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Abstract 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.

Simple Summary: The invasive freshwater jellyfish Craspedacusta sowerbii exists as a microscopic polyp stage and a more visible, pelagic jellyfish-like medusa stage. Current methods to collect these polyps are challenging and time consuming, so we developed a more efficient method involving glass and plastic microscope slides. Polyps became established on these slides, confirming the efficacy of our method. Current sampling methods for detecting the presence of the invasive freshwater hydrozoan Craspedacusta sowerbii rely mainly on visual confirmation of the medusa stage. Confirming the presence of the polyp stage is equally important for observing medusae since typical late summer/early fall occurrences or observations of medusae are sporadic though are becoming more frequent. The polyp stage is important as it is the organism's primary stage and is present throughout the year depending on water temperatures. Therefore, sampling methods for the polyp stage are, commonly, the collection of substrates such as rocks, plants, or pieces of wood in a given body of water, and these can be cumbersome to examine. Polyps are also small, transparent, and difficult to see on natural substrates. Based on a preliminary culturing of the polyp stage on glass and plastic microscope slides in the laboratory, we designed a sampling methodology based on submerging four substrate types (glass and plastic microscope slides, Hester-Dendy discs, and small glass Petri dishes) to confirm the presence of C. sowerbii polyps in the field. We tested this method in three lakes in the Illinois–Indiana region (USA). Two of the lakes have recorded sightings of medusae but the third has no record of polyps or medusae. The sampling method we designed was effective in that C. sowerbii polyps were found on both plastic and glass slides. While this method can be sufficient for detection of the polyp stage, it also shows potential for improvement; we highlight abiotic and biotic ecological parameters as significant factors influencing the collection of C. sowerbii polyps to be considered for future methodologies. [ABSTRACT FROM AUTHOR]

As a renewable marine inorganic material, Coscinodiscus sp. has significant potential in the field of rapid hemostasis. However, the low yield of Coscinodiscus sp. seriously limits the application. In this study, two new culture modes were adopted to increase the production of Coscinodiscus sp., the effect of changes in culture conditions and growth status on the hemostatic activity of diatoms was detected. To prevent Coscinodiscus sp. from sinking in culture, the suspension culture mode was realized by adding 0.5% agar. The semi-continuous high nutrient concentration culture mode increased the cell density of Coscinodiscus sp. to 11000 cells mL−1 and shorten the culture cycle to 5 d. In terms of coagulation activity, the addition of frustules reduced the in vitro coagulation time by half and the activation time of coagulation by 70%. The hemolysis rate and cytotoxicity of frustules harvested in the two culture modes did not change significantly. The results showed that suspension culture mode and high nutrient concentration culture mode only changed the growth state of Coscinodiscus sp., while the hemostatic performance remained stable. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Current sampling methods for detecting the presence of the invasive freshwater hydrozoan Craspedacusta sowerbii rely mainly on visual confirmation of the medusa stage. Confirming the presence of the polyp stage is equally important for observing medusae since typical late summer/early fall occurrences or observations of medusae are sporadic though are becoming more frequent. The polyp stage is important as it is the organism’s primary stage and is present throughout the year depending on water temperatures. Therefore, sampling methods for the polyp stage are, commonly, the collection of substrates such as rocks, plants, or pieces of wood in a given body of water, and these can be cumbersome to examine. Polyps are also small, transparent, and difficult to see on natural substrates. Based on a preliminary culturing of the polyp stage on glass and plastic microscope slides in the laboratory, we designed a sampling methodology based on submerging four substrate types (glass and plastic microscope slides, Hester-Dendy discs, and small glass Petri dishes) to confirm the presence of C. sowerbii polyps in the field. We tested this method in three lakes in the Illinois–Indiana region (USA). Two of the lakes have recorded sightings of medusae but the third has no record of polyps or medusae. The sampling method we designed was effective in that C. sowerbii polyps were found on both plastic and glass slides. While this method can be sufficient for detection of the polyp stage, it also shows potential for improvement; we highlight abiotic and biotic ecological parameters as significant factors influencing the collection of C. sowerbii polyps to be considered for future methodologies.

