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SUMMARY: With global climate change, the high‐temperature environment has severely impacted the community structure and phenotype of marine diatoms. Phaeodactylum tricornutum, a model species of marine diatom, is sensitive to high temperature, which grow slowly under high temperature. However, the regulatory mechanism of P. tricornutum in response to high‐temperature is still unclear. In this study, we found that the expression level of the HSP70A in the wild type (WT) increased 28 times when exposed to high temperature (26°C) for 1 h, indicating that HSP70A plays a role in high temperature in P. tricornutum. Furthermore, overexpression and interference of HSP70A have great impact on the exponential growth phase of P. tricornutum under 26°C. Moreover, the results of Co‐immunoprecipitation (Co‐IP) suggested that HSP70A potentially involved in the correct folding of the photosynthetic system‐related proteins (D1/D2), preventing aggregation. The photosynthetic activity results demonstrated that overexpression of HSP70A improves non‐photochemical quenching (NPQ) activity under high‐temperature stress. These results reveal that HSP70A regulates the photosynthetic activity of P. tricornutum under high temperatures. This study not only helps us to understand the photosynthetic activity of marine diatoms to high temperature but also provides a molecular mechanism for HSP70A in P. tricornutum under high‐temperature stress. [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]

Phaeodactylum tricornutum a prominent source of industrial fucoxanthin production, faces challenges in its application due to its tolerance to high-temperature environments. This study investigates the physiological responses of P. tricornutum to high-temperature stress and its impact on fucoxanthin content, with a specific focus on the role of cis-zeatin. The results reveal that high-temperature stress inhibits P. tricornutum's growth and photosynthetic activity, leading to a decrease in fucoxanthin content. Transcriptome analysis shows that high temperature suppresses the expression of genes related to photosynthesis (e.g., psbO, psbQ, and OEC) and fucoxanthin biosynthesis (e.g., PYS, PDS1, and PSD2), underscoring the negative effects of high temperature on P. tricornutum. Interestingly, genes associated with cis-zeatin biosynthesis and cytokinesis signaling pathways exhibited increased expression under high-temperature conditions, indicating a potential role of cis-zeatin signaling in response to elevated temperatures. Content measurements confirm that high temperature enhances cis-zeatin content. Furthermore, the exogenous addition of cytokinesis mimetics or inhibitors significant ly affected P. tricornutum's high-temperature resistance. Overexpression of the cis-zeatin biosynthetic enzyme gene tRNA DMATase enhanced P. tricornutum's resistance to high-temperature stress, while genetic knockout of tRNA DMATase reduced its resistance to high temperatures. Therefore, this research not only uncovers a novel mechanism for high-temperature resistance in P. tricornutum but also offers a possible alga species that can withstand high temperatures for the industrial production of fucoxanthin, offeri ng valuable insights for practical utilization. [ABSTRACT FROM AUTHOR]

Acute liver failure is an infrequent yet fatal condition marked by rapid liver function decline, leading to abnormalities in blood clotting and cognitive impairment among individuals without prior liver ailments. The primary reasons for liver failure are infection with hepatitis virus or overdose of certain medicines, such as acetaminophen. Phaeodactylum tricornutum (PT), a type of microalgae known as a diatom species, has been reported to contain an active ingredient with anti-inflammatory and anti-obesity effects. In this study, we evaluated the preventive and therapeutic activities of PT extract in acute liver failure. To achieve our purpose, we used two different acute liver failure models: acetaminophen- and D-GalN/LPS-induced acute liver failure. PT extract showed protective activity against acetaminophen-induced acute liver failure through attenuation of the inflammatory response. However, we failed to demonstrate the protective effects of PT against acute liver injury in the D-GalN/LPS model. Although the PT extract did not show protective activity against two different acute liver failure animal models, this study clearly demonstrates the importance of considering the differences among animal models when selecting an acute liver failure model for evaluation. [ABSTRACT FROM AUTHOR]

Ocean acidification influences photosynthesis, respiration, and metabolism in marine diatoms, leading to changes in diatom growth performance and shifts in phytoplankton communities. Previous studies have demonstrated that increases in seawater CO2 concentrations affect the uptake of trace metals such as iron, zinc, copper, and cobalt by marine diatoms. However, the influence of increased CO2 on calcium, which plays a vital role as a secondary messenger in various signaling pathways within organisms, has received limited attention so far. This study examined the effect of increased CO2 on Ca homeostasis and signaling in the marine diatom Phaeodactylum tricornutum. While seawater acidification had little effect on the diatom's growth, it significantly changed cell properties (surface topography, adhesion, and surface potential). Elevated CO2 concentrations reduced calcium accumulation P. tricornutum and lowered the rise of cytosolic Ca2+ transients stimulated by toxic aldehyde, phosphorus supplement, and hypo‐osmotic stress. Our results suggest that a continuous rise in atmospheric CO2 may alter diatoms' response to environmental cues. [ABSTRACT FROM AUTHOR]

Diversity and its drivers and consequences are at the heart of ecological research. Mostly, studies have focused on different species, but if the causes for increases or decreases in diversity are general, the observed patterns should also be observable within genotypes. As previous research shows that there is higher variability in nitrogen to phosphorus ratios (N/P) between slow-growing unicellular algal populations, compared to fast-growing ones, we expected to observe similar patterns within genetically identical strains growing at different rates. We tested this hypothesis in a laboratory experiment performed with a monoculture of the diatom Phaeodactylum tricornutum. Using a growth rate gradient obtained with 10 chemostats, we were able to determine the effect of growth rate on the diatom's elemental stoichiometry as well as on selected traits, such as cell size and shape. Our results showed indeed less intercellular variability (in the selected traits assessed on single-cell level) in the faster-growing populations, which was accompanied by a downward trend in bulk N/P ratios. We pose that this higher variability at lower growth rates potentially results in higher variability of the food sources available for higher trophic levels with potential consequences for the transfer efficiency of energy and matter in marine food webs. [ABSTRACT FROM AUTHOR]

Long time series of spatiotemporally continuous phytoplankton functional type (PFT) products are essential for understanding marine ecosystems, global biogeochemical cycles, and effective marine management. In this study, by integrating artificial intelligence (AI) technology with multi-source marine big data, we have developed a Spatial–Temporal–Ecological Ensemble model based on Deep Learning (STEE-DL), and then generated the first AI-driven Global Daily gap-free 4 km PFTs product from 1998 to 2023 (AIGD-PFT), significantly enhancing the accuracy and spatiotemporal coverage of quantifying eight major PFTs (i.e., Diatoms, Dinoflagellates, Haptophytes, Pelagophytes, Cryptophytes, Green Algae, Prokaryotes, and Prochlorococcus). The input data encompass physical oceanographic, biogeochemical, spatiotemporal information, and ocean color data (OC-CCI v6.0) that have been gap-filled using a Discrete Cosine Transform with a Penalized Least Square (DCT-PLS) approach. The STEE-DL model utilizes an ensemble strategy with 100 ResNet models, applying Monte Carlo and bootstrapping methods to estimate optimal PFT values and assess model uncertainty through ensemble means and standard deviations. The model's performance was validated using multiple cross-validation strategies—random, spatial-block, and temporal-block—combined with in-situ data, demonstrating STEE-DL's robustness and generalization capability. The daily updates and seamless nature of the AIGD-PFT product capture the complex dynamics of coastal regions effectively. Finally, through a comparative analysis using a triple-collocation (TC) approach, the competitive advantages of the AIGD-PFT product over existing products were validated. The AIGD-PFT product not only provides the foundation for detailed analyses of PFT trends, interannual variability, and the impacts of climate change on phytoplankton composition across various temporal and spatial scales, but also has the potential to facilitate precise quantification of marine carbon flux and enhances the accuracy of biogeochemical models. A video demonstration is available at https://doi.org/10.5446/67366 (Zhang and Shen, 2024a). The complete product dataset (1998–2023) can be freely downloaded at https://doi.org/10.11888/RemoteSen.tpdc.301164 (Zhang and Shen, 2024b). [ABSTRACT FROM AUTHOR]

