This study stresses the role of specific bacterial outer structures (such as glycocalix and parietal polymers) on calcium carbonate crystallization in terrestrial environments. The aim is to compare calcium carbonate crystals obtained in bacterial cultures with those obtained during abiotically mediated synthesis to show implications of exopolysaccharides and amino acids in the mineralogy and morphology of calcium carbonate crystals produced by living bacteria. This is done using various amounts of purified exopolysaccharide (xanthan EPS) and L-amino acids with a range of acidities. Amino acids and increasing xanthan content enhance sphere formation in calcite and vaterite. Regarding calcite, the morphology of crystals evolves from rhombohedral to needle shape. This evolution is characterized by stretching along the c axis as the amino acid changes from glutamine to aspartic acid and as the medium is progressively enriched in EPS. Regarding vaterite, the spherulitic habit is preserved throughout the morphological sequence and starts with spheres formed by the agglomeration of short needles, which are produced in a xanthan-free medium with glutamine. Monocrystals forming spheres increase in size as xanthan is added and the acidity of amino acids (glutamic and aspartic acids) is increased. At high xanthan concentrations, amino acids, and mainly aspartic and glutamic acids, induce vaterite precipitation. The role of the carboxyl group is also probably critical because bacterial outer structures associated with peptidoglycan commonly contain carboxyl groups. This role, combined with the results presented here, clearly demonstrate the influence of bacterial outer structure composition on the morphology and mineralogy of bacterially induced calcium carbonate. This point should not be neglected in the interpretation of calcite cements and carbonate accumulations in terrestrial environments.

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In freshwater environments such as river and stream bottoms, rocks and submerged vegetation are covered with a biological felt (also called a periphyton, microbial mat, biofilm, etc.) that is susceptible to calcification. Compilation of an extensive bibliography and our own observations have allowed the identification of 44 species of Coccogonophyceae, 122 Hormogonophyceae, 2 Chrysophyceae, 35 Chlorophyceae, 3 Xanthophyceae, 2 diatoms, and 3 Rhodophyceae that grow on calcareous tufa and coat vegetation. Diverse genera include species that are also calcified but impossible to determine because they lack reproductive organs. Crystals have been described from 74 species in the literature and we have observed 53 others. They can be classified into 10 groups: (1) platelets on cell walls (Volvocales, analogues of coccolithophorids) (2) crystals in mucilage (Synechococcus, diatoms, Hydrurus) and calcified stalks (Oocardium) (3) sheaths containing crystals in the form of simple or three‐branched needles, dendritic crystals, and crystals with box‐work fabric (Geitleria, Scytonema) (4) sheaths containing calcite spherulites (5) stalks intersecting a large crystal (Cymbella) (6) micrite tubes (Phormidium, Schizothrix) (7) isolated rhombohedra (Zygnema, Scytonema), rhombohedra in clusters or chains (Nostoc parmelioides) (8) sparite platelets (Vaucheria) or isodiametric crystals (Scytonema, Chaetophora) (9) large crystals crosscut by many parallel filaments (Rivularia, Batrachospermum), and (10) fan‐like crystals (Phormidium). These crystals can be arranged in clusters or form regular laminations. They can transform into isodiametric sparite crystals to form fan‐like or radial palisadic structures. Knowledge of primary crystals and their diagenetic transformations is necessary to correctly interpret freshwater stromatolites. The latter always result from intense calcification and are a diagenetic transformation of a biological felt made of many prokaryotic and eukaryotic algal species, small invertebrates, and organic and mineral debris.

SummaryRock-Eval pyrolysis was designed for petroleum exploration to determine the type and quality of organic matter in rock samples. Nevertheless, this technique can be used for bulk characterization of the immature organic matter in soil samples and recent sediments. We studied 76 samples from seven soil classes and showed that their pyrograms can be described by a combination of four elementary Gaussian components: F1, F2, F3 and F4. These four components are related to major classes of organic constituents differing in origin and their resistance to pyrolysis: labile biological constituents (F1), resistant biological constituents (F2), immature non-biotic constituents (F3) and a mature refractory fraction (F4). We discriminated the relative contributions of these components and used them to derive two indices: (i) to quantify the relative contributions of labile and resistant biological constituents and (ii) to quantify the degradation stage of the soil organic matter. The practical applications are illustrated via the influence of vegetal cover on soil organic matter dynamics and peat development in a Holocene sedimentary sequence, but we suggest that the approach is of much wider application.

