Control of biosilica morphology and mechanical performance by the conserved diatom gene Silicanin-1

Simultaneous Effect of Diameter and Concentration of Multi-Walled Carbon Nanotubes on Mechanical and Electrical Properties of Cement Mortars: With and without Biosilica

In this work, the effect of multi-walled carbon nanotubes (MWCNT1, MWCNT2, and MWCNT3) with different outer diameters and specific surface areas on the mechanical and electrical properties of cement mortar have been investigated. Various concentrations of MWCNTs were used (0.05, 0.10, and 0.15%), the effective dispersion of which was carried out by an Ultrasonic machine (for 40 min with 160 W power and a 24 kHz frequency) using a surfactant. Composites have been processed with a biosilica content of 10% by weight of cement and without it. Compressive strength tests were carried out on days 7 and 28 of curing. The 7-day compressive strength of samples prepared without biosilica increased compared to the result of the control sample (6.4% for MWCNT1, 7.4% for MWCNT2, and 10.8% for MWCNT3), as did those using biosilica (6.7% in the case of MWCNT1, 29.2% for MWCNT2, and 2.1% for MWCNT3). Compressive strength tests of 28-day specimens yielded the following results: 21.7% for MWCNT1, 3.8% for MWCNT2, and 4.2% for MWCNT3 in the absence of biosilica and 8.5%, 12.6%, and 6.3% with biosilica, respectively. The maximum increase in compressive strength was observed in the composites treated with a 0.1% MWCNT concentration, while in the case of 0.05 and 0.15% concentrations, the compressive strengths were relatively low. The MWCNT-reinforced cement matrix obtained electrical properties due to the high electrical conductivity of these particles. The effect of MWCNT concentrations of 0.05, 0.10, and 0.15 wt% on the electrical properties of cement mortar, especially the bulk electrical resistivity and piezoresistive characteristics of cement mortar, was studied in this work. At a concentration of 0.05%, the lowest value of resistivity was obtained, and then it started to increase. The obtained results show that all investigated specimens have piezoresistive properties and that the measurements led to a deviation in fractional change in resistivity.

A biogenic geodesic dome of the silica skeleton in Phaeodaria

Unique architectures of microbial skeletons are viewed as a model for the architectural design of artificial structural materials. In particular, the specific geometric arrangement of a spherical skeleton 0.5-1.5 mm in diameter of shell-bearing protists, Phaeodaria (Aulosphaera sp.), is remarkably interesting because of its similarity to a geodesic polyhedron, which is a hollow framework with 6-branched nodes that requires minimal building material for maximal strength. A phaeodarian skeleton composed of silica rods 5-10 µm in diameter was characterized as a distorted dome that is based on an icosahedron sectioned with a 7-frequency subdivision. The major difference of the biogenic architecture from the ideal geodesic dome is the coexistence of 7- and 5-branched nodes with the distortion of the frames and the presence of radial spines. From a microscopic perspective, the frames and radial spines were revealed to be hollow tubes having inner fibers and lamellar walls consisting of silica nanoparticles 4-8 nm in diameter with interlayer organic matter. The high degradability of the silica skeleton in seawater after cell mortality is ascribed to the specific nanometric composite structure. The biological architectonics sheds light on the production of environmentally friendly, lightweight structural materials and microdevices.

The draft genome of Nitzschia closterium f. minutissima and transcriptome analysis reveals novel insights into diatom biosilicification

BACKGROUND

Nitzschia closterium f. minutissima is a commonly available diatom that plays important roles in marine aquaculture. It was originally classified as Nitzschia (Bacillariaceae, Bacillariophyta) but is currently regarded as a heterotypic synonym of Phaeodactylum tricornutum. The aim of this study was to obtain the draft genome of the marine microalga N. closterium f. minutissima to understand its phylogenetic placement and evolutionary specialization. Given that the ornate hierarchical silicified cell walls (frustules) of diatoms have immense applications in nanotechnology for biomedical fields, biosensors and optoelectric devices, transcriptomic data were generated by using reference genome-based read mapping to identify significantly differentially expressed genes and elucidate the molecular processes involved in diatom biosilicification.

RESULTS

In this study, we generated 13.81 Gb of pass reads from the PromethION sequencer. The draft genome of N. closterium f. minutissima has a total length of 29.28 Mb, and contains 28 contigs with an N50 value of 1.23 Mb. The GC content was 48.55%, and approximately 18.36% of the genome assembly contained repeat sequences. Gene annotation revealed 9,132 protein-coding genes. The results of comparative genomic analysis showed that N. closterium f. minutissima was clustered as a sister lineage of Phaeodactylum tricornutum and the divergence time between them was estimated to be approximately 17.2 million years ago (Mya). CAFF analysis demonstrated that 220 gene families that significantly changed were unique to N. closterium f. minutissima and that 154 were specific to P. tricornutum, moreover, only 26 gene families overlapped between these two species. A total of 818 DEGs in response to silicon were identified in N. closterium f. minutissima through RNA sequencing, these genes are involved in various molecular processes such as transcription regulator activity. Several genes encoding proteins, including silicon transporters, heat shock factors, methyltransferases, ankyrin repeat domains, cGMP-mediated signaling pathways-related proteins, cytoskeleton-associated proteins, polyamines, glycoproteins and saturated fatty acids may contribute to the formation of frustules in N. closterium f. minutissima.

