Organic Envelopes Research Articles

Characterization of calcite spines of planktonic foraminifers (Globigerinidae)

Spines projecting from a trochospiral test of a spinose planktonic foraminifer are a single-crystal-like calcite that has a nanogranular texture containing microstrain and an organic envelope.

Study on the Soft Magnetic Properties of FeSiB/EP Composites by Direct Ink Writing

Fe-based amorphous alloy has excellent soft magnetic properties; traditionally, Fe-based amorphous alloy such as soft magnetic devices was fabricated by insulation enveloping and suppression molding methods. In this process, the aging of organic envelope materials and the crystallization of Fe-based amorphous alloy were usually occurring, accompanying with low magnetic induction and poor mechanical properties. The direct ink writing (DIW) technique can make complex-shaped parts and needs no heating treatment after forming, which can avoid the effect of traditional molding process. In the present study, varying mass fraction FeSiB/EP composite parts were prepared by the DIW technique with the Fe-based amorphous alloy powder and epoxy resin, in which microscopic morphology, magnetic properties, and mechanical properties of FeSiB/EP soft magnetic composites were studied. The results indicate that the slurry with iron powder mass fraction of 92.3, 92.6, and 92.8 wt% has good printing performance and self-support ability, which is suitable for DIW. The density of the printed parts is about 4.317, 4.449, and 4.537 g/cm3, which is almost similar with the iron powder. The tensile strength and elongation of printing parts are significantly improved compared with the pure epoxy resin. From the photos of microscopic morphology of printing parts, it can be seen that FeSiB powders are evenly dispersed in EP, no pores, and defects, with the proportion increasing of powders; the insulation coating thickness decreases; and the magnetic performance improves. The optimal sample is 92.8 wt% FeSiB/EP, in which saturation magnetic induction strength is 137.9759 emu/g and coercivity is 4.6523 A/m.

Heterogeneous distribution of shell matrix proteins in the pearl oyster prismatic layer

Shell formation in molluscan bivalves is regulated by organic matrices composed of biological macromolecules, but how these macromolecules assemble in vitro remains elusive. Prismatic layer in the pearl oyster Pinctada fucata consists of polygonal prisms enveloped by thick organic matrices. In this study, we found that the organic matrices were heterogeneously distributed, with highly acidic fractions (EDTA-soluble and EDTA-insoluble) embedded inside the prism columns, while basic EDTA-insoluble faction as inter-column framework enveloping the prisms. The intra-column matrix was enriched in aspartic acid whereas the inter-column matrix was enriched in glycine, tyrosine and phenylalanine. Moreover, the intra-column matrix contained sulfo group further contributing to its acidic property. Proteomics data showed that the intra-column proteins mainly consisted of acidic proteins, while some typical matrix proteins were absent. The absent matrix proteins such as shematrin family and KRMP family were highly basic and contained aromatic amino acids, suggesting that electric charge and hydrophobic effect might play a role in the matrix heterogeneity. Interestingly, chitin metabolism related proteins were abundant in the inter-column matrix, which may be involved in reconstructing the prism organic matrix. Overall, our study suggests that each single prism grew in an enclosed organic envelope and the organic matrix undergoes rearrangement, thus leading to the peculiar growth of the prismatic layer.

Organic Stabilization of Extracellular Elemental Sulfur in a Sulfurovum-Rich Biofilm: A New Role for Extracellular Polymeric Substances?

This work shines light on the role of extracellular polymeric substance (EPS) in the formation and preservation of elemental sulfur biominerals produced by sulfur-oxidizing bacteria. We characterized elemental sulfur particles produced within a Sulfurovum-rich biofilm in the Frasassi Cave System (Italy). The particles adopt spherical and bipyramidal morphologies, and display both stable (α-S8) and metastable (β-S8) crystal structures. Elemental sulfur is embedded within a dense matrix of EPS, and the particles are surrounded by organic envelopes rich in amide and carboxylic groups. Organic encapsulation and the presence of metastable crystal structures are consistent with elemental sulfur organomineralization, i.e., the formation and stabilization of elemental sulfur in the presence of organics, a mechanism that has previously been observed in laboratory studies. This research provides new evidence for the important role of microbial EPS in mineral formation in the environment. We hypothesize that the extracellular organics are used by sulfur-oxidizing bacteria for the stabilization of elemental sulfur minerals outside of the cell wall as a store of chemical energy. The stabilization of energy sources (in the form of a solid electron acceptor) in biofilms is a potential new role for microbial EPS that requires further investigation.

