Characterization of calcium oxalates generated as biominerals in cacti

The chemical composition and morphology of solid material isolated from various Cactaceae species have been analyzed. All of the tested specimens deposited high-purity calcium oxalate crystals in their succulent modified stems. These deposits occurred most frequently as round-shaped druses that sometimes coexist with abundant crystal sand in the tissue. The biominerals were identified either as CaC(2)O(4).2H(2)O (weddellite) or as CaC(2)O(4).H(2)O (whewellite). Seven different species from the Opuntioideae subfamily showed the presence of whewellite, and an equal number of species from the Cereoideae subfamily showed the deposition of weddellite. The chemical nature of these deposits was assessed by infrared spectroscopy. The crystal morphology of the crystals was visualized by both conventional light and scanning electron microscopy. Weddellite druses were made up of tetragonal crystallites, whereas those from whewellite were most often recognized by their acute points and general star-like shape. These studies clearly demonstrated that members from the main traditional subfamilies of the Cactaceae family could synthesize different chemical forms of calcium oxalate, suggesting a definite but different genetic control. The direct relationship established between a given Cactaceae species and a definite calcium oxalate biomineral seems to be a useful tool for plant identification and chemotaxonomy.     

Biomineral electron backscatter diffraction for palaeontology

Electron backscatter diffraction (EBSD) originated in materials science and has transferred to biomineral research providing insight into fossil and modern biominerals. An electron microscopy technique, EBSD requires a fine polished sample surface where the electron beam diffracts in the first few lattice layers, identifying mineral, polymorph and crystallographic orientation. The technique is particularly well suited for the analysis of modern and fossil calcium carbonate biominerals, where it provides key insight into biological control of mineral formation such as in molluscs and brachiopods. EBSD readily identifies original and secondary mineralogy, which helps to inform our understanding of biomineral evolution such as the identification of original aragonite in Silurian trimerellid brachiopods. As a technique to identify and thus avoid the inclusion of secondary minerals in proxy organisms such as corals, EBSD can be used to ensure accuracy of palaeoproxy data. Even when fossil systems have no modern equivalents, EBSD can provide key data to determine functional mechanisms such as in the lenses of schizochroal eyes of phacopine trilobites. These few examples illustrate that EBSD is proving to be a valuable component of the palaeontology toolkit.     

Factors controlling spatial distribution of soil acidification and Al forms in forest soils

Soil acidification and Al release in forest soils is controlled by a number of factors, like acid deposition, forest type, parent rock, altitude, etc. This paper studies the principal stand factors affecting spatial distribution of the content of KCl-extractable Al (Al(KCl), mainly exchangeable), Na4P2O7-extractable Al (Al(Na4P2O7), mainly organically bound), and other soil characteristics related to acidification in surface organic (O) and subsurface mineral (B) horizons in the Jizera Mountains region. Geostatistical methods were exploited. The highest Al(KCl) contents in the O horizons were related to high S and N content, low pH and low Ca and Mg content in soil. Liming decreased Al(KCl) contents in the O horizons. Al(Na4P2O7) in the O horizons was more abundant under spruce than under beech; in both horizons it was increased on the immission clear-cut areas populated by grass. Surface horizons are more sensitive to external influence (acid deposition, liming) and their spatial variation is stronger. In the mineral horizons, the effect of pedogenetic processes is more important. The effect of stand factors on Al behaviour is complex and often indirect, mediated for example by organic matter or soil reaction. It is difficult to clearly distinguish the effects of the particular factors.     