CONCLUSIONS

Here, we described a draft genome of N. closterium f. minutissima and compared it with those of eight other diatoms, which provided new insight into its evolutionary features. Transcriptome analysis to identify DEGs in response to silicon will help to elucidate the underlying molecular mechanism of diatom biosilicification in N. closterium f. minutissima.

The Physiological Inorganic Polymers Biosilica and Polyphosphate as Key Drivers for Biomedical Materials in Regenerative Nanomedicine

There is a need for novel nanomaterials with properties not yet exploited in regenerative nanomedicine. Based on lessons learned from the oldest metazoan phylum, sponges, it has been recognized that two previously ignored or insufficiently recognized principles play an essential role in tissue regeneration, including biomineral formation/repair and wound healing. Firstly, the dependence on enzymes as a driving force and secondly, the availability of metabolic energy. The discovery of enzymatic synthesis and regenerative activity of amorphous biosilica that builds the mineral skeleton of siliceous sponges formed the basis for the development of successful strategies for the treatment of osteochondral impairments in humans. In addition, the elucidation of the functional significance of a second regeneratively active inorganic material, namely inorganic polyphosphate (polyP) and its amorphous nanoparticles, present from sponges to humans, has pushed forward the development of innovative materials for both soft (skin, cartilage) and hard tissue (bone) repair. This energy-rich molecule exhibits a property not shown by any other biopolymer: the delivery of metabolic energy, even extracellularly, necessary for the ATP-dependent tissue regeneration. This review summarizes the latest developments in nanobiomaterials based on these two evolutionarily old, regeneratively active materials, amorphous silica and amorphous polyP, highlighting their specific, partly unique properties and mode of action, and discussing their possible applications in human therapy. The results of initial proof-of-concept studies on patients demonstrating complete healing of chronic wounds are outlined.

Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects

Initially discovered over 35 years ago in the bacterium Escherichia coli as a defense system against invasion of viral (or other exogenous) DNA into the genome, CRISPR/Cas has ushered in a new era of functional genetics and served as a versatile genetic tool in all branches of life science. CRISPR/Cas has revolutionized the methodology of gene knockout with simplicity and rapidity, but it is also powerful for gene knock-in and gene modification. In the field of marine biology and ecology, this tool has been instrumental in the functional characterization of 'dark' genes and the documentation of the functional differentiation of gene paralogs. Powerful as it is, challenges exist that have hindered the advances in functional genetics in some important lineages. This review examines the status of applications of CRISPR/Cas in marine research and assesses the prospect of quickly expanding the deployment of this powerful tool to address the myriad fundamental marine biology and biological oceanography questions.

Synthesis and Antimicrobial Activity of 3D Micro-Nanostructured Diatom Biosilica Coated by Epitaxially Growing Ag-AgCl Hybrid Nanoparticles

The 3D (three-dimensional) micro-nanostructured diatom biosilica obtained from cultivated diatoms was used as a support to immobilize epitaxially growing AgCl-Ag hybrid nanoparticles ((Ag-AgCl)NPs) for the synthesis of nanocomposites with antimicrobial properties. The prepared composites that contained epitaxially grown (Ag-AgCl)NPs were investigated in terms of their morphological and structural characteristics, elemental and mineral composition, crystalline forms, zeta potential, and photoluminescence properties using a variety of instrumental methods including SEM (scanning electron microscopy), TEM (transmission electron microscopy), EDX (energy-dispersive X-ray spectroscopy), XRD (X-ray powder diffraction), zeta-potential measurement, and photoluminescence spectroscopy. The content of (AgCl-Ag)NPs in the hybrid composites amounted to 4.6 mg/g and 8.4 mg/g with AgClNPs/AgNPs ratios as a percentage of 86/14 and 51/49, respectively. Hybrid nanoparticles were evenly dispersed with a dominant size of 5 to 25 nm in composite with an amount of 8.4 mg/g of silver. The average size of the nanoparticles was 7.5 nm; also, there were nanoparticles with a size of 1-2 nm and particles that were 20-40 nm. The synthesis of (Ag-AgCl)NPs and their potential mechanism were studied. The MIC (the minimum inhibitory concentration method) approach was used to investigate the antimicrobial activity against microorganisms Klebsiella pneumoniae, Escherichia coli, and Staphylococcus aureus. The nanocomposites containing (Ag-AgCl)NPs and natural diatom biosilica showed resistance to bacterial strains from the American Type Cultures Collection and clinical isolates (diabetic foot infection and wound isolates).

