens of interest. Biological samples are particularly sensitive due to their composition of light elements suspended in an aqueous medium. Early investigators developed techniques of embedding and staining with heavy metal salts for contrast enhancement. Indeed, the Nobel Prize in 1974 recognized Claude, de Duve, and Palade for establishment of the field of cell biology, largely due to their developments in separation and preservation of cellular components for electron microscopy. A decade later, cryogenic fixation was introduced. Vitrification of the water avoids the need for dehydration and provides an ideal matrix in which the organic macromolecules are suspended; the specimen represents a native state, suddenly frozen in time at temperatures below -150 °C. The low temperature maintains a low vapor pressure for the electron microscope, and the amorphous nature of the medium avoids diffraction contrast from crystalline ice. Such samples are extremely delicate, however, and cryo-EM imaging is a race for information in the face of ongoing damage by electron irradiation. Through this journey, cryo-EM enhanced the resolution scale from membranes to molecules and most recently to atoms. Cryo-EM pioneers, Dubochet, Frank, and Henderson, were awarded the Nobel Prize in 2017 for high resolution structure determination of biological macromolecules.A relatively untapped feature of cryo-EM is its preservation of composition. Nothing is added and nothing removed. Analytical spectroscopies based on electron energy loss or X-ray emission can be applied, but the very small interaction cross sections conflict with the weak exposures required to preserve sample integrity. To what extent can we interpret quantitatively the pixel intensities in images themselves? Conventional cryo-transmission electron microscopy (TEM) is limited in this respect, due to the strong dependence of the contrast transfer on defocus and the absence of contrast at low spatial frequencies.Inspiration comes largely from a different modality for cryo-tomography, using soft X-rays. Contrast depends on the difference in atomic absorption between carbon and oxygen in a region of the spectrum between their core level ionization energies, the so-called water window. Three dimensional (3D) reconstruction provides a map of the local X-ray absorption coefficient. The quantitative contrast enables the visualization of organic materials without stain and measurement of their concentration quantitatively. We asked, what aspects of the quantitative contrast might be transferred to cryo-electron microscopy?Compositional contrast is accessible in scanning transmission EM (STEM) via incoherent elastic scattering, which is sensitive to the atomic number Z. STEM can be regarded as a high energy, low angle diffraction measurement performed pixel by pixel with a weakly convergent beam. When coherent diffraction effects are absent, that is, in amorphous materials, a dark field signal measures quantitatively the flux scattered from the specimen integrated over the detector area. Learning to interpret these signals will open a new dimension in cryo-EM. This Account describes our efforts so far to introduce STEM for cryo-EM and tomography of biological specimens. We conclude with some thoughts on further developments.

In situ fiducial markers for 3D correlative cryo-fluorescence and FIB-SEM imaging

Imaging of cells and tissues has improved significantly over the last decade. Dual-beam instruments with a focused ion beam mounted on a scanning electron microscope (FIB-SEM), offering high-resolution 3D imaging of large volumes and fields-of-view are becoming widely used in the life sciences. FIB-SEM has most recently been implemented on fully hydrated, cryo-immobilized, biological samples. Correlative light and electron microscopy workflows combining fluorescence microscopy (FM) with FIB-SEM imaging exist, whereas workflows combining cryo-FM and cryo-FIB-SEM imaging are not yet commonly available. Here, we demonstrate that fluorescently labeled lipid droplets can serve as in situ fiducial markers for correlating cryo-FM and FIB-SEM datasets and that this approach can be used to target the acquisition of large FIB-SEM stacks spanning tens of microns under cryogenic conditions. We also show that cryo-FIB-SEM imaging is particularly informative for questions related to organelle structure and inter-organellar contacts, nuclear organization, and mineral deposits in cells.

