Salinity-dependent diatom biosilicification implies an important role of external ionic strength

Enhancement of hemostatic properties of Cyclotella cryptica frustule through genetic manipulation

BACKGROUND

The silicified cell wall of diatoms, also known as frustule, shows huge potential as an outstanding bio-nanomaterial for hemostatic applications due to its high hemostatic efficiency, good biocompatibility, and ready availability. As the architectural features of the frustule determine its hemostatic performance, it is of great interest to develop an effective method to modify the frustule morphology into desired patterns to further improve hemostatic efficiency.

RESULTS

In this study, the gene encoding Silicalemma Associated Protein 2 (a silicalemma-spanning protein) of Cyclotella cryptica (CcSAP2) was identified as a key gene in frustule morphogenesis. Thus, it was overexpressed and knocked down, respectively. The frustule of the overexpress lines showed no obvious alteration in morphology compared to the wild type (WT), while the size, specific surface area (BET), pore volume, and pore diameter of the knockdown strains changed greatly. Particularly, the knockdown frustules achieved a more pronounced coagulation effect and in vivo hemostatic performance than the WT strains. Such observations suggested that silicalemma proteins are ideal genetic encoding targets for manipulating frustule morphology associated hemostatic properties. Furthermore, the Mantel test was adopted to identify the key morphologies associated with C. cryptica bleeding control. Finally, based on our results and recent advances, the mechanism of frustule morphogenesis was discussed.

CONCLUSION

This study explores a new strategy for enhancing the hemostatic efficiency of the frustule based on genetic morphology modification and may provide insights into a better understanding of the frustule morphogenesis mechanism.

A novel effective bio-originated methylene blue adsorbent: the porous biosilica from three marine diatom strains of Nanofrustulum spp. (Bacillariophyta)

In the present paper, for the first time the ability of the porous biosilica originated from three marine diatom strains of 'Nanofrustulum spp.' viz. N. wachnickianum (SZCZCH193), N. shiloi (SZCZM1342), N. cf. shiloi (SZCZP1809), to eliminate MB from aqueous solutions was investigated. The highest biomass was achieved under silicate enrichment for N. wachnickianum and N. shiloi (0.98 g L-1 DW and 0.93 g L-1 DW respectively), and under 15 °C for N. cf. shiloi (2.2 g L-1 DW). The siliceous skeletons of the strains were purified with hydrogen peroxide and characterized by SEM, EDS, the N2 adsorption/desorption, XRD, TGA, and ATR-FTIR. The porous biosilica (20 mg DW) obtained from the strains i.e. SZCZCH193, SZCZM1342, SZCZP1809, showed efficiency in 77.6%, 96.8%, and 98.1% of 14 mg L-1 MB removal under pH 7 for 180 min, and the maximum adsorption capacity was calculated as 8.39, 19.02, and 15.17 mg g-1, respectively. Additionally, it was possible to increase the MB removal efficiency in alkaline (pH = 11) conditions up to 99.08% for SZCZP1809 after 120 min. Modelling revealed that the adsorption of MB follows Pseudo-first order, Bangham's pore diffusion and Sips isotherm models.

Removal of the Basic and Diazo Dyes from Aqueous Solution by the Frustules of Halamphora cf. salinicola (Bacillariophyta)

Industrial wastes with hazardous dyes serve as a major source of water pollution, which is considered to have an enormous impact on public health. In this study, an eco-friendly adsorbent, the porous siliceous frustules extracted from the diatom species Halamphora cf. salinicola, grown under laboratory conditions, has been identified. The porous architecture and negative surface charge under a pH of 7, provided by the various functional groups via Si-O, N-H, and O-H on these surfaces, revealed by SEM, the N₂ adsorption/desorption isotherm, Zeta-potential measurement, and ATR-FTIR, respectively, made the frustules an efficient mean of removal of the diazo and basic dyes from the aqueous solutions, 74.9%, 94.02%, and 99.81% against Congo Red (CR), Crystal Violet (CV), and Malachite Green (MG), respectively. The maximum adsorption capacities were calculated from isotherms, as follows: 13.04 mg g^-1, 41.97 mg g^-1, and 33.19 mg g^-1 against CR, CV, and MG, respectively. Kinetic and isotherm models showed a higher correlation to Pore diffusion and Sips models for CR, and Pseudo-Second Order and Freundlich models for CV and MG. Therefore, the cleaned frustules of the thermal spring-originated diatom strain Halamphora cf. salinicola could be used as a novel adsorbent of a biological origin against anionic and basic dyes.

Integrative effects of morphology, silicification, and light on diatom vertical movements

Diatoms represent the most abundant and diversified class of primary producers in present oceans; their distinctive trait is the ability to incorporate silicic acid in a silica outer shell called frustule. Numerous adaptative functions are ascribed to frustules, including the control of vertical movements through the water column; this indirectly determines cell access to fundamental resources such as light and nutrients, and favors diatom escape from predators. At the same time, light guides phototroph movements in the water column by affecting cell density (e.g., by modulating Si deposition in diatoms, vacuole volume, and/or solution). We investigated how the tremendous diversity in morphology and silicification that characterizes the frustule and the crucial role of light in diatom spatial distribution govern diatom sinking capacity. To test their integrative effects, we acclimated four diatoms distinguished by frustule traits (Chaetoceros muelleri, Conticribra weissflogii, Phaeodactylum tricornutum, and Cylindrotheca fusiformis) to different light conditions and evaluated their physiological performance in terms of growth, elemental composition, morphological changes, and their in vivo sinking capacity. What emerged from this study was that silicification, more than other morphological characteristics, controls species vertical movements, while a higher energy availability enhances cell floating independently from the silica content.