Thalassiosira pseudonana (Cyclotella nana) (Hustedt) Hasle et Heimdal (Bacillariophyceae): A genetically tractable model organism for studying diatom biology, including biological silica formation

In 2004, Thalassiosira pseudonana was the first eukaryotic marine alga to have its genome sequenced. Since then, this species has quickly emerged as a valuable model species for investigating the molecular underpinnings of essentially all aspects of diatom life, particularly bio-morphogenesis of the cell wall. An important prerequisite for the model status of T. pseudonana is the ongoing development of increasingly precise tools to study the function of gene networks and their encoded proteins in vivo. Here, we briefly review the current toolbox for genetic manipulation, highlight specific examples of its application in studying diatom metabolism, and provide a peek into the role of diatoms in the emerging field of silica biotechnology.

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.

Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs

The order Parmales (class Bolidophyceae) is a minor group of pico-sized eukaryotic marine phytoplankton that contains species with cells surrounded by silica plates. Previous studies revealed that Parmales is a member of ochrophytes and sister to diatoms (phylum Bacillariophyta), the most successful phytoplankton group in the modern ocean. Therefore, parmalean genomes can serve as a reference to elucidate both the evolutionary events that differentiated these two lineages and the genomic basis for the ecological success of diatoms vs. the more cryptic lifestyle of parmaleans. Here, we compare the genomes of eight parmaleans and five diatoms to explore their physiological and evolutionary differences. Parmaleans are predicted to be phago-mixotrophs. By contrast, diatoms have lost genes related to phagocytosis, indicating the ecological specialization from phago-mixotrophy to photoautotrophy in their early evolution. Furthermore, diatoms show significant enrichment in gene sets involved in nutrient uptake and metabolism, including iron and silica, in comparison with parmaleans. Overall, our results suggest a strong evolutionary link between the loss of phago-mixotrophy and specialization to a silicified photoautotrophic life stage early in diatom evolution after diverging from the Parmales lineage.

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.

Genome engineering via gene editing technologies in microalgae

CRISPR-Cas has revolutionized genetic modification with its comparative simplicity and accuracy, and it can be used even at the genomic level. Microalgae are excellent feedstocks for biofuels and nutraceuticals because they contain high levels of fatty acids, carotenoids, and other metabolites; however, genome engineering for microalgae is not yet as developed as for other model organisms. Microalgal engineering at the genetic and metabolic levels is relatively well established, and a few genomic resources are available. Their genomic information was used for a "safe harbor" site for stable transgene expression in microalgae. This review proposes further genome engineering schemes including the construction of sgRNA libraries, pan-genomic and epigenomic resources, and mini-genomes, which can together be developed into synthetic biology for carbon-based engineering in microalgae. Acetyl-CoA is at the center of carbon metabolic pathways and is further reviewed for the production of molecules including terpenoids in microalgae.

The molecular basis for pore pattern morphogenesis in diatom silica

Biomineral-forming organisms produce inorganic materials with complex, genetically encoded morphologies that are unmatched by current synthetic chemistry. It is poorly understood which genes are involved in biomineral morphogenesis and how the encoded proteins guide this process. We addressed these questions using diatoms, which are paradigms for the self-assembly of hierarchically meso- and macroporous silica under mild reaction conditions. Proteomics analysis of the intracellular organelle for silica biosynthesis led to the identification of new biomineralization proteins. Three of these, coined dAnk1-3, contain a common protein-protein interaction domain (ankyrin repeats), indicating a role in coordinating assembly of the silica biomineralization machinery. Knocking out individual dank genes led to aberrations in silica biogenesis that are consistent with liquid-liquid phase separation as underlying mechanism for pore pattern morphogenesis. Our work provides an unprecedented path for the synthesis of tailored mesoporous silica materials using synthetic biology.

