Revealing the molecular secrets of marine diatoms

Transcriptomic analysis of Chaetoceros muelleri in response to different nitrogen concentrations reveals the activation of pathways to enable efficient nitrogen uptake

Nitrogen is the principal nutrient deficiency that increases lipids and carbohydrate content in diatoms but negatively affects biomass production. Marine diatom Chaetoceros muelleri is characterized by lipid and carbohydrate accumulation under low nitrogen concentration without affecting biomass. To elucidate the molecular effects of nitrogen concentrations, we performed an RNA-seq analysis of C. muelleri grown under four nitrogen concentrations (3.53 mM, 1.76 mM, 0.44 mM, and 0.18 mM of NaNO3). This research revealed that changes in global transcription in C. muelleri are differentially expressed by nitrogen concentration. "Energetic metabolism", "Carbohydrate metabolism" and "Lipid metabolism" pathways were identified as the most upregulated by N deficiency. Due to N limitation, alternative pathways to self-supply nitrogen employed by microalgal cells were identified. Additionally, nitrogen limitation decreased chlorophyll content and caused a greater response at the transcriptional level with a higher number of unigenes differentially expressed. By contrast, the highest N concentration (3.53 mM) recorded the lowest number of differentially expressed genes. Amt1, Nrt2, Fad2, Skn7, Wrky19, and Dgat2 genes were evaluated by RT-qPCR. In conclusion, C. muelleri modify their metabolic pathways to optimize nitrogen utilization and minimize nitrogen losses. On the other hand, the assembled transcriptome serves as the basis for metabolic engineering focused on improving the quantity and quality of the diatom for biotechnological applications. However, proteomic and metabolomic analysis is also required to compare gene expression, protein, and metabolite accumulation.

Skeletonema marinoi ecotypes show specific habitat-related responses to fluctuating light supporting high potential for growth under photobioreactor light regime

Diatoms are a diverse group of phytoplankton usually dominating areas characterized by rapidly shifting light conditions. Because of their high growth rates and interesting biochemical profile, their biomass is considered for various commercial applications. This study aimed at identifying strains with superior growth in a photobioreactor (PBR) by screening the natural intraspecific diversity of ecotypes isolated from different habitats. We investigated the effect of PBR light fluctuating on a millisecond scale (FL, simulating the light in a PBR) on 19 ecotypes of the diatom Skeletonema marinoi isolated from the North Sea-Baltic Sea area. We compare growth, pigment ratios, phylogeny, photo-physiological variables and photoacclimation strategies between all strains and perform qPCR and absorption spectra analysis on a subset of strains. Our results show that the ecotypes responded differently to FL, and have contrasting photo-physiological and photoprotective strategies. The strains from Kattegat performed better in FL, and shared common photoacclimation and photoprotection strategies that are the results of adaptation to the specific light climate of the Kattegat area. The strains that performed better with FL conditions had a high light (HL)-acclimated phenotype coupled with unique nonphotochemical quenching features. Based on their characteristics, three strains were identified as good candidates for growth in PBRs.

Electric Field Susceptibility of Chlorophyll c Leads to Unexpected Excitation Dynamics in the Major Light-Harvesting Complex of Diatoms

Diatoms are one of the most abundant photosynthetic organisms on earth and contribute largely to atmospheric oxygen production. They contain fucoxanthin and chlorophyll-a/c binding proteins (FCPs) as light-harvesting complexes with a remarkable adaptation to the fluctuating light on ocean surfaces. To understand the basis of the photosynthetic process in diatoms, the excitation energy funneling within FCPs must be probed. A state-of-the-art multiscale analysis within a quantum mechanics/molecular mechanics framework has been employed. To this end, the chlorophyll (Chl) excitation energies within the FCP complex from the diatom Phaeodactylum tricornutum have been determined. The Chl-c excitation energies were found to be 5-fold more susceptible to electric fields than those of Chl-a pigments and thus are significantly lower in FCP than in organic solvents. This finding challenges the general belief that the excitation energy of Chl-c is always higher than that of Chl-a in FCP proteins and reveals that Chl-c molecules are much more sensitive to electric fields within protein scaffolds than in Chl-a pigments. The analysis of the linear absorption spectrum and the two-dimensional electronic spectra of the FCP complex strongly supports these findings and allows us to study the excitation transfer within the FCP complex.

Oligotrophic waters of the Northwest Atlantic support taxonomically diverse diatom communities that are distinct from coastal waters

Diatoms are important components of the marine food web and one of the most species-rich groups of phytoplankton. The diversity and composition of diatoms in eutrophic nearshore habitats have been well documented due to the outsized influence of diatoms on coastal ecosystem functioning. In contrast, patterns of both diatom diversity and community composition in offshore oligotrophic regions where diatom biomass is low have been poorly resolved. To compare the diatom diversity and community composition in oligotrophic and eutrophic waters, diatom communities were sampled along a 1,250 km transect from the oligotrophic Sargasso Sea to the coastal waters of the northeast US shelf. Diatom community composition was determined by amplifying and sequencing the 18S rDNA V4 region. Of the 301 amplicon sequence variants (ASVs) identified along the transect, the majority (70%) were sampled exclusively from oligotrophic waters of the Gulf Stream and Sargasso Sea and included the genera Bacteriastrum, Haslea, Hemiaulus, Pseudo-nitzschia, and Nitzschia. Diatom ASV richness did not vary along the transect, indicating that the oligotrophic Sargasso Sea and Gulf Stream are occupied by a diverse diatom community. Although ASV richness was similar between oligotrophic and coastal waters, diatom community composition in these regions differed significantly and was correlated with temperature and phosphate, two environmental variables known to influence diatom metabolism and geographic distribution. In sum, oligotrophic waters of the western North Atlantic harbor diverse diatom assemblages that are distinct from coastal regions, and these open ocean diatoms warrant additional study, as they may play critical roles in oligotrophic ecosystems.

