Graphitizing anthracene-based cokes and non-graphitizing saccharose-based chars were processed at temperatures from 450°C to 2900°C at ambient pressure. This offers a whole set of samples that ...greatly differ in structure. Here, their structural evolution was monitored by combining XRD and visible (green) Raman spectroscopy as well as, for the first time, near-infrared Raman and synchrotron-based C-XANES spectroscopies. These different techniques provide complementary information especially regarding the spatial resolution they achieved. However, despite its importance, the quantitative comparison between the structural parameters extracted from these techniques is difficult. Based on a new signal deconvolution procedure to extract quantitative structural information from C-XANES data and the achievement of a new dataset on a complete series of graphitization, the reliability and the precision of the information which can be retrieved from each technique are discussed. C-XANES spectroscopy appears to provide reliable proxies for the extent of aromatic layers of graphitic compounds and an empirical calibration is proposed.
Cyanobacteria have long been thought to induce the formation of Ca‐carbonates as secondary by‐products of their metabolic activity, by shifting the chemical composition of their extracellular ...environment to conditions favoring mineral precipitation. Some cyanobacterial species forming Ca‐carbonates intracellularly were recently discovered. However, the environmental conditions under which this intracellular biomineralization process can occur and the impact of cyanobacterial species forming Ca‐carbonates intracellularly on extracellular carbonatogenesis are not known. Here, we show that these cyanobacteria can form Ca‐carbonates intracellularly while growing in extracellular solutions undersaturated with respect to all Ca‐carbonate phases, that is, conditions thermodynamically unfavorable to mineral precipitation. This shows that intracellular Ca‐carbonate biomineralization is an active process; that is, it costs energy provided by the cells. The cost of energy may be due to the active accumulation of Ca intracellularly. Moreover, unlike cyanobacterial strains that have been usually considered before by studies on Ca‐carbonate biomineralization, cyanobacteria forming intracellular carbonates may slow down or hamper extracellular carbonatogenesis, by decreasing the saturation index of their extracellular solution following the buffering of the concentration of extracellular calcium to low levels.
The search for microfossils in the geological record has been a long-term challenge. Part of the problem comes from the difficulty of identifying such microfossils unambiguously, since they can be ...morphologically confused with abiotic biomorphs. One route to improve our ability to correctly identify microfossils involves studying fossilization processes affecting bacteria in modern settings. We studied the initial stages of fossilization of cyanobacterial cells in modern microbialites from Lake Alchichica (Mexico), a Mg-rich hyperalkaline crater lake (pH 8.9) hosting currently growing stromatolites composed of aragonite CaCO3 and hydromagnesite Mg5(CO3)4(OH)2 · 4(H2O). Most of the biomass associated with the microbialites is composed of cyanobacteria. Scanning electron microscopy analyses coupled with confocal laser scanning microscopy observations were conducted to co-localize cyanobacterial cells and associated minerals. These observations showed that cyanobacterial cells affiliated with the order Pleurocapsales become specifically encrusted within aragonite with an apparent preservation of cell morphology. Encrustation gradients from non-encrusted to totally encrusted cells spanning distances of a few hundred micrometers were observed. Cells exhibiting increased levels of encrustation along this gradient were studied down to the nm scale using a combination of focused ion beam (FIB) milling, transmission electron microscopy (TEM) and scanning transmission x-ray microscopy (STXM) at the C, O and N K-edges. Two different types of aragonite crystals were observed: one type was composed of needle-shaped nano-crystals growing outward from the cell body with a crystallographic orientation perpendicular to the cell wall, and another type was composed of larger crystals that progressively filled the cell interior. Exopolymeric substances (EPS), initially co-localized with the cells, decreased in concentration and dispersed away from the cells while crystal growth occurred. As encrustation developed, EPS progressively disappeared, but remaining EPS showed the same spectroscopic signature. In the most advanced stages of fossilization, only the textural organization of the two types of aragonite recorded the initial cell morphology and spatial distribution.
