Genetic basis of stony coral biomineralization: History,trends and future prospects

Despite their simple body plan, stony corals (order Scleractinia, phylum Cnidaria) can produce massive and complex exoskeletal structures in shallow, tropical and subtropical regions of Earth’s oceans. The species-specific macromorphologies of their aragonite skeletons suggest a highly coordinated biomineralization process that is rooted in their genomes, and which has persisted across major climatic shifts over the past 400 + million years. The mechanisms by which stony corals produce their skeletons has been the subject of interest for at least the last 160 years, and the pace of understanding the process has increased dramatically in the past decade since the sequencing of the first coral genome in 2011. In this review, we detail what is known to date about the genetic basis of the stony coral biomineralization process, with a focus on advances in the last several years as well as ways that physical and chemical tools can be combined with genetics, and then propose next steps forward for the coming decade.     

Otolith crystals (in Carapidae): growth and habit

The biomineralization of otoliths results mainly from the release of soluble Ca(2+), which is in turn precipitated as CaCO(3) crystals. In some Carapidae, sagittae sections have been shown to reveal a three-dimensional asymmetry with a nucleus close to the sulcal side, an unusual position. This study seeks to understand otolith formation in Carapus boraborensis. The unusual shape of the otolith is partly explained by the distribution of the epithelium cells, and particularly the sensory epithelium. Experimental evidence shows for the first time that aragonite growth takes place along the c-axis. These aragonite needles present two different habits. On the sulcal side is found the acicular form resulting from rapid growth during a short period of time. On the anti-sulcal side, the prismatic form seen there is due to a slower growth speed over longer periods. The otolith surface was observed each hour during a period of 24h in fishes reared in similar conditions. This allowed for the first time the direct observation on the otolith surface of the deposition of the two layers (L-zone and D-zone). In C. boraborensis, the organic-rich layer (D-zone) develops during the day, whereas the CaCO(3) layer (L-zone) seems to be deposited during the night.     

Taphonomic windows and molluscan preservation

Recent studies on silicified fossil biotas have suggested that substantial skewing of the molluscan record resulted from early aragonite dissolution in mid-outer carbonate ramp settings. If those rare skeletal lagerstätten are representative, then the quality and completeness of the molluscan record are thrown into doubt. Yet database studies suggest that the bivalve fossil record is actually relatively complete. If so, then biodiversity must be captured by other processes that preserved shells vulnerable to early dissolution, and which operated on a relatively high frequency, i.e., less than the species duration for bivalves.Storm beds, shell plasters and submarine hardgrounds are identified as fossil deposits that can preserve the labile aragonitic component of the fauna and thus represent potential taphonomic windows. Many storm event beds include rich accumulations of shelly benthos. Differences between storm bed faunas and those of the background facies could reflect transportation effects. However, some storm bed assemblages are rich in originally aragonitic infaunal bivalves that are not represented in background facies or more proximal shelf equivalents, and here rapid burial and removal of organic matter by winnowing may be the keys to aragonite shell preservation. Despite Palaeozoic to Cenozoic changes in the thickness and frequency of shell beds that reflect the predominant bioclast producers, shallow infaunas are commonly concentrated together with epifauna in such deposits.Some low energy, organic-rich mud-dominated settings are associated with preservation of aragonitic molluscs. Infaunal bivalves are a prominent component of shell plasters or pavements in such settings, linked to episodic bottom water anoxia. Decaying algal blooms drew the redox boundary up above the sediment–water interface, and brought populations of infaunal bivalves to the surface where they died. Isolated from the oxic taphonomically active zone, the shells were not dissolved and were buried as thin shell layers. In similar settings, aragonitic shells were preserved as moulds through early pyritisation, or even through preservation of original shell aragonite.In oxic environments, bioturbational reworking of surface sediment destroyed moulds of aragonitic shells after early dissolution. In some hardgrounds, these delicate moulds were preserved due to synsedimentary cementation, probably using carbonate released by aragonite dissolution. The examples included here come from both intervals of “calcite” and “aragonite” seas, and it is not possible to assess whether the saturation state (with respect to aragonite) of the ambient sea water played a role in the selective removal of aragonitic shells.While taphonomic windows may have captured the diversity of individual groups, it is clear from quantitative data involving skeletal lagerstätten that the scale of loss from early aragonite dissolution has drastically altered the trophic composition of some fossil assemblages commonly used as the basis for reconstructions of past communities.     