Characterization of biominerals in species of Canna (Cannaceae)

Plant biominerals are not always well characterized, although this information is important for plant physiology and can be useful for taxonomic purposes. In this work, fresh plant material of seven wild neotropical species of genus Canna, C. ascendens, C. coccinea, C. indica, C. glauca, C. plurituberosa, C. variegatifolia and C. fuchsina sp. ined., taken from different habitats, were studied to characterize the biominerals in their internal tissues. For the first time, samples from primary and secondary veins of leaves were investigated by means of infrared spectroscopy, complemented with X-ray powder diffractometry and scanning electron microscopy. The spectroscopic results, supported by X-ray powder diffractometry, suggest that the calcium oxalate is present in the form of whewellite (CaC2O4 x H2O) in all the investigated samples. It is interesting to emphasize that all IR spectra obtained were strongly similar in all species studied, thus indicating an identical chemical composition in terms of the biominerals found. In this sense, the results suggest that the species of Canna show similar ability to produce biogenic silica and produce an identical type of calcium oxalate within their tissues. These results can be an additional trait to support the relationship among the families of Zingiberales.     

MMS6 protein regulates crystal morphology during nano-sized magnetite biomineralization in vivo

Biomineralization, the process by which minerals are deposited by organisms, has attracted considerable attention because this mechanism has shown great potential to inspire bottom-up material syntheses. To understand the mechanism for morphological regulation that occurs during biomineralization, many regulatory proteins have been isolated from various biominerals. However, the molecular mechanisms that regulate the morphology of biominerals remain unclear because there is a lack of in vivo evidence. Magnetotactic bacteria synthesize intracellular magnetosomes that comprise membrane-enveloped single crystalline magnetite (Fe(3)O(4)). These nano-sized magnetite crystals (<100 nm) are bacterial species dependent in shape and size. Mms6 is a protein that is tightly associated with magnetite crystals. Based on in vitro experiments, this protein was first implicated in morphological regulation during nano-sized magnetite biomineralization. In this study, we analyzed the mms6 gene deletion mutant (Δmms6) of Magnetospirillum magneticum (M. magneticum) AMB-1. Surprisingly, the Δmms6 strain was found to synthesize the smaller magnetite crystals with uncommon crystal faces, while the wild-type and complementation strains synthesized highly ordered cubo-octahedral crystals. Furthermore, deletion of mms6 gene led to drastic changes in the profiles of the proteins tightly bound to magnetite crystals. It was found that Mms6 plays a role in the in vivo regulation of the crystal structure to impart the cubo-octahedral morphology to the crystals during biomineralization in magnetotactic bacteria. Magnetotactic bacteria synthesize magnetite crystals under ambient conditions via a highly controlled morphological regulation system that uses biological molecules.     

The sea urchin (<Emphasis Type="Italic">Strongylocentrotus purpuratus</Emphasis>) test and spine proteomes

Background  

The organic matrix of biominerals plays an important role in biomineral formation and in determining biomineral properties. However, most components of biomineral matrices remain unknown at present. In sea urchin, which is an important model organism for developmental biology and biomineralization, only few matrix components have been identified and characterized at the protein level. The recent publication of the Strongylocentrotus purpuratus genome sequence rendered possible not only the identification of possible matrix proteins at the gene level, but also the direct identification of proteins contained in matrices of skeletal elements by in-depth, high-accuracy, proteomic analysis.     

Characterization of the calcium biomineral in the radular teeth of Chiton pelliserpentis

The radula in a group of molluscan invertebrates, the chitons (Polyplacophora), is a ribbon-like apparatus used for feeding and which bears a series of distinctive mineralized teeth called the major lateral teeth. While some chiton species deposit only iron biominerals in these teeth, many others deposit both iron and calcium. In this study, the calcium biomineral in the teeth of one of the latter types of species, the Australian east-coast chiton, Chiton pelliserpentis, has been isolated and examined for the first time. Spectroscopic and crystallographic techniques have identified the biomineral as a carbonate-substituted apatite with significant fluoride substitution also likely. Fourier-transform infrared and laser Raman spectroscopy indicated that the carbonate content was less than that of either bovine tibia cortical bone or human tooth enamel. X-ray diffraction analysis showed the biomineral to be poorly crystalline due to small crystal size and appreciable anionic substitution. The lattice parameters were calculated to be a=9.382?Å and c=6.883?Å, which are suggestive of a fluorapatite material. It is postulated that structural and biochemical differences in the tooth organic matrix of different chiton species will ultimately determine if the teeth become partly calcified or iron mineralized only.     

