Diatom microfossils from cretaceous and eocene sediments contain native silica precipitating long‐chain polyamines

Organic molecules from known biological sources (biomarkers) that are preserved over geological time are critical tools in the study of past conditions and events on earth. Polar molecules are typically recycled rapidly in marine environments and do not survive burial within aquatic sediments in unambiguously recognizable form. As such, geological biomarkers are formed almost exclusively from precursor biomolecules that have been altered, limiting their utility as paleoproxies. Here, we report that nitrogen‐rich aliphatic long‐chain polyamines (LCPAs), biosynthesized by diatoms in species‐specific assemblages for the precipitation of nanopatterned siliceous cell walls (frustules), are preserved unaltered in the oldest available diatom fossils dating to the Lower Cretaceous (early Albian, 115–110 Ma). We further show that the cumulative LCPA pool accounts for 60% of the total C and 80% of the total N preserved in the Cretaceous age sediments. We suggest that silica glass formation by diatoms constitutes an important preservation mechanism for source‐specific, polar biomolecules, protecting them indefinitely by encapsulation within the silicified frustule. LCPAs are a unique, source‐specific carbon and nitrogen archive of diatom biomass, offering a promising tool for reconstruction of global cycles of carbon and nitrogen over geological timescales.     

Frustule morphogenesis of raphid pennate diatom <Emphasis Type="Italic">Encyonema ventricosum</Emphasis> (Agardh) Grunow

Diatoms stand out among other microalgae due to the high diversity of species-specific silica frustules whose components (valves and girdle bands) are formed within the cell in special organelles called silica deposition vesicles (SDVs). Research on cell structure and morphogenesis of frustule elements in diatoms of different taxonomic groups has been carried out since the 1950s but is still relevant today. Here, cytological features and valve morphogenesis in the freshwater raphid pennate diatom Encyonema ventricosum (Agardh) Grunow have been studied using light and transmission electron microscopy of cleaned frustules and ultrathin sections of cells, and scanning electron and atomic force microscopy of the frustule surface. Data have been obtained on chloroplast structure: the pyrenoid is spherical, penetrated by a lamella (a stack of two thylakoids); the girdle lamella consists of several short lamellae. The basic stages of frustule morphogenesis characteristic of raphid pennate diatoms have been traced, with the presence of cytoskeletal elements near SDVs being observed throughout this process. Degradation of the plasmalemma and silicalemma is shown to take place when the newly formed valve is released into the space between sister cells. The role of vesicular transport and exocytosis in the gliding of pennate diatoms is discussed.     

Genotypic and phenotypic variation in diatom silicification under paleo‐oceanographic conditions

Diatoms have co‐evolved with the silicon cycle and are largely responsible for reducing surface concentrations of silicate in the ocean to their present levels. We quantify silicification in marine diatoms at a range of high silicate concentrations representative of environments found over their geological history. The species examined include Stephanopyxis turris, an ancient centric species found throughout the Cenozoic, Thalassiosira pseudonana and Thalassiosira weissflogii, two younger centric species, and two pennate ecotypes of Staurosirella pinnata isolated from different nutrient regimes. Frustule thickness and micromorphological structure are strongly affected by silicate concentration. All species become increasingly silicified with silicate concentrations at concentrations vastly in excess of surface ocean concentrations today. In contrast, the half‐saturation constant for silicate uptake for most modern diatoms is below 2 μm . Based on the results, we hypothesize that silicate uptake is multiphasic in diatoms and that multiple silicate transport systems may have evolved in response to decreases in surface silicate concentration over geological time. The oldest species examined is more heavily silicified than the more modern species, presumably reflecting the conditions under which it originated. Yet diversification in silicification can be rapid, as illustrated by greater silicification in onshore versus the offshore ecotype of the same modern species. This work suggests that silicification of fossil frustules may eventually provide a paleoproxy for surface silicate concentrations over the Cenozoic, although development of species‐specific calibrations will be necessary and the effects of a range of environmental conditions must be investigated.     