The Roles of Mg over the Precipitation of Carbonate and Morphological Formation in the Presence of Arthrobacter sp. Strain MF-2

Microbial mineralization of carbonate is a research subject widely studied in the past decades. The magnesium ions (Mg²⁺), present in water systems, are a key determinant in biomineralization process of carbonate and they are widely found in calcium-based biominerals as an accessory component. However, the crystallization mechanism and morphological change of carbonate polymorphs in the presence of Mg²⁺ ions has not been clarified sufficiently. In this report, a series of culture experiments were performed for 50 days using the Arthrobacter sp. strain MF-2 in a M2 culture medium using Mg/Ca molar ratios (R) of 0, 1.5, 3, 6, 9, and 12 in solution. And the roles of Mg²⁺ ions on the crystal growth and morphological change of biogenic carbonate were investigated. Experimental results show: (1) MF-2 could induce aragonite, high-Mg calcite, and Ca-dolomite formation in M2 culture media with different R values. The increased stability of amorphous calcium carbonate suggests Mg²⁺ ions inhibit carbonate crystallization. (2) The mineral morphologies were varied (rod-shaped, dumbbell-shaped, cauliflower-like, spherical, etc.) in the medium with R = 1.5, but they became simple (spherical and lamellar) in high Mg²⁺ concentrations (Mg > 0.15 M, R > 3). (3) The increased ionic strength of Mg²⁺ ions in the environment has an influence on the polymorphs and morphologies of carbonate formed by controlling the metabolism of strain MF-2 and the activity of carbonic anhydrase.     

Preparation and characterization of cockle shell aragonite nanocomposite porous 3D scaffolds for bone repair

The demands for applicable tissue-engineered scaffolds that can be used to repair load-bearing segmental bone defects (SBDs) is vital and in increasing demand. In this study, seven different combinations of 3 dimensional (3D) novel nanocomposite porous structured scaffolds were fabricated to rebuild SBDs using an extraordinary blend of cockle shells (CaCo₃) nanoparticles (CCN), gelatin, dextran and dextrin to structure an ideal bone scaffold with adequate degradation rate using the Freeze Drying Method (FDM) and labeled as 5211, 5400, 6211, 6300, 7101, 7200 and 8100. The micron sized cockle shells powder obtained (75 µm) was made into nanoparticles using mechano-chemical, top-down method of nanoparticles synthesis with the presence of the surfactant BS-12 (dodecyl dimethyl bataine). The phase purity and crystallographic structures, the chemical functionality and the thermal characterization of the scaffolds’ powder were recognized using X-Ray Diffractometer (XRD), Fourier transform infrared (FTIR) spectrophotometer and Differential Scanning Calorimetry (DSC) respectively. Characterizations of the scaffolds were assessed by Scanning Electron Microscopy (SEM), Degradation Manner, Water Absorption Test, Swelling Test, Mechanical Test and Porosity Test. Top-down method produced cockle shell nanoparticles having averagely range 37.8±3–55.2±9 nm in size, which were determined using Transmission Electron Microscope (TEM). A mainly aragonite form of calcium carbonate was identified in both XRD and FTIR for all scaffolds, while the melting (Tm) and transition (Tg) temperatures were identified using DSC with the range of Tm 62.4–75.5 °C and of Tg 230.6–232.5 °C. The newly prepared scaffolds were with the following characteristics: (i) good biocompatibility and biodegradability, (ii) appropriate surface chemistry and (iii) highly porous, with interconnected pore network. Engineering analyses showed that scaffold 5211 possessed 3D interconnected homogenous porous structure with a porosity of about 49%, pore sizes ranging from 8.97 to 337 µm, mechanical strength 20.3 MPa, Young's Modulus 271±63 MPa and enzymatic degradation rate 22.7 within 14 days.     