Organic biomorphs may be better preserved than microorganisms in early Earth sediments

Abstract The Precambrian rock record contains numerous examples of microscopic organic filaments and spheres, commonly interpreted as fossil microorganisms. Microfossils are among the oldest traces of life on Earth, making their correct identification crucial to our understanding of early evolution. Yet, spherical and filamentous microscopic objects composed of organic carbon and sulfur can form in the abiogenic reaction of sulfide with organic compounds. Termed organic biomorphs, these objects form under geochemical conditions relevant to the sulfidic environments of early Earth. Furthermore, they adopt a diversity of morphologies that closely mimic a number of microfossil examples from the Precambrian record. Here, we tested the potential for organic biomorphs to be preserved in cherts; i.e., siliceous rocks hosting abundant microbial fossils. We performed experimental silicification of the biomorphs along with the sulfur bacterium Thiothrix. We show that the original morphologies of the biomorphs are well preserved through encrustation by nano-colloidal silica, while the shapes of Thiothrix cells degrade. Sulfur diffuses from the interior of both biomorphs and Thiothrix during silicification, leaving behind empty organic envelopes. Although the organic composition of the biomorphs differs from that of Thiothrix cells, both types of objects present similar nitrogen/carbon ratios after silicification. During silicification, sulfur accumulates along the organic envelopes of the biomorphs, which may promote sulfurization and preservation through diagenesis. Organic biomorphs possessing morphological and chemical characteristics of microfossils may thus be an important component in Precambrian cherts, challenging our understanding of the early life record.

Qualitative evaluation of organic envelopes on subsurface drainage performance*

AbstractThe purpose of this study was to investigate the efficiency of organic matter such as rice husk and palm‐leaf stalk as envelopes in drainage pipes. For this purpose, to simulate field conditions in vitro, we used a physical model consisting of a plexiglass cylinder with a height of 200 mm and diameter of 100 mm, with five holes attached to the manometers and an inlet at the bottommost part and an outlet at the topmost part with a water tank which provided a fixed head. Experiments were carried out with five types of organic matter (i.e. rice husk, three types of powder and palm‐leaf fibres) on Ramshir agricultural soil which required envelopes according to existing standards. The results showed that among the envelopes utilized, the highest outflow (discharge) rate was related to powder No. 3 (the most coarse‐grained powder) in a gradient of 0.5. By increasing the gradient to 2, envelope hydraulic fracturing was observed, which means that it was unable to retain soil particles with finally an inadequate filtering function for this organic material. In gradient 2, the highest output discharge was related to palm stalk and leaf fibres, which is reflected in the proper hydraulic performance of this envelope and its high filtering properties. Finally, comparing the value of the gradient ratio in the higher gradients confirmed the results.

Tightly shut: flexible valve margins and microstructural asymmetry in pterioid bivalves

An organic-rich columnar prismatic outer shell layer, which extends far beyond the underlying nacre, has allowed pterioid bivalves (the pearl oysters and their allies) to develop flexible valve margins, allowing a tight hermetic seal when shut. In some taxa, the microstructural arrangement is known to be asymmetrically developed between the two valves. The asymmetry was surveyed across 29 taxa of pterioids (including representatives of known genera) confirming that it is typically the right valve which has a greater expanse of prism-only shell (and less nacre) and showing that this portion of the right valve has more organic content (more than twice the value in some instances) than the equivalent in the left. A more detailed investigation of prismatic material in Pteria penguin comparing the right and left valves revealed that the right valve flange has a higher density of smaller prisms, each with its organic envelope, and not a greater thickness of the organic envelopes themselves. The flange is also thinner on the right valve and shown here to be very flexible when wet. This allows it to bend against the rigid left valve when the shell is closed. Comparison of this structural asymmetry in the pterioids with five outgroup taxa in the Ostreidae and Pinnidae suggests that clades with the asymmetry have been freed from the constraints of a flattened valve morphology and to develop inequivalved forms.

