Rare earth element geochemistry of scleractinian coral skeleton during meteoric diagenesis: A sequence through neomorphism of aragonite to calcite

Rare earth element geochemistry in carbonate rocks is utilized increasingly for studying both modern oceans and palaeoceanography, with additional applications for investigating water–rock interactions in groundwater and carbonate diagenesis. However, the study of rare earth element geochemistry in ancient rocks requires the preservation of their distribution patterns through subsequent diagenesis. The subjects of this study, Pleistocene scleractinian coral skeletons from Windley Key, Florida, have undergone partial to complete neomorphism from aragonite to calcite in a meteoric setting; they allow direct comparison of rare earth element distributions in original coral skeleton and in neomorphic calcite. Neomorphism occurred in a vadose setting along a thin film, with degradation of organic matter playing an initial role in controlling the morphology of the diagenetic front. As expected, minor element concentrations vary significantly between skeletal aragonite and neomorphic calcite, with Sr, Ba and U decreasing in concentration and Mn increasing in concentration in the calcite, suggesting that neomorphism took place in an open system. However, rare earth elements were largely retained during neomorphism, with precipitating cements taking up excess rare earth elements released from dissolved carbonates from higher in the karst system. Preserved rare earth element patterns in the stabilized calcite closely reflect the original rare earth element patterns of the corals and associated reef carbonates. However, minor increases in light rare earth element depletion and negative Ce anomalies may reflect shallow oxidized groundwater processes, whereas decreasing light rare earth element depletion may reflect mixing of rare earth elements from associated microbialites or contamination from insoluble residues. Regardless of these minor disturbances, the results indicate that rare earth elements, unlike many minor elements, behave very conservatively during meteoric diagenesis. As the meteoric transformation of aragonite to calcite is a near worst case scenario for survival of original marine trace element distributions, this study suggests that original rare earth element patterns may commonly be preserved in ancient limestones, thus providing support for the use of ancient marine limestones as proxies for marine rare earth element geochemistry.

Reply to the discussion by Karen Johannesson on “Rare earth element geochemistry of scleractinian coral skeleton during meteoric diagenesis: a sequence through neomorphism of aragonite to calcite” by Webb et al., Sedimentology, 56, 1433-1463

Webb et al. (2009) described a late Pleistocenecoral sample wherein the diagenetic stabilization of original coral aragonite to meteoric calcite was halted more or less mid-way through the process, allowing direct comparison of pre-diagenetic and post-diagenetic microstructure and trace element distributions. Those authors found that the rare earth elements (REEs) were relatively stable during meteoric diagenesis, unlike divalent cations such as Sr,and it was thus concluded that original, in this case marine, REE distributions potentially could be preserved through the meteoric carbonate stabilization process that must have affected many, if not most, ancient limestones. Although this was not the case in the analysed sample, they noted that where such diagenesis took place in laterally transported groundwater, trace elements derived from that groundwater could be incorporated into diagenetic calcite, thus altering the initial REE distribution (Banner et al., 1988). Hence, the paper was concerned with the diagenetic behaviour of REEs in a groundwater-dominated karst system. The comment offered by Johannesson (2011) does not question those research results, but rather, seeks to clarify an interpretation made by Webb et al. (2009) of an earlier paper, Johannesson et al. (2006).

Calcite precipitation induced by clay-bleach cation exchange in andesitic reservoir rocks

Experiments were carried out on the sodium hypochlorite bleach sensitivity of a deep subsurface andesitic reservoir in order to predict possible deleterious mineral transformations during a downhole clean-up job. Experiments involved examination of core samples from the reservoir using an Environmental Scanning Electron Microscope (ESEM) with an attached Energy Dispersive Spectrometer (EDS) before and after the samples were immersed in bleach. Bleach immersion of whole-rock samples resulted in rapid (less than 1 min) precipitation of abundant 3.0-10.0-μm-wide calcite rhombs within clay-associated micropores and on clay and feldspar grain surfaces. Abundant microporefilling calcite rhombs also formed in pure separates of constituent chlorite/corrensite, whereas no calcite formed in a pure separate of constituent zeolite. These experiments indicate that corrensite is the likely calcium source in this experimental fluid-rock system. Formation of calcite occurs via a cation exchange reaction in which calcium in the smectitic interlayers of corrensite exchanges for sodium in the bleach. Serious formation damage due to calcite precipitation would have occurred in the andesite reservoir had it been exposed to bleach. This finding gives credence to earlier suggestions that cation exchange reactions have the potential to cause calcite precipitation in some sandstone reservoirs when exposed to drilling, completion or stimulation fluids. © 1993.