Summer monsoon precipitation variations in central China over the past 750 years derived from a high-resolution absolute-dated stalagmite

A 2–3-year resolution record of stalagmite oxygen isotope variations from the south flank of the Qinling Mountains, central China, has revealed the Asian summer monsoon (ASM) precipitation variations in the investigated area over the past 750 years. The summer monsoon precipitation gradually increased since 1249 AD, reaching its highest values in the period 1535–1685 AD, and then decreased with substantial decadal- to centennial-scale fluctuations. The monsoon precipitation increased again between 1920 and 1970 AD. Three intervals of high monsoon precipitation were identified: 1535–1685 AD, 1755–1835 AD, and 1920–1970 AD. Three intervals of low precipitation were inferred in 1249–1325 AD, 1390–1420 AD, and 1890–1915 AD. The δ¹⁸O composition and lithological features of the stalagmite coincidently indicate a wetter climate during the Little Ice Age (LIA), which is also confirmed by climate records from Chinese historical documents within this area. A comparison with other high-resolution speleothem records indicates regional differences in monsoon precipitation variability from the south to the north of central China in the last 750 years on decadal- to centennial-scale. Power spectrum analysis of the δ¹⁸O record shows significant 117.8-, 34.6-, 14-, 10.3-, and ~ 6-year periodicities. These periodicities are widely observed in the climate records from ASM-controlled areas of China and are consistent with the Gleissburg periodicity, Brϋckner periodicity, sunspot periodicity of solar activity, and El Nińo–Southern Oscillation (ENSO) periodicity. These correlations suggest that both solar activity and ENSO periodicity may have had important influences on ASM precipitation in China over the past 750 years.     

Structure and composition of the septal nacreous layer of Nautilus macromphalus L. (Mollusca, Cephalopoda)

The nacreous layer of Mollusca is the best-known aragonitic structure and is the usual model for biomineralization. However, data are based on less than 10 species. In situ observations of the septal nacreous layer of the cephalopod Nautilus shell has revealed that the tablets are composed of acicular laths. These laths are composed of round nanograins surrounded by an organic sheet. No hole has been observed in the decalcified interlamellar membranes. A set of combined analytical data shows that the organic matrices extracted from the nacreous layer are glycoproteins. In both soluble and insoluble matrices, S amino acids are rare and the soluble organic matrices have a higher sulfated sugar content than the insoluble matrices. It is possible that the observed differences in the structure and composition of the nacreous layers of the outer wall and septa of the Nautilus shell have a dual origin: evolution and functional adaptation. However, we have no appropriate data as yet to answer this question.     

Carbonate Precipitation of Bacterial Strains Isolated from Sediments and Seawater: Formation Mechanisms

This article presents a research study on carbonate formation in solid and liquid media by Thalassospira sp., Halomonas sp., Bacillus pumilus, and Pseudomonas grimontii, four bacterial strains isolated from sediments and deep seawater. As part of this study, we analyzed carbonic anhydrase activity, pH, adsorption of calcium and magnesium ions, and total organic and inorganic carbon. The geochemical program PHREEQC was also used to calculate the mineral saturation indexes in all the cultures. The minerals formed were studied with X-ray diffraction, X-ray dispersive energy microanalysis, and scanning electron microscopy. In addition, all four bacterial strains were found to induce carbonate precipitation and to have carbonic anhydrase activity. Sterile control experiments did not precipitate carbonate. In solid M1 and B4 media, all of the strains precipitated magnesium calcite, whereas in the liquid media, they precipitated different percentages of magnesium calcite, aragonite, and monohydrocalcite. In both cases, small amounts of amorphous precipitates were also produced. This article discusses carbonate formation and the possible role played by metabolic activity, bacterial surfaces and carbonic anhydrase in this process. Finally, the results obtained lead to a hypothesis regarding the importance of carbonate precipitation for the survival of bacteria populations in certain habitats.     

Analysis of tissue condition based on interaction between inorganic and organic matter in cuttlefish bone

The absorption properties of an inner layer of cuttlefish bone were measured using a transmission terahertz time-domain spectrometer in a band from approximately 0.1 to 4 THz. For oriented samples, an absorption peak related to the behavior of calcium carbonate appeared at approximately 2 THz. The peak magnitude and frequency depended on the direction of the incident terahertz electric field, indicating that calcium carbonate crystals constituting the inner layer were oriented in a certain direction. The absorbance of a sample heated to 350 °C for 0 to 2 h to remove organic matter tended to decrease with heating time in the oriented direction, while the peak frequency shifted to higher frequencies. Furthermore, we showed that the peak frequency depended on the interaction area within the unheated sample and we thus obtained a two-dimensional image reflecting crystal regularity inside the cuttlefish bone from the spectral data at each position.