Tightly shut: flexible valve margins and microstructural asymmetry in pterioid bivalves

An organic-rich columnar prismatic outer shell layer, which extends far beyond the underlying nacre, has allowed pterioid bivalves (the pearl oysters and their allies) to develop flexible valve margins, allowing a tight hermetic seal when shut. In some taxa, the microstructural arrangement is known to be asymmetrically developed between the two valves. The asymmetry was surveyed across 29 taxa of pterioids (including representatives of known genera) confirming that it is typically the right valve which has a greater expanse of prism-only shell (and less nacre) and showing that this portion of the right valve has more organic content (more than twice the value in some instances) than the equivalent in the left. A more detailed investigation of prismatic material in Pteria penguin comparing the right and left valves revealed that the right valve flange has a higher density of smaller prisms, each with its organic envelope, and not a greater thickness of the organic envelopes themselves. The flange is also thinner on the right valve and shown here to be very flexible when wet. This allows it to bend against the rigid left valve when the shell is closed. Comparison of this structural asymmetry in the pterioids with five outgroup taxa in the Ostreidae and Pinnidae suggests that clades with the asymmetry have been freed from the constraints of a flattened valve morphology and to develop inequivalved forms.

Elemental Sulfur Formation by Sulfuricurvum kujiense Is Mediated by Extracellular Organic Compounds.

Elemental sulfur [S(0)] is a central and ecologically important intermediate in the sulfur cycle, which can be used by a wide diversity of microorganisms that gain energy from its oxidation, reduction, or disproportionation. S(0) is formed by oxidation of reduced sulfur species, which can be chemically or microbially mediated. A variety of sulfur-oxidizing bacteria can biomineralize S(0), either intracellularly or extracellularly. The details and mechanisms of extracellular S(0) formation by bacteria have been in particular understudied so far. An important question in this respect is how extracellular S(0) minerals can be formed and remain stable in the environment outside of their thermodynamic stability domain. It was recently discovered that S(0) minerals could be formed and stabilized by oxidizing sulfide in the presence of dissolved organic compounds, a process called S(0) organomineralization. S(0) particles formed through this mechanism possess specific signatures such as morphologies that differ from that of their inorganically precipitated counterparts, encapsulation within an organic envelope, and metastable crystal structures (presence of the monoclinic β- and γ-S8 allotropes). Here, we investigated S(0) formation by the chemolithoautotrophic sulfur-oxidizing and nitrate-reducing bacterium Sulfuricurvum kujiense (Epsilonproteobacteria). We performed a thorough characterization of the S(0) minerals produced extracellularly in cultures of this microorganism, and showed that they present all the specific signatures (morphology, association with organics, and crystal structures) of organomineralized S(0). Using “spent medium” experiments, we furthermore demonstrated that soluble extracellular compounds produced by S. kujiense are necessary to form and stabilize S(0) minerals outside of the cells. This study provides the first experimental evidence of the importance of organomineralization in microbial S(0) formation. The prevalence of organomineralization in extracellular S(0) precipitation by other sulfur bacteria remains to be investigated, and the biological role of this mechanism is still unclear. However, we propose that sulfur-oxidizing bacteria could use soluble organics to stabilize stores of bioavailable S(0) outside the cells.

Formation and stabilization of elemental sulfur through organomineralization

Abstract Elemental sulfur (S(0)) is an important intermediate in the biogeochemical cycle of sulfur that is formed by chemical or biological oxidation of more reduced sulfur species. Given the restricted geochemical conditions under which S(0) should persist, the mechanisms whereby S(0) can be stabilized in the environment are not fully understood. Here we identify a process called “S(0) organomineralization”, by which S(0) minerals are produced and stabilized following the oxidation of hydrogen sulfide in the presence of numerous types of dissolved organics, including simple sugars and amino acids. The S(0) particles formed through this mechanism are closely associated with organics, which often form an envelope around the mineral. The organic envelopes are formed by self-assembly of the dissolved organic molecules in the presence of hydrogen sulfide and oxygen, and play in a role in the stabilization of S(0). Organic compound sulfurization probably plays an important role in the self-assembly mechanism, by causing the polymerization of relatively small dissolved organic molecules into solid, macromolecular, polymeric organics. The organomineralized S(0) particles present unique and complex morphologies, which are controlled by the type of dissolved organic compound present in the experimental media. Depending on the organics present, organomineralized S(0) can exist as different combinations of several crystal structures, including the non-thermodynamically stable β- and γ-S8 allotropes, which are most likely stabilized by their close association with the organic phase. We propose that complex particle morphology combined with the presence of metastable S(0) allotropes could be used as a signature of S(0) organomineralization in natural settings. S(0) organomineralization was obtained in the laboratory under a wide range of experimental conditions that span across geochemical conditions which can be encountered in many sulfidic environments. It is possible that the reaction between reduced sulfur species and organics may significantly affect the production and preservation of S(0) in numerous natural systems.