Calcite as a Precursor of Hydroxyapatite in the Early Biomineralization of Differentiating Human Bone-Marrow Mesenchymal Stem Cells

Biomineralization is the process by which living organisms generate organized mineral crystals. In human cells, this phenomenon culminates with the formation of hydroxyapatite, which is a naturally occurring mineral form of calcium apatite. The mechanism that explains the genesis within the cell and the propagation of the mineral in the extracellular matrix still remains largely unexplained, and its characterization is highly controversial, especially in humans. In fact, up to now, biomineralization core knowledge has been provided by investigations on the advanced phases of this process. In this study, we characterize the contents of calcium depositions in human bone mesenchymal stem cells exposed to an osteogenic cocktail for 4 and 10 days using synchrotron-based cryo-soft-X-ray tomography and cryo-XANES microscopy. The reported results suggest crystalline calcite as a precursor of hydroxyapatite depositions within the cells in the biomineralization process. In particular, both calcite and hydroxyapatite were detected within the cell during the early phase of osteogenic differentiation. This striking finding may redefine most of the biomineralization models published so far, taking into account that they have been formulated using murine samples while studies in human cell lines are still scarce.

Coccolith crystals: Pure calcite or organic-mineral composite structures?

The localization of organic material within biominerals is central to developing biomineral formation mechanisms. Coccoliths, morphologically sophisticated calcite platelets of intracellularly calcifying coccolithophores, are not only eco-physiologically important, but also influence biogeochemical cycles through mass production. Despite their importance and over a century of research, the formation mechanism of coccoliths is still poorly understood. Crucial unsolved questions include the localization of organic material within coccoliths. In extracellular calcifiers the discovery of an organics-containing nano-structure within seemingly single crystals has led to the formulation of a two-step crystallization mechanism. Coccoliths are traditionally thought of as being formed by a different mechanism, but it is unclear whether coccolith crystals possess a nano-structure. Here we review the evidence for and against such a nano-structure. Current SXPD analyses suggest a nano-structure of some kind, while imaging methods (SEM, TEM, AFM) provide evidence against it. We suggest directions for future research which should help solve this puzzle. STATEMENT OF SIGNIFICANCE: Coccolithophores, unicellular calcifying algae, are important primary producers and contribute significantly to pelagic calcium carbonate export. Their calcite platelets, the coccoliths, are amongst the most sophisticated biomineral structures. Understanding the crystallization mechanism of coccolith crystals is not only central to coccolithophore cell biology but also lies at the heart of biomineralization research more generally. The crystallization mechanism of coccoliths has remained largely elusive, not least because it is still an open question whether the micron sized coccolith crystals are pure calcite, or contain organic material. Here we review the state of the art and suggest a way to solve this central problem.

Exploring Intracellular Ion Pools in Coccolithophores Using Live-Cell Imaging

Some microorganisms, such as coccolithophores, produce an intricate exoskeleton made of inorganic solids. Coccoliths, the calcium carbonate scales of coccolithophores, are examples of the precise bioproduction of such complex 3D structures. However, the understanding of the cellular mechanisms that control mineral formation inside the cell, specifically the ability of these microalgae to transport high fluxes of inorganic building blocks, is still limited. Recently, using cryo-electron and X-ray microscopy, several intracellular compartments are shown to store high concentrations of calcium and phosphorous and are suggested to have a dominant role in the intracellular mineralization pathway. Here, live-cell confocal microscopy and fluorescent markers are used to examine the dynamics of ion stores in coccolithophores. Using calcein and 4',6-diamidino-2-phenylindole (DAPI) as fluorescent proxies for calcium and polyphosphates, the experiments reveal an unexpected plethora of organelles with distinct fluorescent signatures over a wide range of strains and conditions. Surprisingly, the fluorescent labeling does not show changes along the calcification process and is similar between calcifying and noncalcifying cells, suggesting that these ion pools may not be a dynamic avenue for calcium transport. In such a case, the enigma behind the ability of coccolithophores to sustain intracellular calcification still awaits comprehensive elucidation.

Micropearls and other intracellular inclusions of amorphous calcium carbonate: an unsuspected biomineralization capacity shared by diverse microorganisms

An unsuspected biomineralization process, which produces intracellular inclusions of amorphous calcium carbonate (ACC), was recently discovered in unicellular eukaryotes. These mineral inclusions, called micropearls, can be highly enriched with other alkaline‐earth metals (AEM) such as Sr and Ba. Similar intracellular inclusions of ACC have also been observed in prokaryotic organisms. These comparable biomineralization processes involving phylogenetically distant microorganisms are not entirely understood yet. This review gives a broad vision of the topic in order to establish a basis for discussion on the possible molecular processes behind the formation of the inclusions, their physiological role, the impact of these microorganisms on the geochemical cycles of AEM and their evolutionary relationship. Finally, some insights are provided to guide future research.

Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging

Eukaryotic phytoplankton have a small global biomass but play major roles in primary production and climate. Despite improved understanding of phytoplankton diversity and evolution, we largely ignore the cellular bases of their environmental plasticity. By comparative 3D morphometric analysis across seven distant phytoplankton taxa, we observe constant volume occupancy by the main organelles and preserved volumetric ratios between plastids and mitochondria. We hypothesise that phytoplankton subcellular topology is modulated by energy-management constraints. Consistent with this, shifting the diatom Phaeodactylum from low to high light enhances photosynthesis and respiration, increases cell-volume occupancy by mitochondria and the plastid CO₂-fixing pyrenoid, and boosts plastid-mitochondria contacts. Changes in organelle architectures and interactions also accompany Nannochloropsis acclimation to different trophic lifestyles, along with respiratory and photosynthetic responses. By revealing evolutionarily-conserved topologies of energy-managing organelles, and their role in phytoplankton acclimation, this work deciphers phytoplankton responses at subcellular scales.

Coccolithophore calcification: Changing paradigms in changing oceans

Coccolithophores represent a major component of the marine phytoplankton and contribute to the bulk of biogenic calcite formation on Earth. These unicellular protists produce minute calcite scales (coccoliths) within the cell, which are secreted to the cell surface. Individual coccoliths and their arrangements on the cell surface display a wide range of morphological variations. This review explores some of the recent evidence that points to similarities and differences in the mechanisms of calcification, focussing on the transport mechanisms that bring substrates to, and remove products from the site of calcification, together with new findings on factors that regulate coccolith morphology. We argue that better knowledge of these mechanisms and their variations is needed to inform more generally how different species of coccolithophore are likely to respond to changes in ocean chemistry. STATEMENT OF SIGNIFICANCE: Coccolithophores, minute single celled phytoplankton are the major producers of biogenic carbonate on Earth. They also represent an important component of the ocean's biota and contribute significantly to global carbon fluxes. Coccolithophores produce intricate calcite scales (coccoliths) internally that they secrete onto their external surface. This review presents some recent key findings on the mechanisms underlying the production of coccoliths. It also considers the factors that regulate the rate of production as well as the variety of shapes of individual coccoliths and their arrangements at the cell surface. Understanding these processes is needed to allow better predictions of how coccolithophores may respond to changing ocean chemistry associated with climate change.

Cellular pathways of calcium transport and concentration toward mineral formation in sea urchin larvae

Sea urchin larvae have an endoskeleton consisting of two calcitic spicules. The primary mesenchyme cells (PMCs) are the cells that are responsible for spicule formation. PMCs endocytose sea water from the larval internal body cavity into a network of vacuoles and vesicles, where calcium ions are concentrated until they precipitate in the form of amorphous calcium carbonate (ACC). The mineral is subsequently transferred to the syncytium, where the spicule forms. Using cryo-soft X-ray microscopy we imaged intracellular calcium-containing particles in the PMCs and acquired Ca-L2,3 X-ray absorption near-edge spectra of these Ca-rich particles. Using the prepeak/main peak (L2'/ L2) intensity ratio, which reflects the atomic order in the first Ca coordination shell, we determined the state of the calcium ions in each particle. The concentration of Ca in each of the particles was also determined by the integrated area in the main Ca absorption peak. We observed about 700 Ca-rich particles with order parameters, L2'/ L2, ranging from solution to hydrated and anhydrous ACC, and with concentrations ranging between 1 and 15 M. We conclude that in each cell the calcium ions exist in a continuum of states. This implies that most, but not all, water is expelled from the particles. This cellular process of calcium concentration may represent a widespread pathway in mineralizing organisms.