THE EVOLUTION OF ELONGATE SHAPE IN DIATOMS1

Diatoms have been classified historically as either centric or pennate based on a number of features, cell outline foremost among them. The consensus among nearly every estimate of the diatom phylogeny is that the traditional pennate diatoms (Pennales) constitute a well‐supported clade, whereas centric diatoms do not. The problem with the centric–pennate classification was highlighted by some recent analyses concerning the phylogenetic position of Toxarium, whereby it was concluded that this “centric” diatom independently evolved several pennate‐like characters including an elongate, pennate‐like cell outline. We performed several phylogenetic analyses to test the hypothesis that Toxarium evolved its elongate shape independently from Pennales. First, we reanalyzed the original data set used to infer the phylogenetic position of Toxarium and found that a more thorough heuristic search was necessary to find the optimal tree. Second, we aligned 181 diatom and eight outgroup SSU rDNA sequences to maximize the juxtapositioning of similar primary and secondary structure of the 18S rRNA molecule over a much broader sampling of diatoms. We then performed a number of phylogenetic analyses purposely based on disparate sets of assumptions and found that none of these analyses supported the conclusion that Toxarium acquired its pennate‐like outline independently from Pennales. Our results suggest that elongate outline is congruent with SSU rDNA data and may be synapomorphic for a larger, more inclusive clade than the traditional Pennales.     

Spatial heterogeneity of diatom silicification and growth in a eutrophic reservoir

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Luminescence properties of a nanoporous freshwater diatom

Freshwater diatom frustules show special optical properties. In this paper we observed luminescence properties of the freshwater diatom Cyclotella meneghiniana. To confirm the morphological properties we present scanning electron microscopy (SEM) images. X‐ray diffraction (XRD) studies were carried out to visualize the structural properties of the frustules, confirming that silica present in diatom frustules crystallizes in an α‐quartz structure. Study of the optical properties of the silica frustules of diatoms using ultra‐violet‐visible (UV‐vis) spectroscopy and photoluminescence spectroscopy confirmed that the diatom C. meneghiniana shows luminescence in the blue region of the electromagnetic spectrum when irradiated with UV light. This property of diatoms can be exploited to obtain many applications in day‐to‐day life. Also, using time‐resolved photoluminescence spectroscopy (TRPL) it was confirmed that this species of diatom shows bi‐exponential decay. Copyright © 2011 John Wiley & Sons, Ltd.     

Seasonal changes on planktonic diatom communities along an inshore-offshore gradient in the Gulf of Gabes (Tunisia)

We investigated the composition, biomass and cell size dynamics of the marine planktonic diatom species along a coastal-open sea gradient in relation to the hydrological characteristics, during four oceanographic cruises in July 2005, May–June 2006, September 2006 and March 2007 in the Gulf of Gabes. The study of the marine planktonic diatoms throughout the sampling period showed the presence of 40 different species belonging to 22 pennate and 18 centric diatom species. Centric diatoms were more abundant than the pennate ones; 56% and 44% of total diatom abundance, respectively. Diatoms were very abundant, representing about 60% of the total phytoplankton abundance, with an exception in July 2005 (19%) during which Dictyochophyceae were the most dominant group (41% of the total phytoplankton abundance). Diatoms, which were dominant in the coastal samples, mainly proliferate in the semi-mixing conditions (May–June 2006), whereas they declined in the offshore area, most likely due to silicate shortage. In this period, in spite of the high abundance of diatom planktonic cells, only diatom biomass was correlated with silica amount, proving that biomass was a better ecological bio-indicator than abundance. The results suggest that the marine planktonic diatoms taxa were generally adapted to specific hydrological structure. In fact, the dominance index of diatoms showed that the biodiversity of diatoms increased gradually along the coastal-open sea gradient except in May–June 2006 during which a slight decrease along the inshore towards offshore areas was observed. This index increase depended on a coastal-open sea distance during thermal stratification (July 2005 and September 2006) and mixing periods (March 2007).     