Growth and competition of Cytisus scoparius,an invasive shrub,and Australian native shrubs

English broom (Cytisus scoparius) is an aggressive invasive shrub in native sclerophyll forests of South Australia. We studied its relative growth rate (RGR) and competitive ability in soils from invaded and uninvaded woodlands, in comparison to three native species it commonly displaces:Hakea rostrata, Acacia verniciflua, and A. myrtifolia. Hakea was the slowest growing species throughout the year. Both native species had their highest RGR during spring. The RGR of broom was higher than that of both hakea and acacia in the winter and spring. Despite losing its leaves in the summer, the RGR of broom through the year was higher than that of either of the native species. Soil from the invaded stands had higher organic C, N and soluble P than that from uninvaded sites. Broom and acacia grew better in the higher nutrient soil than in the lower nutrient soil. Competition did not decrease the final biomass of any of the species in low nutrient soil. In the higher nutrient soil the biomass of broom was reduced by competition with acacia, but not by competition with hakea. Competition by broom reduced the biomass of hakea but not that of acacia. Broom's earlier and higher RGR, high competitiveness in nutrient rich soils, and probably its ability to change nutrient availability could be important contributors to the mechanisms by which it invades native woodlands.     

In-depth,high-accuracy proteomics of sea urchin tooth organic matrix

Background  

The organic matrix contained in biominerals plays an important role in regulating mineralization and in determining biomineral properties. However, most components of biomineral matrices remain unknown at present. In sea urchin tooth, which is an important model for developmental biology and biomineralization, only few matrix components have been identified. The recent publication of the Strongylocentrotus purpuratus genome sequence rendered possible not only the identification of genes potentially coding for matrix proteins, but also the direct identification of proteins contained in matrices of skeletal elements by in-depth, high-accuracy proteomic analysis.     

Structural and functional analyses of organic molecules regulating biomineralization

ABSTRACT

Biomineralization by living organisms are common phenomena observed everywhere. Molluskan shells are representative biominerals that have fine microstructures with controlled morphology, polymorph, and orientation of CaCO₃ crystals. A few organic molecules involved in the biominerals play important roles in the formation of such microstructures. Analyses of structure–function relationships for matrix proteins in biominerals revealed that almost all matrix proteins have an acidic region for the binding of calcium ion in CaCO₃ crystals and interaction domains for other organic molecules. On the other hand, biomineralization of metal nanoparticles by microorganisms were also investigated. Gold nanoparticles and quantum dots containing cadmium were successfully synthesized by bacteria or a fungus. The analyses of components revealed that glycolipids, oligosaccharides, and lactic acids have key roles to synthesize the gold nanoparticle in Lactobacillus casei as reductants and dispersants. These researches about biomineralization will give new insights for material and environmental sciences in the human society.     

Chemical taphonomy of biomineralized tissues

Biomineralized tissues are chemically altered after death, and this diagenetic alteration can obscure original biological chemical features or provide new chemical information about the depositional environment. To use the chemistry of fossil biominerals to reconstruct biological, environmental or taphonomic information, a solid appreciation of biomineralization, mineral diagenesis and biomineral–water interaction is needed. Here, I summarize the key recent developments in the fields of biomineralization and post‐mortem trace element exchange that have significant implications for our understanding of the diagenetic behaviour of biominerals and the ways in which biomineral chemistry can be used in palaeontological and taphonomic research.     