Precipitation of Calcium Carbonate Inside Giant Unilamellar Vesicles Composed of Fluid-Phase Lipids

Biomineralization of CaCO₃ commonly involves the formation of amorphous CaCO₃ precursor particles that are produced in a confined space surrounded by a lipid bilayer. While the influence of confinement itself has been investigated with different model systems, the impact of an enclosing continuous lipid bilayer on CaCO₃ formation in a confined space is still poorly understood as appropriate model systems are rare. Here, we present a new versatile method based on droplet-based microfluidics to produce fluid-phase giant unilamellar vesicles (GUVs) in the presence of high CaCl₂ concentrations. These GUVs can be readily investigated by means of confocal laser scanning microscopy in combination with bright-field microscopy, demonstrating that the formed CaCO₃ particles are in conformal contact with the fluid-phase lipid bilayer and thus suggesting a strong interaction between the particle and the membrane. Atomic force microscopy adhesion studies with membrane-coated spheres on different CaCO₃ crystals corroborated this notion of a strong interaction between the lipids and CaCO₃.

Serial cryoFIB/SEM Reveals Cytoarchitectural Disruptions in Leigh Syndrome Patient Cells

The advancement of serial cryoFIB/SEM offers an opportunity to study large volumes of near-native, fully hydrated frozen cells and tissues at voxel sizes of 10 nm and below. We explored this capability for pathologic characterization of vitrified human patient cells by developing and optimizing a serial cryoFIB/SEM volume imaging workflow. We demonstrate profound disruption of subcellular architecture in primary fibroblasts from a Leigh syndrome patient harboring a disease-causing mutation in USMG5 protein responsible for impaired mitochondrial energy production.

•

Developed and optimized a serial cryoFIB/SEM volume imaging workflow

•

Visualized the 3D structure of an entire cell under native conditions

•

Revealed a disruption of cellular structures in primary LS patient fibroblasts

•

Demonstrated the potential for clinical phenotyping of pathogenic tissues

Imaging and quantifying homeostatic levels of intracellular silicon in diatoms

Diatoms are an abundant group of microalgae, known for their ability to form an intricate cell wall made of silica. Silicon levels in seawater are in the micromolar range, making it a challenge for diatoms to supply the rapid intracellular silicification process with the needed flux of soluble silicon. Here, we use three-dimensional cryo-electron microscopy and spectroscopy to quantitatively analyze, at submicrometer spatial resolution and sensitivity in the millimolar range, intracellular silicon in diatom cells. Our results show that the internal silicon concentration inside the cell is ~150 mM in average, three orders of magnitude higher than the external environment. The cellular silicon content is not compartmentalized, but rather unevenly distributed throughout the cell. Unexpectedly, under silicon starvation, the internal silicon pool is not depleted, reminiscent of a constitutive metabolite. Our spatially resolved approach to analyze intracellular silicon opens avenues to investigate this homeostatic trait of diatoms.

Association of Phosphatidylinositol-Specific Phospholipase C with Calcium-Induced Biomineralization in the Coccolithophore Emiliania huxleyi

Biomineralization by calcifying microalgae is a precisely controlled intracellular calcification process that produces delicate calcite scales (or coccoliths) in the coccolithophore Emiliania huxleyi (Haptophycea). Despite its importance in biogeochemical cycles and the marine environment globally, the underlying molecular mechanism of intracellular coccolith formation, which requires calcium, bicarbonate, and coccolith-polysaccharides, remains unclear. In E. huxleyi CCMP 371, we demonstrated that reducing the calcium concentration from 10 (ambient seawater) to 0.1 mM strongly restricted coccolith production, which was then recovered by adding 10 mM calcium, irrespective of inorganic phosphate conditions, indicating that coccolith production could be finely controlled by the calcium supply. Using this strain, we investigated the expression of differentially expressed genes (DEGs) to observe the cellular events induced by changes in calcium concentrations. Intriguingly, DEG analysis revealed that the phosphatidylinositol-specific phospholipase C (PI-PLC) gene was upregulated and coccolith production by cells was blocked by the PI-PLC inhibitor U73122 under conditions closely associated with calcium-induced calcification. These findings imply that PI-PLC plays an important role in the biomineralization process of the coccolithophore E. huxleyi.