Computational modelling of diatom silicic acid transporters predicts a conserved fold with implications for their function and evolution

Diatoms are an important group of algae that can produce intricate silicified cell walls (frustules). The complex process of silicification involves a set of enigmatic integral membrane proteins that are thought to actively transport the soluble precursor of biosilica, dissolved silicic acid. Full-length silicic acid transporters are found widely across the diatoms while homologous shorter proteins have now been identified in a range of other organisms. It has been suggested that modern silicic acid transporters arose from the union of such partial sequences. Here, we present a computational study of the silicic acid transporters and related transporter-like sequences to help understand the structure, function and evolution of this class of membrane protein. The AlphaFold software predicts that all of the protein sequences studied here share a common fold in the membrane domain which is entirely different from the predicted folds of non-homologous silicic acid transporters from plants. Substrate docking reveals how conserved polar residues could interact with silicic acid at a central solvent-accessible binding site, consistent with an alternating access mechanism of transport. The structural conservation between these proteins supports a model where modern silicon transporters evolved from smaller ancestral proteins by gene fusion.

Morphological plasticity in response to salinity change in the euryhaline diatom Pleurosira laevis (Bacillariophyta)

Pleurosira laevis is a salt-tolerant diatom distributed around the world. The valve of P. laevis has distinct structures called ocelli, which are sharply defined areas with fine, densely packed pores. Two formae of this diatom, P. laevis f. laevis and P. laevis f. polymorpha, are distinguished from each other by their flat or dome-shaped valve faces and degree of elevation of the ocelli, respectively. In this study, we established 4 strains of P. laevis isolated from freshwaters or coastal areas in Japan and the United States, and tracked the formation of newly formed valves with the fluorescent SDV-specific dye PDMPO in culture under several salinity conditions. The result clearly demonstrated the morphological plasticity of the valves, controlled by environmental salinity. The laevis form and polymorpha form valves were produced at salinities of 2 and 7, respectively. The salinity thresholds dictating the morphological plasticity of the valve were consistent in all 4 strains. A similar morphology to the polymorpha form was reproduced in a freshwater medium with the addition of sorbitol, suggesting that osmotic pressure plays a key role in this morphological plasticity. The highly reproducible and easily manipulated change in morphology makes this diatom an ideal model for lab experiments focusing on the molecular and genetic factors involved with valve morphogenesis.

Solids retention time dependent, tunable diatom hierarchical micro/nanostructures and their effect on nutrient removal

The hierarchical three-dimensional (3D) micro/nanostructures of diatoms make them a promising biomaterial for fabricating nanomaterials, producing bioactive pharmaceuticals or nutraceuticals, and removing micropollutants. For diatom production in a continuous flow system, little is known how bioreactor operating parameters, especially solids retention time (SRT), affect the 3D structures of diatoms. This study demonstrated that tunable diatom micro/nanostructures could be produced by varying the SRT of membrane bioreactors (MBRs). A diatom strain (Stephanodiscus hantzschii) was cultivated in two identical MBRs with a fixed hydraulic retention time (HRT) of 24 h and staged SRTs from 5, to 10, and to 20 d. As SRTs increased from 5 to 20 d, important characteristics of diatom micro/nanostructures showed linear decreases: the diameters of foramina on the areola layer decreased from 170 ± 10 to 130 ± 12 nm, the numbers of nanopores per cribrum layer decreased from 20 ± 3 to 12 ± 2, and the specific surface areas of the diatoms decreased from 36.01 ± 1.27 to 12.67 ± 2.45 m²·g^-1. However, the average diatom heights increased from 2.9 ± 0.3 to 3.9 ± 0.4 µm, while diatom cell diameter (5 µm) and nanopore size (20 nm) remained unchanged. The silicon content of diatoms also linearly increased with SRT. The decrease in diatom porosity and increase in silicon content were probably due to the reduced diatom growth rates (likely resulting in less pores) at increasing SRTs, which also facilitated silica deposition as the overall diatom population stayed longer in the MBRs. As the SRTs increased from 5 to 10, and to 20 d, the nitrate (NO₃^-) removal efficiency decreased from 75% to 70%, and to 60%, respectively, whereas phosphorus (P) removal efficiency increased from 74% to 80%, and to 90%, respectively. The opposite trends in efficiencies were because NO₃^--N was removed by cellular uptake and biomass waste whereas P was mainly removed through diatom-assisted chemical precipitation.

Fractal-like R5 assembly promote the condensation of silicic acid into silica particles

HYPOTHESIS

Despite advances in understanding the R5 (SSKKSGSYSGKSGSKRRIL) peptide-driven bio-silica process, there remains significant discrepancies regarding the physicochemical characterization and the self-assembling mechanistic driving forces of the supramolecular R5 template. This paper investigates the self-assembly of R5 as a function of monovalent (sodium chloride) and multivalent salt (phosphate) to determine if assembly is phosphate ion concentration dependent. Additionally, we hypothesize that the assembled R5 aggregates do not resemble a micelle or unimer structure as proposed in current literature.

EXPERIMENTS

R5 peptides were synthesized, and aggregates evaluated for their size, morphology, and association state as a function of salt and ionic strength concentration via dynamic and static light scattering, small angle X-ray and neutron scattering and cryogenic transmission electron microscopy. Furthermore, we compare the proposed R5 template to precipitated silica by scanning electron microscopy.