Investigating the reduction of sodium adsorption ratio from agricultural waste by rice husk in batch scale and physical model of drain envelop

Sodium adsorption ratio (SAR) is one of the water quality indexes that whose is important due to reuse or depletion to environment. Solutes in drain water can be controlled by adsorption, chemical or biological reaction, organic envelope of drainage. Rice husk is the common option of drainage envelops in paddy fields. In this study, the ability of reduction of SAR by rice husk was evaluated in batch scale and physical model of drain envelops. In the batch experiments, the adsorption of SAR parameters was investigated by adding 2 g of rice husk into a 100 ml of sodium chloride solution. The results indicated that rice husk absorbed calcium, magnesium and sodium, respectively. By increasing the temperature, contact time and pH, adsorption of calcium, magnesium and sodium was increased; however, the higher concentration of sodium in soil solution reduced the percentage of adsorption. In a more realistic state, physical models of subsurface drainage in the paddy fields were made. Drainage envelope treatments included of rice husk (H), combination of 20 and 60 % of husk with gravel (H20G80 and H60G40) and a pipe without envelope (NE). Due to higher drain discharge and more sodium removal (lower SAR in drain water), treatment H with the discharge of 16.2 ml/min and SAR of 1.27 (meq/l)0.5 was better in comparison with other treatments.

Limpet Shells from the Aterian Level 8 of El Harhoura 2 Cave (Témara, Morocco): Preservation State of Crossed-Foliated Layers.

The exploitation of mollusks by the first anatomically modern humans is a central question for archaeologists. This paper focuses on level 8 (dated around ∼ 100 ka BP) of El Harhoura 2 Cave, located along the coastline in the Rabat-Témara region (Morocco). The large quantity of Patella sp. shells found in this level highlights questions regarding their origin and preservation. This study presents an estimation of the preservation status of these shells. We focus here on the diagenetic evolution of both the microstructural patterns and organic components of crossed-foliated shell layers, in order to assess the viability of further investigations based on shell layer minor elements, isotopic or biochemical compositions. The results show that the shells seem to be well conserved, with microstructural patterns preserved down to sub-micrometric scales, and that some organic components are still present in situ. But faint taphonomic degradations affecting both mineral and organic components are nonetheless evidenced, such as the disappearance of organic envelopes surrounding crossed-foliated lamellae, combined with a partial recrystallization of the lamellae. Our results provide a solid case-study of the early stages of the diagenetic evolution of crossed-foliated shell layers. Moreover, they highlight the fact that extreme caution must be taken before using fossil shells for palaeoenvironmental or geochronological reconstructions. Without thorough investigation, the alteration patterns illustrated here would easily have gone unnoticed. However, these degradations are liable to bias any proxy based on the elemental, isotopic or biochemical composition of the shells. This study also provides significant data concerning human subsistence behavior: the presence of notches and the good preservation state of limpet shells (no dissolution/recrystallization, no bioerosion and no abrasion/fragmentation aspects) would attest that limpets were gathered alive with tools by Middle Palaeolithic (Aterian) populations in North Africa for consumption.