Diatoms are single-celled algae that biosynthesize cell walls of biogenic silica called "frustules" that are intricately patterned at the submicron- and nanoscale. In this study, we amplified the intrinsic luminescent properties of antibody-functionalized diatom biosilica frustules for enhanced, label-free, photoluminescence (PL) detection of immunocomplex formation. It was hypothesized that metabolically doped GeO centers in antibody-functionalized diatom biosilica would enhance PL emission associated with nucleophilic immunocomplex formation. Germanium (Ge) was metabolically inserted into the frustule biosilica by two-stage cell cultivation of the centric diatom Cyclotella sp. The biosilica frustules were isolated by hydrogen peroxide treatment and thermally annealed to convert Ge oxides in the biosilica (0.4 wt% Ge) to luminescent GeO centers. The Ge-doped biosilica frustules were then functionalized with Rabbit Immunoglobulin G (IgG). Upon immunocomplex formation with its complimentary antigen goat anti-Rabbit IgG, the Ge-oxide doped, antibody-functionalized frustule biosilica increased the intensity of PL emission by a factor of 2.6 relative to immunocomplex formation by antibody-functionalized frustule biosilica without Ge. It is proposed that the luminescent GeO centers in the Ge-oxide doped frustule biosilica were more sensitive to radiative recombination than luminescent silanol groups in frustule biosilica without Ge, resulting in a higher PL emission upon immunocomplex formation. [ABSTRACT FROM AUTHOR]

Abstract The microstructure of diatom frustules found in mud sediments along the coast of Boryeong- city, South Korea, was observed using a scanning electron microscopy (SEM), and the constituent elements of diatoms were analyzed using energy-dispersive X-ray spectroscopy (EDS). Diatom frustules and clay minerals were present in the SEM images of the mud powder. High-magnification SEM images revealed that the surface of the frustules contained identically shaped circular pores, measuring 1 μm in diameter, arranged at regular intervals. This study revealed that the diatom shell fragments in the mud powder ranged in size from 3 to 30 μm, with an average thickness of approximately 2.5 μm. The elements Si, Al, Fe, K, Na, Mg, and Ti were detected while analyzing the frustule constituents, with Si being the primary component with the highest content.

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. [ABSTRACT FROM AUTHOR]

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.

The microstructure of diatom frustules found in mud sediments along the coast of Boryeong- city, South Korea, was observed using a scanning electron microscopy (SEM), and the constituent elements of diatoms were analyzed using energy-dispersive X-ray spectroscopy (EDS). Diatom frustules and clay minerals were present in the SEM images of the mud powder. High-magnification SEM images revealed that the surface of the frustules contained identically shaped circular pores, measuring 1 μm in diameter, arranged at regular intervals. This study revealed that the diatom shell fragments in the mud powder ranged in size from 3 to 30 μm, with an average thickness of approximately 2.5 μm. The elements Si, Al, Fe, K, Na, Mg, and Ti were detected while analyzing the frustule constituents, with Si being the primary component with the highest content. [ABSTRACT FROM AUTHOR]

frustul diatom Navicula sp TAD was isolated by acid washing and burning. Cells of Navicula sp TAD were cultivated for 7 days at room temperature under a light intensity of 5000 lux to obtain high cell density and biomass. The highest cell density was obtained at 72.167 × 105 ± 0.946 cells mL-1. Dry biomass was obtained at 11.459 g with biomass productivity of 0.1364 gL-1 h - 1. Frustul Navicula sp TAD results from 20% HCl washing and burning at 600 oC has a whiter frustul color. The frustul characterization showed that the structure with nanopores on the frustul surface was clearly visible. Frustul from Navicula sp TAD is composed of silicon and oxygen. [ABSTRACT FROM AUTHOR]