Many diatoms form long chains and the distribution of chain lengths within a species depends on several environmental factors, among them grazing risk. Larger grazers, such as copepods, efficiently handle and ingest even very long chains but are less efficient with individual cells, whereas most smaller grazers are unable to feed on chains exceeding a few cells in length. Copepod cues make several species shorten their chain length, and theory predicts that cues from small grazers should induce increased, but this remains to be tested, despite the importance of diatoms in marine food webs. Here, we expose three species of chain‐forming diatoms, Skeletonema marinoi, Chaetoceros affinis, and Thalassiosira rotula to cues from various actively feeding micrograzers and record their response. The effect of grazer presence on chain length varies depending on both the type of grazer and the diatom species. For example, S. marinoi increased its chain length when exposed to grazing cues from the heterotrophic dinoflagellate Gyrodinium dominans and the ciliate Euplotes sp. but not to a copepod nauplii (Temora longicornis). C. affinis also responded to cues from grazing G. dominans by increasing chain length, and the response increased with exposure time. Finally, T. rotula did not respond to grazing cues from G. dominans, but rather inhibited the dinoflagellates' ability to feed, presumably through the release of chemical compounds. Our results suggest that some chainforming diatoms can sense and appropriately respond to fast‐growing micrograzers, thus contributing to the success of diatoms in marine environments. [ABSTRACT FROM AUTHOR]

Phytoplankton blooms fuel marine food webs with labile dissolved carbon and also lead to the formation of particulate organic matter composed of living and dead algal cells. These particles contribute to carbon sequestration and are sites of intense algal-bacterial interactions, providing diverse niches for microbes to thrive. We analyzed 16S and 18S ribosomal RNA gene amplicon sequences obtained from 51 time points and metaproteomes from 3 time points during a spring phytoplankton bloom in a shallow location (6-10 m depth) in the North Sea. Particulate fractions larger than 10 µm diameter were collected at near daily intervals between early March and late May in 2018. Network analysis identified two major modules representing bacteria co-occurring with diatoms and with dinoflagellates, respectively. The diatom network module included known sulfate-reducing Desulfobacterota as well as potentially sulfur-oxidizing Ectothiorhodospiraceae. Metaproteome analyses confirmed presence of key enzymes involved in dissimilatory sulfate reduction, a process known to occur in sinking particles at greater depths and in sediments. Our results indicate the presence of sufficiently anoxic niches in the particle fraction of an active phytoplankton bloom to sustain sulfate reduction, and an important role of benthic-pelagic coupling for microbiomes in shallow environments. Our findings may have implications for the understanding of algal-bacterial interactions and carbon export during blooms in shallow-water coastal areas. [ABSTRACT FROM AUTHOR]

Laminarin, a β(1,3)‐glucan, serves as a storage polysaccharide in marine microalgae such as diatoms. Its abundance, water solubility and simple structure make it an appealing substrate for marine bacteria. Consequently, many marine bacteria have evolved strategies to scavenge and decompose laminarin, employing carbohydrate‐binding modules (CBMs) as crucial components. In this study, we characterized two previously unassigned domains as laminarin‐binding CBMs in multimodular proteins from the marine bacterium Christiangramia forsetii KT0803T, thereby introducing the new laminarin‐binding CBM families CBM102 and CBM103. We identified four CBM102s in a surface glycan‐binding protein (SGBP) and a single CBM103 linked to a glycoside hydrolase module from family 16 (GH16_3). Our analysis revealed that both modular proteins have an elongated shape, with GH16_3 exhibiting greater flexibility than SGBP. This flexibility may aid in the recognition and/or degradation of laminarin, while the constraints in SGBP could facilitate the docking of laminarin onto the bacterial surface. Exploration of bacterial metagenome‐assembled genomes (MAGs) from phytoplankton blooms in the North Sea showed that both laminarin‐binding CBM families are widespread among marine Bacteroidota. The high protein abundance of CBM102‐ and CBM103‐containing proteins during phytoplankton blooms further emphasizes their significance in marine laminarin utilization. [ABSTRACT FROM AUTHOR]

Background: Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), belonging to ω-3 long-chain polyunsaturated fatty acids (ω3-LC-PUFAs), are essential components of human diet. They are mainly supplemented by marine fish consumption, although their native producers are oleaginous microalgae. Currently, increasing demand for fish oils is insufficient to meet the entire global needs, which puts pressure on searching for the alternative solutions. One possibility may be metabolic engineering of plants with an introduced enzymatic pathway producing ω3-LC-PUFAs. Result: In this study we focused on the acyl-CoA:diacylglycerol acyltransferase2b (PtDGAT2b) from the diatom Phaeodactylum tricornutum, an enzyme responsible for triacylglycerol (TAG) biosynthesis via acyl-CoA-dependent pathway. Gene encoding PtDGAT2b, incorporated into TAG-deficient yeast strain H1246, was used to confirm its activity and conduct biochemical characterization. PtDGAT2b exhibited a broad acyl-CoA preference with both di-16:0-DAG and di-18:1-DAG, whereas di-18:1-DAG was favored. The highest preference for acyl donors was observed for 16:1-, 10:0- and 12:0-CoA. PtDGAT2b also very efficiently utilized CoA-conjugated ω-3 LC-PUFAs (stearidonic acid, eicosatetraenoic acid and EPA). Additionally, verification of the potential role of PtDGAT2b in planta, through its transient expression in tobacco leaves, indicated increased TAG production with its relative amount increasing to 8%. Its co-expression with the gene combinations aimed at EPA biosynthesis led to, beside elevated TAG accumulation, efficient accumulation of EPA which constituted even 25.1% of synthesized non-native fatty acids (9.2% of all fatty acids in TAG pool). Conclusions: This set of experiments provides a comprehensive biochemical characterization of DGAT enzyme from marine microalgae. Additionally, this study elucidates that PtDGAT2b can be used successfully in metabolic engineering of plants designed to obtain a boosted TAG level, enriched not only in ω-3 LC-PUFAs but also in medium-chain and ω-7 fatty acids. [ABSTRACT FROM AUTHOR]

This study is focused on analysing polyphenols and carbohydrates released by Phaeodactylum tricornutum (P. tricornutum) diatoms cultured in natural seawater enriched with sublethal and lethal Cu doses. Cu concentrations of 0.31, 0.79 and 1.57 µM reduced cell densities by 37, 82 and 91%, respectively, compared to the control. The total sum of all identified polyphenols and total carbohydrates released by cells grown under lethal Cu levels increased up to 18.8 and 107.4 times, respectively, compared to data from a control experiment. Four different in vitro assays were used to estimate the antioxidant activities of the extracellular compounds: 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical inhibition, cupric ion reducing antioxidant capacity (CUPRAC), ferric reducing antioxidant power and Cu complexing ability (CCA). The highest antioxidant activities were observed in the Cu lethal treatments, where the CCA assay exhibited a greater increase (up to 32.2 times higher than that found in the control experiment) to reduce the concentration of free Cu in the medium and its toxicity. The presence of Cu stimulated the release of polyphenols and carbohydrates to the medium as a detoxification mechanism to survive under lethal levels of Cu regulating its speciation. [ABSTRACT FROM AUTHOR]