Evidence of a Biological Control over Origin, Growth and End of the Calcite Prisms in the Shells of Pinctada margaritifera (Pelecypod, Pterioidea)

Consistently classified among the references for calcite simple prisms, the microstructural units that form the outer layer of the Pinctada margaritifera have been investigated through a series of morphological, crystallographical and biochemical characterizations. It is often said that the polygonal transverse shape of the prisms result from the competition for space between adjacent crystals. In contrast to this classical scheme the Pinctada prisms appear to be composed of four successive developmental stages from the concentrically growing disks on the internal side of the periostracum to the morphological, structural and compositional changes in both envelopes and mineral components at the end of the prisms. These latest structural and compositional changes predate nacre deposition, so that the end of prism growth is not caused by occurrence of nacre, but by metabolic changes in the secretory epithelium. This sequence makes obvious the permanent biological control exerted by the outer cell layer of the mantle in both organic envelopes and mineralizing organic phases.

Crystallography of calcite in pearls

Mineralization in pearls is used as a ‘study model’ to understand basic mechanisms of calcium carbonate biomineralization. In addition to nacre formation, vaterite and calcite can be found in pearls, with the occurrence of calcite being the least studied. In this study, two calcite microstructures, prisms and “pseudo-prisms”, are described. Electron backscatter diffraction (EBSD) analyses show that there is no unique crystallographic orientation for a single calcite microstructure and, instead, each is composed of microcrystals with different orientations. Furthermore, general crystallographic orientations are found for prisms, with c-axis parallel to the long axis, and “pseudo-prisms” with the c-axis perpendicular to their elongation. Pseudo-prisms tend to be grouped in crystallographic domains. Overall, the formation of calcite structures in pearls may not be compared to biomineral structures in shells, which are better defined in terms of crystal habit and present a more constrained crystallographic control, in addition to having a strong correlation between crystallization and the formation of organic envelopes.

Metal nanoparticles in organic field-effect transistor: Transition from charge trapping to conduction mechanism

Self-assembled monolayers of metal nanoparticles (NPs) are envisioned for various devices and have been investigated for possible applications. However, organic envelope of NPs which is required for self-assembling must be often removed prior further device fabrication. Here, we report on effect of ozonolysis on monolayer of silver NPs (Ag NPs) with size of 8nm and its impact on Ag NPs utilization in organic field-effect transistor. It was found that Ag NPs covered by organics serve like a traps and removal of insulating organics decreases number of traps and consequently increases Ag NPs monolayer conductivity.

QUANTITATIVE NANOMECHANICAL MAPPING OF MARINE DIATOM IN SEAWATER USING PEAK FORCE TAPPING ATOMIC FORCE MICROSCOPY(1).

It is generally accepted that a diatom cell wall is characterized by a siliceous skeleton covered by an organic envelope essentially composed of polysaccharides and proteins. Understanding of how the organic component is associated with the silica structure provides an important insight into the biomineralization process and patterning on the cellular level. Using a novel atomic force microscopy (AFM) imaging technique (Peak Force Tapping), we characterized nanomechanical properties (elasticity and deformation) of a weakly silicified marine diatom Cylindrotheca closterium (Ehrenb.) Reimann et J. C. Lewin (strain CCNA1). The nanomechanical properties were measured over the entire cell surface in seawater at a resolution that was not achieved previously. The fibulae were the stiffest (200 MPa) and the least deformable (only 1 nm). Girdle band region appeared as a series of parallel stripes characterized by two sets of values of Young's modulus and deformation: one for silica stripes (43.7 Mpa, 3.7 nm) and the other between the stripes (21.3 MPa, 13.4 nm). The valve region was complex with average values of Young's modulus (29.8 MPa) and deformation (10.2 nm) with high standard deviations. After acid treatment, we identified 15 nm sized silica spheres in the valve region connecting raphe with the girdle bands. The silica spheres were neither fused together nor forming a nanopattern. A cell wall model is proposed with individual silica nanoparticles incorporated in an organic matrix. Such organization of girdle band and valve regions enables the high flexibility needed for movement and adaptation to different environments while maintaining the integrity of the cell.