The frustule of diatoms has an exceptional structure composed of inorganic and organic molecules. In the organic fraction, protein families were identified whose members are expected to have a complex cellular targeting to their final location within the frustule. Here we investigated for frustule-targeting signals two representatives of the cingulin family, the proteins CinY2 and CinW2; beside an already known, classical signal peptide, we have identified further regions involved in cellular targeting. By using these regions as a search criteria we were able to identify two new frustule proteins. In addition, we showed that the temporal regulation of the gene expression determines the final location of one cingulin. Our results therefore point to a sophisticated cellular and extracellular targeting of frustule components to build the fascinating frustule structure of a diatom. [ABSTRACT FROM AUTHOR]

The frustule of diatoms has an exceptional structure composed of inorganic and organic molecules. In the organic fraction, protein families were identified whose members are expected to have a complex cellular targeting to their final location within the frustule. Here we investigated for frustule-targeting signals two representatives of the cingulin family, the proteins CinY2 and CinW2; beside an already known, classical signal peptide, we have identified further regions involved in cellular targeting. By using these regions as a search criteria we were able to identify two new frustule proteins. In addition, we showed that the temporal regulation of the gene expression determines the final location of one cingulin. Our results therefore point to a sophisticated cellular and extracellular targeting of frustule components to build the fascinating frustule structure of a diatom.

Diatoms are single-celled algae that biosynthesize cell walls of biogenic silica called “frustules” that are intricately patterned at the submicron- and nanoscale. In this study, we amplified the intrinsic luminescent properties of antibody-functionalized diatom biosilica frustules for enhanced, label-free, photoluminescence (PL) detection of immunocomplex formation. It was hypothesized that metabolically doped GeO centers in antibody-functionalized diatom biosilica would enhance PL emission associated with nucleophilic immunocomplex formation. Germanium (Ge) was metabolically inserted into the frustule biosilica by two-stage cell cultivation of the centric diatom Cyclotella sp. The biosilica frustules were isolated by hydrogen peroxide treatment and thermally annealed to convert Ge oxides in the biosilica (0.4 wt% Ge) to luminescent GeO centers. The Ge-doped biosilica frustules were then functionalized with Rabbit Immunoglobulin G (IgG). Upon immunocomplex formation with its complimentary antigen goat anti-Rabbit IgG, the Ge-oxide doped, antibody-functionalized frustule biosilica increased the intensity of PL emission by a factor of 2.6 relative to immunocomplex formation by antibody-functionalized frustule biosilica without Ge. It is proposed that the luminescent GeO centers in the Ge-oxide doped frustule biosilica were more sensitive to radiative recombination than luminescent silanol groups in frustule biosilica without Ge, resulting in a higher PL emission upon immunocomplex formation.

(1) An approach with great potential for fast and cost-effective profiling and identification of diatoms in lake ecosystems is presented herein. This approach takes advantage of Raman spectroscopy. (2) The study was based on the analysis of 790 Raman spectra from 29 species, belonging to 15 genera, 12 families, 9 orders and 4 subclasses, which were analysed using chemometric methods. The Raman data were first analysed by a partial least squares regression discriminant analysis (PLS-DA) to characterise the diatom species. Furthermore, a method was developed to streamline the integrated interpretation of PLS-DA when a high number of significant components is extracted. Subsequently, an artificial neural network (ANN) was used for taxa identification from Raman data. (3) The PLS interpretation produced a Raman profile for each species reflecting its biochemical composition. The ANN models were useful to identify various taxa with high accuracy. (4) Compared to studies in the literature, involving huge datasets one to four orders of magnitude larger than ours, high sensitivity was found for the identification of Achnanthidium exiguum (67%), Fragilaria pararumpens (67%), Amphora pediculus (71%), Achnanthidium minutissimum (80%) and Melosira varians (82%). [ABSTRACT FROM AUTHOR]