Background: Fucoxanthin has been widely investigated owing to its beneficial biological properties, and the model diatom Phaeodactylum tricornutum, possessing fucoxanthin (Fux) chlorophyll proteins as light-harvesting systems, is considered to have the potential to become a commercial cell factory for the pigment production. Results: Here, we compared the pigment contents in 10 different P. tricornutum strains from the globe, and found that strain CCMP631 (Pt6) exhibited the highest Fux content but with a low biomass. Comparison of mRNA levels revealed that higher Fux content in Pt6 was related with the higher expression of gene violaxanthin de-epoxidase-like (VDL) protein 1 (VDL1), which encodes the enzyme catalyzing the tautomerization of violaxanthin to neoxanthin in Fux biosynthesis pathway. Single nucleotide variants of VDL1 gene and allele-specific expression in strains Pt1 (the whole genome sequenced strain CCMP632) and Pt6 were analyzed, and overexpressing of each of the 4 VDL1 alleles, two from Pt1 and two from Pt6, in strain Pt1 leads to an increase in downstream product diadinoxanthin and channels the pigments towards Fux biosynthesis. All the 8 VDL1 overexpression (OE) lines showed significant increases by 8.2 to 41.7% in Fux content without compromising growth, and VDL1 Allele 2 OE lines even exhibited the higher cell density on day 8, with an increase by 24.2–28.7% in two Pt1VDL1-allele 2 OE lines and 7.1–11.1% in two Pt6VDL1-allele 2 OE lines, respectively. Conclusions: The results reveal VDL1, localized in the plastid stroma, plays a key role in Fux over-accumulation in P. tricornutum. Overexpressing VDL1, especially allele 2, improved both the Fux content and growth rate, which provides a new strategy for the manipulation of Fux production in the future. [ABSTRACT FROM AUTHOR]

Southern Ocean phytoplankton growth is limited by low iron (Fe) supply and irradiance, impacting the strength of the biological carbon pump. Unfavorable upper ocean conditions, such as low nutrient concentrations, can lead to the formation of deep chlorophyll or biomass maxima (DCM/DBM). While common in the Southern Ocean, these features remain understudied due to their subsurface location. To increase our understanding of their occurrence, we studied the responses of phytoplankton communities from a Southern Ocean DCM to increasing light, Fe, and manganese (Mn) levels. The DCM communities were light‐ and Fe‐limited, but light limitation did not increase phytoplankton Fe requirements. The greatest physiological responses were observed under combined Fe/light additions, which stimulated macronutrient drawdown, biomass production and the growth of large diatoms. Combined Mn/light additions induced subtle changes in Fe uptake rates and community composition, suggesting species‐specific Mn requirements. These results provide valuable information on Southern Ocean DCM phytoplankton physiology. [ABSTRACT FROM AUTHOR]

Coastal upwelling currents such as the California Current System (CCS) comprise some of the most productive biological systems on the planet. Diatoms dominate these upwelling events in part due to their rapid response to nutrient entrainment. In this region, they may also be limited by the micronutrient iron (Fe), an important trace element primarily involved in photosynthesis and nitrogen assimilation. The mechanisms behind how diatoms physiologically acclimate to the different stages of the upwelling conveyor belt cycle remain largely uncharacterized. Here, we explore their physiological and metatranscriptomic response to the upwelling cycle with respect to the Fe limitation mosaic that exists in the CCS. Subsurface, natural plankton assemblages that would potentially seed surface blooms were examined over wide and narrow shelf regions. The initial biomass and physiological state of the phytoplankton community had a large impact on the overall response to simulated upwelling. Following on‐deck incubations under varying Fe physiological states, our results suggest that diatoms quickly dominated the blooms by "frontloading" nitrogen assimilation genes prior to upwelling. However, diatoms subjected to induced Fe limitation exhibited reductions in carbon and nitrogen uptake and decreasing biomass accumulation. Simultaneously, they exhibited a distinct gene expression response which included increased expression of Fe‐starvation induced proteins and decreased expression of nitrogen assimilation and photosynthesis genes. These findings may have significant implications for upwelling events in future oceans, where changes in ocean conditions are projected to amplify the gradient of Fe limitation in coastal upwelling regions. [ABSTRACT FROM AUTHOR]

During the cultivation of Ulva fenestrata in a land-based aquaculture system, the colonisation of the water tanks' surfaces and eventually the macroalgal biomass by the biofouling diatom Fragilariopsis oceanica compromises the production process. Since germanium dioxide (GeO2) is an effective growth inhibitor of diatoms, this study aimed to understand how it affects the presence of F. oceanica and the photosynthesis and growth of U. fenestrata as a primary parameter contribution to the biomass production. A toxicological dose-response experiment showed that the diatom's growth was inhibited at the low GeO2 concentration of 0.014 mg l−1. In contrast, the photosynthetic performances and growth rates of U. fenestrata remained unaffected under a wide GeO2 concentration range (0.022–2.235 mg l−1) in small- and large-scale experiments in 1-l glass beakers and 100-l Plexiglass water tanks, respectively. In the latter, the diatom density in the tanks was reduced by 40 %. The costs arising from the use of GeO2 can range between €2.35 and €8.35 kg−1 fresh weight of produced U. fenestrata biomass under growth conditions resulting in growth rates of 20 and 11.5 % d−1, respectively. GeO2 is an effective agent to control biofouling diatoms such as F. oceanica during the land-based biomass production of U. fenestrata. [ABSTRACT FROM AUTHOR]

Aureochromes are light-responsive transcription factors found in photosynthetic stramenopile algae, including diatoms. They contain a blue light-sensitive LOV domain and a DNA-binding bZIP domain. Aureochromes can form homo- and heterodimers, activating the expression of intermediate regulatory factors in diatoms. These photoreceptors are important for sustaining the aquatic food web and have unique properties that allow them to directly bind to target DNA upon blue light activation. The study of aureochromes in diatoms, particularly in the model organism Phaeodactylum tricornutum, has provided insights into their role in gene regulation and their interactions with other transcription factors. Further research is needed to explore the regulatory network components and the diversity of aureochromes in different stramenopile species. [Extracted from the article]

Aureochromes (AUREOs) are unique blue light receptors and transcription factors found only in stramenopile algae. While each of the four AUREOs identified in the diatom Phaeodactylum tricornutum may have a specific function, PtAUREO1a has been shown to have a strong impact on overall gene regulation, when light changes from red to blue light conditions. Despite its significance, the molecular mechanism of PtAUREO1a is largely unexplored. To comprehend the overall process of gene regulation by PtAUREO1a, we conducted a series of in vitro and in vivo experiments, including pull-down assays, yeast one-hybrid experiments, and phenotypical characterization using recombinant PtAUREOs and diatom mutant lines expressing a modified PtAureo1a gene. We describe the distinct light absorption properties of four PtAUREOs and the formation of all combinations of their potential dimers. We demonstrate the capability of PtAUREO1a and 1b to activate the genes, diatom-specific cyclin 2 , PtAureo1a , and PtAureo1c under both light and dark conditions. Using mutant lines expressing a modified PtAUREO1a protein with a considerably reduced light absorption, we found novel evidence that PtAUREO1a regulates the expression of PtLHCF15, which is essential for red light acclimation. Based on current knowledge, we present a working model of PtAUREO1a gene regulation properties. [ABSTRACT FROM AUTHOR]

Phytoplankton are photosynthetic marine microbes that affect food webs, nutrient cycles and climate regulation. Their roles are determined by correlated phytoplankton functional traits including cell size, chlorophyll content and cellular composition. Here, we explore patterns of evolution in interrelated trait values and correlations. Because both chance events and natural selection contribute to phytoplankton trait evolution, we used population bottlenecks to diversify six genotypes of Thalassiosirid diatoms. We then evolved them as large populations in two environments. Interspecific variation and within-species evolution were visualized for nine traits and their correlations using reduced axes (a trait-scape). Our main findings are that shifts in trait values resulted in movement of evolving populations within the trait-scape in both environments, but were more frequent when large populations evolved in a novel environment. Which trait relationships evolved was population-specific, but greater departures from ancestral trait correlations were associated with lower population growth rates. There was no single master trait that could be used to understand multi-trait evolution. Instead, repeatable multi-trait evolution occurred along a major axis of variation defined by several diatom traits and trait relationships. Because trait-scapes capture changes in trait relationships and values together, they offer an insightful way to study multi-trait variation. [ABSTRACT FROM AUTHOR]