Xenophyophores (Rhizaria, Foraminifera) from the Nazaré Canyon (Portuguese margin, NE Atlantic)

Xenophyophores are abundant on a terrace of the lower Nazaré Canyon (4300 m water depth) on the Portuguese margin. Here, the most abundant species, Reticulammina cerebreformis sp. nov., occurs in densities of up to 21 individuals/m 2. This large species has a soft, friable hemispherical test up to 10 cm in diameter consisting of curved, sinuous plates (lamellae) that branch and anastomose. The plates are separated by deep furrows and other depressions to form a distinctive ‘brain-like’ structure. The outer test layer is thin, weakly cemented and is dominated by fine sediment particles; the internal xenophyae include a higher proportion of larger mineral grains. The second new species at the 4300-m site, Nazareammina tenera gen. et sp. nov., is much less common. The test is basically plate-like, but towards the interior it is perforated by oval spaces, which typically merge into complex system of bar-like features, sometimes with irregular excrescences. The granellare system (cell body and its organic envelope) is packed with tiny mineral grains of various sizes and shapes, including titanium-bearing particles. Also common at this deep site are clusters, with a maximum diameter up to 10 cm or occasionally more, of irregular tubes belonging to Aschemonella ramuliformis Brady 1884, a species previously known mainly from isolated tubes. Rather than being single individuals, these clusters comprise a large number of separate branched tubes. Finally, Syringammina fragillissima Brady 1883, a well-known species that is widely distributed on the NW European margin, occurred on steep sediment-covered slopes at a shallower (1555 m water depth) site in the upper canyon. Almost complete SSU rDNA gene sequences obtained from A. ramuliformis and R. cerebreformis confirm that these xenophyophores are foraminifera. Together with two previously sequenced xenophophores ( Shinkaia lindsayi Lecroq, Gooday, Tsuchiya, Pawlowski 2009 and Syringammina corbicula Richardson 2001), and the foraminiferan Rhizammina algaeformis, they constitute a clade within the radiation of monothalamous foraminifera. In situ photographs of R. cerebreformis and A. ramuliformis reveal no evidence of pseudopodia deployed onto the sediment surface. Instead, these species probably trap sediment within their complex, folded test surface ( R. cerebreformis) or intercept suspended particles ( A. ramuliformis).

Shell layers of the black-lip pearl oyster Pinctada margaritifera: Matching microstructure and composition

The nacre-prism transition of the mollusc shell Pinctada margaritifera was studied using scanning electron microscopy, electron probe micro-analysis (EPMA) and time-of-flight secondary ion mass spectrometry (TOF-SIMS). Mineralogical change is correlated with a change in organic matrix. Previous analyses had shown that sugars were involved in the transition layer (fibrous aragonite). The new Energy Dispersive Spectrometry (EDS) and TOF-SIMS maps show that the modifications at the layer boundary are complex, and that proteins and lipids are also involved. Detailed TOF-SIMS maps show that the thick organic envelopes surrounding the prisms, and between the prisms and the fibrous aragonitic layer, are not composed by regular layers, but are a patchwork of various molecules. The amino acid compositions of the nacreous and prismatic layer are compared thanks to the TOF-SIMS localized analyses.

Erosion of the prismatic layer by the organic matrix during the formation of the nacre-prism transition layer in the shell of Pinctada fucata (Bivalvia, Mollusca)

Three variants of the sequence of formation of the nacre-prism transition layer were observed in Pinctada fucata (Bivalvia, Mollusca) shells. In each case, the layer was formed by the organic matrix secreted by the mantle, together with the interprismatic organic envelope. The continuity of the organic phase throughout the shell was maintained as the new nacreous layer was formed on the nacre-prism transition layer. Changes in the interprismatic organic envelopes on either side of the nacre-prism transition zone indicated that the organic matrix of the nacre-prism transition layer becomes embedded into the organic phase of the prismatic layer. It is concluded that penetration and erosion of the prisms by the organic matrix generates a strong bond between the prismatic and nacreous layers.

A possible mechanism for the formation of annual growth lines in bivalve shells

We report a unique shell margin that differed from the usual shell structure of Pinctada fucata. We observed empty organic envelopes in the prismatic layer and the formation of the nacreous layer in the shell margin. All the characteristics of the growing margin indicated that the shell was growing rapidly. To explain this anomaly, we propose the concept of "jumping development". During jumping development, the center of growth in the bivalve shell jumps forward over a short time interval when the position of the mantle changes. Jumping development explains the unusual structure of the anomalous shell and the development of annual growth lines in typical shells. Annual growth lines are the result of a discontinuity in the shell microstructure induced by jumping development.