The role of the transmembrane domain of silicanin-1: Reconstitution of the full-length protein in artificial membranes

Biosilica formation in diatoms is a membrane-confined process that occurs in so-called silica deposition vesicles (SDVs). As SDVs have as yet not been successfully isolated, the impact of the SDV membrane on silica morphogenesis is not well understood. However, recently the first SDV transmembrane protein, silicanin-1 (Sin1) has been identified that appears to be involved in biosilica formation. In this study, we recombinantly expressed and isolated full-length Sin1 from E. coli and investigated its reconstitution behavior in artificial membranes. A reconstitution efficiency in vesicles of up to 80% was achieved by a co-micellization method. By using a chymotrypsin digest, the orientation of Sin1 in unilamellar vesicles was analyzed indicating a positioning of the large N-terminal domain to the outside of the vesicles. These proteoliposomes were capable of precipitating silica in the presence of long-chain polyamines. Supported lipid bilayers were produced by proteoliposome spreading on lipid monolayers to form continuous lipid bilayers with Sin1 confined to the membrane. Successful Sin1 reconstitution into these planar membranes was shown by means of immunostaining with purified primary anti-Sin1 and secondary fluorescent antibodies. The established planar model membrane system, amenable for surface sensitive and microscopy techniques, will pave the way to investigate SDV-membrane interactions with other SDV associated biomolecules and its role in silica biogenesis.

Diminished carbon and nitrate assimilation drive changes in diatom elemental stoichiometry independent of silicification in an iron-limited assemblage

In the California Current Ecosystem, upwelled water low in dissolved iron (Fe) can limit phytoplankton growth, altering the elemental stoichiometry of the particulate matter and dissolved macronutrients. Iron-limited diatoms can increase biogenic silica (bSi) content >2-fold relative to that of particulate organic carbon (C) and nitrogen (N), which has implications for carbon export efficiency given the ballasted nature of the silica-based diatom cell wall. Understanding the molecular and physiological drivers of this altered cellular stoichiometry would foster a predictive understanding of how low Fe affects diatom carbon export. In an artificial upwelling experiment, water from 96 m depth was incubated shipboard and left untreated or amended with dissolved Fe or the Fe-binding siderophore desferrioxamine-B (+DFB) to induce Fe-limitation. After 120 h, diatoms dominated the communities in all treatments and displayed hallmark signatures of Fe-limitation in the +DFB treatment, including elevated particulate Si:C and Si:N ratios. Single-cell, taxon-resolved measurements revealed no increase in bSi content during Fe-limitation despite higher transcript abundance of silicon transporters and silicanin-1. Based on these findings we posit that the observed increase in bSi relative to C and N was primarily due to reductions in C fixation and N assimilation, driven by lower transcript expression of key Fe-dependent genes.

Diatom biosilica: Source, Physical-chemical characterization, modification, and application

Growing research interest in the use of diatomaceous biosilica results from its unique properties, such as chemical inertness, biocompatibility, high mechanical and thermal stability, low thermal conductivity, homogeneous porous structure with a large specific surface. Unlike the production of synthetic silica materials with a micro- or nano-scale structure in an expensive conventional manufacturing process, diatomaceous biosilica can be produced in huge quantities without significant expenditure of energy and materials. This fact makes it an unlimited, easily accessible, natural, inexpensive, and renewable material. Moreover, the production of bio-silica is extremely environmentally friendly, as there is essentially no toxic waste, and the process does not require more energy compared to the production of synthetic silica-based materials. For all these reasons, diatoms are an intriguing alternative to synthetic materials in developing cheap biomaterials used in a different branch of industry. In review has been reported the state-of-art of biosilica materials, their characteristics approaches, and possible way of application. This article is protected by copyright. All rights reserved.

Shedding light on silica biomineralization by comparative analysis of the silica-associated proteomes from three diatom species

Morphogenesis of the intricate patterns of diatom silica cell walls is a protein-guided process, yet to date only very few such silica biomineralization proteins have been identified. Therefore, it is currently unknown whether all diatoms share conserved proteins of a basal silica forming machinery, and whether unique proteins are responsible for the morphogenesis of species-specific silica patterns. To answer these questions, we extracted proteins from the silica of three diatom species (Thalassiosira pseudonana, Thalassiosira oceanica, and Cyclotella cryptica) by complete demineralization of the cell walls. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) analysis of the extracts identified 92 proteins that we name 'soluble silicome proteins' (SSPs). Surprisingly, no SSPs are common to all three species, and most SSPs showed very low similarity to one another in sequence alignments. In-depth bioinformatics analyses revealed that SSPs could be grouped into distinct classes based on short unconventional sequence motifs whose functions are yet unknown. The results from the in vivo localization of selected SSPs indicates that proteins, which lack sequence homology but share unconventional sequence motifs may exert similar functions in the morphogenesis of the diatom silica cell wall.