SUMMARY: 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. Significance Statement: This comprehensive analysis of silica‐associated diatom proteins employs a combination of proteomics, bioinformatics, and protein localization studies to identify candidate proteins involved in silica biogenesis. Through in‐depth statistical analysis and phylogenomics, we show that these proteins are dominated by intrinsically disordered domains, are enriched in unconventional sequence motifs, and identify potential members of the basal silica biomineralization machinery as well as proteins that probably exert species‐specific functions in this process. [ABSTRACT FROM AUTHOR]

In this study, we investigated cell physiological and biochemical responses to copper (Cu) accumulation in the marine diatom Phaeodactylum tricornutum under different nitrogen (N) and phosphorus (P) conditions. Cells with sufficient N and P (+N+P) showed the highest total Cu concentrations and displayed a higher metal-tolerance ability. In the +N+P treatments, 36.5% of dissolved Cu was adsorbed on the frustules (cell walls), 54.9% was occluded in organelles, and 8.6% was in the soluble fraction. In comparison, cells with N and/or P shortages (+N−P, −N+P, and −N−P) adsorbed 10.8–13.1% of the total Cu onto their cell walls, 74.5–80% was occluded in organelles, and 9.2–12.4% was in the soluble fraction. The Cu2+ influx on the +N+P cell wall was faster due to sufficient metal ligands on the cell walls and up-regulated metal-related transporters. A significant increase in protein content occurred under N and/or P shortages, which was accompanied by the inhibition of the antioxidative enzymatic system and cell membrane damage. Our findings indicate that N and P play an important role in both Cu adsorption (cell surface) and uptake (intracellular), and they provide multifaceted evidence of the Cu acquisition mechanism in P. tricornutum under different macronutrient conditions.

Predation is one of the strongest selection pressures phytoplankton has evolved strategies to cope with. Concurrently, phytoplankton growth must deal with resource acquisition. Experiments on mono- and mixed cultures of morphologically different diatoms exposed to copepods were performed to assess if size and shape were primary drivers in avoiding predation. Additionally, frustule silicification was investigated as a potential factor affecting prey selection by copepods. Thalassiosira pseudonana, Conticribra weissflogii, Cylindrotheca closterium, and Phaeodactylum tricornutum were exposed to the presence of Temora longicornis, a calanoid copepod. The physiological response in terms of growth, elemental composition and morphology was determined. The power of Image Flow Cytometry allowed functional single-cell analyses of mixed cultures in the presence and absence of copepods. Results highlighted that T. pseudonana although the most eaten by copepods in monospecific cultures, was not the preferred prey when the bigger C. weissflogii was added to the culture. When pennates were co-cultured with centric diatoms, their growth was unaffected by predators. Our data suggested that the frustule morphology contributes to long-term prey-predator interaction since the elongated thinner frustule, which evolved more recently, benefited cells in escaping from predators also when facing competition for resources.

Silica granulomas have been described on the skin and are rare; however, this is the first report of a sarcoid‐like granulomatous reaction because of siliceous diatom frustules in the subcutis, making this an unprecedented case. A 41‐year‐old female presented with a subcutaneous nodule on the right forearm clinically suggestive of cyst, foreign body, or lipoma. Excisional biopsy revealed subcutis with a sarcoid‐like granulomatous reaction in a background of fibrosis, containing abundant semitransparent, exquisitely geometric particles, mildly refringent under polarized light, highlighted by phase contrast microscopy; special stains were negative for microorganisms. Definitive characterization of the peculiar fragments was accomplished by confocal laser microscopy, scanning electron microscopy, and energy dispersive X‐ray spectroscopy, revealing them as diatom frustules made of silicon dioxide (SiO2) or silica. Diatoms are unicellular algae, their skeletons (frustules) made of silica have collected on the bottom of rivers, lakes, and oceans for thousands or millions of years and form what we know as diatomite or diatomaceous earth, which is widely used in different industries and easily available in the market. The mechanism whereby diatom frustules gained access to the patient's subcutis is enigmatic. [ABSTRACT FROM AUTHOR]