The fate of carbonates in the Earth's mantle plays a key role in the geodynamical carbon cycle. Although iron is a major component of the Earth's lower mantle, the stability of Fe‐bearing carbonates ...has rarely been studied. Here we present experimental results on the stability of Fe‐rich carbonates at pressures ranging from 40 to 105 GPa and temperatures of 1450–3600 K, corresponding to depths within the Earth's lower mantle of about 1000–2400 km. Samples of iron oxides and iron‐magnesium oxides were loaded into CO2 gas and laser heated in a diamond‐anvil cell. The nature of crystalline run products was determined in situ by X‐ray diffraction, and the recovered samples were studied by analytical transmission electron microscopy and scanning transmission X‐ray microscopy. We show that Fe(II) is systematically involved in redox reactions with CO2 yielding to Fe(III)‐bearing phases and diamonds. We also report a new Fe(III)‐bearing high‐pressure phase resulting from the transformation of FeCO3 at pressures exceeding 40 GPa. The presence of both diamonds and an oxidized C‐bearing phase suggests that oxidized and reduced forms of carbon might coexist in the deep mantle. Finally, the observed reactions potentially provide a new mechanism for diamond formation at great depth.
Key Points
Observation of a new high‐pressure phase
Redox state of carbon in the deep mantle
Microbial anaerobic Fe(II) oxidation at neutral pH produces poorly soluble Fe(III) which is expected to bind to cell surfaces causing cell encrustation and potentially impeding cell metabolism. The ...challenge for Fe(II)-oxidizing prokaryotes therefore is to avoid encrustation with Fe(III). Using different microscopic techniques we tracked Fe(III) minerals at the cell surface and within cells of phylogenetically distinct phototrophic and nitrate-reducing Fe(II)-oxidizing bacteria. While some strains successfully prevented encrustation others precipitated Fe(III) minerals at the cell surface and in the periplasm. Our results indicate differences in the cellular mechanisms of Fe(II) oxidation, transport of Fe(II)/Fe(III) ions, and Fe(III) mineral precipitation.
Iron‐oxidizing bacteria are important actors of the geochemical cycle of iron in modern environments and may have played a key role all over Earth’s history. However, in order to better assess that ...role on the modern and the past Earth, there is a need for better understanding the mechanisms of bacterial iron oxidation and for defining potential biosignatures to be looked for in the geologic record. In this study, we investigated experimentally and at the nanometre scale the mineralization of iron‐oxidizing bacteria with a combination of synchrotron‐based scanning transmission X‐ray microscopy (STXM), scanning transmission electron microscopy (STEM) and cryo‐transmission electron microscopy (cryo‐TEM). We show that the use of cryo‐TEM instead of conventional microscopy provides detailed information of the successive iron biomineralization stages in anaerobic nitrate‐reducing iron‐oxidizing bacteria. These results suggest the existence of preferential Fe‐binding and Fe‐oxidizing sites on the outer face of the plasma membrane leading to the nucleation and growth of Fe minerals within the periplasm of these cells that eventually become completely encrusted. In contrast, the septa of dividing cells remain nonmineralized. In addition, the use of cryo‐TEM offers a detailed view of the exceptional preservation of protein globules and the peptidoglycan within the Fe‐mineralized cell walls of these bacteria. These organic molecules and ultrastructural details might be protected from further degradation by entrapment in the mineral matrix down to the nanometre scale. This is discussed in the light of previous studies on the properties of Fe–organic interactions and more generally on the fossilization of mineral–organic assemblies.
Laser-induced breakdown spectroscopy (LIBS) and Raman spectroscopy are complementary techniques providing respectively chemical and structural information on the sample target. These techniques are ...increasingly used in Earth and Planetary sciences, and often together. LIBS is locally destructive for the target, and the laser-induced effects due to LIBS laser shots on the structure and on the Raman fingerprint of a set of geological samples relevant to Mars exploration are here investigated by Raman spectroscopy and electron microscopy. Experiments show that the structure of samples with low optical absorption coefficients is preserved as well as the structural information carried by Raman spectra. By contrast, minerals with high optical absorption coefficient can be severely affected by LIBS laser shots with local amorphization, melting and/or phase transformation. Thermal modeling shows that the temperature can reach several thousands of degrees at the surface for such samples during a LIBS laser shot, but decreases rapidly with time and in space. In 2020, NASA Mars 2020 mission will send a rover equiped with a combined LIBS/Raman instrument for remote analysis (SuperCam) as well as proximity science instruments at fine scale for X-ray fluorescence called PIXL for Planetary Instrument for X-ray Lithochemistry, and deep UV Raman spectroscopy called SHERLOC for Scanning Habitable Environments with Raman & Luminescence for Organics & Chemicals. We discuss the implications of our results for the operation of these instruments and show that (i) the SuperCam analytical footprint for Raman spectroscopy is many times larger than the LIBS crater, minimizing any effects and (ii) SHERLOC and PIXL analysis may be affected if they analyze within a LIBS crater created by SuperCam LIBS.
