Automicrites in modern cyanobacterial stromatolitic deposits of Rangiroa, Tuamotu Archipelago, French Polynesia: Biochemical parameters underlaying their formation

This paper provides evidence of the role of the proteinaceous constituents of the sedimentary organic matter in the control of (Ca, Mg) carbonate precipitation within recent stromatolitic sediments belonging to the kopara-type (Rangiroa, Tuamotu Archipelago, French Polynesia). Millimeter- to cm-thick alternating carbonate-rich and carbonate-poor layers allow the separation by hand of these two contrasted types of layers (with respect to carbonate content). The study aims, (1) to decipher the potential compartments (cyanobacterially derived and dissolved organic matter) for proteins that interact with divalent cations, to compare their biochemical composition with those of the intramineral organic matrices that incorporate fine authigenic micrites when they form; (2) to discriminate the ageing processes of organic matter, including OM mineralized by CaCO3; (3) to correlate the biochemical features of protein-rich molecules dissolved in natural pore waters, extracted from different sediment layers (either carbonate-rich or carbonate-poor), with experimental tests of the efficiency of these same protein-rich molecules in the role of calcium carbonate inhibitors. The extracted natural macromolecules definitely control the rate of in vitro calcium carbonate precipitation: they exert an inhibiting effect, which strength depends on the type of layer–carbonate-rich or carbonate-poor–out of which they have been extracted. The quality (with respect to their aspartic and/or glutamic acid contents), as well as the amount of soluble protein-rich macromolecules present in the pore waters in each layer, plays a key role in active calcification processes. As a matter of fact, pore waters of carbonate-poor layers deliver high concentrations of dissolved, aspartic-rich macromolecules that are shown to inhibit strongly calcium carbonate precipitation in experimental conditions. The consequence of such experimentally based results, as well as the correlation with the actual intensity of calcification in natural sediment layers, is crucial for discussing calcium carbonate balance or the formation of laminations in paleoenvironments

Reply to “Reply to comments on defining biominerals and organominerals: Direct and indirect indicators of life [Perry et al., Sedimentary Geology, 201, 157–179]” by R.S. Perry and M.A. Sephton: [Sedimentary Geology 213 (2009) 156]

International audienceThis is a reply to R.S. Perry and M.A. Sephton's “Reply to comments on defining biominerals and organominerals: direct and indirect indicators of life [Perry et al., Sedimentary Geology, 201, 157–179]” [Sedimentary Geology 213 (2009) 156]

Syndepositional cements associated with nannofossils in the Marmolada Massif: Evidences of microbially mediated primary marine cements? (Middle Triassic, Dolomites, Italy)

The Marmolada platform is characterized by striking globose masses (“evinosponges”), arranged in concentric bands, of fibrous calcite cements ranging in size from centimeters to several decimeters. The lithogenetic importance of these peculiar cements has been recognized in many Middle Triassic buildups of the Western Tethys. EDS microanalyses revealed that these fibrous cements contain 1–3 mol% of Mg and detectable amounts of Sr, over 1000 ppm, sometimes exceeding 10,000 ppm. The strontium geochemical signature in neomorphic calcite could reflect the replacement of an aragonitic carbonate precursor. The boundaries between the fibrous calcite bands are marked by alignments of microcrystalline aggregates of fluorapatite and/or dolomite. The presence of fluorapatite may indicate a depositional microenvironment eutrophic or rich in microbial communities. Epifluorescence analyses showed bright bands alternated to dark ones, confirming that organic matter remains occur within the studied cements and could have played a significant role in supporting the widespread syndepositional cementation. High magnification SEM observations on bright epifluorescent bands showed the presence of widespread, more or less spherical bodies ranging in size 100–300 nm. These bodies could represent the relicts of nannobacterial cells

Defining organominerals: Comment on ‘Defining biominerals and organominerals: Direct and indirect indicators of life' by Perry et al.