Ecosystem Level Impacts of Invasive Acacia saligna in the South African Fynbos

Recent efforts to clear invasive plants from the fynbos of South Africa forces managers to think about how N₂‐fixing invasives have altered ecosystem processes and the implications of these changes for community development. This study investigated the changes in nitrogen (N) cycling regimes in fynbos with the invasion of Acacia saligna, the effects of clear‐cutting acacia stands on soil microclimate and N cycling, and how altered N resources affected the growth of a weedy grass species. Litterfall, litter quality, soil nutrient pools, and ion exchange resin (IER)‐available soil N were measured in uninvaded fynbos, intact acacia, and cleared acacia stands. In addition, a bioassay experiment was used to ascertain whether the changes in soil nutrient availability associated with acacia would enhance the success of a weedy grass species. Acacia plots had greater amounts of litterfall, which had higher concentrations of N. This led to larger quantities of organic matter, total N, and IER‐available N in the soil. Clearing acacia stands caused changes in soil moisture and temperature, but did not result in differences in IER‐available N. The alteration of N availability by acacias was shown to increase growth rates of the weedy grass Ehrharta calycina, suggesting that secondary invasions by nitrophilous weedy species may occur after clearing N₂‐fixing alien species in the fynbos. It is suggested that managers use controlled burns, the addition of mulch, and the addition of fynbos seed after clearing to lower the levels of available N in the soil and initiate the return of native vegetation.     

Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past

Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo‐) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro‐) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA extraction, high‐throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome‐scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA research, with the potential to reconstruct the evolutionary history of molluscs, microbial communities and pathogens in the face of environmental changes. Other future applications include conservation of endangered mollusc species and aquaculture management.     

Studies of Biominerals Relevant to the Search for Life on Mars

The evidence of the water erosion on Mars is particularly interesting since present climatic conditions are such that liquid water cannot exist at the surface. But, if water was present on the planet in the past, there may have been life, too. Since the discovery of carbonates on Mars also may have very important implications on the possibility that life developed there, we are studying minerals that can have biotic or abiotic origin: calcite (CaCO₃) and aragonite, a metastable state of calcite. We have analysed biomineral aragonite, in the form of recent sea shells, as well as crystals of mineral aragonite. Infrared spectroscopy in the 2–25 μm wavelength range reveals that, after thermal processing, the biotic samples have a different spectral behaviour from the abiotic ones. As a result, it is possible to distinguish abiotic mineral aragonite from aragonite of recent biological origin. Obviously, if life existed in the past on the Red Planet, we could expect to find “ancient” biotic carbonates, which should therefore be investigated, in order to search for a way of discriminating them from abiotic minerals. For this reason, at the beginning we have considered samples of crushed fossil shells of aragonite composition. Afterwards, in order to take into account that fossilization processes almost always produce a transformation of metastable form (aragonite) into more stable form (calcite), we also studied samples of mineral calcite and different types of fossils completely transformed into calcite. All these biotic fossil samples show the same spectral behaviour as the fresh biotic material after thermal annealing at 485°C. Instead, the calcite behaves like abiotic aragonite. Furthermore, it is known that seashells and other biominerals are formed through an intimate association of inorganic materials with organic macromolecules. The macromolecules control the nucleation, structure, morphology, crystal orientation and spatial confinement of the inorganic phase: this differentiates biominerals from minerals. Analysing the aragonite or calcite fossils with a Scanning Electron Microscope, we found that the fossilization process did not modify the structure of the biominerals which maintain their microscopic characteristics. Looking at the morphology of fossil biominerals, it is evident that the crystals are arranged in complex architectures compared with the compact structure of the mineral crystals. In conclusion, the properties and structure of the biominerals are different from those of the minerals. The rapid increase of the crystalline structure developed under biotic conditions makes these minerals less resistant to thermal treatments, compared with samples of abiotic origin. This result holds both for recent shells as well as all fossil samples. The spectroscopic behaviour of all analysed calcium carbonates of biotic origin is different from that of the abiotic one. Therefore, the infrared spectroscopy is a valid technique to discern the origin of the samples and a powerful tool for analysing in-situ and “sample-return” Mars missions specimens. Also Optical and Scanning Electron Microscopy can be useful to support this type of studies. ^*Presented at: National Workshop on Astrobiology: Search for Life in the Solar System, Capri, Italy, 26 to 28 October, 2005     