FINDINGS

R5 peptides assemble into large aggregates due to multivalence bridging and the decrease in electrostatic repulsion due to ionic strength. We elucidate the structure of R5 aggregates as mass-fractals composed of small spherical aggregates. Moreover, we discover that phosphate ions not only have a significant role in driving the growth of the R5 scaffold, but additionally in driving the polycondensation of silicic acid during the bio-silification process via electrostatic interactions.

A review on diatom biosilicification and their adaptive ability to uptake other metals into their frustules for potential application in bone repair

Diatoms are unicellular eukaryotic algae that have a distinctive siliceous cell wall (frustule) with unique architectures. The nanotopography of the frustule is perfectly replicated between generations, offering a source of highly intricate and identical silica microparticles. In recent years, the ability to alter their cell wall chemistry both in terms of functionalisation with organic moieties or by incorporation of the metal ions in their frustules has increased interest in their utility for catalysis technologies, and semiconductor and biomedical applications. Herein we review the fundamental biological mechanisms in which diatoms produce their frustule and their ability to substitute different metal ions in their frustule fabrication process. The review focuses on the potential of diatom frustules as a naturally derived biomaterial in bone tissue engineering applications and how their cell walls, comprising biogenic silica, could either partially or fully incorporate other bone therapeutic metal ions, e.g., titanium or calcium, into their frustule. The use of diatom frustules in bone repair also potentially offers a 'greener', more environmentally friendly, biomaterial as they can naturally synthesise oxides of silicon and other metals into their frustules under ambient conditions at a relatively neutral pH. This process would negate the use of harsh organic chemicals and high-temperature processing conditions, often used in the fabrication of silica based biomaterials, e.g., bioactive glass.

Filament extrusion of bioresorbable PDLGA for additive manufacturing utilising diatom biosilica to inhibit process-induced thermal degradation

Bone scaffolds are often fabricated by initially producing custom-made filaments by twin-screw extruder and subsequently fabricating into 3D scaffolds using fused deposition modelling. This study aims to directly compare the effect of two alternative silica-rich filler materials on the thermo-mechanical properties of such scaffolds after extrusion and printing. Poly (DL-lactide-co-glycolide) (PDLGA) was blended with either 45S5 Bioglass (5 wt %) or Biosilica (1 and 5 wt%) isolated from Cyclotella meneghiniana a freshwater diatom were tested. Diatom-PDLGA was found to have similar mechanical strength and ductility to pure-PDLGA, whereas Bioglass-PDLGA was found induce a more brittle behaviour. Bioglass-PDLGA was also found to have the lowest toughness in terms of energy absorption to failure. The TGA results suggested that significant thermal degradation in both the Bioglass filaments and scaffolds had occurred as a result of processing. However, diatom biosilica was found to inhibit thermal degradation of the PDLGA. Furthermore, evidence suggested the agglomeration of Bioglass particles occurred during processing the Bioglass-PDLGA filaments. Overall, diatom biosilica was found to be a promising candidate as a bone filler additive in 3D printed PDLGA scaffolds, whereas Bioglass caused some potentially detrimental effects on performance.

The Probable Mechanism for Silicon Capture by Diatom Algae: Assimilation of Polycarbonic Acids with Diatoms-Is Endocytosis a Key Stage in Building of Siliceous Frustules?

Many organisms including unicellular (diatoms, radiolaria, and chrysophytes), higher plants (rice and horsetail) and animals (sponges) use silica as a main part of skeletons. The bioavailable form of silicon is silicic acid and the mechanism of silicic acid penetration into living cells is still an enigma. Macropinocytosis was assumed as a key stage of the silicon capture by diatoms but assimilation of monomeric silicic acid by this way requires enormous amounts of water to be passed through the cell. We hypothesized that silicon can be captured by diatoms via endocytosis in the form of partially condensed silicic acid (oligosilicates) whose formation on the diatom surface was supposed. Oligosilicates are negatively charged nanoparticles and similar to coils of poly(acrylic acid) (PAA). We have synthesized fluorescent tagged PAA as well as several neutral and positively charged polymers. Cultivation of the diatom Ulnaria ferefusiformis in the presence of these polymers showed that only PAA is able to penetrate into siliceous frustules. The presence of PAA in the frustules was confirmed with chromatography and PAA causes various aberrations of the valve morphology. Growth of U. ferefusiformis and two other diatoms in the presence of tri- and tetracarbonic fluorescent tagged acids points to the ability of diatoms to recognize substances that bear four acidic groups and to include them into siliceous frustules. Thus, partial condensation of silicic acid is a plausible first stage of silicon assimilation.

Modifying the thickness, pore size, and composition of diatom frustule in Pinnularia sp. with Al3+ ions

Diatoms are unicellular photosynthetic algae that produce a silica exoskeleton (frustule) which exposes a highly ordered nano to micro scale morphology. In recent years there has been a growing interest in modifying diatom frustules for technological applications. This is achieved by adding non-essential metals to the growth medium of diatoms which in turn modifies morphology, composition, and resulting properties of the frustule. Here, we investigate the frustule formation in diatom Pinnularia sp., including changes to overall morphology, silica thickness, and composition, in the presence of Al³⁺ ions at different concentrations. Our results show that in the presence of Al³⁺ the total silica uptake from the growth medium increases, although a decrease in the growth rate is observed. This leads to a higher inorganic content per diatom resulting in a decreased pore diameter and a thicker frustule as evidenced by electron microscopy. Furthermore, ²⁷Al solid-state NMR, FIB-SEM, and EDS results confirm that Al³⁺ becomes incorporated into the frustule during the silicification process, thus, improving hydrolysis resistance. This approach may be extended to a broad range of elements and diatom species towards the scalable production of silica materials with tunable hierarchical morphology and chemical composition.