International audienceThe paper by Perry et al. (2007, Defining biominerals and organominerals: Direct and indirect indicators of life, Sedimentary Geology, 201, 157-179) proposes to introduce “the new term ‘organomineral'” to describe mineral products whose formation is induced by by-products of biological activity, dead and decaying organisms, or nonbiological organic compounds, to be distinguished from the biomineral components of living organisms. The substantive ‘organomineral', however, is not new: it was first introduced in 1993, with basically the same definition and distinction from biominerals, at the 7th International Symposium on Biomineralization (Défarge and Trichet, 1995, From biominerals to ‘organominerals': The example of the modern lacustrine calcareous stromatolites from Polynesian atolls, Bulletin de l'Institut Océanographique de Monaco, n° spéc. 14, vol. 2, pp. 265-271). Thereafter, more than twenty-five papers by various authors have been devoted to organominerals and organomineral formation (‘organomineralization') processes. Only two of these papers are cited by Perry et al., and without any reference to the definitions, or even the terms ‘organomineral' or ‘organomineralization', which they included. Moreover, Perry et al. tend to enlarge the original concept of organomineral to encompass all minerals containing organic matter, whether these organic compounds are active or passive in the mineralization, which introduces ambiguities detrimental to a fine understanding of present and past geobiological processes. Finally, Perry et al. propose to consider organominerals as indirect biosignatures that could be used in the search for evidence of life in the geological record and extraterrestrial bodies. This latter proposition also is problematical, in that organominerals may be formed in association with prebiotic or abiotic organic matter

Dynamic of dissolved organic matter and trace elements in a steady state lake bottom layer : molecular size fractionation.

International audienceDissolved organic matter (DOM) in aquatic systems interacts with most processes including redox reactions, trace elements complexation, sorption and sedimentation. The complex nature of DOM in natural waters suggests that all the fractions constituting it do not contribute in the same way to its reactivity. The total stock of DOM can be split by various means like the difference in size of the molecules or the difference in affinity for adsorbent phases. The deep and stable layers of meromictic lakes are of a particular interest for the study of the mechanisms controlling the behaviour of chemical elements in natural systems. Quasi stationary conditions unroll and stratify the processes through a certain thickness of the water column. In the deep layer of the lake Pavin (Massif-Central, France), solutes dispersing from the water-sediment interface (92 meter depth) cross a succession of levels characterized by different physicochemical and microbiological conditions (redox conditions, interactions with neoformed or settling particles, bacterial metabolic types) before to reach the oxic layer around 60 meter depth (Viollier et al., 1995, 1997, Lehours et al., 2003)

Molecular fossils and other organic markers as palaeoenvironmental indicators of the Messinian Calcare di Base Formation: normal versus stressed marine deposition (Rossano Basin, northern Calabria, Italy)

A multidisciplinary study has been carried out on the Late Miocene (Messinian) Calcare di Base Formation in northern Calabria, Italy, with the aim of understanding the depositional conditions of these enigmatic carbonate sediments that have been interpreted as evaporitic or diagenetic limestone. The research has been developed through sedimentological (microfacies), organic petrography and geochemical analyses (palynofacies, Rock-Eval pyrolysis and gas chromatography/mass spectrometry). The carbonates studied preserve their original mineralogy (aragonite) and microstructure. The prevailing microfacies consists of clotted peloidal micrite with antigravitative fabric. Larger and darker cylindrical–subcylindrical micritic grains, attributable to faecal pellets, are more or less randomly dispersed in the peloidal micrite. The faecal pellets have been ascribed to copepods because zooclasts of these arthropods were observed in the palynofacies. Bright epifluorescence characterizes the faecal pellets and peloidal micrite, indicating their high content of organic matter. Detrital and stromatolitic microfacies occur rarely (around a few percent). The detrital microfacies is characterized by silt-sized grains organized in thin, sometimes bioturbated, graded laminae. The stromatolitic microfacies shows planar to gently curved/wrinkled laminae organized in dark and light couplets. The associated sedimentary organic matter shows low maturity, and preserves the original signatures of the source organisms. Rock-Eval pyrolysis revealed a transitional composition between Type II and Type III kerogen, suggesting a mixture of marine and terrigenous organic matter input. The molecular biogeochemical data indicate three main biological signatures: algae, bacteria and higher plants. Organic markers together with sedimentary evidence indicate a marine depositional scenario influenced by freshwater input rather than evaporitic concentration. We conclude that the most probable bacterial process involved in carbonate precipitation of the Calcare di Base, considering the freshwater input and consequent probable enrichment in organic matter and Ca2+ ions, is ammonification of amino-acids in aerobic conditions

Electron Paramagnetic Resonance Study of a Photosynthetic Microbial Mat and Comparison with Archean Cherts