Application of cyanobacteria for bioproduction, bioremediation and biotransformation is being increasingly explored. Photoautotrophs are carbon-negative by default, offering a direct pathway to reducing emissions in production systems. More robust and versatile host strains are needed for constructing production strains that would function as efficient and carbon-neutral cyanofactories. We have tested if the engineering of sigma factors, regulatory units of the bacterial RNA polymerase, could be used to generate better host strains of the model cyanobacterium Synechocystis sp. PCC 6803. Overexpressing the stress-responsive sigB gene under the strong psbA2 promoter (SigB-oe) led to improved tolerance against heat, oxidative stress and toxic end-products. By targeting transcription initiation in the SigB-oe strain, we could simultaneously activate a wide spectrum of cellular protective mechanisms, including carotenoids, the HspA heat shock protein, and highly activated non-photochemical quenching. Yellow fluorescent protein was used to test the capacity of the SigB-oe strain to produce heterologous proteins. In standard conditions, the SigB-oe strain reached a similar production as the control strain, but when cultures were challenged with oxidative stress, the production capacity of SigB-oe surpassed the control strain. We also tested the production of growth-rate-controlled host strains via manipulation of RNA polymerase, but post-transcriptional regulation prevented excessive overexpression of the primary sigma factor SigA, and overproduction of the growth-restricting SigC factor was lethal. Thus, more research is needed before cyanobacteria growth can be manipulated by engineering RNA polymerase. [ABSTRACT FROM AUTHOR]

Diatoms, efficient carbon capture organisms, contribute to 20% of global carbon fixation and 40% of ocean primary productivity, garnering significant attention to their growth. Despite their significance, the synthesis mechanism of polyamines (PAs), especially spermidine (Spd), which are crucial for growth in various organisms, remains unexplored in diatoms. This study reveals the vital role of Spd, synthesized through the spermidine synthase (SDS)-based pathway, in the growth of the diatom Phaeodactylum tricornutum. PtSDS1 and PtSDS2 in the P. tricornutum genome were confirmed as SDS enzymes through enzyme-substrate selectivity assays. Their distinct activities are governed primarily by the Y79 active site. Overexpression of a singular gene revealed that PtSDS1, PtSDS2, and PtSAMDC from the SDS-based synthesis pathway are all situated in the cytoplasm, with no significant impact on PA content or diatom growth. Co-overexpression of PtSDS1 and PtSAMDC proved essential for elevating Spd levels, indicating multifactorial regulation. Elevated Spd content promotes diatom growth, providing a foundation for exploring PA functions and regulation in diatoms. [ABSTRACT FROM AUTHOR]

Lipoxygenases make several biological functions in cells, based on the products of the catalyzed reactions. In diatoms, microalgae ubiquitous in aquatic ecosystems, lipoxygenases have been noted for the oxygenation of fatty acids with the production of oxylipins, which are involved in many physiological and pathological processes in marine organisms. The interest in diatoms' lipoxygenases and oxylipins has increased due to their possible biotechnological applications, ranging from ecology to medicine. We investigated using bioinformatics and molecular docking tools the lipoxygenases of diatoms and the possible interaction with substrates. A large-scale analysis of sequence resources allowed us to retrieve 45 sequences of lipoxygenases from diatoms. We compared and analyzed the sequences by multiple alignments and phylogenetic trees, suggesting the possible clustering in phylogenetic groups. Then, we modelled the 3D structure of representative enzymes from the different groups and investigated in detail the structural and functional properties by docking simulations with possible substrates. The results allowed us to propose a classification of the lipoxygenases from diatoms based on their sequence features, which may be reflected in specific structural differences and possible substrate specificity. [ABSTRACT FROM AUTHOR]

Two members of the marine diatom genus Falcula, which has been little known for a long time, were found from the surface of some Japanese seaweeds; one was assigned to F. cf. media and the other was described as a new species, F. rectangularis sp. nov. Aside from the arcuate valves and slit-like apical fields, typical of the genus, detailed morphological observations using light and scanning electron microscopy revealed resemblance between F. cf. media and F. rectangularis in areolae, stria density and lack of costae. However, the two species can be distinguished based on several morphological features, including the valve length, plastid arrangement, and frustules in girdle view. A three-gene molecular phylogeny recovered these two species as monophyletic with a high interspecific rbcL difference, which in turn were sister to the clade containing taxa that belong to the orders Cyclophorales and Protoraphidales with low support. The members in this poorly supported assemblage share apical fields composed of slits. The two species of Falcula were phylogenetically distinct from Pseudofalcula hyalina, a member previously assigned to Falcula. [ABSTRACT FROM AUTHOR]

Summary: Fucoxanthin, a natural carotenoid that has substantial pharmaceutical value due to its anticancer, antioxidant, antiobesity, and antidiabetic properties, is biosynthesized from glyceraldehyde‐3‐phosphate (G3P) via a series of enzymatic reactions. However, our understanding of the transcriptional mechanisms involved in fucoxanthin biosynthesis remains limited.Using reverse genetics, the med8 mutant was identified based on its phenotype of reduced fucoxanthin content, and the biological functions of MED8 in fucoxanthin synthesis were characterized using approaches such as gene expression, protein subcellular localization, protein–protein interaction and chromatin immunoprecipitation assay.Gene‐editing mutants of MED8 exhibited decreased fucoxanthin content as well as reduced expression levels of six key genes involved in fucoxanthin synthesis, namely DXS, PSY1, ZDS‐like, CRTISO5, ZEP1, and ZEP3, when compared to the wild‐type (WT) strain. Furthermore, we showed that MED8 interacts with HSF3, and genetic analysis revealed their shared involvement in the genetic pathway governing fucoxanthin synthesis. Additionally, HSF3 was required for MED8 association with the promoters of the six fucoxanthin synthesis genes.In conclusion, MED8 and HSF3 are involved in fucoxanthin synthesis by modulating the expression of the fucoxanthin synthesis genes. Our results increase the understanding of the molecular regulation mechanisms underlying fucoxanthin synthesis in the diatom P. tricornutum. [ABSTRACT FROM AUTHOR]

Summary: Diatoms are a highly successful group of phytoplankton, well adapted also to oligotrophic environments and capable of handling nutrient fluctuations in the ocean, particularly nitrate. The presence of a large vacuole is an important trait contributing to their adaptive features. It confers diatoms the ability to accumulate and store nutrients, such as nitrate, when they are abundant outside and then to reallocate them into the cytosol to meet deficiencies, in a process called luxury uptake.The molecular mechanisms that regulate these nitrate fluxes are still not known in diatoms. In this work, we provide new insights into the function of Phaeodactylum tricornutum NPF1, a putative low‐affinity nitrate transporter. To accomplish this, we generated overexpressing strains and CRISPR/Cas9 loss‐of‐function mutants.Microscopy observations confirmed predictions that PtNPF1 is localized on the vacuole membrane. Furthermore, functional characterizations performed on knock‐out mutants revealed a transient growth delay phenotype linked to altered nitrate uptake.Together, these results allowed us to hypothesize that PtNPF1 is presumably involved in modulating intracellular nitrogen fluxes, managing intracellular nutrient availability. This ability might allow diatoms to fine‐tune the assimilation, storage and reallocation of nitrate, conferring them a strong advantage in oligotrophic environments. [ABSTRACT FROM AUTHOR]

Summary: Lysophosphatidic acid acyltransferases (LPAATs) catalyze the formation of phosphatidic acid (PA), a central metabolite in both prokaryotic and eukaryotic organisms for glycerolipid biosynthesis. Phaeodactylum tricornutum contains at least two plastid‐localized LPAATs (ptATS2a and ptATS2b), but their roles in lipid synthesis remain unknown.Both ptATS2a and ptATS2b could complement the high temperature sensitivity of the bacterial plsC mutant deficient in LPAAT. In vitro enzyme assays showed that they prefer lysophosphatidic acid over other lysophospholipids.ptATS2a is localized in the plastid inner envelope membrane and CRISPR/Cas9‐generated ptATS2a mutants showed compromised cell growth, significantly changed plastid and extra‐plastidial membrane lipids at nitrogen‐replete condition and reduced triacylglycerols (TAGs) under nitrogen‐depleted condition. ptATS2b is localized in thylakoid membranes and its knockout led to reduced growth rate and TAG content but slightly altered molecular composition of membrane lipids.The changes in glycerolipid profiles are consistent with the role of both LPAATs in the sn‐2 acylation of sn‐1‐acyl‐glycerol‐3‐phosphate substrates harboring 20:5 at the sn‐1 position. Our findings suggest that both LPAATs are important for membrane lipids and TAG biosynthesis in P. tricornutum and further highlight that 20:5‐Lyso‐PA is likely involved in the massive import of 20:5 back to the plastid to feed plastid glycerolipid syntheses. [ABSTRACT FROM AUTHOR]