An improved blood hemorrhaging treatment using diatoms frustules, by alternating Ca and light levels in cultures

Hemorrhage control requires hemostatic materials that are both effective and biocompatible. Among these, diatom biosilica (DBs) could significantly improve hemorrhage control, but it induces hemolysis (the hemolysis rate > 5%). Thus, the purpose of this study was to explore the influence of Ca2+ biomineralization on DBs for developing fast hemostatic materials with a low hemolysis rate. Here, CaCl2 was added to the diatom medium under high light (cool white, fluorescent lamps, 67.5 µmol m-2 s-1), producing Ca-DBs-3 with a particle size of 40-50 μm and a Ca2+ content of Ca-DBs-3 obtained from the higher concentration CaCl2 group (6.7 mmol L-1) of 0.16%. The liquid absorption capacity of Ca-DBs-3 was 30.43 ± 0.57 times its dry weight; the in vitro clotting time was comparable to QuikClot® zeolite; the hemostatic time and blood loss using the rat tail amputation model were 36.40 ± 2.52 s and 0.39 ± 0.12 g, which were 40.72% and 19.50% of QuikClot® zeolite, respectively. Ca-DBs-3 showed no apparent toxicity to L929 cells (cell viability > 80%) and was non-hemolysis (the hemolysis rate < 2%). This study prepared Ca-DBs-3 with a rapid hemostatic effect and good biocompatibility, providing a path to develop diatom biosilica hemostatic materials.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00180-3.

Evaluation of the antioxidative response of diatoms grown on emerging steroidal contaminants

With increasing anthropic activities, a myriad of typical contaminants from industries, hospitals, and municipal discharges have been found which fail to be categorized under regulatory standards and are hence considered contaminants of "emerging concern". Since these pollutants are not removed effectively even by the conventional treatment systems, they tend to inflict potential threats to both human and aquatic life. However, microalgae-mediated remediation strategies have recently gained worldwide importance owing to their role in carbon fixation, low operational cost, and production of high-value products. In this study, centric diatom Chaetoceros neogracilis was exposed to different concentrations of estradiol (E2)-induced synthetic media ranging from 0 to 2 mg L^-1, and its impact on the antioxidative system of algae was investigated. The results demonstrate that the nutrient stress caused a strong oxidative response elevating the superoxide dismutase (SOD) activity and malondialdehyde (MDA) content in the 2 mg L^-1 E2-treated diatom cultures. However, the specific activity of the H₂O₂ radical scavenging enzymes like catalase (CAT) was inhibited by the E2 treatment, while that of ascorbate peroxidase (APX) remained comparable to the control (0 mg L^-1 of E2). Thus, the study reveals the scope of diatoms as potential indicators of environmental stress even under the varying concentration of a single contaminant (E2).

New recorded diatoms in Holocene sediment cores from the Gonggeom-ji Wetland in Korea

The Gonggeom-ji reservoir is an agricultural one built for rice farming during the Proto-Three Kingdoms period and was designated as Gyeongsangbuk-do monument No. 121 because of its high historical value. The Nakdonggang National Institute of Biological Resources has been conducting paleontological and paleoenvironmental studies on major wetlands from Korea since 2016, as well as diatom, geological, and depth distribution analyses on the sedimentary soil of Gonggeom-ji. This study summarized the description and ecological characteristics of six newly recorded diatoms (Gomphonema lacusrankala, Pinnularia diandae, P. gibba var. hyaline, P. lacunarum, Sellaphora labda var. nipponica, Stauroneis angustilancea) found in samples collected through drilling in Gonggeom-ji in 2019.

Biochemical Characterization of a Novel Redox-Regulated Metacaspase in a Marine Diatom

Programmed cell death (PCD) in marine microalgae was suggested to be one of the mechanisms that facilitates bloom demise, yet its molecular components in phytoplankton are unknown. Phytoplankton are completely lacking any of the canonical components of PCD, such as caspases, but possess metacaspases. Metacaspases were shown to regulate PCD in plants and some protists, but their roles in algae and other organisms are still elusive. Here, we identified and biochemically characterized a type III metacaspase from the model diatom Phaeodactylum tricornutum, termed PtMCA-IIIc. Through expression of recombinant PtMCA-IIIc in E. coli, we revealed that PtMCA-IIIc exhibits a calcium-dependent protease activity, including auto-processing and cleavage after arginine. Similar metacaspase activity was detected in P. tricornutum cell extracts. PtMCA-IIIc overexpressing cells exhibited higher metacaspase activity, while CRISPR/Cas9-mediated knockout cells had decreased metacaspase activity compared to WT cells. Site-directed mutagenesis of cysteines that were predicted to form a disulfide bond decreased recombinant PtMCA-IIIc activity, suggesting its enhancement under oxidizing conditions. One of those cysteines was oxidized, detected in redox proteomics, specifically in response to lethal concentrations of hydrogen peroxide and a diatom derived aldehyde. Phylogenetic analysis revealed that this cysteine-pair is unique and widespread among diatom type III metacaspases. The characterization of a cell death associated protein in diatoms provides insights into the evolutionary origins of PCD and its ecological significance in algal bloom dynamics.

Benthic Diatoms in River Biomonitoring—Present and Future Perspectives within the Water Framework Directive

The European Water Framework Directive 2000/60/EC (WFD) has been implemented over the past 20 years, using physicochemical, biological and hydromorphological elements to assess the ecological status of surface waters. Benthic diatoms (i.e., phytobenthos) are one of the most common biological quality elements (BQEs) used in surface water monitoring and are particularly successful in detecting eutrophication, organic pollution and acidification. Herein, we reviewed their implementation in river biomonitoring for the purposes of the WFD, highlighting their advantages and disadvantages over other BQEs, and we discuss recent advances that could be applied in future biomonitoring. Until now, phytobenthos have been intercalibrated by the vast majority (26 out of 28) of EU Member States (MS) in 54% of the total water bodies assessed and was the most commonly used BQE after benthic invertebrates (85% of water bodies), followed by fish (53%), macrophytes (27%) and phytoplankton (4%). To meet the WFD demands, numerous taxonomy-based quality indices have been developed among MS, presenting, however, uncertainties possibly related to species biogeography. Recent development of different types of quality indices (trait-based, DNA sequencing and predictive modeling) could provide more accurate results in biomonitoring, but should be validated and intercalibrated among MS before their wide application in water quality assessments.

