Morphometry and composition of aragonite and vaterite otoliths of deformed laboratory reared juvenile herring from two populations

Vaterite otoliths were sampled from two reared populations (Celtic and Clyde Seas) of juvenile herring Clupea harengus. The crystallography, elemental composition and morphometry were analysed and compared with those of normal aragonite otoliths. The incidence of vaterite otoliths in the juveniles sampled (n = 601) ranged from 7·8% in the Clyde population to 13·9% in the Celtic Sea population, and was 5·5% in the small sample (n = 36) of wild adults examined. In all but one case fish had only one vaterite otolith; the corresponding otolith of the pair was completely aragonite. Although the majority of the juveniles sampled showed craniofacial deformities, there was no link between the skull or jaw malformation and the incidence of vaterite otoliths. All vaterite otoliths had an aragonite inner area, and vaterite deposition began sometime after the age of 90 days. The vaterite otoliths were larger and lighter than their corresponding aragonite partners, and were less dense as a consequence of the vaterite crystal structure. The vaterite areas of the otoliths were depleted in Sr, Na and K. Concentrations of Mn were higher in the vaterite areas. The transition between the aragonite inner areas and the vaterite areas was sharply delineated. Within a small spatial scale (20 μm³) in the vaterite areas, however, there was co‐precipitation of both vaterite and aragonite. The composition of the aragonite cores in the vaterite otoliths was the same as in the cores of the normal aragonite otoliths indicating that the composition of the aragonite cores did not seed the shift to vaterite. Vaterite is less dense than aragonite, yet the concentrations of Ca analysed with wavelength‐dispersive spectrometry (WDS) were the same between the two polymorphs, indicating that Ca concentrations measured with WDS are not a good indicator of hypermineralized zones with high mineral density. The asymmetry in density and size of the otoliths may cause disruptions of hearing and pressure sensitivity for individual fish with one vaterite otolith, however, the presence of vaterite otoliths did not seem to affect the growth of these laboratory reared juvenile herring.     

Competitive Formation of Hydroxycarbonate Green Rust 1 versus Hydroxysulphate Green Rust 2 in Shewanella putrefaciens Cultures

The formation of hydroxysulphate green rust 2, a Fe(II-III) compound commonly found during corrosion processes of iron-based materials in seawater, has not yet been reported in bacterial cultures. Here we used Shewanella putrefaciens, a dissimilatory iron-reducing bacterium to anaerobically catalyze the transformation of a ferric oxyhydroxide, lepidocrocite (γ-FeOOH), into Fe(II) in the presence of various sulphate concentrations. Biotransformation assays of γ-FeOOH were performed with formate as the electron donor under a variety of concentrations. The results showed that the competitive formation of hydroxycarbonate green rust 1 (GR1(CO₃ ^2?)) and hydroxysulphate green rust 2 (GR2(SO₄ ^{2 ?})) depended upon the relative ratio (R) of bicarbonate and sulphate concentrations. When R ≥ 0.17, GR1(CO₃ ^{2 ?}) only was formed whereas when R < 0.17, a mixture of GR2(SO₄ ^{2 ?}) and GR1(CO₃ ^{2 ?}) was obtained. These results demonstrated that the hydroxysulphate GR2 can originate from the microbial reduction of γ-FeOOH and confirmed the preference for carbonate over sulphate during green rust precipitation. The solid phases were characterized by X-ray diffraction, transmission Mössbauer spectroscopy and scanning electron microscopy. Diffuse reflectance infrared Fourier transform spectroscopy confirmed the presence of intercalated carbonate and sulphate in green rust's structure. This study sheds light on the influence of dissimilatory iron-reducing bacteria on microbiologically influenced corrosion.     

Bio-deposition of a calcium carbonate layer on degraded limestone by Bacillus species

To obtain a restoring and protective calcite layer on degraded limestone, five different strains of the Bacillus sphaericus group and one strain of Bacillus lentus were tested for their ureolytic driven calcium carbonate precipitation. Although all the Bacillus strains were capable of depositing calcium carbonate, differences occurred in the amount of precipitated calcium carbonate on agar plate colonies. Seven parameters involved in the process were examined: calcite deposition on limestone cubes, pH increase, urea degrading capacity, extracellular polymeric substances (EPS)-production, biofilm formation, ζ-potential and deposition of dense crystal layers. The strain selection for optimal deposition of a dense CaCO₃ layer on limestone, was based on decrease in water absorption rate by treated limestone. Not all of the bacterial strains were effective in the restoration of deteriorated Euville limestone. The best calcite precipitating strains were characterised by high ureolytic efficiency, homogeneous calcite deposition on limestone cubes and a very negative ζ-potential.     