(1) An approach with great potential for fast and cost-effective profiling and identification of diatoms in lake ecosystems is presented herein. This approach takes advantage of Raman spectroscopy. (2) The study was based on the analysis of 790 Raman spectra from 29 species, belonging to 15 genera, 12 families, 9 orders and 4 subclasses, which were analysed using chemometric methods. The Raman data were first analysed by a partial least squares regression discriminant analysis (PLS-DA) to characterise the diatom species. Furthermore, a method was developed to streamline the integrated interpretation of PLS-DA when a high number of significant components is extracted. Subsequently, an artificial neural network (ANN) was used for taxa identification from Raman data. (3) The PLS interpretation produced a Raman profile for each species reflecting its biochemical composition. The ANN models were useful to identify various taxa with high accuracy. (4) Compared to studies in the literature, involving huge datasets one to four orders of magnitude larger than ours, high sensitivity was found for the identification of Achnanthidium exiguum (67%), Fragilaria pararumpens (67%), Amphora pediculus (71%), Achnanthidium minutissimum (80%) and Melosira varians (82%).

Abstract The external skeleton, frustule, of a diatom is composed of hydrous amorphous silica and amino acids. In this study, the structural changes in the frustule of Chaetoceros calcitrans after thermal treatment up to 1200 °C were investigated using X-ray diffraction and attenuated total reflection infrared spectroscopy and Raman spectroscopy. Their structural changes after thermal treatment give important information to elucidate the unheated structure of the frustule and its crystallization process. In addition, this study is almost the first report to discuss the structure of diatom frustule in detail with Raman spectrum. The unheated structure of the frustule has the relatively ordered and dominant six-membered ring structure made of SiO4 tetrahedra. The sample heated at 800 °C has the more ordered six-membered ring structure observed in quartz or cristobalite. Water molecules and silanol (Si–OH) included in the frustule are dehydrated at this temperature. This dehydration may promote the formation of ordered and polymerized structure. The structure of the frustule after heating at 1200 °C is similar to that of low-cristobalite. However, additional heating is required for complete crystallization.

Diatoms constitute an important group of eukaryotic phytoplankton possessing genetic ability to mineralize amorphous silica into complex structures. Phylogenetic analysis was performed using dnadist module of PHYLIP package, and neighbor-joining method was employed to generate the phylogenetic relationship among the sequences. In order to investigate the phylogenetic relationships among the diatoms at higher taxonomic levels, nucleotide sequence of the nuclear-encoded SSU rRNA coding regions from 21 different diatoms were compared to homologous coding regions from other heterokonts. To provide more accuracy and information to the identification and phylogenetic placement of the analyzed sequences, the highly similar closest matches were used in phylogenetic analysis. In the present investigation, the phylogenetic analysis revealed that the 21 different diatoms of the four study sites could be clustered into six major clades on the basis of their 18S rDNA sequence homology. This finding could further be used for phylogenetic placement of more diatom flora and for proper selection of diatoms to be exploited in nanotechnology. [ABSTRACT FROM AUTHOR]

Highlights • AQ1 diatom frustules were advantageously adopted for lysozyme purification from chicken egg white. • The surface area and cation exchange capacity of AQ1 frustules were about 400 m2/g and 140 μmol/mL. • Through batch purification, the lysozyme recovery was 80–89% with a purity of 90–98% by AQ1 frustules. • In flow-through mode, the lysozyme purity could be notably increased to 99%. Abstract A nontoxic chromatographic matrix, with low cost and high adsorption capacity, is always a major goal for therapeutic protein purification. In this study, the frustules from two cultured diatoms, Nitzschia bilobata (AQ1) and Psammodictyon panduriforme (NP), were investigated as cation exchange materials for lysozyme purification from chicken egg white. The surface area and cation exchange capacity of frustules were about 400 m2/g and 140 μmol/mL for AQ1, 390 m2/g and 130 µmol/mL for NP. The optimal pH was 9 for adsorption. Through batch purification, the lysozyme recovery was 86% with a purity of 95% by AQ1 frustules, which was higher than that by NP frustules (82% with a purity of 90%). In the flow-through system, the purity using AQ1 frustules notably increased to 99%, higher than the result of 91% using NP frustules. Diatom frustules from AQ1 are more effective and could be an alternative chromatographic matrix for lysozyme purification. [ABSTRACT FROM AUTHOR]

