The regulation of carbon metabolism in the diatom Phaeodactylum tricornutum at the cell, metabolite, and gene expression levels in exponential fed-batch cultures is reported. Transcriptional profiles and cell chemistry sampled simultaneously at all time points provide a comprehensive data set on carbon incorporation, fate, and regulation. An increase in Nile Red fluorescence (a proxy for cellular neutral lipids) was observed throughout the light period, and water-soluble glucans increased rapidly in the light period. A near-linear decline in both glucans and lipids was observed during the dark period, and transcription profile data indicated that this decline was associated with the onset of mitosis. More than 4,500 transcripts that were differentially regulated during the light/dark cycle are identified, many of which were associated with carbohydrate and lipid metabolism. Genes not previously described in algae and their regulation in response to light were integrated in this analysis together with proposed roles in metabolic processes. Some very fast light-responding genes in, for example, fatty acid biosynthesis were identified and allocated to biosynthetic processes. Transcripts and cell chemistry data reflect the link between light energy availability and light energy-consuming metabolic processes. Our data confirm the spatial localization of processes in carbon metabolism to either plastids or mitochondria or to glycolysis/gluconeogenesis, which are localized to the cytosol, chloroplast, and mitochondria. Localization and diel expression pattern may be of help to determine the roles of different isoenzymes and the mining of genes involved in light responses and circadian rhythms.

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The ecological success of diatoms is emphasized by regular blooms of many different species in all aquatic systems, but the reason behind their success is not fully understood. A special feature of the diatom cell is the frustule, a nano-patterned cell encasement made of amorphous biosilica. The optical properties of a cleaned single valve (one half of a frustule) from the diatom Coscinodiscus centralis were studied using confocal micro-spectroscopy. A photonic crystal function in the frustule was observed, and analysis of the hyperspectral mapping revealed an enhancement of transmitted light around 636 and 663 nm. These wavelengths match the absorption maxima of chlorophyll a and c, respectively. Additionally, we demonstrate that a highly efficient light trapping mechanism occurred, resulting from strong asymmetry between the cribrum and foramen pseudo-periodic structures. This effect may prevent transmitted light from being backscattered and in turn enhance the light absorption. Based on our results, we hypothesize that the multi-scaled layered structure of the frustule improves photosynthetic efficiency by these three mechanisms. The optical properties of the frustule described here may contribute to the ecological success of diatoms in both lentic and marine ecosystems, and should be studies further in vivo.

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The diatom cell wall, or frustule, is a highly complex, three-dimensional structure consisting of nanopatterned silica as well as proteins and other organic components. While some key components have been identified, knowledge on frustule biosynthesis is still fragmented. The model diatom Thalassiosira pseudonana was subjected to silicon (Si) shift-up and shift-down situations. Cellular and molecular signatures, dynamic changes and co-regulated clusters representing the hallmarks of cellular and molecular responses to changing Si availabilities were characterised. Ten new proteins with silaffin-like motifs, two kinases and a novel family of putatively frustule-associated transmembrane proteins induced by Si shift-up with a possible role in frustule biosynthesis were identified. A separate cluster analysis performed on all significantly regulated silaffin-like proteins (SFLPs), as well as silaffin-like motifs, resulted in the classification of silaffins, cingulins and SFLPs into distinct clusters. A majority of the genes in the Si-responsive clusters are highly divergent, but positive selection does not seem to be the driver behind this variability. This study provides a high-resolution map over transcriptional responses to changes in Si availability in T. pseudonana. Hallmark Si-responsive genes are identified, characteristic motifs and domains are classified, and taxonomic and evolutionary implications outlined and discussed.

Microalgae are regarded as a promising alternative that can replace fishmeal and fish oil in aquaculture. Under N-limitation, many microalgae species change their carbon storage patterns in favor of neutral lipids (NLs) mainly in the form of triacylglycerol (TAG), but fatty acids in polar lipids (PL) are nutritionally more available for fish than those esterified into NLs. In the present study, the effect of N-limitation on the lipid content and fatty acid profiles in different lipid classes of Phaeodactylum tricornutum, Isochrysis aff. galbana clone T-Iso, Rhodomonas baltica, and Nannochloropsis oceanica were investigated. The microalgae cells were cultivated by two different methods, batch and semi-continuous culture, to create strong and moderate N-limitation, and this in turn will significantly affect the biomass and lipid productivity. All four species accumulated lipids mainly in the form of TAG, in response to strong nitrogen limitation. N. oceanica, however, accumulated 51% of the dry weight as lipid in moderate nitrogen limitation and up to 87% of the fatty acid was in TAG. Isochrysis aff. galbana clone T-Iso was the only species where the fraction of polyunsaturated fatty acid (PUFA), especially the fraction of docosahexaenoic acid (DHA), increased with increasing nitrogen limitation. Total lipid productivity showed no increase in batch culture although stronger nitrogen limitation led to lipid accumulation. P. tricornutum had the highest eicosapentaenoic acid (EPA) content, while N. oceanica showed the highest EPA productivity due to the high content of lipid. The highest DHA productivity was found in Isochrysis aff. galbana clone T-Iso from moderate N-limitation, mainly due to the high biomass productivity. Based on the results from the current study, N. oceanica and T-Iso are two promising microalgae strains ass long-term sustainable sources of n-3 long chain-PUFAs under moderate N-limitation. As shown in the present study, increased lipid content in microalgal cells due to strong N-limitation induction may not increase the lipid productivity because biomass production is usually reduced. Therefore, a combination of approaches such as metabolic engineering, conditioning and selection may be needed to further increase the n-3 LC-PUFA productivity without substantial loss of biomass.

To study the use of nuclear magnetic resonance (NMR) spectroscopy as a method of classification, we performed high-resolution magic angle spinning proton (HR MAS 1 H) NMR spectroscopy analysis of whole-cell samples of Dunaliella sp. (Chlorophyceae), Amphidinium carterae (Dinophyceae), Phaeodactylum tricornutum and Thalassiosira pseudonana (Bacillariophyceae). Emphasising the potential use of NMR spectroscopy as a routine analysis of microalgae we chose a straightforward procedure for culturing and harvesting, without extraction or radioactive labelling. We obtained well-resolved HR MAS 1 H NMR spectra from the 4 algae, despite the fact that our samples contained whole cells and some residual sea water. Selected parts of 5 replicate spectra from each microalga were used as input in 2 multivariate pattern-recognition strategies (principal component analysis and fuzzy clustering), both analyses showing clear grouping of the different species. Two spectra from a previous sample run (cultures grown under the same conditions) were also included, and both were correctly classified. We therefore consider HR MAS 1 H NMR spectroscopy to be a potential method of classification for microalgae, with statistical data processing indicating replicability and robustness of the method.