Digital expression profiling of novel diatom transcripts provides insight into their biological functions

Background: Diatoms represent the predominant group of eukaryotic phytoplankton in the oceans and are responsible for around 20% of global photosynthesis. Two whole genome sequences are now available. Notwithstanding, our knowledge of diatom biology remains limited because only around half of their genes can be ascribed a function based onhomology-based methods. High throughput tools are needed, therefore, to associate functions with diatom-specific genes. Results: We have performed a systematic analysis of 130,000 ESTs derived from Phaeodactylum tricornutum cells grown in 16 different conditions. These include different sources of nitrogen, different concentrations of carbon dioxide, silicate and iron, and abiotic stresses such as low temperature and low salinity. Based on unbiased statistical methods, we have catalogued transcripts with similar expression profiles and identified transcripts differentially expressed in response to specific treatments. Functional annotation of these transcripts provides insights into expression patterns of genes involved in various metabolic and regulatory pathways and into the roles of novel genes with unknown functions. Specific growth conditions could be associated with enhanced gene diversity, known gene product functions, and over-representation of novel transcripts. Comparative analysis of data from the other sequenced diatom, Thalassiosira pseudonana, helped identify several unique diatom genes that are specifically regulated under particular conditions, thus facilitating studies of gene function, genome annotation and the molecular basis of species diversity. Conclusions: The digital gene expression database represents a new resource for identifying candidate diatom-specific genes involved in processes of major ecological relevance

Genome-Wide Transcriptome Analyses of Silicon Metabolism in Phaeodactylum tricornutum Reveal the Multilevel Regulation of Silicic Acid Transporters

BACKGROUND:Diatoms are largely responsible for production of biogenic silica in the global ocean. However, in surface seawater, Si(OH)(4) can be a major limiting factor for diatom productivity. Analyzing at the global scale the genes networks involved in Si transport and metabolism is critical in order to elucidate Si biomineralization, and to understand diatoms contribution to biogeochemical cycles. METHODOLOGY/PRINCIPAL FINDINGS:Using whole genome expression analyses we evaluated the transcriptional response to Si availability for the model species Phaeodactylum tricornutum. Among the differentially regulated genes we found genes involved in glutamine-nitrogen pathways, encoding putative extracellular matrix components, or involved in iron regulation. Some of these compounds may be good candidates for intracellular intermediates involved in silicic acid storage and/or intracellular transport, which are very important processes that remain mysterious in diatoms. Expression analyses and localization studies gave the first picture of the spatial distribution of a silicic acid transporter in a diatom model species, and support the existence of transcriptional and post-transcriptional regulations. CONCLUSIONS/SIGNIFICANCE:Our global analyses revealed that about one fourth of the differentially expressed genes are organized in clusters, underlying a possible evolution of P. tricornutum genome, and perhaps other pennate diatoms, toward a better optimization of its response to variable environmental stimuli. High fitness and adaptation of diatoms to various Si levels in marine environments might arise in part by global regulations from gene (expression level) to genomic (organization in clusters, dosage compensation by gene duplication), and by post-transcriptional regulation and spatial distribution of SIT proteins

Locomotion speed of a benthic foraminifer Ammonia tepida exposed to different nitrogen and carbon sources

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Physiological and photophysiological responses of the benthic diatom Entomoneis paludosa (Bacillariophyceae) to dissolved inorganic and organic nitrogen in culture

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Photorespiration in continuous of Dunaliella tertiolecta (Chlorophyta) : relationships between serine, glycine, and extracellular glycolate

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Photorespiration in continuous culture of Dunaliella tertiolecta (Chlorophyta): relationships between serine, glycine, and extracellular glycolate

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Dilution of 15N in Dunaliella tertiolecta by uptake of an unidentified compound following nitrate exhaustion

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Physiological and photophysiological responses of the benthic diatom Entomoneis paludosa (Bacillariophyceae) to dissolved inorganic and organic nitrogen in culture

International audienceBenthic diatoms are dominant primary producers in intertidal flats. This study investigated the effect of different nitrogen sources and concentrations on Entomoneis paludosa growth and physiological responses. Six nitrogen sources either inorganic (nitrate and ammonium) or organic (urea, arginine, glutamine and glycine) supplied at two concentrations (40 and 400 mu M-N) induced significant effects on growth, carbon, nitrogen, pigment content and maximum PSII quantum efficiency (F-v/F-m). Entomoneis paludosa grew under all nitrogen sources albeit showing differences in lag phase, growth rate and cell yield. Inorganic nitrogen, urea and arginine induced higher growth, whereas glycine did not support high biomass. F-v/F-m showed variability dependent on nitrogen source and C/N ratio. F-v/F-m varied between 0.55 and 0.65 at 400 mu M-N with the highest values observed in glycine, glutamine and urea, whereas nitrate, ammonium and arginine induced lower F-v/F-m. All cellular components decreased in the 40 mu M-N treatments, with nitrogen and pigments being lower than carbon content. Light-harvesting pigment ratios Chl c/Chl a and photoprotective pigment ratios (diatoxanthin + diadinoxanthin)/Chl a increased, while fucoxanthin/Chl a ratios were unaffected by N-limitations. Entomoneis paludosa was capable of quickly adapting and using a wide variety of nitrogen sources. This adaptability may contribute to microphytobenthos diatom ecological success in mudflat ecosystems

Growth and biochemical composition of a microphytobenthic diatom (Entomoneis paludosa) exposed to shorebird (Calidris alpina) droppings

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Growth-compensating phenomena in continuous cultures of Dunaliella tertiolecta limited simultaneously by light and nitrate

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