In this study, transmission electron microscopy (TEM) and cryo‐scanning electron microscopy (cryo‐SEM) were evaluated for their ability to detect lipid bodies in microalgae. To do so, Phaeodactylum tricornutum and Nannochloropsis oculata cells were harvested in both the mid‐exponential and early stationary growth phase. Two different cryo‐SEM cutting methods were compared: cryo‐planing and freeze‐fracturing. The results showed that, despite the longer preparation time, TEM visualisation preceded by cryo‐immobilisation allows a clear detection of lipid bodies and is preferable to cryo‐SEM. Using freeze‐fracturing, lipid bodies were rarely detected. This was only feasible if crystalline layers in the internal structure, most likely related to sterol esters or di‐saturated triacylglycerols, were revealed. Furthermore, lipid bodies could not be detected using cryo‐planing. Cryo‐SEM is also not the preferred technique to recognise other organelles besides lipid bodies, yet it did reveal chloroplasts in both species and filament‐containing organelles in cryo‐planed Nannochloropsis oculata samples. LAY DESCRIPTION: Lipid bodies are cellular organelles, which serve as a storage for lipids inside the cell. Microalgae can accumulate up to more than 50% of their dry weight as lipids. These lipids can be of interest for application in the production of biofuel and for application in food products. Certain microalgae can grow fast and have a high yield, making them an interesting alternative lipid source. The amount of lipids in microalgae increases when the cells are grown under unfavourable conditions such as nutrient limitation. The goal of this study was to compare advanced microscopy techniques to visualise lipid bodies in two different microalgae species. The first technique is transmission electron microscopy (TEM), whereby samples are high‐pressure frozen, freeze‐substituted and cut into thin slices before visualisation. The second technique is cryo‐scanning electron microscopy (cryo‐SEM), preceded by two different cutting methods to reveal the sample's inner structure. After being quickly frozen, samples are either roughly broken (freeze‐fractured) or cut with a sharp knife to obtain a flat surface (cryo‐planing). For each microalgae species, cells in the mid‐exponential and early stationary growth phase were examined, lipid bodies are expected to be more numerous in the latter ones. The results showed that TEM visualisation preceded by cryo‐immobilisation allows the detection of lipid bodies, and is preferable to cryo‐SEM, despite the longer preparation time. Using freeze‐fracturing, only occasionally a few lipid bodies were detected as the fracturing plane needs to cross the lipid bodies revealing the internal structure (layers), which is necessary for lipid body identification. Cryo‐planing was not useful for lipid body detection in these samples as this technique resulted in flat cell surfaces. In addition, TEM reveals the highest amount of other cell organelles while cryo‐SEM could only reveal chloroplasts and filament‐containing organelles. Our findings could help other researchers in choosing an appropriate electron microscopy technique for visualising lipid bodies in biological samples or the microstructure of food matrices. [ABSTRACT FROM AUTHOR]

Summary: Marine diatoms express genes encoding potential phosphate transporter and alkaline phosphatase (APase) under phosphate‐limited (−P) condition. This indicates that diatoms use high‐affinity phosphate uptake system with organic phosphate hydration. The function of molecules playing roles for Pi uptake was determined in this study.Pi uptake and APase activity of two marine diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana, were monitored during acclimation to −P condition. The transcript levels of Pi transporter were analyzed, and Pi transporters were localized with GFP tagging in diatom cells. KO mutants of plasma membrane solute carrier proteins (SLC34s) or APase were established, and their phenotype was evaluated.Some Na+/Pi transporter candidates, SLC34s in P. tricornutum and T. pseudonana, increased transcript under −P condition. Whole‐cell Pi transport was specifically stimulated by sodium ion but independent of potassium, lithium, or proton. Genome‐editing KO of PtSLC34‐5 and APase (Pt49678) in P. tricornutum was highly inhibitory for Pi uptake, and KO of TpSLC34‐2 was also highly inhibitory for Pi uptake in T. pseudonana.SLC34s and APase were co‐expressed under −P conditions in marine diatoms. SLC34s play a major role in the initial acclimation stage of diatom cells to −P condition and APase plays an increasing role in the prolonged Pi‐starved condition. [ABSTRACT FROM AUTHOR]

The document is a program for the Eighth European Phycological Congress (EPC8), which aims to bring together phycologists from Europe and beyond. The program includes symposia, poster sessions, and workshops covering various topics in phycology, such as algae biodiversity, algal cell biology, and the potential uses of algae in different industries. The organizers have made efforts to ensure gender balance and diversity among the speakers and conveners. The document provides a detailed schedule of the conference, including dates, times, and locations of the events and presentations. [Extracted from the article]

The ability to utilize dissolved organic phosphorus (DOP) gives phytoplankton competitive advantages in P-limited environments. Our previous research indicates that the diatom Phaeodactylum tricornutum could grow on glyphosate, a DOP with carbon-phosphorus (C-P) bond and an herbicide, as sole P source. However, direct evidence and mechanism of glyphosate utilization are still lacking. In this study, using physiological and isotopic analysis, combined with transcriptomic profiling, we demonstrated the uptake of glyphosate by P. tricornutum and revealed the candidate responsible genes. Our data showed a low efficiency of glyphosate utilization by P. tricornutum, suggesting that glyphosate utilization costs energy and that the alga possessed an herbicide-resistant type of 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase. Compared to the P-limited cultures, the glyphosate-grown P. tricornutum cells up-regulated genes involved in DNA replication, cell growth, transcription, translation, carbon metabolism, and many genes encoding antioxidants. Additionally, cellular C and silicon (Si) increased remarkably while cellular nitrogen (N) declined in the glyphosate-grown P. tricornutum, leading to higher Si:C and Si:N ratios, which corresponded to the up-regulation of genes involved in the C metabolism and Si uptake and the down-regulation of those encoding N uptake. This has the potential to enhance C and Si export to the deep sea when P is limited but phosphonate is available. In sum, our study documented how P. tricornutum could utilize the herbicide glyphosate as P nutrient and how glyphosate utilization may affect the element content and stoichiometry in this diatom, which have important ecological implications in the future ocean. [ABSTRACT FROM AUTHOR]

The article titled "Putting together the polyphosphate puzzle for microalgae" discusses the challenges and recent advancements in understanding the role of polyphosphate (polyP) in microalgae. PolyP is a chain of orthophosphate groups linked together and has various functions related to cellular stress responses and nutrient metabolism. The article focuses on a study that characterizes polyP dynamics in the freshwater diatom Achnanthidium minutissimum using a combination of techniques including microscopy and biochemical assays. The study reveals insights into the accumulation and utilization of polyP in response to phosphorus availability, expanding our understanding of polyP dynamics in microalgae. Further research is needed to explore the molecular mechanisms and ecological implications of polyP in microalgal systems. [Extracted from the article]