On the fate of sinking diatoms: the transport of active buoyancy-regulating cells in the ocean

Diatoms are one of the most abundant, diverse and ecologically relevant phytoplanktonic group, contributing enormously to global biogeochemical processes like the carbon and silica cycles. This large success has been partly attributed to the mechanical and optical properties of the silica shell (the frustule) that envelops their body. But since they lack motility it is difficult to conceive how they cope with the fast-fluctuating environment they live in and where distributions of resources are very heterogeneous and dynamical. This pinpoints an important but yet poorly understood feature of diatoms physiology: buoyancy regulation that helps them controlling their sinking speed and position in the water column. While buoyancy regulation by light and nutrients availability has been well studied, the effect of hydromechanical stress via fluid shear has been rather overlooked when considering diatoms dynamics. Here, we aim to start filling this gap by first presenting direct experimental evidences for buoyancy control in response to hydro-mechanical stress and then review recent theoretical models where simple couplings between local shear and buoyancy control always result in heterogeneous cell distributions, specific accumulation regions within complex flows and increased sedimentation times to the depths, features of direct ecological relevance. We conclude by suggesting future experiments aiming to unveil such coupling and therefore gain better understanding on the fate of these fascinating microorganisms in their natural habitat. This article is part of the theme issue 'Stokes at 200 (part 2)'.

Wealth from waste: Diatoms as tools for phycoremediation of wastewater and for obtaining value from the biomass

Diatoms are a type of microalgae with diverse capabilities which make them useful for multiple applications. The abundance of diatoms in water bodies facilitates the removal of pollutants from wastewater originating from different industries, such as agriculture and other anthropogenic sources. The unique photosynthetic, cellular and metabolic characteristics of diatoms allows them to utilize pollutants like nitrate, iron, phosphate, molybdenum, silica, and heavy metals, such as copper, cadmium, chromium, lead, etc., which make diatoms a good option for wastewater treatment. In addition, the biomass produced by diatoms growth on wastewaters has diverse applications and can, therefore, be valuable. This review focusses on the unique capabilities of diatoms for wastewater remediation and the capture of carbon dioxide, concomitant with the generation of valuable products. Diatom biorefinery can be a sustainable solution to wastewater management, and the biomass obtained from treatment can be turned into biofuels, biofertilizers, nutritional supplements for animal production, and used for pharmaceutical applications containing bioactive compounds like EPA, DHA and pigments such as fucoxanthin.

Evolution of Codon Usage Bias in Diatoms

Codon usage bias (CUB)-preferential use of one of the synonymous codons, has been described in a wide range of organisms from bacteria to mammals, but it has not yet been studied in marine phytoplankton. CUB is thought to be caused by weak selection for translational accuracy and efficiency. Weak selection can overpower genetic drift only in species with large effective population sizes, such as Drosophila that has relatively strong CUB, while organisms with smaller population sizes (e.g., mammals) have weak CUB. Marine plankton species tend to have extremely large populations, suggesting that CUB should be very strong. Here we test this prediction and describe the patterns of codon usage in a wide range of diatom species belonging to 35 genera from 4 classes. We report that most of the diatom species studied have surprisingly modest CUB (mean Effective Number of Codons, ENC = 56), with some exceptions showing stronger codon bias (ENC = 44). Modest codon bias in most studied diatom species may reflect extreme disparity between astronomically large census and modest effective population size (N_e), with fluctuations in population size and linked selection limiting long-term N_e and rendering selection for optimal codons less efficient. For example, genetic diversity (pi ~0.02 at silent sites) in Skeletonema marinoi corresponds to N_e of about 10 million individuals, which is likely many orders of magnitude lower than its census size. Still, N_e ~10⁷ should be large enough to make selection for optimal codons efficient. Thus, we propose that an alternative process-frequent changes of preferred codons, may be a more plausible reason for low CUB despite highly efficient selection for preferred codons in diatom populations. The shifts in the set of optimal codons should result in the changes of the direction of selection for codon usage, so the actual codon usage never catches up with the moving target of the optimal set of codons and the species never develop strong CUB. Indeed, we detected strong shifts in preferential codon usage within some diatom genera, with switches between preferentially GC-rich and AT-rich 3^rd codon positions (GC3). For example, GC3 ranges from 0.6 to 1 in most Chaetoceros species, while for Chaetoceros dichaeta GC3 = 0.1. Both variation in selection intensity and mutation spectrum may drive such shifts in codon usage and limit the observed CUB. Our study represents the first genome-wide analysis of CUB in diatoms and the first such analysis for a major phytoplankton group.

Turbulence induces clustering and segregation of non-motile, buoyancy-regulating phytoplankton

Turbulence plays a major role in shaping marine community structure as it affects organism dispersal and guides fundamental ecological interactions. Below oceanographic mesoscale dynamics, turbulence also impinges on subtle physical-biological coupling at the single cell level, setting a sea of chemical gradients and determining microbial interactions with profound effects on scales much larger than the organisms themselves. It has been only recently that we have started to disentangle details of this coupling for swimming microorganisms. However, for non-motile species, which comprise some of the most abundant phytoplankton groups on Earth, a similar level of mechanistic understanding is still missing. Here, we explore by means of extensive numerical simulations the interplay between buoyancy regulation in non-motile phytoplankton and cellular responses to turbulent mechanical cues. Using a minimal mechano-response model, we show how such a mechanism would contribute to spatial heterogeneity and affect vertical fluxes and trigger community segregation.