Production and particle characterization of the frustules of Cyclotella cryptica in comparison with siliceous earth

Diatoms are photoautotrophic micro-organisms that use inorganic carbon sources and light in photosynthesis. Diatom frustules were characterized in terms of particle techniques and compared with siliceous earth, i.e. depositions of diatoms that have wide technical applications. To obtain enough biomass for frustule characterization Cyclotella cryptica has been cultivated in a 15 l photobioreactor under controlled conditions. Native diatom frustules are characterized by a 1.5-fold lower density and 80-fold higher specific surface than siliceous earth. Therefore, native diatom frustules provides a material with novel properties which might be interesting for special technical application.     

Grazing-induced changes in cell wall silicification in a marine diatom

In aquatic environments, diatoms (Bacillariophyceae) constitute a central group of microalgae which contribute to about 40% of the oceanic primary production. Diatoms have an absolute requirement for silicon to build-up their silicified cell wall in the form of two shells (the frustule). To date, changes in diatom cell wall silicification have been only studied in response to changes in the growth environment, with consistent increase in diatom silica content when specific growth rates decrease under nutrient or light limitations. Here, we report the first evidence for grazing-induced changes in cell wall silicification in a marine diatom. Cells grown in preconditioned media that had contained both diatoms and herbivores are significantly more silicified than diatoms grown in media that have contained diatoms alone or starved herbivores. These observations suggest that grazing-induced increase in cell wall silicification can be viewed as an adaptive reaction in habitats with variable grazing pressure, and demonstrate that silicification in diatoms is not only a constitutive mechanical protection for the cell, but also a phenotypically plastic trait modulated by grazing. In turn, our results corroborate the idea that plant-herbivore interactions, beyond grazing sensu stricto, contribute to drive ecosystem structure and biogeochemical cycles in the ocean.     

The fascinating diatom frustule—can it play a role for attenuation of UV radiation?

Diatoms are ubiquitous organisms in aquatic environments and are estimated to be responsible for 20–25 % of the total global primary production. A unique feature of diatoms is the silica wall, called the frustule. The frustule is characterized by species-specific intricate nanopatterning in the same size range as wavelengths of visible and ultraviolet (UV) light. This has prompted research into the possible role of the frustule in mediating light for the diatoms’ photosynthesis as well as into possible photonic applications of the diatom frustule. One of the possible biological roles, as well as area of potential application, is UV protection. In this review, we explore the possible adaptive value of the silica frustule with focus on research on the effect of UV radiation on diatoms. We also explore the possible effect of the frustules on UV radiation, from a theoretical, biological, and applied perspective, including recent experimental data on UV transmission of diatom frustules.     