Pelagic Sargassum spp. capture CO2 and produce calcite

Pelagic Sargassum is considered an ecological plague that is causing adverse economic impacts to the tourist and fishing industries in the Caribbean. However, its proliferation might be playing an important role to reduce global warming, as it removes a high content of CO2 from the atmosphere and transforms it into calcium carbonate, in its calcite phase, producing sediment after it dies. We quantified the amount of calcite in Sargassum samples collected from the Mexican Caribbean coast in 2019. Samples were divided into three parts: vesicles, thallus, and leaves. In each part, the amount of carbon, oxygen, and calcium was determined by means of X-ray energy dispersion to confirm the existence of a calcite crystalline phase. Imaging methodologies and IR spectroscopy complemented the structural studies. The thermogravimetric analysis determined that approximately 5% of the CO2 captured by the Sargassum was converted into calcite. Thus, by extrapolation, the Atlantic Sargasso Belt retained approximately 19.3 million tons of CO2 from 2011 to 2019.

High resolution spatial analyses of trace elements in coccoliths reveal new insights into element incorporation in coccolithophore calcite

Coccolithophores are phytoplanktonic algae which produce an exoskeleton made of single platelets of calcite named coccoliths. They are widespread in all oceans and directly impact the short- and long-term C cycle. The study of coccolith size, morphology and elemental composition reveals important information regarding the ability of the cell to calcify and on the factors that influence this process. In this regard, very little is known about coccolith composition and its changes under altered environmental conditions. Here, we present high resolution (50 × 50 nm) elemental spatial distribution in pristine coccoliths of Coccolithus pelagicus and Gephyrocapsa oceanica reconstructed via X-ray fluorescence analyses at synchrotron. The studied specimens are from control culture and metal-enriched (V, Ni, Zn and Pb) experiments. The analysed specimens produced under stress conditions, display an irregular shape and are thinner, especially in the external rim, with ca. 1/3 lower Ca concentrations compared to specimens from the control. The same specimens also have higher Sr/Ca ratio with highest values in the coccolith external rim, suggesting that difficulty in calcification is additionally reflected in increased Sr/Ca ratios. Selenium is found in the coccolith as possible substitute of carbonate in the calcite. V and Pb apparently did not interact with the coccoliths while Zn and Ni were deposited on the coccolith surface.

Microbe-Mediated Extracellular and Intracellular Mineralization: Environmental, Industrial, and Biotechnological Applications

Microbe-mediated mineralization is ubiquitous in nature, involving bacteria, fungi, viruses, and algae. These mineralization processes comprise calcification, silicification, and iron mineralization. The mechanisms for mineral formation include extracellular and intracellular biomineralization. The mineral precipitating capability of microbes is often harnessed for green synthesis of metal nanoparticles, which are relatively less toxic compared with those synthesized through physical or chemical methods. Microbe-mediated mineralization has important applications ranging from pollutant removal and nonreactive carriers, to other industrial and biomedical applications. Herein, the different types of microbe-mediated biomineralization that occur in nature, their mechanisms, as well as their applications are elucidated to create a backdrop for future research.

Cryo-FIB-SEM as a promising tool for localizing proteins in 3D

Focused Ion Beam-Scanning Electron Microscopy (FIB-SEM) is an invaluable tool to visualize the 3D architecture of cell constituents and map cell networks. Recently, amorphous ice embedding techniques have been associated with FIB-SEM to ensure that the biological material remains as close as possible to its native state. Here we have vitrified human HeLa cells and directly imaged them by cryo-FIB-SEM with the secondary electron InLens detector at cryogenic temperature and without any staining. Image stacks were aligned and processed by denoising, removal of ion beam milling artefacts and local charge imbalance. Images were assembled into a 3D volume and the major cell constituents were modelled. The data illustrate the power of the workflow to provide a detailed view of the internal architecture of the fully hydrated, close-to-native, entire HeLa cell. In addition, we have studied the feasibility of combining cryo-FIB-SEM imaging with live-cell protein detection. We demonstrate that internalized gold particles can be visualized by detecting back scattered primary electrons at low kV while simultaneously acquiring signals from the secondary electron detector to image major cell features. Furthermore, gold-conjugated antibodies directed against RNA polymerase II could be observed in the endo-lysosomal pathway while labelling of the enzyme in the nucleus was not detected, a shortcoming likely due to the inadequacy between the size of the gold particles and the voxel size. With further refinements, this method promises to have a variety of applications where the goal is to localize cellular antigens while visualizing the entire native cell in three dimensions.