Insights into the mechanisms and dynamics of energy transfer in plant light-harvesting complexes from two-dimensional electronic spectroscopy

During the past two decades, two-dimensional electronic spectroscopy (2DES) and related techniques have emerged as a potent experimental toolset to study the ultrafast elementary steps of photosynthesis. Apart from the highly engaging albeit controversial analysis of the role of quantum coherences in the photosynthetic processes, 2DES has been applied to resolve the dynamics and pathways of energy and electron transport in various light-harvesting antenna systems and reaction centres, providing unsurpassed level of detail. In this paper we discuss the main technical approaches and their applicability for solving specific problems in photosynthesis. We then recount applications of 2DES to study the exciton dynamics in plant and photosynthetic light-harvesting complexes, especially light-harvesting complex II (LHCII) and the fucoxanthin-chlorophyll proteins of diatoms, with emphasis on the types of unique information about such systems that 2DES is capable to deliver. This article is part of a Special Issue entitled Light harvesting, edited by Dr. Roberta Croce.

Diatom isoprenoids: Advances and biotechnological potential

Diatoms are among the most productive and ecologically important groups of microalgae in contemporary oceans. Due to their distinctive metabolic and physiological features, they offer exciting opportunities for a broad range of commercial and industrial applications. One such feature is their ability to synthesize a wide diversity of isoprenoid compounds. However, limited understanding of how these molecules are synthesized have until recently hindered their exploitation. Following comprehensive genomic and transcriptomic analysis of various diatom species, the biosynthetic mechanisms and regulation of the different branches of the pathway are now beginning to be elucidated. In this review, we provide a summary of the recent advances in understanding diatom isoprenoid synthesis and discuss the exploitation potential of diatoms as chassis for high-value isoprenoid synthesis.

Dark metabolism: a molecular insight into how the Antarctic sea-ice diatom Fragilariopsis cylindrus survives long-term darkness

Light underneath Antarctic sea-ice is below detectable limits for up to 4 months of the year. The ability of Antarctic sea-ice diatoms to survive this prolonged darkness relies on their metabolic capability. This study is the first to examine the proteome of a prominent sea-ice diatom in response to extended darkness, focusing on the protein-level mechanisms of dark survival. The Antarctic diatom Fragilariopsis cylindrus was grown under continuous light or darkness for 120 d. The whole cell proteome was quantitatively analysed by nano-LC-MS/MS to investigate metabolic changes that occur during sustained darkness and during recovery under illumination. Enzymes of metabolic pathways, particularly those involved in respiratory processes, tricarboxylic acid cycle, glycolysis, the Entner-Doudoroff pathway, the urea cycle and the mitochondrial electron transport chain became more abundant in the dark. Within the plastid, carbon fixation halted while the upper sections of the glycolysis, gluconeogenesis and pentose phosphate pathways became less active. We have discovered how F. cylindrus utilises an ancient alternative metabolic mechanism that enables its capacity for long-term dark survival. By sustaining essential metabolic processes in the dark, F. cylindrus retains the functionality of the photosynthetic apparatus, ensuring rapid recovery upon re-illumination.

Marine biofilms: diversity of communities and of chemical cues

Surfaces immersed in seawater are rapidly colonized by various microorganisms, resulting in the formation of heterogenic marine biofilms. These communities are known to influence the settlement of algae spores and invertebrate larvae, triggering a succession of fouling events, with significant environmental and economic impacts. This review covers recent research regarding the differences in composition of biofilms isolated from different artificial surface types and the influence of environmental factors on their formation. One particular phenomenon - bacterial quorum sensing (QS) - allows bacteria to coordinate swarming, biofilm formation among other phenomena. Some other marine biofilm chemical cues are believed to modulate the settlement and the succession of macrofouling organisms, and they are also reviewed here. Finally, since the formation of a marine biofilm is considered to be an initial, QS-dependent step in the development of marine fouling events, QS inhibition is discussed on its potential as a tool for antibiofouling control in marine settings.

Transgene-free genome editing in marine algae by bacterial conjugation - comparison with biolistic CRISPR/Cas9 transformation

The CRISPR/Cas9 technology has opened the possibility for targeted genome editing in various organisms including diatom model organisms. One standard method for delivery of vectors to diatom cells is by biolistic particle bombardment. Recently delivery by conjugation was added to the tool-box. An important difference between these methods is that biolistic transformation results in transgene integration of vector DNA into the algae genome, whereas conjugative transformation allows the vector to be maintained as an episome in the recipient cells. In this study, we have used both transformation methods to deliver the CRISPR/Cas9 system to the marine diatom Phaeodactylum tricornutum aiming to induce mutations in a common target gene. This allowed us to compare the two CRISPR/Cas9 delivery systems with regard to mutation efficiency, and to assess potential problems connected to constitutive expression of Cas9. We found that the percentage of CRISPR-induced targeted biallelic mutations are similar for both methods, but an extended growth period might be needed to induce biallelic mutations when the CRISPR/Cas9 system is episomal. Independent of the CRISPR/Cas9 vector system, constitutive expression of Cas9 can cause re-editing of mutant lines with small indels. Complications associated with the biolistic transformation system like the permanent and random integration of foreign DNA into the host genome and unstable mutant lines caused by constitutive expression of Cas9 can be avoided using the episomal CRISPR/Cas9 system. The episomal vector can be eliminated from the diatom cells by removal of selection pressure, resulting in transient Cas9 expression and non-transgenic mutant lines. Depending on legislation, such lines might be considered as non-GMOs.

Effect of iron on the growth of Phaeodactylum tricornutum via photosynthesis

Iron is a limiting factor that controls the phytoplankton biomass in the modern ocean, and iron fertilization of the ocean could lead to blooms dominated by diatoms. Thus, iron plays an important role in controlling the distribution of diatoms. In this study, we measured the growth rate and photosynthetic activity of the model diatom Phaeodactylum tricornutum cultured under different iron concentrations and found that it grew more rapidly and had a much higher photosynthetic efficiency under higher iron concentrations. In order to explore the unique mechanism of the response of diatoms to iron, a proteomic analysis was carried out, and the results indicated that iron promotes the Calvin cycle of P. tricornutum. Diatoms can tolerate the pressure of iron limitation by replacing iron-rich proteins with flavodoxin, and so on. Moreover, we found that the photosystem I (PSI) activity of iron-limited algae that were treated by N',N',N',N'-tetramethyl-p-phenylenediamine (TMPD) was increased significantly. As TMPD plays the role of a cytochrome b₆ /f complex that transfers electrons from photosystem II to PSI, the cytochrome b₆ /f complex is the key to photosynthesis regulation. Iron could influence the growth of P. tricornutum by regulating its biosynthesis. All of the results suggest that iron might affect the growth of diatoms through the Calvin cycle and the cytochrome b₆ /f complex.