Ultrastructure of setae of a planktonic diatom, Chaetoceros coarctatus

Silica frustules of most planktonic diatoms have many shallow holes in which the length (L) is smaller than the width (W). The present study focuses on a silica ultrastructure of setae of a planktonic diatom having deep (L/W > 1) holes. Here, we characterized microscopically patterned nanoholes on the silica walls of thick, robust, and hollow setae of a colony of Chaetoceros coarctatus. Basically, tetragonal poroid arrangements with and without a costa pattern are observed on the inner and outer surfaces, respectively, for three kinds of curving hollow setae attached to the anterior, intercalary, and posterior parts of the colony. The seta structures including specific poroid arrangements and continuity of deep nanoholes depend on the location. The deep nanoholes ∼90 nm wide are elongated from 150 to 1500 nm (L/W ∼17) with an increase in the wall thickness of the polygonal tubes of the setae. The inside poroid array, with a period of 190 nm in the extension direction of setae, is lined by parallel plates of the costae. However, the poroid arrangement on the outer surface is disordered, with several holes obstructed with increasing wall thickness of the posterior terminal setae. According to the movement of a colony in a fluid microchannel, the thick curving terminal setae is suggested to involve attitude control and mechanical protection. Using an optical simulation, the patterned deep through-holes on the intercalary setae were suggested to contribute anti-reflection of blue light in the wavelength range of 400 to 500 nm for the promotion of photosynthesis in seawater.

Investigating the Morphology and Mechanics of Biogenic Hierarchical Materials at and below Micrometer Scale

Investigating and understanding the intrinsic material properties of biogenic materials, which have evolved over millions of years into admirable structures with difficult to mimic hierarchical levels, holds the potential of replacing trial-and-error-based materials optimization in our efforts to make synthetic materials of similarly advanced complexity and properties. An excellent example is biogenic silica which is found in the exoskeleton of unicellular photosynthetic algae termed diatoms. Because of the complex micro- and nanostructures found in their exoskeleton, determining the intrinsic mechanical properties of biosilica in diatoms has only partly been accomplished. Here, a general method is presented in which a combination of in situ deformation tests inside an SEM with a realistic 3D model of the frustule of diatom Craspedostauros sp. (C. sp.) obtained by electron tomography, alongside finite element method (FEM) simulations, enables quantification of the Young’s modulus (E = 2.3 ± 0.1 GPa) of this biogenic hierarchical silica. The workflow presented can be readily extended to other diatom species, biominerals, or even synthetic hierarchical materials.

Solid-State NMR Investigations of Extracellular Matrixes and Cell Walls of Algae, Bacteria, Fungi, and Plants

Extracellular matrixes (ECMs), such as the cell walls and biofilms, are important for supporting cell integrity and function and regulating intercellular communication. These biomaterials are also of significant interest to the production of biofuels and the development of antimicrobial treatment. Solid-state nuclear magnetic resonance (ssNMR) and magic-angle spinning-dynamic nuclear polarization (MAS-DNP) are uniquely powerful for understanding the conformational structure, dynamical characteristics, and supramolecular assemblies of carbohydrates and other biomolecules in ECMs. This review highlights the recent high-resolution investigations of intact ECMs and native cells in many organisms spanning across plants, bacteria, fungi, and algae. We spotlight the structural principles identified in ECMs, discuss the current technical limitation and underexplored biochemical topics, and point out the promising opportunities enabled by the recent advances of the rapidly evolving ssNMR technology.

In Situ Manipulation and Micromechanical Characterization of Diatom Frustule Constituents Using Focused Ion Beam Scanning Electron Microscopy

Biocomposite structures are difficult to characterize by bulk approaches due to their morphological complexity and compositional heterogeneity. Therefore, a versatile method is required to assess, for example, the mechanical properties of geometrically simple parts of biocomposites at the relevant length scales. Here, it is demonstrated how a combination of Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) and micromanipulators can be used to isolate, transfer, and determine the mechanical properties of frustule constituents of diatom Thalassiosira pseudonana (T.p.). Specifically, two parts of the diatom frustule, girdle bands and valves, are separated by FIB milling and manipulated using a sharp tungsten tip without compromising their physical or chemical integrity. In situ mechanical studies on isolated girdle bands combined with Finite Element Method (FEM) simulations, enables the quantitative assessment of the Young's modulus of this biosilica; E = 40.0 GPa. In addition, the mechanical strength of isolated valves could be measured by transferring and mounting them on top of premilled holes in the sample support. This approach may be extended to any hierarchical biocomposite material, regardless of its chemical composition, to isolate, transfer, and investigate the mechanical properties of selected constituents or specific regions.

Structural evidence for extracellular silica formation by diatoms

The silica cell wall of diatoms, a widespread group of unicellular microalgae, is an exquisite example for the ability of organisms to finely sculpt minerals under strict biological control. The prevailing paradigm for diatom silicification is that this is invariably an intracellular process, occurring inside specialized silica deposition vesicles that are responsible for silica precipitation and morphogenesis. Here, we study the formation of long silicified extensions that characterize many diatom species. We use cryo-electron tomography to image silica formation in situ, in 3D, and at a nanometer-scale resolution. Remarkably, our data suggest that, contradictory to the ruling paradigm, these intricate structures form outside the cytoplasm. In addition, the formation of these silica extensions is halted at low silicon concentrations that still support the formation of other cell wall elements, further alluding to a different silicification mechanism. The identification of this unconventional strategy expands the suite of mechanisms that diatoms use for silicification.