In Vivo Shaping of Inorganic Functional Devices using Microalgae

The usage of biomineralization processes performed by living microalgae to create 3D nanostructured materials are advantageous compared to conventional synthesis routes. Exploitation of in vivo shaping using living cells leads to inorganic intricate biominerals, produced with low environmental impact. Since biomineralization processes are genetically controlled, the formation of nanostructured materials is highly reproducible. The shells of microalgae, like coccoliths, are particularly of great interest. This study shows the generation of mesoporous highly structured functional materials with induced optoelectronical properties using in vivo processes of the microalga species Emiliania huxleyi. It demonstrates the metabolically driven incorporation of the lanthanide terbium into the coccoliths of E. huxleyi as a route for the synthesis of finely patterned photoluminescent particles by feeding the microalgae with this luminescent element. The resulting green luminescent particles have hierarchical ordered pores on the nano- and microscale and may act as powerful tools for many applications; they may serve as imaging probes for biomedical applications, or in microoptics. The luminescent coccoliths combine a unique hierarchical structure with a characteristic luminescence pattern, which make them superior to conventional produced Tb doted material. With this study, the possibility of the further exploitation of coccoliths as advanced functional materials for nanotechnological applications is given.

Across the spectrum: integrating multidimensional metal analytics for in situ metallomic imaging

To know how much of a metal species is in a particular location within a biological context at any given time is essential for understanding the intricate roles of metals in biology and is the fundamental question upon which the field of metallomics was born. Simply put, seeing is powerful. With the combination of spectroscopy and microscopy, we can now see metals within complex biological matrices complemented by information about associated molecules and their structures. With the addition of mass spectrometry and particle beam based techniques, the field of view grows to cover greater sensitivities and spatial resolutions, addressing structural, functional and quantitative metallomic questions from the atomic level to whole body processes. In this perspective, I present a paradigm shift in the way we relate to and integrate current and developing metallomic analytics, highlighting both familiar and perhaps less well-known state of the art techniques for in situ metallomic imaging, specific biological applications, and their use in correlative studies. There is a genuine need to abandon scientific silos and, through the establishment of a metallomic scientific platform for further development of multidimensional analytics for in situ metallomic imaging, we have an incredible opportunity to enhance the field of metallomics and demonstrate how discovery research can be done more effectively.

Biomineral Precursor Formation Is Initiated by Transporting Calcium and Phosphorus Clusters from the Endoplasmic Reticulum to Mitochondria

Mineral granules in the mitochondria of bone-forming cells are thought to be the origin of biomineral precursors, which are transported to extracellular matrices to initiate cell-mediated biomineralization. However, no evidence has revealed how mitochondrial granules form. This study indicates that mitochondrial granules are initiated by transporting calcium and phosphorus clusters from the endoplasmic reticulum (ER) to mitochondria based on detailed observations of the continuous process of mouse parietal bone development as well as in vitro biomineralization in bone-forming cells. Nanosized biomineral precursors (≈30 nm in diameter), which originate from mitochondrial granules, initiate intrafibrillar mineralization of collagen as early as embryonic day 14.5. Both in vivo and in vitro studies further reveal that formation of mitochondrial granules is induced by the ER. Elevated levels of intracellular calcium or phosphate ions, which can be induced by treatment with ionomycin and black phosphorus, respectively, accelerate formation of the calcium and phosphorus clusters on ER membranes and ultimately promote biomineralization. These findings provide a novel insight into biomineralization and bone formation.

Fully automated, sequential focused ion beam milling for cryo-electron tomography

Cryo-electron tomography (cryoET) has become a powerful technique at the interface of structural biology and cell biology, due to its unique ability for imaging cells in their native state and determining structures of macromolecular complexes in their cellular context. A limitation of cryoET is its restriction to relatively thin samples. Sample thinning by cryo-focused ion beam (cryoFIB) milling has significantly expanded the range of samples that can be analyzed by cryoET. Unfortunately, cryoFIB milling is low-throughput, time-consuming and manual. Here, we report a method for fully automated sequential cryoFIB preparation of high-quality lamellae, including rough milling and polishing. We reproducibly applied this method to eukaryotic and bacterial model organisms, and show that the resulting lamellae are suitable for cryoET imaging and subtomogram averaging. Since our method reduces the time required for lamella preparation and minimizes the need for user input, we envision the technique will render previously inaccessible projects feasible.