Endogenous physical regulation of population density in the freshwater protozoan Paramecium caudatum

Studies confirm physical long-range cell-cell communication, most evidently based on electromagnetic fields. Effects concern induction or inhibition of cell growth. Their natural function is unclear. With the protozoan Paramecium caudatum I tested whether the signals regulate cell density and are electromagnetic. Up to 300 cells/mL, cell growth in clones of this study is decreasingly pronounced. Using cuvettes as chemical barriers enabling physical communication  I  placed 5 indicator cells/mL, the inducer populations, into smaller cuvettes that stand in bigger and contained 50, 100, 200 or 300 cells/mL. Under conditions of total darkness such pairs were mutually exposed for 48 hours. The hypothesis was that indicator cells, too, grow less the more neighbor cells there are. The bigger inducer populations were in the beginning the less they grew. The indicator populations grew accordingly; the more cells they were surrounded by the less they grew. The suppressing neighbors-effect disappeared when inner cuvettes were shielded by graphite known to shield electromagnetic radiation from GHz to PHz, i.e. to absorb energy from microwaves to light. These are the first results demonstrating non-contact physical quorum sensing for cell population density regulation. I assume rules intrinsic to electromagnetic fields interacting with matter and life.

Defense related decadienal elicits membrane lipid remodeling in the diatom Phaeodactylum tricornutum

Diatoms rapidly release extracellular oxylipins (oxygenated lipids) including polyunsaturated aldehydes in response to herbivory and other stresses. Oxylipins have several defense-related activities including inhibition of reproduction in herbivores and signaling to distant diatoms. Physiological changes in diatoms exposed to varying levels of oxylipins are only beginning to be understood. In this study, Phaeodactylum tricornutum cultures were treated with sublethal concentrations of the polyunsaturated aldehyde trans,trans-2,4-decadienal (DD) to assess effects on lipid composition and membrane permeability. In cells treated with DD for 3 hr, all measured saturated and unsaturated fatty acids significantly decreased (0.46–0.69 fold of levels in solvent control cells) except for 18:2 (decreased but not significantly). The decrease was greater in the polyunsaturated fatty acid pool than the saturated and monounsaturated fatty acid pool. Analysis of lipid classes revealed increased abundances of phosphatidylethanolamine and phosphatidylcholine at 3 and 6 hr. Concomitantly, these and other membrane lipids exhibited increased saturated and monounsaturated acyl chains content relative to polyunsaturated acyl chains compared to control cells. Evidence of decreased plasma membrane permeability in DD treated cells was obtained, based on reduced uptake of two of three dyes relative to control cells. Additionally, cells pre-conditioned with a sublethal DD dose for 3 hr then treated with a lethal DD dose for 2 hr exhibited greater membrane integrity than solvent pre-conditioned control cells that were similarly treated. Taken together, the data are supportive of the hypothesis that membrane remodeling induced by sublethal DD is a key element in the development of cellular resistance in diatoms to varying and potentially toxic levels of polyunsaturated aldehydes in environments impacted by herbivory or other stresses.

Bioinspired carbide-derived carbons with hierarchical pore structure for the adsorptive removal of mercury from aqueous solution

Biosilica of the diatom species Thalassiosira pseudonana is used as hard template for the synthesis of silicon carbide-derived carbons.

Gold Nanoparticle-Decorated Diatom Biosilica: A Favorable Catalyst for the Oxidation of d-Glucose

Diatoms are unicellular algae of enormous biodiversity that occur in all water habitats on earth. Their cell walls are composed of amorphous biosilica and exhibit species-specific nanoporous to microporous and macroporous patterning. Therefore, diatom biosilica is a promising renewable material for various applications, such as in catalysis, drug-delivery systems, and biophotonics. In this study, diatom biosilica of three different species (Stephanopyxis turris, Eucampia zodiacus, and Thalassiosira pseudonana) was used as support material for gold nanoparticles using a covalent coupling method. The resulting catalysts were applied for the oxidation of d-glucose to d-gluconic acid. Because of its high specific surface area, well-established transport pores, and the presence of small, homogeneously distributed gold nanoparticles on the surface, diatom biosilica provides a highly catalytically active surface and advanced accessibility to the active sites. In comparison to those of the used reference supports, higher catalytic activities (up to 3.28 × 10^-4 mmol_Glc s^-1 mg_Au ^-1 for T. pseudonana biosilica) and slower deactivation were observed for two of the diatom biosilica materials. In addition, diatom biosilica showed very high gold-loading capacities (up to 45 wt %), with a homogeneous nanoparticle distribution.

Effects of titanium dioxide nanoparticles derived from consumer products on the marine diatom Thalassiosira pseudonana

Increased manufacture of TiO₂ nanoproducts has caused concern about the potential toxicity of these products to the environment and in public health. Identification and confirmation of the presence of TiO₂ nanoparticles derived from consumer products as opposed to industrial TiO₂ NPs warrant examination in exploring the significance of their release and resultant impacts on the environment. To this end, we examined the significance of the release of these particles and their toxic effect on the marine diatom algae Thalassiosira pseudonana. Our results indicate that nano-TiO₂ sunscreen and toothpaste exhibit more toxicity in comparison to industrial TiO₂ and inhibited the growth of the marine diatom T. pseudonana. This inhibition was proportional to the exposure time and concentrations of nano-TiO₂. Our findings indicate a significant effect, and therefore, further research is warranted in evaluation and assessment of the toxicity of modified nano-TiO₂ derived from consumer products and their physicochemical properties.