Study on the Hemostasis Characteristics of Biomaterial Frustules Obtained from Diatom Navicula australoshetlandica sp

Diatoms, known as photosynthetic unicellular algae, can produce natural biosilica frustules that exhibit great biocompatibility, superhydrophilicity, and superhemophilicity. In our study, the diatom Navicula australoshetlandica sp. was isolated from aquaculture wastewater and pretreated to obtain frustules so as to explore their hemostasis characteristics. A special “porous web” (6–8 nm) substructure in the ordered nanopores (165–350 nm) of boat-shaped diatom frustule was observed in Navicula australoshetlandica sp. using SEM and TEM analysis. Moreover, X-ray, N₂ adsorption–desorption isotherms, and BET analysis showed that the diatom frustule is a mesoporous material with a surface area of 401.45 m² g⁻¹ amorphous silica. FTIR analysis showed that Navicula australoshetlandica sp. frustules possessed abundant OH functional groups. A low hemolysis ratio was observed for 1–5 mg mL⁻¹ diatom frustules that did not exceed 1.55 ± 0.06%, which indicates favorable hemocompatibility. The diatom frustules exhibited the shortest clotting time (134.99 ± 7.00 s) with a hemostasis material/blood (mg/μL) ratio of 1:100, which is 1.83 times (112.32 s) shorter than that of chitosan. The activated partial thromboplastin time (aPTT) of diatom frustule was also 44.53 s shorter than the control. Our results demonstrate the potential of Navicula australoshetlandica sp. diatom frustules to be used as medical hemostasis material.

New paradigm in diatom omics and genetic manipulation

Diatoms are one of the most heterogeneous eukaryotic plankton known for regulating earth's biogeochemical cycles and maintaining the marine ecosystems ever since the late Eocene epoch. The advent of multidisciplinary omics approach has both epitomized and revolutionized the nature of their chimeric genetic toolkit, ecophysiology, and metabolic adaptability as well as their interaction with other communities. In addition, advanced functional annotation of transcriptomic and proteomic data using cutting edge bioinformatics tools together with high-resolution genome-scale mathematical modeling has effectively proven as the catapult in solving genetic bottlenecks in microbial as well as diatom exploration. In this review, a corroborative summation of the robust work done in manipulating, engineering, and sequencing of the diatom genomes besides underpinning the holistic application of omics in transcription and translation has been discussed in order to shrewd their multifarious novel potential in the field of biotechnology and provide an insight into their dynamic evolutionary relevance.

Biomimetic and bioinspired silicifications: Recent advances for biomaterial design and applications

The rational design and controllable synthesis of functional silica-based materials have gained increased interest in a variety of biomedical and biotechnological applications due to their unique properties. The current review shows that marine organisms, such as siliceous sponges and diatoms, could be the inspiration for the fabrication of advanced biohybrid materials. Several biomolecules were involved in the molecular mechanism of biosilicification in vivo. Mimicking their behavior, functional silica-based biomaterials have been generated via biomimetic and bioinspired silicification in vitro. Additionally, several advanced technologies were developed for in vitro and in vivo immobilization of biomolecules with potential applications in biocatalysis, biosensors, bioimaging, and immunoassays. A thin silica layer could coat a single living cell or virus as a protective shell offering new opportunities in biotechnology and nanomedicine fields. Promising nanotechnologies have been developed for drug encapsulation and delivery in a targeted and controlled manner, in particular for poorly soluble hydrophobic drugs. Moreover, biomimetic silica, as a morphogenetically active biocompatible material, has been utilized in the field of bone regeneration and in the development of biomedical implantable devices. STATEMENT OF SIGNIFICANCE: In nature, silica-based biomaterials, such as diatom frustules and sponge spicules, with high mechanical and physical properties were created under biocompatible conditions. The fundamental knowledge underlying the molecular mechanisms of biosilica formation could inspire engineers and chemists to design novel hybrid biomaterials using molecular biomimetic strategies. The production of such biohybrid materials brings the biosilicification field closer to practical applications. This review starts with the biosilicification process of sponges and diatoms with recently updated researches. Then, this article covers recent advances in the design of silica-based biomaterials and their potential applications in the fields of biotechnology and nanomedicine, highlighting several promising technologies for encapsulation of functional proteins and living cells, drug delivery and the preparation of scaffolds for bone regeneration.