Coccolith Ultrastructure and Biomineralisation

The relationship between calcite biomineralisation and coccolith ultrastructure is analysed across the diversity of calcifying haptophytes. The emphasis is on integration of evidence from crystallographic and ultrastructural studies but additional relevant information from biochemical and phylogenetic work is reviewed. We attempt to identify aspects of ultrastructure which are most likely to be the product of self-organising processes. The principal topics reviewed are heterococcolith rim nucleation, including reassessment of the V/R model; crystal growth regulation in heterococcoliths; holococcolith biomineralisation; and the diversity of other biomineralisation modes in haptophytes. It is concluded that the diverse range of calcareous structures produced by haptophytes probably has a common phylogenetic origin and is produced via operation of a limited set of mainly shared genetic and biochemical pathways.     

Computer-integrated polarisation (CIP) in the analysis of fossils: a case of study in a Palaeozoic coral (Sinopora,Syringoporicae, Carboniferous)

Computer-integrated polarisation (CIP) method has been applied satisfactorily in the study of fossils skeletons of Sinopora (tabulate coral, Auloporida and Carboniferous). A previous characterisation of sample by scanning electron microscopy, atomic force microscopy and cathodoluminescence (CL) with the purpose of distinguishing the diagenetical alteration was done. Subsequently, a crystallographic comparison between CIP and electron-backscattering diffraction has been made getting a very good correlation between both methods. The CIP method allows obtaining c-axis orientation images, pole figures, and measure and mapping the misorientation of uniaxial biominerals in recent and fossil skeletons. This technique can only be used in uniaxial biominerals (calcite, quartz and hydroxylapatite), limiting its use for biaxial or bimineralic and polimineralic biominerals. CIP method has good spatial resolution (limited by camera); in our example 90 nm. The main advantage of this technique, versus other with similar properties, is the fast acquisition of data in low and high magnifications. This method does not require special treatment of samples and can be very useful for the analysis of microstructures in thin and ultra-thin sections. CIP method detects diagenetic alterations in fossil skeletons by modifications in the inner arrangement of biominerals, which combined with CL offers valuable geochemical and crystallographic information.     

Microbial influence on dolomite and authigenic clay mineralisation in dolocrete profiles of NW Australia

Dolomite (CaMg(CO₃)₂) precipitation is kinetically inhibited at surface temperatures and pressures. Experimental studies have demonstrated that microbial extracellular polymeric substances (EPS) as well as certain clay minerals may catalyse dolomite precipitation. However, the combined association of EPS with clay minerals and dolomite and their occurrence in the natural environment are not well documented. We investigated the mineral and textural associations within groundwater dolocrete profiles from arid northwest Australia. Microbial EPS is a site of nucleation for both dolomite and authigenic clay minerals in this Late Miocene to Pliocene dolocrete. Dolomite crystals are commonly encased in EPS alveolar structures, which have been mineralised by various clay minerals, including montmorillonite, trioctahedral smectite and palygorskite-sepiolite. Observations of microbial microstructures and their association with minerals resemble textures documented in various lacustrine and marine microbialites, indicating that similar mineralisation processes may have occurred to form these dolocretes. EPS may attract and bind cations that concentrate to form the initial particles for mineral nucleation. The dolomite developed as nanocrystals, likely via a disordered precursor, which coalesced to form larger micritic crystal aggregates and rhombic crystals. Spheroidal dolomite textures, commonly with hollow cores, are also present and may reflect the mineralisation of a biofilm surrounding coccoid bacterial cells. Dolomite formation within an Mg-clay matrix is also observed, more commonly within a shallow pedogenic horizon. The ability of the negatively charged surfaces of clay and EPS to bind and dewater Mg²⁺, as well as the slow diffusion of ions through a viscous clay or EPS matrix, may promote the incorporation of Mg²⁺ into the mineral and overcome the kinetic effects to allow disordered dolomite nucleation and its later growth. The results of this study show that the precipitation of clay and carbonate minerals in alkaline environments may be closely associated and can develop from the same initial amorphous Ca–Mg–Si-rich matrix within EPS. The abundance of EPS preserved within the profiles is evidence of past microbial activity. Local fluctuations in chemistry, such as small increases in alkalinity, associated with the degradation of EPS or microbial activity, were likely important for both clay and dolomite formation. Groundwater environments may be important and hitherto understudied settings for microbially influenced mineralisation and for low-temperature dolomite precipitation.