Diatoms are a group of marine algae that are responsible for a significant part of global oxygen production. Adapted to life in an aqueous environment dominated by the blue–green light, their major light-harvesting antennae—fucoxanthin–chlorophyll protein complexes (FCPs)—exhibit different pigment compositions than of plants. Despite extensive experimental studies, until recently the theoretical description of excitation energy dynamics in these complexes was limited by the lack of high-resolution structural data. In this work, we use the recently resolved crystallographic information of the FCP complex from Phaeodactylum tricornutum diatom [Wang et al., Science 363, 6427 (2019)] and quantum chemistry-based calculations to evaluate the chlorophyll transition dipole moments, atomic transition charges from electrostatic potential, and the inter-chlorophyll couplings in this complex. The obtained structure-based excitonic couplings form the foundation for any modeling of stationary or time-resolved spectroscopic data. We also calculate the inter-pigment Förster energy transfer rates and identify two quickly equilibrating chlorophyll clusters. [ABSTRACT FROM AUTHOR]

Single-cell transcriptomics has the potential to provide novel insights into poorly studied microbial eukaryotes. Although several such technologies are available and benchmarked on mammalian cells, few have been tested on protists. Here, we applied a microarray single-cell sequencing (MASC-seq) technology, that generates microscope images of cells in parallel with capturing their transcriptomes, on three species representing important plankton groups with different cell structures; the ciliate Tetrahymena thermophila, the diatom Phaeodactylum tricornutum, and the dinoflagellate Heterocapsa sp. Both the cell fixation and permeabilization steps were adjusted. For the ciliate and dinoflagellate, the number of transcripts of microarray spots with single cells were significantly higher than for background spots, and the overall expression patterns were correlated with that of bulk RNA, while for the much smaller diatom cells, it was not possible to separate single-cell transcripts from background. The MASC-seq method holds promise for investigating "microbial dark matter", although further optimizations are necessary to increase the signal-to-noise ratio. [ABSTRACT FROM AUTHOR]

Summary: Diatoms are eukaryotic microalgae responsible for nearly half of the marine productivity. RNA interference (RNAi) is a mechanism of regulation of gene expression mediated by small RNAs (sRNAs) processed by the endoribonuclease Dicer (DCR). To date, the mechanism and physiological role of RNAi in diatoms are unknown.We mined diatom genomes and transcriptomes for key RNAi effectors and retraced their phylogenetic history. We generated DCR knockout lines in the model diatom species Phaeodactylum tricornutum and analyzed their mRNA and sRNA populations, repression‐associated histone marks, and acclimatory response to nitrogen starvation.Diatoms presented a diversification of key RNAi effectors whose distribution across species suggests the presence of distinct RNAi pathways. P. tricornutum DCR was found to process 26–31‐nt‐long double‐stranded sRNAs originating mostly from transposons covered by repression‐associated epigenetic marks. In parallel, P. tricornutum DCR was necessary for the maintenance of the repression‐associated histone marks H3K9me2/3 and H3K27me3. Finally, PtDCR‐KO lines presented a compromised recovery post nitrogen starvation suggesting a role for P. tricornutum DCR in the acclimation to nutrient stress.Our study characterized the molecular function of the single DCR homolog of P. tricornutum suggesting an association between RNAi and heterochromatin maintenance in this model diatom species. [ABSTRACT FROM AUTHOR]

SUMMARY: Phaeodactylum tricornutum plastid is surrounded by four membranes, and its protein composition and function remain mysterious. In this study, the P. tricornutum plastid‐enriched fraction was obtained and 2850 proteins were identified, including 92 plastid‐encoded proteins, through label‐free quantitative proteomic technology. Among them, 839 nuclear‐encoded proteins were further determined to be plastidial proteins based on the BLAST alignments within Plant Proteome DataBase and subcellular localization prediction, in spite of the strong contamination by mitochondria‐encoded proteins and putative plasma membrane proteins. According to our proteomic data, we reconstructed the metabolic pathways and highlighted the hybrid nature of this diatom plastid. Triacylglycerol (TAG) hydrolysis and glycolysis, as well as photosynthesis, glycan metabolism, and tocopherol and triterpene biosynthesis, occur in the plastid. In addition, the synthesis of long‐chain acyl‐CoAs, elongation, and desaturation of fatty acids (FAs), and synthesis of lipids including TAG are confined in the four‐layered‐membrane plastid based on the proteomic and GFP‐fusion localization data. The whole process of generation of docosahexaenoic acid (22:6) from palmitic acid (16:0), via elongation and desaturation of FAs, occurs in the chloroplast endoplasmic reticulum membrane, the outermost membrane of the plastid. Desaturation that generates 16:4 from 16:0 occurs in the plastid stroma and outer envelope membrane. Quantitative analysis of glycerolipids between whole cells and isolated plastids shows similar composition, and the FA profile of TAG was not different. This study shows that the diatom plastid combines functions usually separated in photosynthetic eukaryotes, and differs from green alga and plant chloroplasts by undertaking the whole process of lipid biosynthesis. [ABSTRACT FROM AUTHOR]

The marine diatom Phaeodactylum tricornutum is an emerging host for metabolic engineering, but little is known about how introduced pathways are integrated into the existing metabolic framework of the host or influence transgene expression. In this study, we expressed the heterologous poly-3-hydroxybutyrate (PHB) pathway using episomal expression, which draws on the precursor acetyl coenzyme-A (AcCoA). By experimentally perturbing cultivation conditions, we gained insight into the regulation of the endogenous metabolism in transgenic lines under various environmental scenarios, as well as on alterations in AcCoA flux within the host cell. Biosynthesis of PHB led to distinct shifts in the metabolome of the host, and further analysis revealed a condition-dependent relationship between endogenous and transgenic metabolic pathways. Under N limitation, which induced a significant increase in neutral lipid content, both metabolic and transcriptomic data suggest that AcCoA was preferably shunted into the endogenous pathway for lipid biosynthesis over the transgenic PHB pathway. In contrast, supply of organic carbon in the form of glycerol supported both fatty acid and PHB biosynthesis, suggesting cross-talk between cytosolic and plastidial AcCoA precursors. This is the first study to investigate the transcriptomic and metabolomic response of diatom cell lines expressing a heterologous multi-gene pathway under different environmental conditions, providing useful insights for future engineering attempts for pathways based on the precursor AcCoA. Key points: • PHB expression had minimal effects on transcription of adjacent pathways. • N limitation favoured native lipid rather than transgenic PHB synthesis. • Glycerol addition allowed simultaneous lipid and PHB accumulation. [ABSTRACT FROM AUTHOR]

Marine algae are a valuable source of sulfated polysaccharides presenting varied structural characteristics and biological activities. Regarding sulfated polysaccharides extracted from marine microalgae, molecular characteristics and bioactivity have yet to be fully explored, especially in diatoms. Sulfated polysaccharides from marine diatoms have great potential to produce numerous health benefits and lead to new biomedical materials. Nevertheless, these potential applications are based on the polysaccharide molecular characteristics, which define their functional properties. Therefore, a detailed understanding of sulfated polysaccharides from marine diatoms may represent the starting point for a broad development of innovative applications, especially in the biomedical area. In this context, the present manuscript aims to review marine diatom sulfated polysaccharides' molecular characteristics and biological activity, looking for a more profound knowledge of these macromolecules and their potential applications. [ABSTRACT FROM AUTHOR]

Phytoplanktonic communities have been moulded from a higher level in the food web by zooplankton predation. Diatoms, which are the major primary producers in present day oceans, have evolved many strategies to thrive in the presence of copepods, their predators. Chemical signals are released in the aquatic environment by microarthropods and elicit morphological, behavioural and/or physiological modifications in diatom cells which allow them to cope with predators. Other than the most studied effects of copepod signals on the release of toxins by diatoms, the role of chemical cues on growth and biology of non-toxic diatoms has been little investigated, although it may broaden our knowledge of co-evolutive physiological mechanisms. To examine the response of diatoms to copepod-derived signals, Phaeodactylum tricornutum, Chaetoceros muelleri and Cylindrotheca fusiformis (Bacillariophyceae) were grown in the presence of copepod cues. Physiological modifications occurred and differed in sign and magnitude between species: i) in P. tricornutum cell density was higher, and dry weight lower, suggesting energy allocation into cell division at the expense of lipid and protein quotas; ii) C. muelleri showed a very homeostatic behaviour; and iii) in C. fusiformis cell density was lower and lipid content higher, showing energy allocation into lipids, which likely act as deterrent to feeders. Copepod cues are here suggested to have ruled diatom species composition in the ocean by affecting species-specific growth performance and the energy allocation into macromolecules. [ABSTRACT FROM AUTHOR]