Tunable Surface Wrinkling by a Bio-Inspired Polyamine Anion Coacervation Process that Mediates the Assembly of Polyoxometalate Nanoclusters

A bio-inspired method is used to render controlled wrinkling surface patterns on supramolecular architectures assembled from polyoxometalate (POM) clusters. It involves a polyamine-multivalent anion interaction generating positively charged coacervates, which while dictating the assembly of POM into spherical structures further facilitate an interesting surface morphogenesis with wrinkling patterns. This spontaneous surface wrinkling depends on the type of multivalent anion and the pH. As the polyamine-anion interaction becomes stronger, the wrinkles turn denser with lesser depth, which eventually undergoes post-buckling to engender a complex surface pattern. Interestingly, the order of influence exerted by different anions on the morphology follows the Hofmeister series. Moreover, the mild synthesis conditions keep the functional POM units dispersed in the sphere with a structural transformability to their lacunary form.

Levels of Diatom Minor Sterols Respond to Changes in Temperature and Salinity

Diatoms are a broadly distributed and evolutionarily diversified group of microalgae that produce a diverse range of sterol compounds. Sterols are triterpenoids that play essential roles in membrane-related processes in eukaryotic cells. Some sterol compounds possess bioactivities that promote human health and are currently used as nutraceuticals. The relationship between sterol diversity in diatoms and their acclimation to different environments is not well understood. In this study, we investigated the occurrence of different sterol types across twelve diatom species, as well as the effect of temperature reduction and changes in salinity on the sterol contents of three model diatom species. In the diatoms Thalassiosira pseudonana, Phaeodactylum tricornutum and Chaetoceros muelleri, we found that changes in the relative contents of minor sterols accompanied shifts in temperature and salinity. This may be indicative of acquired adaptive traits in diatom metabolism.

Salinity-dependent nanostructures and composition of cell surface and its relation to Cd toxicity in an estuarine diatom

The interactions between metal and phytoplankton are affected by salinity in estuarine environments. While water chemistry is an important factor regulating the metal bioavailability in phytoplankton, the physiological adaptation of the algae cells may also change their intrinsic response to metals. In this work, we tried to interpret the salinity-dependent Cd toxicity in a pennate diatom Nitzchia closterium from a biological side. As with many studies, we observed Cd toxicity to the diatom increased with decreasing salinity. However, changing free Cd ion concentrations may be partly responsible for the enhanced Cd toxicity. Multiple evidences showed that diatom cells acclimated at low salinity had stronger intrinsic Cd adsorption capacity. Salinity significantly affected not only the nanostructures but also the biochemical composition in the cell surface of the diatom. Diatom cells grown at lower salinity had a lower surface potential, higher specific surface area, and more sulfur-containing groups in the cell wall, leading to stronger Cd binding capacity in the cells. Meanwhile, more Si was present as poly-silicic acid when the salinity decreased. The change of Si content and speciation in the cell wall are also considered a major reason for the variations of Cd surface binding. Our study provided new clues for the salinity-dependent metal toxicity in marine diatoms.

Silicon limitation reduced the adsorption of cadmium in marine diatoms

The nitrogen (N) and phosphorus (P) loadings in coastal waters have greatly increased due to anthropogenic input. However, the silicate levels have remained stable in the past decades, leading to nutrient status alternating from N limitation to Si limitation. Few studies have examined the effects of such nutrient imbalance on Cd accumulation in marine diatoms. In the present study, we provide multiple lines of evidence that Si limitation reduced the Cd binding capability in the marine diatom Nitzschia closterium. Diatom cells adapted to lower Si exposure had weaker mechanical strength and less negatively charged surfaces. Close examination of the cell surface revealed that Si shortage changed the biochemical composition of the cell surface and decreased the diatom's silicification ability. The lower density of the silanol groups in the cell wall is the most likely reason for the weaker Cd adsorption ability observed in the Si limited diatom cells. This study demonstrates the significance of Si in controlling the metal accumulation in marine diatoms.

Biosynthetic pathways of glycinebetaine in Thalassiosira pseudonana; functional characterization of enzyme catalyzing three-step methylation of glycine

Betaine (trimethylglycine) is an important compatible solute that accumulates in response to abiotic stresses such as drought and salinity. Biosynthetic pathways of betaine have been extensively studied, but it remains to be clarified on algae. A diatom Thalassiosira pseudonana CCMP1335 is an important component of marine ecosystems. Here we show that the genome sequence of Thalassiosira suggests the presence of two biosynthetic pathways for betaine, via three step methylation of glycine and via two step oxidation of choline. The choline oxidation via choline dehydrogenase was suggested and its sequential characteristics were analyzed. A candidate gene TpORF1 for glycine methylation encodes a protein consisted of 574 amino acids with two putative tandem repeat methyltransferase domains. The TpORF1 was expressed in E. coli, and the purified protein was shown to synthesize betaine via three step methylation of glycine and designated as TpGSDMT. The proteins containing C-terminal half or N-terminal half were expressed in E. coli and exhibited the methyl transferase activities with different substrate specificity for glycine, sarcosine and dimethylglycine. Upregulation of TpGSDMT transcription and betaine levels were observed at high salinity, suggesting the importance of TpGSDMT for salt tolerance in T. pseudonana cells.