Recent 14C-labelled assimilate allocation to Scots pine seedling root and mycorrhizosphere compartments developed on reconstructed podzol humus,E- and B- mineral horizons

In northern boreal forests, podzolic soils prevail that comprise of a distinct upper organic humus/mor (O) horizon that is supported by underlying eluvial (E) and illuvial (B) mineral horizons. The dominant tree species, Scots pine (Pinus sylvestris L.), is known to be highly dependent on root symbiosis with ectomycorrhizal fungi that develop in constituent podzol horizons for growth in these nutrient limited soils. The aim of this microcosm-based study was a quantification of photosynthetically fixed ¹⁴C allocation, following standard pulse-feeding of 7-month-old Scots pine seedling shoots, to respective root and mycorrhizosphere compartments that developed in the reconstructed podzol (O, E and B) profile. Biomass of roots and mycorrhizas decreased with increasing soil depth but no soil origin, control forest vs. clear-cut area, related differences were observed. Similarly, no major soil origin- or podzol horizon-related differences in categorised ectomycorrhizal morphotypes and number of mycorrhizas, in relation to pooled root and mycorrhiza biomass, were detected. However, the total recovery of ¹⁴C-label was significantly higher in clear-cut soil microcosms compared to control counterparts. A significant finding was equivalent ¹⁴C-carbon allocation to roots and ectomycorrhizas in all three major, organic and mineral, podzol profile horizons studied. These carbon allocation data provide additional support for direct (or indirect) roles of roots and symbiotic mycorrhizal fungi in mineral weathering and biodegradation of organic ligands that are central for plant acquisition of growth limiting nutrients and the podzolization process in boreal forest ecosystems.     

The Formation of Otoliths in the Frog Rana esculenta. Scanning Electron Microscopic and X-Ray Diffraction Studies

Two crystal forms of calcium carbonate were observed: calcite (utricle) and aragonite (saccule, lagena, endolymphatic sac). The first step in otolith formation is the appearance of organic structures in the macula. The subsequent step is characterized by fast growing primitive crystals with a prismatic habitus that successively transform into adult or mature crystals. With the metamorphosis, the aragonite crystals of the endolymphatic organ show clear signs of erosion that can be related to a process of CaCO₃ mobilization from such deposits.     

Proteomic analysis of the acid-soluble organic matrix of the chicken calcified eggshell layer

The major difference between inorganic minerals and biominerals is the presence of an organic matrix consisting of proteins, glycoproteins, proteoglycans, and polysaccharides, which is synthesized by specialized cells under genetic control before or during mineralization. The organic matrix is thought to play a major role in the assembly of the biomineral and determination of its mechanical properties. The recent elucidation of the chicken genome provided an opportunity to explore the matrix proteome of a biomineral using up-to-date MS-based technology. We identified 520 proteins in this matrix including the ten matrix proteins already known before. The identified proteins were divided into three abundance groups using the exponentially modified protein abundance index described recently which was roughly calibrated with the few known data on protein yield derived from Edman sequence analysis. A small group of 32 highly abundant proteins contained the presently known eggshell-specific proteins and all of the other known eggshell matrix constituents identified before with much less sensitive conventional methods. The present study, which is the first comprehensive proteomic study of a vertebrate biomineral, is intended as a starting point for the detailed molecular characterization of eggshell matrix proteins, their interactions in the matrix network and functional studies.     