Physical, Chemical, and Genetic Techniques for Diatom Frustule Modification: Applications in Nanotechnology

Diatom frustules represent one of the most complex examples of micro- and nano-structured materials found in nature, being the result of a biomineralization process refined through tens of milions of years of evolution. They are constituted by an intricate, ordered porous silica matrix which recently found several applications in optoelectronics, sensing, solar light harvesting, filtering, and drug delivery, to name a few. The possibility to modify the composition and the structure of frustules can further broaden the range of potential applications, adding new functions and active features to the material. In the present work the most remarkable physical and chemical techniques aimed at frustule modification are reviewed, also examining the most recent genetic techniques developed for its controlled morphological mutation.

Protein-driven biomineralization: Comparing silica formation in grass silica cells to other biomineralization processes

Biomineralization is a common strategy adopted by organisms to support their body structure. Plants practice significant silicon and calcium based biomineralization in which silicon is deposited as silica in cell walls and intracellularly in various cell-types, while calcium is deposited mostly as calcium oxalate in vacuoles of specialized cells. In this review, we compare cellular processes leading to protein-dependent mineralization in plants, diatoms and sponges (phylum Porifera). The mechanisms of biomineralization in these organisms are inherently different. The composite silica structure in diatoms forms inside the cytoplasm in a membrane bound vesicle, which after maturation is exocytosed to the cell surface. In sponges, separate vesicles with the mineral precursor (silicic acid), an inorganic template, and organic molecules, fuse together and are extruded to the extracellular space. In plants, calcium oxalate mineral precipitates in vacuolar crystal chambers containing a protein matrix which is never exocytosed. Silica deposition in grass silica cells takes place outside the cell membrane when the cells secrete the mineralizing protein into the apoplasm rich with silicic acid (the mineral precursor molecules). Our review infers that the organism complexity and precursor reactivity (calcium and oxalate versus silicic acid) are main driving forces for the evolution of varied mineralization mechanisms.

Cloning of Thalassiosira pseudonana's Mitochondrial Genome in Saccharomyces cerevisiae and Escherichia coli

Algae are attractive organisms for biotechnology applications such as the production of biofuels, medicines, and other high-value compounds due to their genetic diversity, varied physical characteristics, and metabolic processes. As new species are being domesticated, rapid nuclear and organelle genome engineering methods need to be developed or optimized. To that end, we have previously demonstrated that the mitochondrial genome of microalgae Phaeodactylum tricornutum can be cloned and engineered in Saccharomyces cerevisiae and Escherichia coli. Here, we show that the same approach can be used to clone mitochondrial genomes of another microalga, Thalassiosira pseudonana. We have demonstrated that these genomes can be cloned in S. cerevisiae as easily as those of P. tricornutum, but they are less stable when propagated in E. coli. Specifically, after approximately 60 generations of propagation in E. coli, 17% of cloned T. pseudonana mitochondrial genomes contained deletions compared to 0% of previously cloned P. tricornutum mitochondrial genomes. This genome instability is potentially due to the lower G+C DNA content of T. pseudonana (30%) compared to P. tricornutum (35%). Consequently, the previously established method can be applied to clone T. pseudonana's mitochondrial genome, however, more frequent analyses of genome integrity will be required following propagation in E. coli prior to use in downstream applications.

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.

Comparative Gene Analysis Focused on Silica Cell Wall Formation: Identification of Diatom-Specific SET Domain Protein Methyltransferases

Silica cell walls of diatoms have attracted attention as a source of nanostructured functional materials and have immense potential for a variety of applications. Previous studies of silica cell wall formation have identified numerous involved proteins, but most of these proteins are species-specific and are not conserved among diatoms. However, because the basic process of diatom cell wall formation is common to all diatom species, ubiquitous proteins and molecules will reveal the mechanisms of cell wall formation. In this study, we assembled de novo transcriptomes of three diatom species, Nitzschia palea, Achnanthes kuwaitensis, and Pseudoleyanella lunata, and compared protein-coding genes of five genome-sequenced diatom species. These analyses revealed a number of diatom-specific genes that encode putative endoplasmic reticulum-targeting proteins. Significant numbers of these proteins showed homology to silicanin-1, which is a conserved diatom protein that reportedly contributes to cell wall formation. These proteins also included a previously unrecognized SET domain protein methyltransferase family that may regulate functions of cell wall formation-related proteins and long-chain polyamines. Proteomic analysis of cell wall-associated proteins in N. palea identified a protein that is also encoded by one of the diatom-specific genes. Expression analysis showed that candidate genes were upregulated in response to silicon, suggesting that these genes play roles in silica cell wall formation. These candidate genes can facilitate further investigations of silica cell wall formation in diatoms.