A Raman spectroscopic comparison of calcite and dolomite

Raman spectroscopy was used to characterize and differentiate the two minerals calcite and dolomite and the bands related to the mineral structure. The (CO3)2− group is characterized by four prominent Raman vibrational modes: (a) the symmetric stretching, (b) the asymmetric deformation, (c) asymmetric stretching and (d) symmetric deformation. These vibrational modes of the calcite and dolomite were observed at 1440, 1088, 715 and 278 cm−1. The significant differences between the minerals calcite and dolomite are observed by Raman spectroscopy. Calcite shows the typical bands observed at 1361, 1047, 715 and 157 cm−1, and the special bands at 1393, 1098, 1069, 1019, 299, 258 and 176 cm−1 for dolomite are observed. The difference is explained on the basis of the structure variation of the two minerals. Calcite has a trigonal structure with two molecules per unit cell, and dolomite has a hexagonal structure. This is more likely to cause the splitting and distorting of the carbonate groups. Another cause for the difference is the cation substituting for Mg in the dolomite mineral.

Earliest diagenesis in scleractinian coral skeletons : implications for palaeoclimate-sensitive geochemical archives

Live-collected samples of four common reef building coral genera (Acropora, Pocillopora, Goniastrea, Porites) from subtidal and intertidal settings of Heron Reef, Great Barrier Reef, show extensive early marine diagenesis where parts of the coralla less than 3 years old contain abundant macro- and microborings and aragonite, high-Mg calcite, low-Mg calcite, and brucite cements. Many types of cement are associated directly with microendoliths and endobionts that inhabit parts of the corallum recently abandoned by coral polyps. The occurrence of cements that generally do not precipitate in normal shallow seawater (e.g., brucite, low-Mg calcite) highlights the importance of microenvironments in coral diagenesis. Cements precipitated in microenvironments may not reXect ambient seawater chemistry. Hence, geochemical sampling of these cements will contaminate trace-element and stable-isotope inventories used for palaeoclimate and dating analysis. Thus, great care must be taken in vetting samples for both bulk and microanalysis of geochemistry. Visual inspection using scanning electron microscopy may be required for vetting in many cases.

Investigation of molecular mechanisms regulating biomineralization of pearl oyster Pinctada maxima

Biomineralization is a process encompassing all mineral containing tissues produced within an organism. The most dynamic example of this process is the formation of the mollusk shell, comprising a variety of crystal phases and microstructures. The organic component incorporated within the shell is said to dictate this remarkable architecture. Subsequently, for the past decade considerable research have been undertaken to identify and characterize the protein components involved in biomineralization. Despite these efforts the general understanding of the process remains ambiguous. This study employs a novel molecular approach to further the elucidation of the shell biomineralization. A microarray platform has been custom generated (PmaxArray 1.0) from the pearl oyster Pinctada maxima. PmaxArray 1.0 consists of 4992 expressed sequence tags (ESTs) originating from the mantle, an organ involved in shell formation. This microarray has been used as the primary tool for three separate investigations in an effort to associate transcriptional gene expression from P. maxima to the process of shell biomineralization. The first investigation analyzes the spatial expression of ESTs throughout the mantle organ. The mantle was dissected into five discrete regions and each analyzed for gene expression with PmaxArray 1.0. Over 2000 ESTs were differentially expressed among the tissue sections, identifying five major expression regions. Three of these regions have been proposed to have shell formation functions belonging to nacre, prismatic calcite and periostracum. The spatial gene expression map was confirmed by in situ hybridization, localizing a subset of ESTs from each expression region to the same mantle area. Comparative sequence analysis of ESTs expressed in the proposed shell formation regions with the BLAST tool, revealed a number of the transcripts were novel while others showed significant sequence similarities to previously characterized shell formation genes. The second investigation correlates temporal EST expression during P. maxima larval ontogeny with transitions in shell mineralization during the same period. A timeline documenting the morphologicat microstructural and mineralogical shell characteristics of P. maxima throughout larval ontogeny has been established. Three different shell types were noted based on the physical characters and termed, prodissoconch I, prodissoconch 11 and dissoconch. PmaxArray 1.0 analyzed ESTs expression of animals throughout the larval development of P. maxima, noting up-regulation of 359 ESTs in association with the shell transitions from prodissoconch 1 to prodissoconch 11 to dissoconch. Comparative sequence analysis of these ESTs indicates a number of the transcripts are novel as well as showing significant sequence similarities between ESTs and known shell matrix associated genes and proteins. These ESTs are discussed in relation to the shell characters associated with their temporal expression. The third investigation uses PmaxArray 1.0 to analyze gene expression in the mantle tissue of P. maxima specimens exposed to sub-lethal concentrations of a shell-deforming toxin, tributyltin (TBT). The shell specific effects of TBT are used in this investigation to interpret differential expression of ESTs with respect to shell formation functions. A lethal and sublethal TBT concentration range was established for P. maxima, noting a concentration of 50 ng L- 1 TBT as sub-lethal over a 21 day period. Mantle tissue from P. maxima animals treated with 50 ng L- 1 TBT was assessed for differential EST expression with untreated control animals. A total of 102 ESTs were identified as differentially expressed in association with TBT exposure, comparative sequence identities included an up-regulation of immunity and detoxification related genes and down-regulation of several shell matrix genes. A number of transcripts encoding novel peptides were additionally identified. The potential actions of these genes are discussed with reference to TBT toxicity and shell biomineralization. This thesis has used a microarray platform to analyze gene expression in spatial, temporal and toxicity investigations, revealing the involvement of numerous gene transcripts in specific shell formation functions. Investigation of thousands of transcripts simultaneously has provided a holistic interpretation of the organic components regulating shell biomineralization.