Biomineralization pathways in calcifying dinoflagellates: Uptake, storage in MgCaP-rich bodies and formation of the shell

Little is known about shell formation of calcareous dinoflagellates, despite the fact that they are one of the major calcifying organisms of the phytoplankton. Here, calcitic cyst formation in two representative members of calcareous dinoflagellates is investigated using cryo-electron microscopy (cryo-SEM and cryo-FIB-SEM) in combination with micro-Raman and infrared spectroscopy. Only calcein-AM and not calcein enters these cells, indicating active uptake of calcium and other divalent cations. Multifunctional vacuoles containing crystalline inclusions are observed, and the crystals are identified as anhydrous guanine in the β-form. The same vacuolar enclosures contain dense magnesium-, calcium-, and phosphorous-rich mineral bodies. These bodies are presumably secreted into the outer matrix where calcite forms. Calcite formation occurs via multiple independent nucleation events, and the different crystals grow with preferred orientation into a dense reticular network that forms the mature calcitic shell. We suggest a biomineralization pathway for calcareous dinoflagellates that includes (1) active uptake of calcium through the membranes, (2) deposition of Mg²⁺- and Ca²⁺-ions inside disordered MgCaP-rich mineral bodies, (3) secretion of these bodies to the inter-membrane space, and (4) Formation and growth of calcite into a dense reticulate network. This study provides new insights into calcium uptake, storage and transport in calcifying dinoflagellates. STATEMENT OF SIGNIFICANCE: Little is known about the shell formation of calcareous dinoflagellates, despite the fact that they are one of the major calcifying organisms of the phytoplankton. We used state-of-the-art cryo-electron microscopy (cryo-SEM and cryo-FIB-SEM) in combination with micro-Raman spectroscopy to provide new insights into mineral formation in calcifying dinoflagellates. To date, intracellular crystalline calcite was assumed to be involved in calcite shell formation. Surprisingly, we identify these crystalline inclusions as anhydrous guanine suggesting that they are not involved in biomineralization. Instead, a key finding is that MgCaP-rich bodies are probably secreted into the outer matrix where the calcite shell is formed. We suggest that these bodies are an essential part of Ca-uptake, -storage and -transport and propose a new biomineralization model.

Mineralized scale patterns on the cell periphery of the chrysophyte Mallomonas determined by comparative 3D Cryo-FIB SEM data processing

Unicellular protists can biomineralize spatially complex and functional shells. A typical cell of the photosynthetic synurophyte Mallomonas is covered by about 60-100 silica scales. Their geometric arrangement, the so-called scale case, mainly depends on the species and on the cell cycle. In this study, the scale case of the synurophyte Mallomonas was preserved in aqueous suspension using high-pressure freezing (HPF). From this specimen, a three-dimensional (3D) data set spanning a volume of about 25.6 μm × 19.2 μm × 4.2 μm with a voxel size of 12.5 nm × 12.5 nm × 25.0 nm was collected by Cryo-FIB SEM in 3 h and 24 min. SEM imaging using In-lens SE detection allowed to clearly differentiate between mineralized, curved scales of less than 0.2 μm thickness and organic cellular ultrastructure or vitrified ice. The three-dimensional spatial orientations and shapes of a minimum set of scales (N = 13) were identified by visual inspection, and manually segmented. Manual and automated segmentation approaches were comparatively applied to one arbitrarily selected reference scale using the differences in grey level between scales and other constituents. Computational automated routines and principal component analysis of the experimentally extracted data created a realistic mathematical model based on the Fibonacci pattern theory. A complete in silico scale case of Mallomonas was reconstructed showing an optimized scale coverage on the cell surface, similarly as it was observed experimentally. The minimum time requirements from harvesting the living cells to the final scale case determination by Cryo-FIB SEM and computational image processing are discussed.