SILICON METABOLISM IN DIATOMS: IMPLICATIONS FOR GROWTH

Diatoms are the world's largest contributors to biosilicification and are one of the predominant contributors to global carbon fixation. Silicon is a major limiting nutrient for diatom growth and hence is a controlling factor in primary productivity. Because our understanding of the cellular metabolism of silicon is limited, we are not fully knowledgeable about intracellular factors that may affect diatom productivity in the oceans. The goal of this review is to present an overview of silicon metabolism in diatoms and to identify areas for future research. Numerous studies have characterized parameters of silicic acid uptake by diatoms, and molecular characterization of transport has begun with the isolation of genes encoding the transporter proteins. Multiple types of silicic acid transporter gene have been identified in a single diatom species, and multiple types appear to be present in all diatom species. The controlled expression and perhaps localization of the transporters in the cell may be factors in the overall regulation of silicic acid uptake. Transport can also be regulated by the rate of silica incorporation into the cell wall, suggesting that an intracellular sensing and control mechanism couples transport with incorporation. Sizable intracellular pools of soluble silicon have been identified in diatoms, at levels well above saturation for silica solubility, yet the mechanism for maintenance of supersaturated levels has not been determined. The mechanism of intracellular transport of silicon is also unknown, but this must be an important part of the silicification process because of the close coupling between silica incorporation and uptake. Although detailed ultrastructural analyses of silica deposition have been reported, we know little about the molecular details of this process. However, proteins occluded within silica that promote silicification in vitro have recently been characterized, and the application of molecular techniques holds the promise of great advances in this area. Cellular energy for silicification and transport comes from aerobic respiration without any direct involvement of photosynthetic energy. As such, diatom silicon metabolism differs from that of other major limiting nutrients such as nitrogen and phosphorous, which are closely linked to photosynthetic metabolism. Cell wall silicification and silicic acid transport are tightly coupled to the cell cycle, which results in a dependency in the extent of silicification on growth rate. Silica dissolution is an important part of diatom cellular silicon metabolism, because dissolution must be prevented in the living cell, and because much of the raw material for mineralization in natural assemblages is supplied by dissolution of dead cells. Perhaps part of the reason for the ecological success of diatoms is due to their use of a silicified cell wall, which has been calculated to impart a substantial energy savings to organisms that have them. However, the growth of diatoms and other siliceous organisms has depleted the oceans of silicon, such that silicon availability is now a major factor in the control of primary productivity. Much new progress in understanding silicon metabolism in diatoms is expected because of the application of molecular approaches and sophisticated analytical techniques. Such insight is likely to lead to a greater understanding of the role of silicon in controlling diatom growth, and hence primary productivity, and of the mechanisms involved in the formation of the intricate silicified structures of the diatom cell wall.     

Comparative genomics of the pennate diatom Phaeodactylum tricornutum

Diatoms are one of the most important constituents of phytoplankton communities in aquatic environments, but in spite of this, only recently have large-scale diatom-sequencing projects been undertaken. With the genome of the centric species Thalassiosira pseudonana available since mid-2004, accumulating sequence information for a pennate model species appears a natural subsequent aim. We have generated over 12,000 expressed sequence tags (ESTs) from the pennate diatom Phaeodactylum tricornutum, and upon assembly into a nonredundant set, 5,108 sequences were obtained. Significant similarity (E < 1E-04) to entries in the GenBank nonredundant protein database, the COG profile database, and the Pfam protein domains database were detected, respectively, in 45.0%, 21.5%, and 37.1% of the nonredundant collection of sequences. This information was employed to functionally annotate the P. tricornutum nonredundant set and to create an internet-accessible queryable diatom EST database. The nonredundant collection was then compared to the putative complete proteomes of the green alga Chlamydomonas reinhardtii, the red alga Cyanidioschyzon merolae, and the centric diatom T. pseudonana. A number of intriguing differences were identified between the pennate and the centric diatoms concerning activities of relevance for general cell metabolism, e.g. genes involved in carbon-concentrating mechanisms, cytosolic acetyl-Coenzyme A production, and fructose-1,6-bisphosphate metabolism. Finally, codon usage and utilization of C and G relative to gene expression (as measured by EST redundance) were studied, and preferences for utilization of C and CpG doublets were noted among the P. tricornutum EST coding sequences.     

UNCOUPLING OF SILICON COMPARED WITH CARBON AND NITROGEN METABOLISMS AND THE ROLE OF THE CELL CYCLE IN CONTINUOUS CULTURES OF THALASSIOSIRA PSEUDONANA (BACILLARIOPHYCEAE) UNDER LIGHT,NITROGEN, AND PHOSPHORUS CONTROL1

The elemental composition and the cell cycle stages of the marine diatom Thalassiosira pseudonana Hasle and Heimdal were studied in continuous cultures over a range of different light‐ (E), nitrogen‐ (N), and phosphorus‐ (P) limited growth rates. In all growth conditions investigated, the decrease in the growth rate was linked with a higher relative contribution of the G2+M phase. The other phases of the cell cycle, G1 and S, showed different patterns, depending on the type of limitation. All experiments showed a highly significant increase in the amount of biogenic silica per cell and per cell surface with decreasing growth rates. At low growth rates, the G2+M elongation allowed an increase of the silicification of the cells. This pattern could be explained by the major uptake of silicon during the G2+M phase and by the independence of this process on the requirements of the other elements. This was illustrated by the elemental ratios Si/C and Si/N that increased from 2‐ to 6‐fold, depending of the type of limitation, whereas the C/N ratio decreased by 10% (E limitation) or increased by 50% (P limitation). The variations of the ratios clearly demonstrate the uncoupling of the Si metabolism compared with the C and N metabolisms. This uncoupling enabled us to explain that in any of the growth condition investigated, the silicification of the cells increased at low growth rates, whereas carbon and nitrogen cellular content are differently regulated, depending of the growth conditions.     