Display omitted
•Laser-induced heating during LIBS analysis depends on the sample optical properties.•Structure of transparent minerals is not affected by LIBS laser shots.•Opaque minerals can be severely affected by LIBS shots due to absorption.
Micrometer‐sized spherical and rod‐shaped forms have been reported in many phosphorites and often interpreted as microbes fossilized by apatite, based on their morphologic resemblance with modern ...bacteria inferred by scanning electron microscopy (SEM) observations. This interpretation supports models involving bacteria in the formation of phosphorites. Here, we studied a phosphatic coprolite of Paleocene age originating from the Ouled Abdoun phosphate basin (Morocco) down to the nanometer‐scale using focused ion beam milling, transmission electron microscopy (TEM), and scanning transmission x‐ray microscopy (STXM) coupled with x‐ray absorption near‐edge structure spectroscopy (XANES). The coprolite, exclusively composed of francolite (a carbonate‐fluroapatite), is formed by the accumulation of spherical objects, delimited by a thin envelope, and whose apparent diameters are between 0.5 and 3 μm. The envelope of the spheres is composed of a continuous crown dense to electrons, which measures 20–40 nm in thickness. It is surrounded by two thinner layers that are more porous and transparent to electrons and enriched in organic carbon. The observed spherical objects are very similar with bacteria encrusting in hydroxyapatite as observed in laboratory experiments. We suggest that they are Gram‐negative bacteria fossilized by francolite, the precipitation of which started within the periplasm of the cells. We discuss the role of bacteria in the fossilization mechanism and propose that they could have played an active role in the formation of francolite. This study shows that ancient phosphorites can contain fossil biological subcellular structures as fine as a bacterial periplasm. Moreover, we demonstrate that while morphological information provided by SEM analyses is valuable, the use of additional nanoscale analyses is a powerful approach to help inferring the biogenicity of biomorphs found in phosphorites. A more systematic use of this approach could considerably improve our knowledge and understanding of the microfossils present in the geological record.
In phosphate-rich environments, vivianite (FeII₃(PO₄)₂, 8H₂O) is an important sink for dissolved Fe(II) and is considered as a very stable mineral due to its low solubility at neutral pH. In the ...present study, we report the mineralogical transformation of vivianite in cultures of the nitrate-reducing iron-oxidizing bacterial strain BoFeN1 in the presence of dissolved Fe(II). Vivianite was first transformed into a greenish phase consisting mostly of an amorphous mixed valence Fe-phosphate. This precipitate became progressively orange and the final product of iron oxidation consisted of an amorphous Fe(III)-phosphate. The sub-micrometer analysis by scanning transmission X-ray microscopy of the iron redox state in samples collected at different stages of the culture indicated that iron was progressively oxidized at the contact of the bacteria and at a distance from the cells in extracellular minerals. Iron oxidation in the extracellular minerals was delayed by a few days compared with cell-associated Fe-minerals. This led to strong differences of Fe redox in between these two types of minerals and finally to local heterogeneities of redox within the sample. In the absence of dissolved Fe(II), vivianite was not significantly transformed by BoFeN1. Whereas Fe(II) oxidation at the cell contact is most probably directly catalyzed by the bacteria, vivianite transformation at a distance from the cells might result from oxidation by nitrite. In addition, processes leading to the export of Fe(III) from bacterial oxidation sites to extracellular minerals are discussed including some involving colloids observed by cryo-transmission electron microscopy in the culture medium.
PDF