Multiple Routes to Smart Nanostructured Materials from Diatom Microalgae: A Chemical Perspective

Diatoms are unicellular photosynthetic microalgae, ubiquitously diffused in both marine and freshwater environments, which exist worldwide with more than 100 000 species, each with different morphologies and dimensions, but typically ranging from 10 to 200 µm. A special feature of diatoms is their production of siliceous micro- to nanoporous cell walls, the frustules, whose hierarchical organization of silica layers produces extraordinarily intricate pore patterns. Due to the high surface area, mechanical resistance, unique optical features, and biocompatibility, a number of applications of diatom frustules have been investigated in photonics, sensing, optoelectronics, biomedicine, and energy conversion and storage. Current progress in diatom-based nanotechnology relies primarily on the availability of various strategies to isolate frustules, retaining their morphological features, and modify their chemical composition for applications that are not restricted to those of the bare biosilica produced by diatoms. Chemical or biological methods that decorate, integrate, convert, or mimic diatoms' biosilica shells while preserving their structural features represent powerful tools in developing scalable, low-cost routes to a wide variety of nanostructured smart materials. Here, the different approaches to chemical modification as the basis for the description of applications relating to the different materials thus obtained are presented.

Pseudo-nitzschia arctica sp. nov., a new cold-water cryptic Pseudo-nitzschia species within the P. pseudodelicatissima complex

A new nontoxic Pseudo-nitzschia species belonging to the P. pseudodelicatissima complex, P. arctica, was isolated from different areas of the Arctic. The erection of P. arctica is mainly supported by molecular data, since the species shares identical ultrastructure with another species in the complex, P. fryxelliana, and represents a new case of crypticity within the genus. Despite their morphological similarity, the two species are not closely related in phylogenies based on LSU, ITS and rbcL. Interestingly, P. arctica is phylogenetically most closely related to P. granii and P. subcurvata, from which the species is, however, morphologically different. P. granii and P. subcurvata lack the central larger interspace which is one of the defining features of the P. pseudodelicatissima complex. The close genetic relationship between P. arctica and the two species P. granii and P. subcurvata is demonstrated by analysis of the secondary structure of ITS2 which revealed no compensatory base changes, two hemi-compensatory base changes, and two deletions in P. arctica with respect to the other two species. These findings emphasize that rates of morphological differentiation, molecular evolution and speciation are often incongruent for Pseudo-nitzschia species, resulting in a restricted phylogenetic value for taxonomic characters used to discriminate species. The description of a new cryptic species, widely distributed in the Arctic and potentially representing an endemic component of the Arctic diatom flora, reinforces the idea of the existence of noncosmopolitan Pseudo-nitzschia species and highlights the need for combined morphological and molecular analyses to assess the distributional patterns of phytoplankton species.

Applications of Imaging Flow Cytometry for Microalgae

The ability to image large numbers of cells at high resolution enhances flow cytometric analysis of cells and cell populations. In particular, the ability to image intracellular features adds a unique aspect to analyses, and can enable correlation between molecular phenomena resulting in alterations in cellular phenotype. Unicellular microalgae are amenable to high-throughput analysis to capture the diversity of cell types in natural samples, or diverse cellular responses in clonal populations, especially using imaging cytometry. Using examples from our laboratory, we review applications of imaging cytometry, specifically using an Amnis(®) ImageStream(®)X instrument, to characterize photosynthetic microalgae. Some of these examples highlight advantages of imaging flow cytometry for certain research objectives, but we also include examples that would not necessarily require imaging and could be performed on a conventional cytometer to demonstrate other concepts in cytometric evaluation of microalgae. We demonstrate the value of these approaches for (1) analysis of populations, (2) documentation of cellular features, and (3) analysis of gene expression.

Diatom silica biomineralization: Parallel development of approaches and understanding

Diatom silica cell walls present an intriguing application of biomineralization in a single celled organism. The ability of diatoms to make an enormous variety of silica structures on the nano- to micro-scale is unparalleled in nature. The process is a whole-cell endeavor, involving diverse cellular components that coordinate "bottom up" and "top down" structure formation processes to reproducibly convert genetic information into physical structure. The study of silicification has been similarly all encompassing, involving the application of diverse analytical techniques to examine different aspects of the process. This review highlights the application of different approaches used to study silicification and the insights they have provided, and documents the progress that has been made. The current status offers the possibility of major breakthroughs in our understanding, by enabling a more widespread identification of genes involved, and direct testing of the role these genes play by genetic manipulation.