The genus Cocconeiopsis was separated from Navicula, but its systematic position is in debate. We sequenced the complete chloroplast and mitochondrial genome of Cocconeidaceae for the first time with Cocconeiopsis kantsiensis and investigated its phylogeny and evolutionary history. Results showed that the plastid genome was 140,415 bp long with 167 genes. The mitochondrial genome was 43,732 bp long with 66 genes. Comparative analysis showed that the plastid genome structure of C. kantsiensis was most similar to those of three Navicula species and Halamphora americana, and its size was significantly smaller than that of a monoraphid species. Its mitochondrial genome was similar to that of related species except for Phaeodactylum tricornutum. The multigene phylogeny reconstruction showed that Cocconeiopsis was sister to Didymosphenia but distant from Naviculaceae. The two-gene phylogenetic analysis containing 255 species showed Cocconeiopsis was sister to Cocconeis, and distant from Naviculaceae as well. Divergence time estimation indicates the common ancestor of cocconeid species occurred about 62.8 Ma and Cocconeiopsis diverged with monoraphid Cocconeis about 58.9 Ma. Our results support the assignment of Cocconeiopsis to Cocconeidaceae and that monoraphid cocconeids were likely evolved from the lineage of Cocconeiopsis. [ABSTRACT FROM AUTHOR]

The study is focused on the ecological and physiological properties, production, and biochemical characteristics of the diatom Nitzschia amabilis. The optimum salinity (35‒36‰), illumination (2.95 klx), and photoperiod (14 h) at which the highest specific cell growth rate is achieved was determined. The coefficient of light saturation (Ik) was calculated and turned out to be lower than one, which indicates the high energy efficiency of photosynthesis. The results of experiments on salinity showed the ability of the alga to grow in the range of 4–68‰, indicating its relatively broad euryhalinity. The biochemical composition of N. amabilis during acumulative cultivation was studied. In general, polyunsaturated fatty acids predominated in the studied strain; eicosapentaenoic, arachidonic, and docosahexaenoic acids were dominant. The main share of saturated fatty acids consisted of palmitic acid. The productivity indicators of N. amabilis in relation to lipids, fucoxanthin, and PUFAs, which were 2.5–3 times higher in the flow cultivation mode than in the cumulative mode, have been established. [ABSTRACT FROM AUTHOR]

We investigated two non-ionising mutagens in the form of ultraviolet radiation (UV) and ethyl methanosulfonate (EMS) and an ionising mutagen (X-ray) as methods to increase fucoxanthin content in the model diatom Phaeodactylum tricornutum. We implemented an ultra-high throughput method using fluorescence-activated cell sorting (FACS) and live culture spectral deconvolution for isolation and screening of potential pigment mutants, and assessed phenotype stability by measuring pigment content over 6 months using high-performance liquid chromatography (HPLC) to investigate the viability of long-term mutants. Both UV and EMS resulted in significantly higher fucoxanthin within the 6 month period after treatment, likely as a result of phenotype instability. A maximum fucoxanthin content of 135 ± 10% wild-type found in the EMS strain, a 35% increase. We found mutants generated using all methods underwent reversion to the wild-type phenotype within a 6 month time period. X-ray treatments produced a consistently unstable phenotype even at the maximum treatment of 1000 Grays, while a UV mutant and an EMS mutant reverted to wild-type after 4 months and 6 months, respectively, despite showing previously higher fucoxanthin than wild-type. This work provides new insights into key areas of microalgal biotechnology, by (i) demonstrating the use of an ionising mutagen (X-ray) on a biotechnologically relevant microalga, and by (ii) introducing temporal analysis of mutants which has substantial implications for strain creation and utility for industrial applications. [ABSTRACT FROM AUTHOR]

The increasing demand for novel natural compounds has prompted the exploration of innovative approaches in bioengineering. This study investigates the bioengineering potential of the marine diatom Phaeodactylum tricornutum through the introduction of cannabis genes, specifically, tetraketide synthase (TKS), and olivetolic acid cyclase (OAC), for the production of the cannabinoid precursor, olivetolic acid (OA). P. tricornutum is a promising biotechnological platform due to its fast growth rate, amenability to genetic manipulation, and ability to produce valuable compounds. Through genetic engineering techniques, we successfully integrated the cannabis genes TKS and OAC into the diatom. P. tricornutum transconjugants expressing these genes showed the production of the recombinant TKS and OAC enzymes, detected via Western blot analysis, and the production of cannabinoids precursor (OA) detected using the HPLC/UV spectrum when compared to the wild-type strain. Quantitative analysis revealed significant olivetolic acid accumulation (0.6–2.6 mg/L), demonstrating the successful integration and functionality of the heterologous genes. Furthermore, the introduction of TKS and OAC genes led to the synthesis of novel molecules, potentially expanding the repertoire of bioactive compounds accessible through diatom-based biotechnology. This study demonstrates the successful bioengineering of P. tricornutum with cannabis genes, enabling the production of OA as a precursor for cannabinoid production and the synthesis of novel molecules with potential pharmaceutical applications. [ABSTRACT FROM AUTHOR]

Beta-glucans are polysaccharides that can be used for different applications, for example as an immunomodulator in food or feed or for managing high cholesterol levels. Certain microalgae species use beta-glucans as energy storage, accumulating them during nutrient depletion. In this study, we examined and compared beta-glucan production during nitrogen depletion in three different algae species, Phaeodactylum tricornutum, Monodopsis subterranea and Cylindrotheca fusiformis, grown in artificially illuminated flat panel airlift reactors, in order to determine the most promising microalgae species for beta-glucan production. Co-products such as fatty acids (especially eicosapentaenoic acid) and the carotenoid fucoxanthin (not produced by M. subterranea) were also considered. Biomass analysis showed that P. tricornutum cultures reached a maximal beta-glucan content of 317 ± 9 mg gDW−1, M. subterranea cultures reached 188 ± 6 mg gDW−1 and C. fusiformis cultures reached 129 ± 13 mg gDW−1. Furthermore, beta-glucan production was faster in P. tricornutum cultures. However, the maximum volumetric beta-glucan concentration reached was higher in M. subterranea cultures compared to P. tricornutum cultures as M. subterranea cultures produced more biomass during nitrogen depletion. In terms of possible co-products, P. tricornutum produced fucoxanthin and EPA, whereas M. subterranea did not produce fucoxanthin. However, M. subterranea exhibited a higher EPA content, which remained above 45 mg g−1 even after several days of nitrogen depletion. Overall, our results suggest that P. tricornutum and M. subterranea are both suitable species for beta-glucan production in flat panel airlift reactors. [ABSTRACT FROM AUTHOR]

Diatoms as important phytoplankton components interact with and are colonized by heterotrophic bacteria. This colonization has been studied extensively in the past but a distinction between the bacterial colonization directly on diatom cells or on the aggregated organic material, exopolymeric substances (EPS), was little addressed. Here we show that the diatom Thalassiosira rotula and EPS were differently colonized by strains of Roseobacteraceae and Flavobacteriaceae in two and tree partner treatments and an enriched natural bacterial community as inoculum. In two partner treatments, the algae and EPS were generally less colonized than in the three partner treatments. Two strains benefitted greatly from the presence of another partner as the proportions of their subpopulations colonizing the diatom cell and the EPS were much enhanced relative to their two partner treatments. Highest proportions of bacteria colonizing the diatom and EPS occurred in the treatment inoculated with the enriched natural bacterial community. Dissolved organic carbon, amino acids and carbohydrates produced by T. rotula were differently used by the bacteria in the two and three partner treatments and most efficiently by the enriched natural bacterial community. Our approach is a valid model system to study physico‐chemical bacteria‐diatom interactions with increasing complexity. [ABSTRACT FROM AUTHOR]