Thermogravimetric analysis-mass spectrometry (TG-MS) of selected Chinese kaolinites

Thermogravimetric analysis-mass spectrometry, X-ray diffraction and scanning electron microscopy (SEM) were used to characterize eight kaolinite samples from China. The results show that the thermal decomposition occurs in three main steps (a) desorption of water below 100 °C, (b) dehydration at about 225 °C, (c) well defined dehydroxylation at around 450 °C. It is also found that decarbonization took place at 710 °C due to the decomposition of calcite impurity in kaolin. The temperature of dehydroxylation of kaolinite is found to be influenced by the degree of disorder of the kaolinite structure and the gases evolved in the decomposition process can be various because of the different amount and kinds of impurities. It is evident by the mass spectra that the interlayer carbonate from impurity of calcite and organic carbon is released as CO2 around 225, 350 and 710 °C in the kaolinite samples.

Synthesis and Raman spectroscopic characterisation of hydrotalcites based on the formula Ca6Al2(CO3)(OH)16· 4H2O

We have successfully synthesized hydrotalcites (HTs) contg. calcium, which are naturally occurring minerals. Insight into the unique structure of HTs has been obtained using a combination of X-ray diffraction (XRD) as well as IR and Raman spectroscopies. Calcium-contg. hydrotalcites (Ca-HTs) of the formula Ca4Al2(CO3)(OH)12·4H2O (2:1 Ca-HT) to Ca8Al2(CO3)(OH)20· 4H2O (4:1 Ca-HT) have been successfully synthesized and characterised by XRD and Raman spectroscopy. XRD has shown that 3:1 calcium HTs have the largest interlayer distance. Raman spectroscopy complemented with selected IR data has been used to characterize the synthesized Ca-HTs. The Raman bands obsd. at around 1086 and 1077 cm-1 were attributed to the ν1 sym. stretching modes of the (CO32-) units of calcite and carbonate intercalated into the HT interlayer. The corresponding ν3 CO32- antisym. stretching modes are found at around 1410 and 1475 cm-1.

A Raman spectroscopic study of the ‘cave’ mineral ardealite Ca2(HPO4)(SO4)•4H2O

The mineral ardealite Ca2(HPO4)(SO4)•4H2O is a ‘cave’ mineral and is formed through the reaction of calcite with bat guano. The mineral shows disorder and the composition varies depending on the origin of the mineral. Raman spectroscopy complimented with infrared spectroscopy has been used to characterise the mineral ardealite. The Raman spectrum is very different from that of gypsum. Bands are assigned to SO42- and HPO42- stretching and bending modes.

Thermal stability of the ‘cave’ mineral brushite CaHPO4•2H2O -mechanism of formation and decomposition

Thermogravimetry combined with evolved gas mass spectrometry has been used to ascertain the stability of the ‘cave’ mineral brushite. X-ray diffraction shows that brushite from the Jenolan Caves is very pure. Thermogravimetric analysis coupled with ion current mass spectrometry shows a mass loss at 111°C due to loss of water of hydration. A further decomposition step occurs at 190°C with the conversion of hydrogen phosphate to a mixture of calcium ortho-phosphate and calcium pyrophosphate. TG-DTG shows the mineral is not stable above 111°C. A mechanism for the formation of brushite on calcite surfaces is proposed, and this mechanism has relevance to the formation of brushite in urinary tracts.