Scolionema suvaense is a medusa belonging to the order Limnomedusae, and commonly lives on seaweed and seagrass. The benthic polyp and planktonic medusa are both stages of the life cycle of S. suvaense. Most of the planulae produced by sexual reproduction by the medusae do not metamorphose into polyps but to motile frustules moving to the bottom, which then metamorphose into polyps. The polyps can asexually produce not only medusae but also motile frustules. At a low temperature (15°C), polyps mostly asexually produce frustules. Extension of the habitat area by motile frustules is suggested to occur during winter and early spring when the temperatures are low. With increasing temperature, the reproduction type of S. suvaense polyps changes to asexual production of medusae. In the medusa stage, S. suvaense can reproduce both sexually and asexually. The relative percentages of asexually-reproducing medusae vs. sexually-reproducing medusae were highest at 20°C. This coincides with the highest abundance recorded for S. suvaense medusae, which showed an abrupt increase between May and June. Moreover, with increasing temperature (over 25°C), the reproductive mode of S. suvaense medusae changes from asexual to sexual, and asexually reproducing medusae are not observed at such high temperatures. Changes in the reproduction type and fluctuations in the subsequent population dynamics of S. suvaense depend on the in situ temperatures. [ABSTRACT FROM AUTHOR]

The external skeleton, frustule, of a diatom is composed of hydrous amorphous silica and amino acids. In this study, the structural changes in the frustule of Chaetoceros calcitrans after thermal treatment up to 1200 °C were investigated using X-ray diffraction and attenuated total reflection infrared spectroscopy and Raman spectroscopy. Their structural changes after thermal treatment give important information to elucidate the unheated structure of the frustule and its crystallization process. In addition, this study is almost the first report to discuss the structure of diatom frustule in detail with Raman spectrum. The unheated structure of the frustule has the relatively ordered and dominant six-membered ring structure made of SiO tetrahedra. The sample heated at 800 °C has the more ordered six-membered ring structure observed in quartz or cristobalite. Water molecules and silanol (Si-OH) included in the frustule are dehydrated at this temperature. This dehydration may promote the formation of ordered and polymerized structure. The structure of the frustule after heating at 1200 °C is similar to that of low-cristobalite. However, additional heating is required for complete crystallization. [ABSTRACT FROM AUTHOR]

Diatoms represent the major component of phytoplankton and are responsible for about 20–25% of global primary production. Hundreds of millions of years of evolution led to tens of thousands of species differing in dimensions and morphologies. In particular, diatom porous silica cell walls, the frustules, are characterized by an extraordinary, species-specific diversity. It is of great interest, among the marine biologists and geneticists community, to shed light on the origin and evolutionary advantage of this variability of dimensions, geometries and pore distributions. In the present article the main reported data related to frustule morphogenesis and functionalities with contributions from fundamental biology, genetics, mathematics, geometry and physics are reviewed. [ABSTRACT FROM AUTHOR]

Coscinodiscus genus , a type of diatoms with complex frustule, has been widely studied and reported because of their delicate nanostructures. In this paper, a dual beam system focused ion beam and scanning electron microscope (FIB-SEM) were applied to precisely investigate the microstructure of diatom cell walls, in particular, aiming to reveal the hierarchical pores of the valve. The microstructures of the valve, valve mantle and girdle bands were illustrated in details through a series of high resolution images after performing the cross section milling of the specific region. The 3D morphology of frustule valve was reconstructed based on the 2D image series, which demonstrated the presence of cribellum in valve, the external foramen, hexagonal cavity and the internal foramen. The four dense porous membranes and girdle bands were characterized clearly based on FIB-SEM dual beam system. An integrated model of Coscinodiscus frustule could be simulated based on the 2D and 3D results. This study provided a systematic approach to measure the morphological features of diatoms at a nanoscale, which could be applied to other nanoporous structure in three dimensions. [ABSTRACT FROM AUTHOR]