Quantum Chemical Studies of Light Harvesting

The design of optimal light-harvesting (supra)molecular systems and materials is one of the most challenging frontiers of science. Theoretical methods and computational models play a fundamental role in this difficult task, as they allow the establishment of structural blueprints inspired by natural photosynthetic organisms that can be applied to the design of novel artificial light-harvesting devices. Among theoretical strategies, the application of quantum chemical tools represents an important reality that has already reached an evident degree of maturity, although it still has to show its real potentials. This Review presents an overview of the state of the art of this strategy, showing the actual fields of applicability but also indicating its current limitations, which need to be solved in future developments.

Quorum sensing is a language of chemical signals and plays an ecological role in algal-bacterial interactions

Algae are ubiquitous in the marine environment, and the ways in which they interact with bacteria are of particular interest in marine ecology field. The interactions between primary producers and bacteria impact the physiology of both partners, alter the chemistry of their environment, and shape microbial diversity. Although algal-bacterial interactions are well known and studied, information regarding the chemical-ecological role of this relationship remains limited, particularly with respect to quorum sensing (QS), which is a system of stimuli and response correlated to population density. In the microbial biosphere, QS is pivotal in driving community structure and regulating behavioral ecology, including biofilm formation, virulence, antibiotic resistance, swarming motility, and secondary metabolite production. Many marine habitats, such as the phycosphere, harbour diverse populations of microorganisms and various signal languages (such as QS-based autoinducers). QS-mediated interactions widely influence algal-bacterial symbiotic relationships, which in turn determine community organization, population structure, and ecosystem functioning. Understanding infochemicals-mediated ecological processes may shed light on the symbiotic interactions between algae host and associated microbes. In this review, we summarize current achievements about how QS modulates microbial behavior, affects symbiotic relationships, and regulates phytoplankton chemical ecological processes. Additionally, we present an overview of QS-modulated co-evolutionary relationships between algae and bacterioplankton, and consider the potential applications and future perspectives of QS.

Molecular tools for the selective detection of nine diatom species biomarkers of various water quality levels

Our understanding of the composition of diatom communities and their response to environmental changes is currently limited by laborious taxonomic identification procedures. Advances in molecular technologies are expected to contribute more efficient, robust and sensitive tools for the detection of these ecologically relevant microorganisms. There is a need to explore and test phylogenetic markers as an alternative to the use of rRNA genes, whose limited sequence divergence does not allow the accurate discrimination of diatoms at the species level. In this work, nine diatom species belonging to eight genera, isolated from epylithic environmental samples collected in central Italy, were chosen to implement a panel of diatoms covering the full range of ecological status of freshwaters. The procedure described in this work relies on the PCR amplification of specific regions in two conserved diatom genes, elongation factor 1-a (eEF1-a) and silicic acid transporter (SIT), as a first step to narrow down the complexity of the targets, followed by microarray hybridization experiments. Oligonucleotide probes with the potential to discriminate closely related species were designed taking into account the genetic polymorphisms found in target genes. These probes were tested, refined and validated on a small-scale prototype DNA chip. Overall, we obtained 17 highly specific probes targeting eEF1-a and SIT, along with 19 probes having lower discriminatory power recognizing at the same time two or three species. This basic array was validated in a laboratory setting and is ready for tests with crude environmental samples eventually to be scaled-up to include a larger panel of diatoms. Its possible use for the simultaneous detection of diatoms selected from the classes of water quality identified by the European Water Framework Directive is discussed.

Interference patterns and extinction ratio of the diatom Coscinodiscus granii

We report experimental and theoretical verification of the nature and position of multiple interference points of visible light transmitted through the valve of the centric diatom species Coscinodiscus granii. Furthermore, by coupling the transmitted light into an optical fiber and moving the diatom valve between constructive and destructive interference points, an extinction ratio of 20 dB is shown.

Microscale patches of nonmotile phytoplankton

Phytoplankton cells have evolved sophisticated strategies for actively responding to environmental signals, most notably to mechanical stresses of hydrodynamic origin. A largely unanswered question, however, is the significance of these cellular responses for the largely heterogeneous spatial distribution of cells found in the oceans. Motivated by the physiological regulation of buoyancy prevalent in nonmotile phytoplankton species, we solve here a minimal model for "active" sinking that incorporates these cellular responses. Within this model, we show how buoyancy regulation leads to intense patchiness for nonmotile species as compared to passive tracers, resulting in important variations in settling speeds and, as a consequence, determining escape rates to the deep ocean.

Supramolecular organization of fucoxanthin-chlorophyll proteins in centric and pennate diatoms

Fucoxanthin-chlorophyll proteins (FCP) are the major light-harvesting proteins of diatom algae, a major contributor to marine carbon fixation. FCP complexes from representatives of centric (Cyclotella meneghiniana) and pennate (Phaeodactylum tricornutum) diatoms were prepared by sucrose gradient centrifugation and studied by means of electron microscopy followed by single particle analysis. The oligomeric FCP from a centric diatom were observed to take the form of unusual chain-like or circular shapes, a very unique supramolecular assembly for such antennas. The existence of the often disputed oligomeric form of FCP in pennate diatoms has been confirmed. Contrary to the centric diatom FCP, pennate diatom FCP oligomers are very similar to oligomeric antennas from related heterokont (Stramenopila) algae. Evolutionary aspects of the presence of novel light-harvesting protein arrangement in centric diatoms are discussed.

António D, Rossi F, Lettieri T. Detection of silver nanoparticles inside marine diatom Thalassiosira pseudonana by electron microscopy and focused ion beam

In the following article an electron/ion microscopy study will be presented which investigates the uptake of silver nanoparticles (AgNPs) by the marine diatom Thalassiosira pseudonana, a primary producer aquatic species. This organism has a characteristic silica exoskeleton that may represent a barrier for the uptake of some chemical pollutants, including nanoparticles (NPs), but that presents a technical challenge when attempting to use electron-microscopy (EM) methods to study NP uptake. Here we present a convenient method to detect the NPs interacting with the diatom cell. It is based on a fixation procedure involving critical point drying which, without prior slicing of the cell, allows its inspection using transmission electron microscopy. Employing a combination of electron and ion microscopy techniques to selectively cut the cell where the NPs were detected, we are able to demonstrate and visualize for the first time the presence of AgNPs inside the cell membrane.