Stromatolites are examples of an iterative system involving radiate accretive growth of microbial mats, biofilm and/or minerals that result from interaction between intrinsic and extrinsic factors, which progressively shape the final morphology. These interactions can neither be easily described by simple mathematical equations, nor by simple physical laws or chemical reactions. Therefore, a holistic approach that will reduce the system to a set of variables (which are combinations of natural variables) is proposed in order to create virtual morphologies which will be compared with their natural counterparts. The combination of both Diffusion Limited Aggregation (DLA) and cellular automata (CA) allows the exploration of the stromatolite morphological space and a representation of the intrinsic and extrinsic factors responsible for natural stromatolite morphogenesis. The holistic approach provides a translation in simple parameters of (1) the way that energy, nutrients and sedimentary particles reach the active surface of a future build-up, (2) how these elements are distributed and used in order to create morphology, and (3) how simple environmental parameters, such as sedimentation, can disturb morphogenesis. In addition, most Precambrian stromatolite morphologies that are impossible to produce with numerical modeling such as the Kardar-Parisi-Zhang (KPZ) equation can be simulated with the DLA-CA model and this, with a minimum set of variables.

Microbial metabolism impacts the degree of carbonate saturation by changing the total alkalinity and calcium availability; this can result in the precipitation of carbonate minerals and thus the formation of microbialites. Here, the microbial metabolic activity, the characteristics and turnover of the extracellular polymeric substances and the physicochemical conditions in the water column and sediments of a hypersaline lake, Big Pond, Bahamas, were determined to identify the driving forces in microbialite formation. A conceptual model for organomineralization within the active part of the microbial mats that cover the lake sediments is presented. Geochemical modelling indicated an oversaturation with respect to carbonates (including calcite, aragonite and dolomite), but these minerals were never observed to precipitate at the mat-water interface. This failure is attributed to the capacity of the water column and upper layers of the microbial mat to bind calcium. A layer of high Mg-calcite was present 4 to 6 mm below the surface of the mat, just beneath the horizons of maximum photosynthesis and aerobic respiration. This carbonate layer was associated with the zone of maximum sulphate reduction. It is postulated that extracellular polymeric substances and low molecular weight organic carbon produced at the surface (i.e. the cyanobacterial layer) of the mat bind calcium. Both aerobic and anaerobic heterotrophic microbes consume extracellular polymeric substances (each process accounting for approximately half of the total consumption) and low molecular weight organic carbon, liberating calcium and producing inorganic carbon. The combination of these geochemical changes can increase the carbonate saturation index, which may result in carbonate precipitation. In conclusion, the formation and degradation of extracellular polymeric substances, as well as sulphate reduction, may play a pivotal role in the formation of microbialites both in marine and hypersaline environments.

No abstract

Needle fibre calcite is one of the most ubiquitous habits of calcite in vadose environments (caves deposits, soil pores, etc.). Its origin, either through inorganic, indirect or direct biological processes, has long been debated. In this study, investigations at 11 sites in Europe, Africa and Central America support arguments for its biogenic origin. The wide range of needle morphologies is the result of a gradual evolution of the simplest type, a rod. This rod is the elementary brick which, by aggregation and welding, builds more complex needles. The absence of cross-welded needles implies that they are welded in a mould, or under a longitudinal and unidirectional constraint, before being released inside the soil pores. The difference between the lengthening of the needles and the c axis can be explained by the existence of needles observed under a scanning electron microscope in organic sleeves, which can act as a mould during rod growth. Complex morphologies with epitaxial outgrowths on straight rods cannot have grown entirely inside organic microtubes; they must result from soil diagenesis after the release of straight rods in a soil-free medium. Whisker crystals are interpreted as the result of growth and coalescence of euhedral crystals on a rod. Rhomb chains are considered to be the consequence of successive epitaxial growth steps on a needle during variations in growth conditions. Isotopic signatures for needle fibre calcite vary from )16AE63& to +1AE10& and from )8AE63& to )2AE25& for d 13 C and d 18 O, respectively. The absence of high d 18 O values for needle fibre calcite precludes a purely physicochemical origin (evaporative) for this particular habit of calcite. As epitaxial growth cannot precipitate in the same conditions as initial needles, needle fibre calcite stable isotopic signatures should be used with caution as a proxy for palaeoenvironmental reconstructions. In addition, it is suggested that the term needle fibre calcite should be kept for the original biogenic form. The other habit should be referred to as epitaxial forms of needle fibre calcite.