Evidence for a regulatory role of diatom silicon transporters in cellular silicon responses

The utilization of silicon by diatoms has both global and small-scale implications, from oceanic primary productivity to nanotechnological applications of their silica cell walls. The sensing and transport of silicic acid are key aspects of understanding diatom silicon utilization. At low silicic acid concentrations (<30 μM), transport mainly occurs through silicic acid transport proteins (SITs), and at higher concentrations it occurs through diffusion. Previous analyses of the SITs were done either in heterologous systems or without a distinction between individual SITs. In the present study, we examined individual SITs in Thalassiosira pseudonana in terms of transcript and protein abundance in response to different silicic acid regimes and examined knockdown lines to evaluate the role of the SITs in transport, silica incorporation, and lipid accumulation resulting from silicon starvation. SIT1 and SIT2 were localized in the plasma membrane, and protein levels were generally inversely correlated with cellular silicon needs, with a distinct response being found when the two SITs were compared. We developed highly effective approaches for RNA interference and antisense knockdowns, the first such approaches developed for a centric diatom. SIT knockdown differentially affected the uptake of silicon and the incorporation of silicic acid and resulted in the induction of lipid accumulation under silicon starvation conditions far earlier than in the wild-type cells, suggesting that the cells were artificially sensing silicon limitation. The data suggest that the transport role of the SITs is relatively minor under conditions with sufficient silicic acid. Their primary role is to sense silicic acid levels to evaluate whether the cell can proceed with its cell wall formation and division processes.

Judging diatoms by their cover: variability in local elasticity of Lithodesmium undulatum undergoing cell division

Unique features of diatoms are their intricate cell covers (frustules) made out of hydrated, amorphous silica. The frustule defines and maintains cell shape and protects cells against grazers and pathogens, yet it must allow for cell expansion during growth and division. Other siliceous structures have also evolved in some chain-forming species as means for holding neighboring cells together. Characterization and quantification of mechanical properties of these structures are crucial for the understanding of the relationship between form and function in diatoms, but thus far only a handful of studies have addressed this issue. We conducted micro-indentation experiments, using atomic force microscopy (AFM), to examine local variations in elastic (Young's) moduli of cells and linking structures in the marine, chain-forming diatom Lithodesmium undulatum. Using a fluorescent tracer that is incorporated into new cell wall components we tested the hypothesis that new siliceous structures differ in elastic modulus from their older counterparts. Results show that the local elastic modulus is a highly dynamic property. Elastic modulus of stained regions was significantly lower than that of unstained regions, suggesting that newly formed cell wall components are generally softer than the ones inherited from the parent cells. This study provides the first evidence of differentiation in local elastic properties in the course of the cell cycle. Hardening of newly formed regions may involve incorporation of additional, possibly organic, material but further studies are needed to elucidate the processes that regulate mechanical properties of the frustule during the cell cycle.

Effect of pretreatment and temperature on the properties of Pinnularia biosilica frustules

Material characteristics of cleaned diatom Pinnularia frustules are investigated and evaluated as adsorbents to remove methylene blue from aqueous solution.

Integration of TiO2 into the diatom Thalassiosira weissflogii during frustule synthesis

Nature has inspired the design of complex hierarchical structures in the field of material science. Diatoms, unicellular algae with a hallmark intricate siliceous cell wall, have provided such a stimulus. Altering the chemistry of the diatom frustule has been explored to expand on the potential application of diatoms. The ability to modify the diatom in vivo opens the possibility to tailor the diatom to the end application. Herein, we report the chemical modification of the living diatom T. weissflogii using a titania precursor, titanium (IV) bis-(ammonium lactato)-dihydroxide (TiBALDH). Incorporation of Ti into the diatom is achieved via repeated treatment of cultures with non-toxic concentrations of TiBALDH. The characteristic architectural features of the diatom are unaltered following chemical modification. Transformation of the living diatom provides opportunity to confer novel structural, chemical or functional properties upon the diatom. We report on a photocatalytic ability imparted upon the TiBALDH-modified diatom.

Putative silicon transport vesicles in the cytoplasm of the diatom Synedra acus during surge uptake of silicon

We studied the growth of the araphid pennate diatom Synedra acus subsp. radians (Kützing) Skabichevskii using a fluorescent dye N(1),N(3)-dimethyl-N(1)-(7-nitro-2,1,3-benzoxadiazol-4-yl)propane-1,3-diamine (NBD-N2), which stains growing siliceous frustules but does not stain other subcellular organelles. We used a clonal culture of S. acus that was synchronized by silicon starvation. Epifluorescence microscopy was performed in two different ways with cells stained by the addition of silicic acid and the dye. Individual cells immobilized on glass were observed during the first 15-20 min following the replenishment of silicic acid after silicon starvation. Alternatively, we examined cells of a batch culture at time intervals during 36 h after the replenishment of silicic acid using fluorescence and confocal microscopy. The addition of silicic acid and NBD-N2 resulted in the rapid (1-2 min) formation of several dozen green fluorescent submicrometer particles (GFSPs) in the cytoplasm, which was accompanied by the accumulation of fluorescent silica inside silica deposition vesicles (SDVs) along their full length. In 5-15 min, GFSPs disappeared from the cytoplasm. Mature siliceous valves were formed within the SDVs during the subsequent 14-16 h. In the next 8-10 h, GFSPs appeared again in the cytoplasm of daughter cells. The data obtained confirm observations about the two-stage mechanism of silicon assimilation, which includes rapid silicon uptake (surge uptake) followed by slow silica deposition. It is likely that the observed GFSPs are silicon transport vesicles, which were first proposed by Schmid and Schulz in (Protoplasma 100:267-288, 1979).

