SciCombinator

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Concept: Diatoms

158

In diatoms, the main photosynthetic pigments are chlorophylls a and c, fucoxanthin, diadinoxanthin and diatoxanthin. The marine pennate diatom Haslea ostrearia has long been known for producing, in addition to these generic pigments, a water-soluble blue pigment, marennine. This pigment, responsible for the greening of oysters in western France, presents different biological activities: allelopathic, antioxidant, antibacterial, antiviral, and growth-inhibiting. A method to extract and purify marennine has been developed, but its chemical structure could hitherto not be resolved. For decades, H. ostrearia was the only organism known to produce marennine, and can be found worldwide. Our knowledge about H. ostrearia-like diatom biodiversity has recently been extended with the discovery of several new species of blue diatoms, the recently described H. karadagensis, H. silbo sp. inedit. and H. provincialis sp. inedit. These blue diatoms produce different marennine-like pigments, which belong to the same chemical family and present similar biological activities. Aside from being a potential source of natural blue pigments, H. ostrearia-like diatoms thus present a commercial potential for aquaculture, cosmetics, food and health industries.

Concepts: Algae, Life, Species, Pigment, Kingdom, Diatom, Diatoms, Pennales

28

Diatoms are major contributors to the photosynthetic productivity of marine phytoplankton. In these organisms, fucoxanthin-chlorophyll proteins (FCPs) serve as light-harvesting proteins. We have explored the FCP complexes in Phaeodactylum tricornutum under low light (LL) and high light (HL) conditions. Sub-fractionating the pool of major FCPs yielded different populations of trimeric complexes. Only Lhcf and Lhc-like proteins were found in the trimers. Under LL, the first polypeptide fraction contained six different Lhcfs and was mainly composed of Lhcf10. It was characterised by the highest amount of fucoxanthin (Fx). The second was dominated by Lhcf10, Lhcf5 and Lhcf2, and had a lower Fx/Chl c ratio. Little Fx/Chl c also characterised the most abundant FCP complexes, found in fraction 3, composed mainly of Lhcf5. These FCPs bound Fx molecules with the strongest bathochromic shift. The last two fractions contained FCP complexes that were built mainly of Lhcf4, harbouring more Fx molecules that absorbed at shorter wavelengths. Under HL, the same main polypeptides were retrieved in the different fractions and spectroscopic features were almost identical except for a higher diadinoxanthin content. The total amount of Lhcf5 was reduced under HL, whereas the amount of the last two fractions and thereby Lhcf4 was increased. Lhcf11 was identified in different LL fractions, but not detected in any HL fraction, while two new Lhc-like proteins were only found under HL. This is the first report on different trimeric FCP complexes in pennate diatoms, which differ in polypeptide composition and pigmentation, and are differentially expressed by light.

Concepts: Algae, Spectroscopy, Peptide, Wavelength, Diatom, Phaeodactylum tricornutum, Diatoms, Planktology

28

Frustules, the silica shells of diatoms, have unique porous architectures with good mechanical strength. In recent years, biologists have learned more about the mechanism of biosilica shells formation; meanwhile, physicists have revealed their optical and microfluidic properties, and chemists have identified ways to modify them into various materials while maintaining their hierarchical structures. These efforts have provided more opportunities to use biosilica structures in microsystems and other commercial products. This review focuses on the preparation of biosilica structures and their applications, especially in the development of microdevices. We discuss existing methods of extracting biosilica from diatomite and diatoms, introduce methods of separating biosilica structures by shape and sizes, and summarize recent studies on diatom-based devices used for biosensing, drug delivery, and energy applications. In addition, we introduce some new findings on diatoms, such as the elastic deformable characteristics of biosilica structures, and offer perspectives on planting diatom biosilica in microsystems.

Concepts: Structure, Silicon, Strength of materials, Diatom, Diatoms, Silicic acid, Frustule, Diatomaceous earth

28

Dispersants are commonly used to mitigate the impact of oil spills, however, the ecological cost associated with their use is uncertain. The toxicity of weathered oil, dispersed weathered oil, and the hydrocarbon-based dispersant Slickgone NS(®), to the diatom Phaeodactylum tricornutum has been examined using standardized toxicity tests. The assumption that most toxicity occurs via narcosis was tested by measuring membrane damage in diatoms after exposure to one of the petroleum products. The mode of toxic action was determined using microarray-based gene expression profiling in diatoms after exposure to one of the petroleum products. The diatoms were found to be much more sensitive to dispersants than to the water accommodated fraction (WAF), and more sensitive to the chemically enhanced WAF (CEWAF) than to either the WAF itself or the dispersants. Exposure to dispersants and CEWAF caused membrane damage, while exposure to WAF did not. The gene expression profiles resulting from exposure to all three petroleum mixtures were highly similar, suggesting a similar mode of action for these compounds. The observed toxicity bore no relationship to PAH concentrations in the water column or to total petroleum hydrocarbon (TPH), suggesting that an undescribed component of the oil was causing toxicity. Taken together, these results suggest that the use of dispersants to clean up oil spills will dramatically increase the oil toxicity to diatoms, and may have implications for ecological processes such as the timing of blooms necessary for recruitment.