Soil properties under Norway spruce differ in spruce dominated and mixed broadleaf forests of the Southern Taiga

In natural forest, disturbance changes tree species composition which in turn affects soil properties. Two areas in the Central Forest State Biosphere Reserve, in the Russian Southern Taiga Zone, differed in the intensity of disturbance: Norway spruce was the dominant species at one site, while at the other spruce was mixed with broadleaves. The presence of broadleaves was due to large gaps in the canopy having been formed, which have triggered vegetation succession. At both sites, five plots were selected to evaluate how the presence of broadleaves influences the properties of the soils under spruce. Soil samples were taken close to spruce trees and the O, A and E horizons were analysed. A difference in the distribution of organic matter in the soil horizons was evident, with a higher concentration in the O and A horizons at the spruce dominated site, while a more homogeneous distribution was found under spruce at the site where broadleaves were abundant. The organic matter did not only differ in quantity, but also in quality as estimated by the C/N ratio, and therefore affected the CEC and element relative availability. No differences at the two sites were found for water-extractable and exchangeable elements, but the ratio between the exchangeable and the acid-extractable forms were different, suggesting a higher relative availability of the elements at the spruce dominated site, and thus potentially higher leaching. Both theoretical and empirical studies have suggested that podzolisation and accumulation of organic matter in the O horizon are related to stagnation of ecosystem processes and ecosystem decline. Our data suggest that the presence to windthrow sites and the inclusion of broadleaf species acts to slow or even reverse podzolisation even in spruce dominated sites.     

Coordinating subdomains of ferritin protein cages with catalysis and biomineralization viewed from the C 4 cage axes

Integrated ferritin protein cage function is the reversible synthesis of protein-caged, solid Fe₂O₃·H₂O minerals from Fe²⁺ for metabolic iron concentrates and oxidant protection; biomineral order differs in different ferritin proteins. The conserved 432 geometric symmetry of ferritin protein cages parallels the subunit dimer, trimer, and tetramer interfaces, and coincides with function at several cage axes. Multiple subdomains distributed in the self-assembling ferritin nanocages have functional relationships to cage symmetry such as Fe²⁺ transport though ion channels (threefold symmetry), biomineral nucleation/order (fourfold symmetry), and mineral dissolution (threefold symmetry) studied in ferritin variants. On the basis of the effects of natural or synthetic subunit dimer cross-links, cage subunit dimers (twofold symmetry) influence iron oxidation and mineral dissolution. 2Fe²⁺/O₂ catalysis in ferritin occurs in single subunits, but with cooperativity (n = 3) that is possibly related to the structure/function of the ion channels, which are constructed from segments of three subunits. Here, we study 2Fe²⁺ + O₂ protein catalysis (diferric peroxo formation) and dissolution of ferritin Fe₂O₃·H₂O biominerals in variants with altered subunit interfaces for trimers (ion channels), E130I, and external dimer surfaces (E88A) as controls, and altered tetramer subunit interfaces (L165I and H169F). The results extend observations on the functional importance of structure at ferritin protein twofold and threefold cage axes to show function at ferritin fourfold cage axes. Here, conserved amino acids facilitate dissolution of ferritin-protein-caged iron biominerals. Biological and nanotechnological uses of ferritin protein cage fourfold symmetry and solid-state mineral properties remain largely unexplored.     

Proteomics Analysis of Avian Eggshell Matrix Proteins: Toward New Advances on Biomineralization

Eggs are widely consumed all over the world. The eggshell is its protective barrier whose original function is to protect the embryo during development. Avian eggshells are made of calcium carbonate with a small amount of organic matrix (proteins and proteoglycans). During eggshell formation, the mineral precursors interact with matrix proteins to regulate the calcification of this highly resistant biomineral. In order to better characterize the functions of matrix proteins in eggshell biominerals, many proteomics studies have been performed during the last 15 years. The chicken eggshell is the main model studied in birds, but there is a need for comparative approaches in order to determine whether there is a general protein toolkits associated with calcitic biomineralization, and to determine its components. The study by Zhu et al., reported in article number 1900011, volume 19, issue 11, is a major step forward as it is the first shell proteomics survey performed on duck. Thus, it will contribute to improved knowledge of the eggshell mineralization process and will provide new insight for shell quality improvement and to guide biomimetic efforts in material sciences.