Multiparametric analyses reveal the pH-dependence of silicon biomineralization in diatoms

Diatoms, the major contributors of the global biogenic silica cycle in modern oceans, account for about 40% of global marine primary productivity. They are an important component of the biological pump in the ocean, and their assemblage can be used as useful climate proxies; it is therefore critical to better understand the changes induced by environmental pH on their physiology, silicification capability and morphology. Here, we show that external pH influences cell growth of the ubiquitous diatom Thalassiosira weissflogii, and modifies intracellular silicic acid and biogenic silica contents per cell. Measurements at the single-cell level reveal that extracellular pH modifications lead to intracellular acidosis. To further understand how variations of the acid-base balance affect silicon metabolism and theca formation, we developed novel imaging techniques to measure the dynamics of valve formation. We demonstrate that the kinetics of valve morphogenesis, at least in the early stages, depends on pH. Analytical modeling results suggest that acidic conditions alter the dynamics of the expansion of the vesicles within which silica polymerization occurs, and probably its internal pH. Morphological analysis of valve patterns reveals that acidification also reduces the dimension of the nanometric pores present on the valves, and concurrently overall valve porosity. Variations in the valve silica network seem to be more correlated to the dynamics and the regulation of the morphogenesis process than the silicon incorporation rate. These multiparametric analyses from single-cell to cell-population levels demonstrate that several higher-level processes are sensitive to the acid-base balance in diatoms, and its regulation is a key factor for the control of pattern formation and silicon metabolism.

Expression, purification, and reconstitution of a diatom silicon transporter

The synthesis and manipulation of silicon materials on the nanoscale are core themes in nanotechnology research. Inspiration is increasingly being taken from the natural world because the biological mineralization of silicon results in precisely controlled, complex silica structures with dimensions from the millimeter to the nanometer. One fascinating example of silicon biomineralization occurs in the diatoms, unicellular algae that sheath themselves in an ornate silica-based cell wall. To harvest silicon from the environment, diatoms have developed a unique family of integral membrane proteins that bind to a soluble form of silica, silicic acid, and transport it across the cell membrane to the cell interior. These are the first proteins shown to directly interact with silicon, but the current understanding of these specific silicon transport proteins is limited by the lack of in vitro studies of structure and function. We report here the recombinant expression, purification, and reconstitution of a silicon transporter from the model diatom Thalassiosira pseudonana. After using GFP fusions to optimize expression and purification protocols, a His(10)-tagged construct was expressed in Saccharomyces cerevisiae, solubilized in the detergent Fos-choline-12, and purified by affinity chromatography. Size-exclusion chromatography and particle sizing by dynamic light scattering showed that the protein was purified as a homotetramer, although nonspecific oligomerization occurred at high protein concentrations. Circular dichroism measurements confirmed sequence-based predictions that silicon transporters are α-helical membrane proteins. Silicic acid transport could be established in reconstituted proteoliposomes, and silicon uptake was found to be dependent upon an applied sodium gradient. Transport data across different substrate concentrations were best fit to the sigmoidal Hill equation, with a K(0.5) of 19.4 ± 1.3 μM and a cooperativity coefficient of 1.6. Sodium binding was noncooperative with a K(m)(app) of 1.7 ± 1.0 mM, suggesting a transport silicic acid:Na(+) stoichiometry of 2:1. These results provide the basis for a full understanding of both silicon transport in the diatom and protein-silicon interactions in general.

Cationic amino acids specific biomimetic silicification in ionic liquid: a quest to understand the formation of 3-D structures in diatoms

The intricate, hierarchical, highly reproducible, and exquisite biosilica structures formed by diatoms have generated great interest to understand biosilicification processes in nature. This curiosity is driven by the quest of researchers to understand nature's complexity, which might enable reproducing these elegant natural diatomaceous structures in our laboratories via biomimetics, which is currently beyond the capabilities of material scientists. To this end, significant understanding of the biomolecules involved in biosilicification has been gained, wherein cationic peptides and proteins are found to play a key role in the formation of these exquisite structures. Although biochemical factors responsible for silica formation in diatoms have been studied for decades, the challenge to mimic biosilica structures similar to those synthesized by diatoms in their natural habitats has not hitherto been successful. This has led to an increasingly interesting debate that physico-chemical environment surrounding diatoms might play an additional critical role towards the control of diatom morphologies. The current study demonstrates this proof of concept by using cationic amino acids as catalyst/template/scaffold towards attaining diatom-like silica morphologies under biomimetic conditions in ionic liquids.

Bioinspired control of colloidal silica in vitro by dual polymeric assemblies of zwitterionic phosphomethylated chitosan and polycations or polyanions

This paper focuses on the effects of biological and synthetic polymers on the formation of amorphous silica. A concise review of relevant literature related to biosilicification is presented. The importance of synergies between polyelectrolytes on the inhibition of silicic acid condensation is discussed. A specific example of a zwitterionic polymer phosphonomethylated chitosan (PCH) is further analyzed for its inhibitory activity. Specifically, the ability of PCH to retard silicic acid condensation at circumneutral pH in aqueous supersaturated solutions is explored. It was discovered that in short-term studies (0-8 h) the inhibitory activity is PCH dosage-independent, but for longer condensation times (>24 h) there is a clear increase in inhibition upon PCH dosage increase. Soluble silicic acid levels reach 300 ppm after 24 h in the presence of 160 ppm PCH. Furthermore, the effects of either purely cationic (polyethyleneimine, PEI) or purely anionic (carboxymethylinulin, CMI) polyelectrolytes on the inhibitory activity of PCH is systematically studied. It was found that the action of inhibitor blends is not cumulative. PCH/PEI blends stabilize the same level of silicic acid as PCH alone in both short-term (8 h) and long-term (72 h) experiments. PCH/CMI combinations on the other hand can only achieve short-term inhibition of silicic acid polymerization, but fail to extend this over the first 8 h. PCH and its combinations with PEI or CMI affect silica particle morphology, studied by SEM. Spherical particles and their aggregates, irregularly shaped particles and porous structures are obtained depending on additive or additive blend. It was demonstrated by FT-IR that PCH is trapped in the colloidal silica matrix.