"Outsourcing" Diatoms in Fabrication of Metal-Doped 3D Biosilica

Diatoms have an ability that is unique among the unicellular photoautotrophic organisms to synthesize an intricately ornamented siliceous (biosilica) exoskeleton with an ordered, hierarchical, three-dimensional structure on a micro- to nanoscale. The unique morphological, structural, mechanical, transport, photonic, and optoelectronic properties of diatomaceous biosilica make it a desirable material for modern technologies. This review presents a summary and discussion of published research on the metabolic insertion of chemical elements with specific functional activity into diatomaceous biosilica. Included in the review is research on innovation in methods of synthesis of a new generation of functional siliceous materials, where the synthesis process is "outsourced" to intelligent microorganisms, referred to here as microtechnologists, by providing them with appropriate conditions and reagents.

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.

Dynamic subcellular translocation of V-type H+ -ATPase is essential for biomineralization of the diatom silica cell wall

Diatom cell walls, called frustules, are main sources of biogenic silica in the ocean and their intricate morphology is an inspiration for nanoengineering. Here we show dynamic aspects of frustule biosynthesis involving acidification of the silica deposition vesicle (SDV) by V-type H⁺  ATPase (VHA). Transgenic Thalassiosira pseudonana expressing the VHA B subunit tagged with enhanced green fluorescent protein (VHA_B -eGFP) enabled subcellular protein localization in live cells. In exponentially growing cultures, VHA_B -eGFP was present in various subcellular localizations including the cytoplasm, SDVs and vacuoles. We studied the role of VHA during frustule biosynthesis in synchronized cell cultures of T. pseudonana. During the making of new biosilica components, VHA_B -eGFP first localized in the girdle band SDVs, and subsequently in valve SDVs. In single cell time-lapse imaging experiments, VHA_B -eGFP localization in SDVs precluded accumulation of the acidotropic silica biomineralization marker PDMPO. Furthermore, pharmacological VHA inhibition prevented PDMPO accumulation in the SDV, frustule biosynthesis and cell division, as well as insertion of the silicalemma-associated protein SAP1 into the SDVs. Finally, partial inhibition of VHA activity affected the nanoscale morphology of the valve. Altogether, these results indicate that VHA is essential for frustule biosynthesis by acidifying the SDVs and regulating the insertion of other structural proteins into the SDV.

Diatom Molecular Research Comes of Age: Model Species for Studying Phytoplankton Biology and Diversity

Diatoms are the world's most diverse group of algae, comprising at least 100,000 species. Contributing ∼20% of annual global carbon fixation, they underpin major aquatic food webs and drive global biogeochemical cycles. Over the past two decades, Thalassiosira pseudonana and Phaeodactylum tricornutum have become the most important model systems for diatom molecular research, ranging from cell biology to ecophysiology, due to their rapid growth rates, small genomes, and the cumulative wealth of associated genetic resources. To explore the evolutionary divergence of diatoms, additional model species are emerging, such as Fragilariopsis cylindrus and Pseudo-nitzschia multistriata Here, we describe how functional genomics and reverse genetics have contributed to our understanding of this important class of microalgae in the context of evolution, cell biology, and metabolic adaptations. Our review will also highlight promising areas of investigation into the diversity of these photosynthetic organisms, including the discovery of new molecular pathways governing the life of secondary plastid-bearing organisms in aquatic environments.

Microbial Nanotechnology: Challenges and Prospects for Green Biocatalytic Synthesis of Nanoscale Materials for Sensoristic and Biomedical Applications

Nanomaterials are increasingly being used in new products and devices with a great impact on different fields from sensoristics to biomedicine. Biosynthesis of nanomaterials by microorganisms is recently attracting interest as a new, exciting approach towards the development of 'greener' nanomanufacturing compared to traditional chemical and physical approaches. This review provides an insight about microbial biosynthesis of nanomaterials by bacteria, yeast, molds, and microalgae for the manufacturing of sensoristic devices and therapeutic/diagnostic applications. The last ten-year literature was selected, focusing on scientific works where aspects like biosynthesis features, characterization, and applications have been described. The knowledge, challenges, and potentiality of microbial-mediated biosynthesis was also described. Bacteria and microalgae are the main microorganism used for nanobiosynthesis, principally for biomedical applications. Some bacteria and microalgae have showed the ability to synthetize unique nanostructures: bacterial nanocellulose, exopolysaccharides, bacterial nanowires, and biomineralized nanoscale materials (magnetosomes, frustules, and coccoliths). Yeasts and molds are characterized by extracellular synthesis, advantageous for possible reuse of cell cultures and reduced purification processes of nanomaterials. The intrinsic variability of the microbiological systems requires a greater protocols standardization to obtain nanomaterials with increasingly uniform and reproducible chemical-physical characteristics. A deeper knowledge about biosynthetic pathways and the opportunities from genetic engineering are stimulating the research towards a breakthrough development of microbial-based nanosynthesis for the future scaling-up and possible industrial exploitation of these promising 'nanofactories'.