Diatoms are the most important contributors to marine primary production, and their most distinctive feature is the silicified cell wall, known as frustule. Recent years, abundant evidences demonstrate that frustule is essential for diatoms metabolic activities, such as nutrients uptake, protection against ultraviolet radiation, deterrent to predation, resistance to parasites, light harvesting, CO 2 capture, and position control. Besides that, due to the uniform composition of silica, internal hollow structure, multilayer porous valve, high thermal stability, and functionally active surface, frustule, as the most exquisite biosilica in the earth, also shows huge potentiality in biomedical field serving as promising bionanomaterials. Considering that the architecture features and physicochemical properties of frustule underlie its biological functions and biomedical applications, therefore, this review starts from the morphological and physicochemical characteristics, and then introduces the biological functions and biomedical applications of the frustule. • Frustule plays essential roles on various metabolic activities of diatom. • Unique composition and architecture make frustule as great bionanomaterial. • Advanced biotechnology gives an opportunity to obtain enabled frustule. • More attentions need to be paid on the discovery of genes related to frustule biogenesis. [ABSTRACT FROM AUTHOR]

Forty-eight isolates of Pseudo- nitzschia species were established from the Miri coast of Sarawak (Malaysian Borneo) and underwent TEM observation and molecular characterization. Ten species were found: P. abrensis, P. batesiana, P. fukuyoi, P. kodamae, P. lundholmiae, P. multistriata, P. pungens, P. subfraudulenta, as well as two additional new morphotypes, herein designated as P. bipertita sp. nov. and P. limii sp. nov. This is the first report of P. abrensis, P. batesiana, P. kodamae, P. fukuyoi, and P. lundholmiae in coastal waters of Malaysian Borneo. Pseudo-nitzschia bipertita differs from its congeners by the number of sectors that divide the poroids, densities of band striae, and its cingular band structure. Pseudo-nitzschia limii, a pseudo-cryptic species in the P. pseudodelicatissima complex sensu lato, is distinct by having wider proximal and distal mantles, a higher number of striae, and greater poroid height in the striae of the valvocopula. The species were further supported by the phylogenetic reconstructions of the nuclear-encoded large subunit ribosomal gene and the second internal transcribed spacer. Phylogenetically, P. bipertita clustered with its sister taxa ( P. subpacifica + P. heimii); P. limii appears as a sister taxon to P. kodamae and P. hasleana in the ITS2 tree. Pairwise comparison of ITS2 transcripts with its closest relatives revealed the presence of both hemi- and compensatory base changes. Toxicity analysis showed detectable levels of domoic acid in P. abrensis, P. batesiana, P. lundholmiae, and P. subfraudulenta, but both new species tested below the detection limit. [ABSTRACT FROM AUTHOR]

Side orientation of cells is usually ambiguous in unicellular organisms, making it impossible to separate components of directional asymmetry (DA) and fluctuating asymmetry (FA). However, frustules of the diatom Luticola poulickovae have biradially symmetric outlines, and their central areas bear ornamentation that is asymmetric across the apical axis. The goal of this study was to explore differentiation of morphometric asymmetry across the apical axis into DA and FA components. Is there detectable DA of the valve outlines of two L. poulickovae strains that may be related to the asymmetric central areas? Given that the life cycle of diatoms involves cell-size diminution, and cell shape is strongly affected by allometry, we also explored the question of whether asymmetry is correlatedwith cell size. The extent of symmetric variation among individuals in each strain, aswell as DA and FA across the apical axis, were quantified using two Procrustes ANOVA models. The results revealed no correlation of either total asymmetry or FA with valve size. DA was significant and considerably more pronounced than FA in both strains, indicating that there is previously unknown systematic asymmetry of valve outlines of L. poulickovae, which may be related to the asymmetry of its central area. [ABSTRACT FROM AUTHOR]