The life of diatoms in the world's oceans

Marine diatoms rose to prominence about 100 million years ago and today generate most of the organic matter that serves as food for life in the sea. They exist in a dilute world where compounds essential for growth are recycled and shared, and they greatly influence global climate, atmospheric carbon dioxide concentration and marine ecosystem function. How these essential organisms will respond to the rapidly changing conditions in today's oceans is critical for the health of the environment and is being uncovered by studies of their genomes.

Plasticity and robustness of pattern formation in the model diatom Phaeodactylum tricornutum

Understanding the morphogenesis of mineralized structures found in shells, bones, teeth, spicules and plant cell walls is difficult because of the complexities underlying biomineralization, and the requirement of accurate models for pattern formation. Here, we investigated the spatial and temporal development of siliceous structures found in a model diatom species, Phaeodactylum tricornutum, for which the entire genome has been sequenced and transformation is routine. Analyses of pattern formation revealed that the process of silicification starts from a 'pi-like' structure that controls the spatial organization of a sternum upon which regular instabilities are initiated and developed. Detailed analyses also demonstrate that morphogenesis of silica is nonuniform. We also tested the sensitivity of pattern formation to perturbation of proton pumps, and found that selective inhibitors of H(+)-V-ATPases affect silica biomineralization both quantitatively and qualitatively. Morphometric analyses of valves purified from isogenic populations of cells show that the morphometric noise of several traits is under exquisite regulation, explaining why the overall valve pattern is reproducibly maintained. Altogether our analyses demonstrate that silica morphogenesis is a robust but nonuniform process, and allow us to propose a model for the dynamic growth of materials within a spatially controlled geometry.

The Glass Menagerie: diatoms for novel applications in nanotechnology

Diatoms are unicellular, eukaryotic, photosynthetic algae that are found in aquatic environments. Diatoms have enormous ecological importance on this planet and display a diversity of patterns and structures at the nano- to millimetre scale. Diatom nanotechnology, a new interdisciplinary area, has spawned collaborations in biology, biochemistry, biotechnology, physics, chemistry, material science and engineering. We survey diatom nanotechnology since 2005, emphasizing recent advances in diatom biomineralization, biophotonics, photoluminescence, microfluidics, compustat domestication, multiscale porosity, silica sequestering of proteins, detection of trace gases, controlled drug delivery and computer design. Diatoms might become the first organisms for which the gap in our knowledge of the relationship between genotype and phenotype is closed.

Silicon uptake in diatoms revisited: a model for saturable and nonsaturable uptake kinetics and the role of silicon transporters

The silicic acid uptake kinetics of diatoms were studied to provide a mechanistic explanation for previous work demonstrating both nonsaturable and Michaelis-Menten-type saturable uptake. Using (68)Ge(OH)(4) as a radiotracer for Si(OH)(4), we showed a time-dependent transition from nonsaturable to saturable uptake kinetics in multiple diatom species. In cells grown under silicon (Si)-replete conditions, Si(OH)(4) uptake was initially nonsaturable but became saturable over time. Cells prestarved for Si for 24 h exhibited immediate saturable kinetics. Data suggest nonsaturability was due to surge uptake when intracellular Si pool capacity was high, and saturability occurred when equilibrium was achieved between pool capacity and cell wall silica incorporation. In Thalassiosira pseudonana at low Si(OH)(4) concentrations, uptake followed sigmoidal kinetics, indicating regulation by an allosteric mechanism. Competition of Si(OH)(4) uptake with Ge(OH)(4) suggested uptake at low Si(OH)(4) concentrations was mediated by Si transporters. At high Si(OH)(4), competition experiments and nonsaturability indicated uptake was not carrier mediated and occurred by diffusion. Zinc did not appear to be directly involved in Si(OH)(4) uptake, in contrast to a previous suggestion. A model for Si(OH)(4) uptake in diatoms is presented that proposes two control mechanisms: active transport by Si transporters at low Si(OH)(4) and diffusional transport controlled by the capacity of intracellular pools in relation to cell wall silica incorporation at high Si(OH)(4). The model integrates kinetic and equilibrium components of diatom Si(OH)(4) uptake and consistently explains results in this and previous investigations.

Prescribing diatom morphology: toward genetic engineering of biological nanomaterials

The formation of inorganic materials with complex form is a widespread biological phenomenon (biomineralization). Among the most spectacular examples of biomineralization is the production by diatoms (a group of eukaryotic microalgae) of intricately nanopatterned to micropatterned cell walls made of silica (SiO2). Understanding the molecular mechanisms of diatom silica biomineralization is not only a fundamental biological problem, but also of great interest in materials engineering, as the biological self-assembly of three-dimensional (3D) inorganic nanomaterials has no man-made analog. Recently, insight into the molecular mechanism of diatom silica formation has been obtained by structural and functional analysis of biomolecules that are involved in this process. Furthermore, the rapid development of diatom molecular genetics has provided new tools for investigating the silica forming machinery of diatoms and for manipulating silica biogenesis. This has opened the door for the production, through genetic engineering, of unique 3D nanomaterials with designed structures and functionalities.