AUXOSPORE FORMATION AND THE MORPHOLOGY OF THE INITIAL CELL OF THE MARINE ARAPHID DIATOM GEPHYRIA MEDIA (BACILLARIOPHYCEAE)1

Recent studies have led to a rapid increase in knowledge of auxospore formation in diatoms. However, these studies have been limited to centric and raphid pennate diatoms, and there is still very little information for the araphid pennate diatoms. Using LM and SEM, we studied the development of the auxospore and the initial cell of the marine epiphytic diatom Gephyria media Arnott. Auxospores were bipolar and curved in side view, as in many other pennate diatoms. SEM revealed many transverse perizonial bands, all of which were incomplete rings. There was an elongate, sprawling, silicified structure beneath the ventral suture of the transverse perizonial bands. This structure is presumably equivalent to the longitudinal perizonial band in other pennate diatoms, although we could not determine the homologous relationship between the two features. Scales were found both in the inner wall of the perizonium and around the primary perizonial bands. The presence or absence of scales may be of phylogenetic significance in diatoms, only during the final stages of auxospore formation because scales are found in early spherical stages. The distinctive finger‐like structures observed throughout all stage of G. media have not been observed before in the other diatom taxa.     

New insights into the complex architecture of siliceous copepod teeth

Copepods belong to the dominant marine zooplankton taxa and play an important role in particle and energy fluxes of the marine water column. Their mandibular gnathobases possess tooth-like structures, so-called teeth. In species feeding on large proportions of diatoms these teeth often contain silica, which is very probably the result of a coevolution with the siliceous diatom frustules. Detailed knowledge of the morphology and composition of the siliceous teeth is essential for understanding their functioning and their significance in the context of feeding interactions between copepods and diatoms. Based on analyses of the gnathobases of the Antarctic copepod Rhincalanus gigas, the present study clearly shows, for the first time, that the silica in the siliceous teeth features large proportions of crystalline silica that is consistent with the mineral α-cristobalite and is doped with aluminium. The siliceous structures have internal chitinous fibre networks, which are assumed to serve as scaffolds during the silicification process. The compact siliceous teeth of R. gigas are accompanied by structures with large proportions of the elastic protein resilin, likely reducing the mechanical damage of the teeth when the copepods feed on diatoms with very stable frustules. The results indicate that the coevolution with diatom frustules has resulted in gnathobases exhibiting highly sophisticated composite structures.     

Density gradient separation of microbenthos from estuarine sediments

Summary The main drawback in investigations on microbenthos in estuarine regions are formed by the presence of detritus, clay minerals and aggregates of these components. Moreover, counts of benthic diatoms in these areas are also made difficult by the presence of empty frustules. Separation of empty frustules from living benthic diatoms is necessary, because identification of specimens must be carried out with empty frustules. Several techniques have been developed to isolate specific groups of organisms from the sediments.For benthic epipelic diatoms the lens-tissue technique was developed; the technique failed for estuarine sediments. Harvest percentages ranged from about 15 to 75%. A more adequate method was obtained by using density gradient centrifugation with the polymer silica Ludox. With a newly developed technique, which will be published in detail elsewhere, it appeared possible to separate about 87% of the total amount of benthic epipelic as well as epipsammic diatoms from empty diatom frustules, clay minerals and sand particles. The diatom fraction still contained a great deal of detritus which, however, does not disturb the microscopical identification of specimens because it can be oxidized.Some meiobenthic groups (copepods, nematodes) can be isolated quantitatively from sediment samples with the density technique. Such fractions contained only a small amount of detritus.     