Concepts: Gene expression, Petroleum, Toxicity, DNA microarray, Diatom, Phaeodactylum tricornutum, Diatoms, Exxon Valdez oil spill

22

The diatom Phaeodactylum tricornutum was cultured in five different growth regimes to obtain cells with different composition. Pairs of populations subjected to different treatments were then mixed in a communal culture regime that differed from those of the origin. After six hours, the ratio between the two populations was verified by flow cytometry. Alterations in this ratio were found when cells previously grown at 1 mM NH4+were mixed with GeO2- and 0.5 mM NH4+-grown cells. The nutritional background may thus make cells differently suited to new environmental conditions and afford advantages in terms of reproductive potential. Competitive interactions between populations may result from the differences in the expressed proteome and/or in the availability of tools for regulatory responses. This may have relevance to the persistence of phenotypically neutral variants present in the population best suited to the new condition, after the interaction of the conspecifics with different nutritional histories. This article is protected by copyright. All rights reserved.

Concepts: Protein, Sociology, Flow cytometry, All rights reserved, Diatom, Phaeodactylum tricornutum, Diatoms, Copyright

7

Glyphosate is a globally popular herbicide to kill weeds and its wide applications may lead to accumulation in coastal oceans as a source of phosphorus (P) nutrient or growth inhibitor of phytoplankton. We studied the physiological effects of glyphosate on fourteen species representing five major coastal phytoplankton phyla (haptophyta, bacillariophyta, dinoflagellata, raphidophyta, and chlorophyta). Based on growth responses to different concentrations of glyphosate under contrasting dissolved inorganic phosphorus (DIP) conditions, we found that phytoplankton species could be classified into five groups. Group I (Emiliania huxleyi, Skeletonema costatum, Phaeodactylum tricornutum) could utilize glyphosate as sole P-source to support growth in axenic culture, but in the presence of DIP, they were inhibited by both 36-μM and 360-μM glyphosate. Group II (Karenia mikimotoi, Prorocentrum minimum, Dunaliella tertiolecta, Symbiodinium sp., Heterosigma akashiwo and Alexandrium catenella) could not utilize glyphosate as sole P-source to support growth, and in the presence of DIP growth was not affected by 36-μM but inhibited by 360-μM glyphosate. Glyphosate consistently enhanced growth of Group III (Isochrysis galbana) and inhibited Group IV (Thalassiosira weissflogii, Thalassiosira pseudonana and Chattonella marina) regardless of DIP condition. Group V (Amphidinium carterae) exhibited no measurable response to glyphosate regardless of DIP condition. This grouping is not congruent with the phylogenetic relationships of the phytoplankton species suggesting functional differentiation driven by environmental pressure. We conclude that glyphosate could be used as P-source by some species while is toxic to some other species and yet has no effects on others. The observed differential effects suggest that the continued use of glyphosate and increasing concentration of this herbicide in the coastal waters will likely exert significant impact on coastal marine phytoplankton community structure.

Concepts: Algae, Phylogenetics, Phosphorus, Coccolithophore, Diatom, Phaeodactylum tricornutum, Diatoms, Planktology

6

In vast areas of the ocean, the scarcity of iron controls the growth and productivity of phytoplankton. Although most dissolved iron in the marine environment is complexed with organic molecules, picomolar amounts of labile inorganic iron species (labile iron) are maintained within the euphotic zone and serve as an important source of iron for eukaryotic phytoplankton and particularly for diatoms. Genome-enabled studies of labile iron utilization by diatoms have previously revealed novel iron-responsive transcripts, including the ferric iron-concentrating protein ISIP2A, but the mechanism behind the acquisition of picomolar labile iron remains unknown. Here we show that ISIP2A is a phytotransferrin that independently and convergently evolved carbonate ion-coordinated ferric iron binding. Deletion of ISIP2A disrupts high-affinity iron uptake in the diatom Phaeodactylum tricornutum, and uptake is restored by complementation with human transferrin. ISIP2A is internalized by endocytosis, and manipulation of the seawater carbonic acid system reveals a second-order dependence on the concentrations of labile iron and carbonate ions. In P. tricornutum, the synergistic interaction of labile iron and carbonate ions occurs at environmentally relevant concentrations, revealing that carbonate availability co-limits iron uptake. Phytotransferrin sequences have a broad taxonomic distribution and are abundant in marine environmental genomic datasets, suggesting that acidification-driven declines in the concentration of seawater carbonate ions will have a negative effect on this globally important eukaryotic iron acquisition mechanism.