Raman spectroscopy of stercorite H(NH4)Na(PO4)•4H2O – a cave mineral from Petrogale Cave, Madura, Eucla, Western Australia

Raman spectroscopy complimented with infrared spectroscopy has been used to characterise the mineral stercorite H(NH4)Na(PO4)·4H2O. The mineral stercorite originated from the Petrogale Cave, Madura, Eucla, Western Australia. This cave is one of many caves in the Nullarbor Plain in the South of Western Australia. These caves have been in existence for eons of time and have been dated at more than 550 million years old. The mineral is formed by the reaction of bat guano chemicals on calcite substrates. A single Raman band at 920 cm−1 defines the presence of phosphate in the mineral. Antisymmetric stretching bands are observed in the infrared spectrum at 1052, 1097, 1135 and 1173 cm−1. Raman spectroscopy shows the mineral is based upon the phosphate anion and not the hydrogen phosphate anion. Raman and infrared bands are found and assigned to PO43−, H2O, OH and NH stretching vibrations. The detection of stercorite by Raman spectroscopy shows that the mineral can be readily determined; as such the application of a portable Raman spectrometer in a ‘cave’ situation enables the detection of minerals, some of which may remain to be identified.

Are the ‘cave’ minerals archerite (K,NH4)H2PO4 and biphosphammite (K,NH4)H2PO4 identical? A molecular structural study

The molecular structure of the mineral archerite ((K,NH4)H2PO4) has been determined and compared with that of biphosphammite ((NH4,K)H2PO4). Raman spectroscopy and infrared spectroscopy has been used to characterise these ‘cave’ minerals. Both minerals originated from the Murra-el-elevyn Cave, Eucla, Western Australia. The mineral is formed by the reaction of the chemicals in bat guano with calcite substrates. Raman and infrared bands are assigned to H2PO4-, OH and NH stretching vibrations. The Raman band at 981 cm-1 is assigned to the HOP stretching vibration. Bands in the 1200 to 1800 cm-1 region are associated with NH4+ bending modes. The molecular structure of the two minerals appear to be very similar, and it is therefore concluded that the two minerals are identical.

Vibrational spectroscopy of synthetic stercorite H(NH4)Na(PO4)•4H2O – a comparison with the natural cave mineral

In order to mimic the chemical reactions in cave systems, the analogue of the mineral stercorite H(NH4)Na(PO4)•4H2O has been synthesised. X-ray diffraction of the stercorite analogue matches the stercorite reference pattern. A comparison is made with the vibrational spectra of synthetic stercorite analogue and the natural Cave mineral. The mineral in nature is formed by the reaction of bat guano chemicals on calcite substrates. A single Raman band at 920 cm-1 (Cave) and 922 cm-1 (synthesised) defines the presence of hydrogen phosphate in the mineral. In the synthetic stercorite analogue, additional bands are observed and are attributed to the dihydrogen and phosphate anions. The vibrational spectra of synthetic stercorite only partly match that of the natural stercorite. It is suggested that natural stercorite is more pure than that of synthesised stercorite. Antisymmetric stretching bands are observed in the infrared spectrum at 1052, 1097, 1135 and 1173 cm-1. Raman spectroscopy shows the stercorite mineral is based upon the hydrogen phosphate anion and not the phosphate anion. Raman and infrared bands are found and assigned to PO43-, H2O, OH and NH stretching vibrations. Raman spectroscopy shows the synthetic analogue is similar to the natural mineral. A mechanism for the formation of stercorite is provided.

Thermal stability of the ‘cave’ mineral ardealite Ca2(HPO4)(SO4)•4H2O

Thermogravimetry combined with evolved gas mass spectrometry has been used to characterise the mineral ardealite and to ascertain the thermal stability of this ‘cave’ mineral. The mineral ardealite Ca2(HPO4)(SO4)•4H2O is formed through the reaction of calcite with bat guano. The mineral shows disorder and the composition varies depending on the origin of the mineral. Thermal analysis shows that the mineral starts to decompose over the temperature range 100 to 150°C with some loss of water. The critical temperature for water loss is around 215°C and above this temperature the mineral structure is altered. It is concluded that the mineral starts to decompose at 125°C, with all waters of hydration being lost after 226°C. Some loss of sulphate occurs over a broad temperature range centred upon 565°C. The final decomposition temperature is 823°C with loss of the sulphate and phosphate anions.