硅藻纳米技术

硅藻是一类微小的单细胞藻类,具有由无定形氧化硅组成的坚硬细胞壁(硅壳).硅壳具有精致的形态和结构,且随硅藻种类和生长条件不同而千变万化.目前估算的硅藻种类超过200 000种,其独特的纳米结构对光子结构、化学生物传感器、新纳米材料和器件的开发具有启发意义.同时硅藻形态形成学和分子生物学的研究,可以推动硅质材料的仿生合成...     

Auxosporulation in Paralia guyana MacGillivary (Bacillariophyta) and Possible New Insights into the Habit of the Earliest Diatoms

Background

Diatoms are one of the most ecologically important aquatic micro-eukaryotes. As a group unambiguously recognized as diatoms, they seem to have appeared relatively recently with a limited record of putative remains from oldest sediments. In contrast, molecular clock estimates for the earliest possible emergence of diatoms suggest a considerably older date. Depending on the analysis, Paralia and Leptocylindrus have been recovered within the basal molecular divergences of diatoms. Thus these genera may be in the position to inform on characters that the earliest diatoms possessed.

Findings

Here we present auxospore development and structure of initial and post-auxospore cells in a representative of the ancient non-polar centric genus Paralia. Their initial frustules showed unusual, but not unprecedented, spore-like morphology. Similarly, initial frustules of Leptocylindrus have been long considered resting spores and a unique peculiarity of this genus. However, even though spore-like in appearance, initial cells of Paralia readily resumed mitotic divisions. In addition, Paralia post-auxospore cells underwent several rounds of mitoses in a multi-step process of building a typical, “perfect” vegetative valve. This degree of heteromorphy immediately post-auxosporulation is thus far unknown among the diatoms.

Implications

A spore-related origin of diatoms has already been considered, most recently in the form of the “multiplate diploid cyst” hypothesis. Our discovery that the initial cells in some of the most ancient diatom lineages are structurally spore-like is consistent with that hypothesis because the earliest diatoms may be expected to look somewhat similar to their ancestors. We speculate that because the earliest diatoms may have appeared less diatom-like and more spore-like, they could have gone unrecognized as such in the Triassic/Jurassic sediments. If correct, diatoms may indeed be much older than the fossil record indicates, and possibly more in line with some molecular clock predictions.     

Mono‐ and digalactosyldiacylglycerol composition of the marennine‐producing diatom,Haslea ostrearia: Comparison to a selection of pennate and centric diatoms

Diatoms are one of the largest groups of primary producers in the oceans, yet despite their environmental importance little is known about their plastidial lipid biochemistry. It has been previously reported that Skeletonema species contain primarily C₁₆/C₁₆ and C₂₀/C₁₆ forms of mono‐ and digalactosyldiacylglycerol (MGDG and DGDG, respectively). Likewise, it was also reported that Phaeodactylum tricornutum contains primarily C₁₆/C₁₆ and C₂₀/C₂₀ forms of MGDG and DGDG. We seek to relate their studies to other diatoms, both in the centrics and pennates, with particular focus on the marennine‐producing pennate diatom, Haslea ostrearia. To this end, the composition and positional distribution of fatty acids of MGDG and DGDG were examined using positive‐ion electrospray ionization/mass spectrometry (ESI/MS). Two centric diatoms, Skeletonema marinoi and Thalassiosira weissflogii, and the pennate diatom, P. tricornutum, contained primarily C₂₀/C₁₆ (sn‐1/sn‐2) and C₁₈/C₁₆ forms of MGDG and DGDG. The other pennate diatoms, H. ostrearia and Navicula perminuta, contained primarily C₁₈/C₁₆ or C₁₈/C₁₈ forms of MGDG and DGDG, indicating a previously unrecognized fatty acid diversity in diatom MGDG and DGDG.