Concepts: Oxygen, Carbon dioxide, Iron, Ocean, Diatom, Phaeodactylum tricornutum, Diatoms, Plankton

4

Diatoms, considered as one of the most diverse and largest groups of algae, can provide the means to reach a sustainable production of petrochemical substitutes and bioactive compounds. However, a prerequisite to achieving this goal is to increase the solar-to-biomass conversion efficiency of photosynthesis, which generally remains less than 5% for most photosynthetic organisms. We have developed and implemented a rapid and effective approach, herein referred to as intracellular spectral recompositioning (ISR) of light, which, through absorption of excess blue light and its intracellular emission in the green spectral band, can improve light utilization. We demonstrate that ISR can be used chemogenically, by using lipophilic fluorophores, or biogenically, through the expression of an enhanced green fluorescent protein (eGFP) in the model diatom Phaeodactylum tricornutum. Engineered P. tricornutum cells expressing eGFP achieved 28% higher efficiency in photosynthesis than the parental strain, along with an increased effective quantum yield and reduced nonphotochemical quenching (NPQ) induction levels under high-light conditions. Further, pond simulator experiments demonstrated that eGFP transformants could outperform their wild-type parental strain by 50% in biomass production rate under simulated outdoor sunlight conditions. Transcriptome analysis identified up-regulation of major photosynthesis genes in the engineered strain in comparison with the wild type, along with down-regulation of NPQ genes involved in light stress response. Our findings provide a proof of concept for a strategy of developing more efficient photosynthetic cell factories to produce algae-based biofuels and bioactive products.

Concepts: Algae, Cyanobacteria, Photosynthesis, Protein, Gene, Diatom, Phaeodactylum tricornutum, Diatoms

3

Diatoms are eukaryotic microalgae that are responsible for up to 40% of the ocean’s primary productivity. How diatoms respond to environmental perturbations such as elevated carbon concentrations in the atmosphere is currently poorly understood. We developed a transcriptional regulatory network based on various transcriptome sequencing expression libraries for different environmental responses to gain insight into the marine diatom’s metabolic and regulatory interactions and provide a comprehensive framework of responses to increasing atmospheric carbon levels. This transcriptional regulatory network was integrated with a recently published genome-scale metabolic model of Phaeodactylum tricornutum to explore the connectivity of the regulatory network and shared metabolites. The integrated regulatory and metabolic model revealed highly connected modules within carbon and nitrogen metabolism. P. tricornutum’s response to rising carbon levels was analyzed by using the recent genome-scale metabolic model with cross comparison to experimental manipulations of carbon dioxide. IMPORTANCE Using a systems biology approach, we studied the response of the marine diatom Phaeodactylum tricornutum to changing atmospheric carbon concentrations on an ocean-wide scale. By integrating an available genome-scale metabolic model and a newly developed transcriptional regulatory network inferred from transcriptome sequencing expression data, we demonstrate that carbon metabolism and nitrogen metabolism are strongly connected and the genes involved are coregulated in this model diatom. These tight regulatory constraints could play a major role during the adaptation of P. tricornutum to increasing carbon levels. The transcriptional regulatory network developed can be further used to study the effects of different environmental perturbations on P. tricornutum’s metabolism.

Concepts: Photosynthesis, Protein, Carbon dioxide, Metabolism, Nitrogen, Diatom, Phaeodactylum tricornutum, Diatoms

3

Environmental fluctuations affect distribution, growth and abundance of diatoms in nature, with iron (Fe) availability playing a central role. Studies on the response of diatoms to low Fe have either utilized continuous (24 hr) illumination or sampled a single time of day, missing any temporal dynamics. We profiled the physiology, metabolite composition, and global transcripts of the pennate diatom Phaeodactylum tricornutum during steady-state growth at low, intermediate, and high levels of dissolved Fe over light:dark cycles, to better understand fundamental aspects of genetic control of physiological acclimation to growth under Fe-limitation. We greatly expand the catalog of genes involved in the low Fe response, highlighting the importance of intracellular trafficking in Fe-limited diatoms. P. tricornutum exhibited transcriptomic hallmarks of slowed growth leading to prolonged periods of cell division/silica deposition, which could impact biogeochemical carbon sequestration in Fe-limited regions. Light harvesting and ribosome biogenesis transcripts were generally reduced under low Fe while transcript levels for genes putatively involved in the acquisition and recycling of Fe were increased. We also noted shifts in expression towards increased synthesis and catabolism of branched chain amino acids in P. tricornutum grown at low Fe whereas expression of genes involved in central core metabolism were relatively unaffected, indicating that essential cellular function is protected. Beyond the response of P. tricornutum to low Fe, we observed major coordinated shifts in transcript control of primary and intermediate metabolism over light:dark cycles which contribute to a new view of the significance of distinctive diatom pathways, such as mitochondrial glycolysis and the ornithine-urea cycle. This study provides new insight into transcriptional modulation of diatom physiology and metabolism across light:dark cycles in response to Fe availability, providing mechanistic understanding for the ability of diatoms to remain metabolically poised to respond quickly to Fe input and revealing strategies underlying their ecological success.

Concepts: DNA, Protein, Gene, Gene expression, Amino acid, Branched-chain amino acids, Diatom, Diatoms