International audienceOrganic radicals in artificially carbonized biomass dominated by oxygenic and non-oxygenic photosynthetic bacteria, Microcoleus chthonoplastes-like and Chloroflexus-like bacteria respectively, were studied by Electron Paramagnetic Resonance (EPR) spectroscopy. The two bacteria species were sampled in mats from a hypersaline lake. They underwent accelerated ageing by cumulative thermal treatments to induce progressive carbonization of the biological material, mimicking the natural maturation of carbonaceous material of Archean age. For thermal treatments at temperatures higher than 620 °C, a drastic increase in the EPR linewidth is observed in the carbonaceous matter from oxygenic photosynthetic bacteria and not anoxygenic photosynthetic bacteria. This selective EPR linewidth broadening reflects the presence of a catalytic element inducing formation of radical aggregates, without affecting the molecular structure or the microstructure of the organic matter, as shown by Raman spectroscopy and Transmission Electron Microscopy. For comparison, we carried out an EPR study of organic radicals in silicified carbonaceous rocks (cherts) from various localities, of different ages (0.42 to 3.5 Gyr) and having undergone various degrees of metamorphism, i.e. various degrees of natural carbonization. EPR linewidth dispersion for the most primitive samples was quite significant, pointing to a selective dipolar broadening similar to that observed for carbonized bacteria. This surprising result merits further evaluation in the light of its potential use as a marker of past bacterial metabolisms, in particular oxygenic photosynthesis, in Archean cherts

Mécanismes de précipitation de carbonate de calcium dans les biofilms photosynthétiques

La précipitation de carbonate de calcium dans les systèmes benthiques est souvent associée aux biofilms photosynthétiques, et notamment observée au sein de structures d'une grande complexité morphologique comme les tapis microbiens, les stromatolithes et les microbialithes. Cette biocalcification modifie les flux de CO2, de calcium et d'alcalinité dans les hydrosystèmes (séquestration du carbone inorganique et d'alcalinité). Ce processus paraît donc très sensible aux impacts anthropiques, e.g. la perturbation globale du cycle du carbone et les contaminations atmosphériques. Son étude revêt une importance capitale pour la compréhension des paléoenvironnements. Différentes hypothèses ont été avancées pour expliquer la biocalcification dans ces biofilms. L'activité photosynthétique des cyanobactéries est souvent mise en cause, mais ce mécanisme est parfois contesté, privilégiant l'activité métabolique des bactéries organohétérotrophes, e.g. les bactéries sulfato-réductrices, qui sont associées aux micro-organismes phototrophes dans les biofilms La calcification peut aussi être contrôlée directement par l'interaction du calcium avec la matière organique, notamment les polymères extracellulaires sécrétés par les microorganismes (EPS) ou les fractions macromoléculaires riches en acides aspartique et glutamique de la matière organique dissoute (MOD)

Characterization and mobility of arsenic and heavy metalsinsoils polluted by the destruction of arsenic-containingshells from the Great War

International audienceDestruction of chemical munitions from World War I has caused extensive local top soil contamination by arsenic and heavy metals. The biogeochemical behavior of toxic elements is poorly documented in this type of environment. Four soils were sampled presenting different levels of contamination. The range of As concentrations in the samples was 1937–72,820 mg/kg. Concentrations of Zn, Cu and Pb reached 90,190 mg/kg, 9113 mg/kg and 5777 mg/kg, respectively. The high clay content of the subsoil and large amounts of charcoal from the use of firewood during the burning process constitute an ample reservoir of metals and As-binding materials. However, SEM–EDS observations showed different forms of association for metals and As. In metal-rich grains, several phases were identified: crystalline phases, where arsenate secondary minerals were detected, and an amorphous phase rich in Fe, Zn, Cu, and As. The secondary arsenate minerals, identified by XRD, were adamite and olivenite (zinc and copper arsenates, respectively) and two pharmacosiderites. The amorphous material was the principal carrier of As and metals in the central part of the site. This singular mineral assemblage probably resulted from the heat treatment of arsenic-containing shells. Microbial characterization included total cell counts, respiration, and determination of As(III)-oxidizing activities. Results showed the presence of microorganisms actively contributing to metabolism of carbon and arsenic, even in the most polluted soil, thereby influencing the fate of bioavailable As on the site. However, the mobility of As correlated mainly with the availability of iron sinks

How to assess cutover Peatland regeneration with combined organic matter indicators ?

International audienceWhen restored, cutover peatlands can favour biodiversity and carbon (C) sequestration. Within the EU program RECIPE, we aimed to identify combinations of site physico-chemical conditions, vegetation composition and below-ground microbiological characteristics that are beneficial to the long-term biodiversity and C sink function regeneration. To unreveal these characteristics, we assessed the bioindicator value of peat organic matter (OM) physico-chemistry from cutover peatlands at various stages of regeneration. Although OM continues to reflect disturbances in the catotelm deep peat, we show that along the chronosequence the regenerated peat tends to be biochemically and physically similar to the one from the non exploited area of the same site. The combination of several indicators provides an efficient assessment of ecological conditions and makes valuable for the management of cutover peatlands