Comparison of oligomeric states and polypeptide compositions of fucoxanthin chlorophyll a/c-binding protein complexes among various diatom species

Fucoxanthin chlorophyll a/c-binding protein (FCP) is a unique light-harvesting apparatus in diatoms. Several biochemical characteristics of FCP oligomer and trimer from different diatom species have been reported previously. However, the integration of information about molecular organizations and polypeptides of FCP through a comparison among diatoms has not been published. In this study, we used two-dimensional clear-native/SDS-PAGE to compare the oligomeric states and polypeptide compositions of FCP complexes from four diatoms: Chaetoceros gracilis, Thalassiosira pseudonana, Cyclotella meneghiniana, and Phaeodactylum tricornutum. FCP oligomer was found in C. gracilis, T. pseudonana, and C. meneghiniana, but not in P. tricornutum. The oligomerization varied among the three diatoms, although a predominant subunit having similar molecular weight was recovered in each FCP oligomer. These results suggest that the predominant subunit is involved in the formation of high FCP oligomerization in each diatom. In contrast, FCP trimer was found in all the diatoms. The trimerizations were quite similar, whereas the polypeptide compositions were markedly different. On the basis of this information and that from mass spectrometric analyses, the gene products in each FCP complex were identified in T. pseudonana and P. tricornutum. Based on these results, we discuss the role of FCP oligomer and trimer from the four diatoms.

Effects of silver nanoparticles in diatom Thalassiosira pseudonana and cyanobacterium Synechococcus sp

The aim of the present study was to investigate the effect of silver nanoparticles (AgNP) of different sizes toward two primary producer aquatic species. Thalassiosira pseudonana and Synechococcus sp. have been selected as representative models for the lower trophic organisms in marine and freshwater habitats, respectively. Time-dependent cellular growth was measured upon exposure to both AgNP and silver nitrate (AgNO(3)). In addition, AgNP behavior in freshwater and marine waters has been followed by CPS disc centrifuge, in the time frame of AgNP exposure studies, and the kinetic release of silver from AgNP of different sizes was measured by dialysis and inductively coupled plasma mass spectrometry (ICP-MS). The combination and interpretation of all these data suggest that a shared effect of AgNP and released silver was responsible for the toxicity in both organisms. Furthermore, the toxic effects induced by AgNP exposure in the present study seem to result from a mixture of parameters including aggregated state, size of the AgNP, stability of the preparation, and speciation of the released silver.

Comparative efficiency of macroalgal extracts and booster biocides as antifouling agents to control growth of three diatom species

The application of 'booster biocides' Diuron, Tolylfluanid and Copper thiocyanate inbantifouling paints, used to prevent development of biofouling, needs to be monitored before assessing their impacts on the environment. An alternative approach aims to propose eco-friendly and effective antifoulants isolated from marine organisms such as seaweeds. In this study, the effects of 'booster biocides' and the ethanol and dichloromethane extracts from a brown (Sargassum muticum) and a red alga (Ceramium botryocarpum) have been compared by algal growth inhibition tests of marine diatoms. The most efficient extracts were ethanol fraction of S. muticum and C. botryocarpum extracts with growth EC(50)=4.74 and 5.3μg mL(-1) respectively, with reversible diatom growth effect. The booster biocides are more efficient EC(50)=0.52μg mL(-1), but are highly toxic. Results validate the use of macroalgal extracts as non toxic antifouling compounds, and they represent valuable environmentally friendly alternatives in comparison with currently used biocides.

Properties of photosystem I antenna protein complexes of the diatom Cyclotella meneghiniana

Analysis of photosystem I (PSI) complexes from Cyclotella meneghiniana cultured under different growth conditions led to the identification of three groups of antenna proteins, having molecular weights of around 19, 18, and 17 kDa. The 19-kDa proteins have earlier been demonstrated to be more peripherally bound to PSI, and their amount in the PSI complexes was significantly reduced when the iron supply in the growth medium was lowered. This polypeptide was almost missing, and thus the total amount of fucoxanthin-chlorophyll proteins (Fcps) bound to PSI was reduced as well. When treating cells with high light in addition, no further changes in antenna polypeptide composition were detected. Xanthophyll cycle pigments were found to be bound to all Fcps of PSI. However, PSI of high light cultures had a significantly higher diatoxanthin to diadinoxanthin ratio, which is assumed to protect against a surplus of excitation energy. PSI complexes from the double-stressed cultures (high light plus reduced iron supply) were slightly more sensitive against destruction by the detergent treatment. This could be seen as a higher 674-nm emission at 77 K in comparison to the PSI complexes isolated from other growth conditions. Two major emission bands of the Fcps bound to PSI at 77 K could be identified, whereby chlorophyll a fluorescing at 697 nm was more strongly coupled to the PSI core than those fluorescing at 685 nm. Thus, the build up of the PSI antenna of several Fcp components enables variable reactions to several stress factors commonly experienced by the diatoms in vivo, in particular diatoxanthin enrichment under high light and reduction of antenna size under reduced iron conditions.

INFLUENCE OF DIFFERENT LIGHT INTENSITIES AND DIFFERENT IRON NUTRITION ON THE PHOTOSYNTHETIC APPARATUS IN THE DIATOM CYCLOTELLA MENEGHINIANA (BACILLARIOPHYCEAE)(1)

The diatom Cyclotella meneghiniana Kütz. (SAG 1020-a) was cultured under high-light (HL) and low-light (LL) conditions with either high (12 μM) or low (1 μM) iron in the media. Changes in cell morphology, especially cell volume and chloroplast size, were observed in cells grown under low iron. In contrast, HL had a much stronger influence on the photosynthetic apparatus. PSII function was unimpaired under lowered iron supply, but its quantum efficiency and reoxidation rate were reduced under HL conditions. As reported before, HL induced changes in antenna polypeptide composition. Especially the amount of Fcp6, an antenna protein related to LI818 and known to be involved in photoprotection, was increased under HL but was significantly reduced under lowered iron. The diatoxanthin content correlated with the amount of Fcp6 in isolated FCPa antenna complexes and was thus increased under HL and reduced under low iron as well. While the diatoxanthin (Dt) content of whole cells was enhanced under HL, no decrease was observed under lowered iron supply, ruling out the possibility that the decreased amounts in FCPa were due to a hampered diadinoxanthin de-epoxidase activity under these conditions. Thus, diatoxanthin not bound to FCPa has to be responsible for protection under the slight reduction in iron supply used here.