Diatoms are prominent and highly diverse microalgae in aquatic environments. Compared with other diatom species, Phaeodactylum tricornutum is an "atypical diatom" displaying three different morphotypes and lacking the usual silica shell. Despite being of limited ecological relevance, its ease of growth in the laboratory and well‐known physiology, alongside the steady increase in genome‐enabled information coupled with effective tools for manipulating gene expression, have meant it has gained increased recognition as a powerful experimental model for molecular research on diatoms. We here present a brief overview of how over the last 25 years P. tricornutum has contributed to the unveiling of fundamental aspects of diatom biology, while also emerging as a new tool for algal process engineering and synthetic biology. [ABSTRACT FROM AUTHOR]

This paper describes the experimental determination of concentration factors (CF) for nickel, ruthenium and antimony in the model diatom Phaeodactylum tricornutum Bohlin (Bacillariophyceae), which was chosen as a representative of marine phytoplankton. Better determinations of these CF are needed to improve the modelling of marine ecosystems at release points, where radioactive pollutants enter the ecosystem, for more accurate predictions of radiation dose to humans caused by these pollutants. A literature study revealed that the currently implemented values of these CF are based on very scarce data, and a computational sensitivity study showed that the radiation dose caused by radioisotopes of these elements depend strongly on the phytoplankton CF. Nutrient-enriched water samples from Swedish coastal waters were used as a medium for growing of the diatom species P. tricornutum and radioactive isotopes of the studied elements were added to the cultures during the exponential growth phase. The radioactivity in the P. tricornutum and in the culture medium were measured separately and used for determination of CF. Conservative estimates of the CF based on this phytoplankton proxy on the present data are 6400 L/kg for nickel, 20,000 L/kg for ruthenium and 890 L/kg for antimony, with P. tricornutum biomass masses referring to dry weight. The estimates for nickel and ruthenium are similar to previously published values, which underpins the credibility of radiation dose calculations based on these values. The estimate for antimony is uncertain, but also, to our knowledge, represents the first published experimentally based data on this CF. [ABSTRACT FROM AUTHOR]

Diatoms are one of the most important phytoplankton on Earth. They comprise at least ten thousand species and contribute to up to 20% of the global primary production. Because of serial endosymbiotic events and horizontal gene transfers, diatoms have developed a "secondary plastid" bounded by four membranes containing a large phase‐separated compartment, termed the pyrenoid. However, the physiological significance of this unique chloroplast morphology is poorly understood. Characterization of fundamental physiological parameters such as local pH in various subcellular compartments should facilitate a greater understanding of the physiological roles of the unique structure of the secondary plastid. A promising method to estimate local pH is the in situ expression of the pH‐sensitive green fluorescent protein. Here, we first developed the molecular tool for the mapping of in situ local pH in the diatom Phaeodactylum tricornutum by heterologously expressing pHluorin2 in the cytosol, periplastidal compartment (PPC; the space in between two sets of outer and inner chloroplast envelopes), chloroplast stroma, and the pyrenoid matrix. Our data suggested that PPC and the pyrenoid matrix are more acidic than the adjacent areas, the cytosol and the chloroplast stroma. Finally, absolute pH values at each compartment were estimated from the ratiometric fluorescence of a recombinant pHluorin2 protein, giving pH values of approximately 7.9, 6.8, 8.0, and 7.5 respectively, for the cytosol, PPC, stroma, and pyrenoid of the P. tricornutum cells, indicating the occurrence of pH gradients and the associated electrochemical potentials at their boundary. [ABSTRACT FROM AUTHOR]

The effects of ocean warming on phytoplankton have been extensively studied, but little has been documented on responses of differently sized diatoms to changes of temperature over wide ranges. We grew three diatom species, Thalassiosira pseudonana, Thalassiosira weissflogii, and Thalassiosira punctigera, with cell volumes of 199, 1805, and 13,599 μm3, respectively, at seven temperatures (5, 10, 15, 20, 25, 30, and 35°C) over 15 generations, and investigated their physiological responses. The optimum growth temperature (Topt), maximum growth rates (μmax), and thermal niche width (w) decreased by 16%, 48%, and 29% per order of magnitude in cell size increment, respectively. The cell volume of each species diminished significantly and linearly with increased temperatures, by 22% in T. punctigera, 17% in T. weissflogii, and 11% in T. pseudonana, respectively. However, the cellular biogenic silica (BSi) contents increased with rising temperature till the optimum growth temperature for growth, with the sensitivity of BSi to temperature changes (Q10BSi) ranging from 1.4 in the largest to 3.4 in the smallest diatom. The largest diatom T. punctigera showed the highest deactivation energy and succumbed to warmer conditions over its Topt, while the smallest was the most tolerant of warming. Although the moderate increase in growth temperature increased the diatoms' BSi levels, warming to temperatures higher than the optimum temperature for growth significantly reduced it. Our results suggest that diatoms acclimated to warmer conditions diminish their cell size but increase their mineralization of silica, which has profound significance in ocean carbon and silica biogeochemical cyclings. [ABSTRACT FROM AUTHOR]

We present a multi‐objective optimization framework for the design of an algal biorefinery with multiple target products. Four environmental endpoint indicators and the economic performance are used as objective functions following the life cycle assessment (LCA) methodology. The process alternatives are modeled as a superstructure covering a total of 720 feasible routes. The proposed method optimizes not only the superstructure route but simultaeously discrete and continuous parameters within the process units. A multi‐objective genetic algorithm (MOGA) is used to solve this nonlinear mixed‐integer optimization problem to design the extraction procedures for all macromolecular fractions. For the extractions, liquid–liquid equilibria (LLE) are predicted with quantum chemical calculations. A microalgae biorefinery for the marine diatom Phaeodactylum tricornutum is considered as case study, including the cultivation and extraction‐supported fractionation of the wet algal biomass to harvest the target products eicosapentaenoic acid (EPA), laminarin and fucoxanthin. 2‐Butanol proved to be the preferred solvent for the initial extraction step of wet biomass. Nutrients and solvent production cause most of the environmental impact of the overall process. A Python package for integrating LCA with multi‐objective superstructure optimization is provided as open source software. It is applicable to any process system design task involving environmental objectives. [ABSTRACT FROM AUTHOR]

Ocean-related global changes have altered phytoplankton community structure, especially the diatom-dinoflagellate competition, which further influences ecosystem structure and functions. The pivotal ecological roles of diatoms and dinoflagellates are strongly related with their biochemical composition, but quantitative comparisons of biochemical changes between diatoms and dinoflagellates under variable environments are still limited. We investigated responses of lipid biomarkers (sterols and fatty acids (FAs)) to different temperatures (12, 18 and 24 °C), nitrogen and phosphorus concentrations and their molar ratios (N:P ratios) of 10:1, 24:1 and 63:1 in marine diatom Phaeodactylum tricornutum and dinoflagellate Prorocentrum minimum. Over these wide ranges of temperature and nutrient conditions, sterol and FA profiles were relatively stable in the two species. For carbon-normalized contents of major lipid biomarkers, warming caused non-significant changes in the diatoms but an increase (up to 153%) in the dinoflagellates. Eutrophication caused an overall decrease (up to 53%) in major lipid biomarker contents in the diatoms but an overall increase (up to 77%) in the dinoflagellates. In contrast, imbalanced N:P ratios caused an overall increase (up to 64%) in major lipid biomarker contents in the diatoms but an overall decrease (up to 53%) in the dinoflagellates. Taken together, our results showed that the contents of major sterols and polyunsaturated FAs would change non-significantly in the diatom P. tricornutum, while those in the dinoflagellate P. minimum would increase (ca. 9–48%) under future ocean warming, eutrophication and imbalanced N:P ratios. This study expands our knowledge on lipid-based indicators of phytoplankton under changing environments, which by systematically linking with several other aspects of food quality will help to understand ecological consequences of diatom-dinoflagellate community changes. [ABSTRACT FROM AUTHOR]