Genome-wide profiling of responses to cadmium in the diatom Phaeodactylum tricornutum

The only group of organisms in which a biological function for cadmium has been shown is the diatoms, which are unicellular phytoplankton. Yet diatoms exhibit similar sensitivity to Cd as other groups of phytoplankton. We have investigated responses of Cd on molecular, metabolic, and physiological levels in the diatom Phaeodactylum tricornutum. P. tricornutum apparently has a high tolerance to Cd; only minor responses were observed on growth, pigment, and transcriptional changes at cadmium concentrations of 123 μg/L. No significant changes in chlorophyll and xanthophyll levels were observed, and the very few transcripts affected strongly indicate that the cells were able to respond to the increased Cd(2+) levels without changing proteins levels. At 10 times this concentration, 1230 μg/L, a much clearer response was observed, including transcripts encoding proteins involved in metal transport, cell signaling, and detoxification processes. Our results point toward putative pathways for the removal or detoxification of Cd and its metabolites as well as a possible Cd uptake mechanism. We predict that ATPase5-1B is involved in removal of Cd by pumping Cd(2+) ions out of the cell, whereas VIT1/CCC1 sequesters Cd(2+) in the vacuole.

Organization of the smallest eukaryotic spindle

In metazoans, plants, and fungi, the spindle checkpoint delays mitosis until each chromosome is attached to one or more of its own kinetochore microtubules (kMTs). Some unicellular eukaryotes, however, have been reported to have fewer kMTs than chromosomes [1-5]. If this is the case, it is unclear how the spindle checkpoint could be satisfied. In the vast majority of the previous studies, mitotic cells were chemically fixed at room temperature, but this does not always preserve dynamic and/or small structures like spindle MTs and kinetochores [6]. Indeed, later higher-resolution studies have reversed some earlier claims [7-11]. Here we show that in Ostreococcus tauri (the smallest eukaryote known), mitosis does involve fewer spindle microtubules than chromosomes. O. tauri cultures were enriched for mitotic cells, high-pressure frozen, and then imaged in 3D both in plastic and in a near-native ("frozen-hydrated") state through electron tomography. Mitotic cells have a distinctive intranuclear heterochromatin-free "spindle tunnel" with approximately four short and occasionally one long, incomplete (unclosed) microtubule at each end of the spindle tunnel. Because other aspects of O. tauri's spindle checkpoint seem typical, these data suggest that O. tauri's 20 chromosomes are physically linked and segregated as just one or a small number of groups.

N-glycans of Phaeodactylum tricornutum diatom and functional characterization of its N-acetylglucosaminyltransferase I enzyme

N-glycosylation, a major co- and post-translational event in the synthesis of proteins in eukaryotes, is unknown in aquatic photosynthetic microalgae. In this paper, we describe the N-glycosylation pathway in the diatom Phaeodactylum tricornutum. Bio-informatic analysis of its genome revealed the presence of a complete set of sequences potentially encoding for proteins involved in the synthesis of the lipid-linked Glc(3)Man(9)GlcNAc(2)-PP-dolichol N-glycan, some subunits of the oligosaccharyltransferase complex, as well as endoplasmic reticulum glucosidases and chaperones required for protein quality control and, finally, the α-mannosidase I involved in the trimming of the N-glycan precursor into Man-5 N-glycan. Moreover, one N-acetylglucosaminyltransferase I, a Golgi glycosyltransferase that initiates the synthesis of complex type N-glycans, was predicted in the P. tricornutum genome. We demonstrated that this gene encodes for an active N-acetylglucosaminyltransferase I, which is able to restore complex type N-glycans maturation in the Chinese hamster ovary Lec1 mutant, defective in its endogeneous N-acetylglucosaminyltransferase I. Consistent with these data, the structural analyses of N-linked glycans demonstrated that P. tricornutum proteins carry mainly high mannose type N-glycans ranging from Man-5 to Man-9. Although representing a minor glycan population, paucimannose N-glycans were also detected, suggesting the occurrence of an N-acetylglucosaminyltransferase I-dependent maturation of N-glycans in this diatom.

Gene biomarkers in diatom Thalassiosira pseudonana exposed to polycyclic aromatic hydrocarbons from contaminated marine surface sediments

Marine diatoms have a key role in the global carbon fixation and therefore in the ecosystem. We used Thalassiosira pseudonana as a model organism to assess the effects of exposure to environmental pollutants at the gene expression level. Diatoms were exposed to polycyclic aromatic hydrocarbons mixture (PAH) from surface sediments collected at a highly PAH contaminated area of the Mediterranean Sea (Genoa, Italy), due to intense industrial and harbor activities. The gene expression data for exposure to the sediment-derived PAH mixture was compared with gene expression data for in vitro exposure to specific polycyclic aromatic hydrocarbons. The data shows that genes involved in stress response, silica uptake, and metabolism were regulated both upon exposure to the sediment-derived PAH mixture and to the single component. Complementary monitoring of silica in the diatom cultures provide further evidence of a reduced cellular uptake of silica as an end-point for benzo[a]pyrene exposure that could be linked with the reduced gene and protein expression of the silicon transporter protein. However some genes showed differences in regulation indicating that mixtures of structurally related chemical compounds can elicit a slightly different gene expression response compared to that of a single component. The paper provides indications on the specific pathways affected by PAH exposure and shows that selected genes (silicon transporter, and silaffin 3) involved in silica uptake and metabolism could be suitable molecular biomarkers of exposure to PAHs.