Defining organominerals: Comment on ‘Defining biominerals and organominerals: Direct and indirect indicators of life’ by Perry et al. (2007, Sedimentary Geology, 201, 157–179)

The 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.     

Structural features of humic acids from a sedimentary sequence in the Guadiana estuary (Portugal–Spain border)

The structural characteristics of humic acids (HAs) from two different depths of a sedimentary sequence representing the last 13 kyr in the valley of Guadiana river estuary (SW Portugal/Spain border) have been approached using a combination of spectroscopic techniques, wet chemical degradation methods (sequential oxidation with sodium persulfate followed by KMnO₄, and oxidation with RuO₄) and analytical pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) in the presence and absence of tetramethylammonium hydroxyde (TMAH). The aim was to obtain complementary information on the sources and alteration of the organic matter (OM) provided by a previous study on the vertical distribution of terrestrial and phytoplankton biogeochemical markers in the sequence. Both the FT-IR (Fourier transformed infrared) and ¹³C NMR (nuclear magnetic resonance) spectra showed a close similarity with the structural characteristics of the HA samples. NMR signals in the alkyl region (0–45 ppm) as well as FT-IR band patterns typical for methoxyl-substituted aromatic rings pointed to the presence of an important aliphatic domain, as well as to lignin-derived compounds. This finding was confirmed using analytical pyrolysis. In addition, the main TMAH thermochemolysis products were typical lignin-derived methoxyphenols with both guaicyl and syringyl nuclei. The detection of methoxyphenol units with three to six carbon atom (C₃–C₆) side chains suggests that lignin and possibly suberin were only partially degraded. Compounds arising from proteins and polysaccharides were also detected, although in lesser and varying amount. The major products from persulfate oxidation were series of n-alkanes (C₁₆–C₃₃ with clear odd/even predominance) and n-fatty acids, both saturated (C₁₀–C₂₆ with strong even/odd predominance) and unsaturated, which may arise from the above aliphatic biomacromolecules. The major products from permanganate oxidation of the persulfate residue were α,ω-diacids (C₆–C₁₁) originating from oxidation of the ether bonds linking the building blocks constituting the core of the HA structure. Aromatic compounds (phenols, methoxy-dimethoxybenzene carboxylic acid and benzene di-, tri-, tetra- and pentacarboxylic acids), most probably derived from the aromatic backbone of the HAs, that may also include lignin moieties as well as other polyphenols (flavonoids and tannins) were also detected. The RuO₄ oxidation also released series of n-alkanes (C₁₆–C₃₃), linear saturated fatty acids (C₁₀–C₂₈) and α,ω-diacids (C₇–C₂₅), as well as traces of benzene polycarboxylic acids. Regarding the usefulness of the various techniques used, they provide complementary information. Indeed, spectroscopic techniques and analytical pyrolysis provide information on the backbone of the HAs, and on their origin, whereas the oxidative degradations provide different information on the structural features of the HA, particularly the nature of the linking between the building blocks. In general, the data support the idea that the HAs still contain information about the signature of aliphatic and aromatic biomacromolecules contributing to the OM deposited. The presence of lignin-derived residues suggests a large input from terrestrial carbon throughout the core.     

Isolation,biodegradation ability and molecular detection of hydrocarbon degrading bacteria in petroleum samples from a Brazilian offshore basin

The detection of microorganisms with potential for biodeterioration and biodegradation in petroleum fields is of great relevance, since these organisms may be related to a decrease in petroleum quality in the reservoirs or damage in the production facilities. In this sense, petroleum formation water and oil samples were collected from the Campos Basin, Brazil, with the aim of isolating microorganisms and evaluating their ability to degrade distinct classes of hydrocarbon biomarkers (9,10-dihydrophenanthrene, phytane, nonadecanoic acid and 5α-cholestane). Twenty eight bacterial isolates were recovered and identified by sequencing their 16S rRNA genes. Biodegradation assays revealed that bacterial metabolism of hydrocarbons occurred through reactions based on oxidation, carbon–carbon bond cleavage and generation of new bonds or by the physical incorporation of hydrocarbons into microbial cell walls. Based on the biodegradation results, selective PCR-based systems were developed for direct detection in petroleum samples of bacterial groups of interest, namely Bacillus spp., Micrococcus spp., Achromobacter xylosoxidans, Dietzia spp. and Bacillus pumilus. Primer sets targeting 16S rRNA genes were designed and their specificity was confirmed in silico (i.e. computational analysis) and in PCR reactions using DNA from reference strains as positive and negative controls. Total DNA from oil was purified and the amplification tests revealed the presence of the target bacteria in the samples, unraveling a significant potential for petroleum deterioration in the reservoirs sampled, once proper conditions are present for hydrocarbon degradation. The application of molecular methods for rapid detection of specific microorganisms in environmental samples would be valuable as a supporting tool for the evaluation of oil quality in production reservoirs.     

Constraints on the application of the MBT/CBT palaeothermometer at high latitude environments (Svalbard,Norway)

Branched glycerol dialkyl glycerol tetraethers (GDGTs) are membrane lipids of unknown bacteria that are ubiquitous in soil and peat. Two indices based on the distribution of these lipids in soils, the Cyclization of Branched Tetraethers (CBT) and the Methylation of Branched Tetraethers (MBT) indices have been shown to correlate with soil pH, and mean annual air temperature (MAT) and soil pH, respectively, and can be used to reconstruct MAT in palaeoenvironments. To verify the extent to which branched GDGTs in marine sediments reflect the distribution pattern on land and whether these proxies are applicable for palaeoclimate reconstruction in high latitude environments with a MAT of <0 °C, we compared the branched GDGT distribution in Svalbard soils and nearby fjord sediments. Although branched GDGT concentrations in the soil are relatively low (0.02–0.95 μg/g dry weight (dw)) because of the cold climate and the short growing season, reconstructed MATs based on the MBT/CBT proxy are ca. ?4 °C, close to the measured MAT (ca. ?6 °C). Concentrations of branched GDGTs (0.01–0.20 μg/g dw) in fjord sediments increased towards the open ocean and the distribution was strikingly different from that in soil, i.e. dominated by GDGTs with one cyclopentane moiety. This resulted in MBT/CBT-reconstructed MAT values of 11–19 °C, well above measured MAT. The results suggest that at least part of the branched GDGTs in marine sediments in settings with a low soil organic matter (OM) input may be produced in situ. In these cases, the application of the MBT/CBT palaeothermometer will generate unrealistic MAT reconstructions. The MBT/CBT proxy should therefore only be used at sites with a substantial input of soil OM relative to the amount of marine OM, i.e. at sites close to the mouth of rivers with a catchment area where sufficient soil formation takes place and the soil thus contains substantial amounts of branched GDGTs.     

Fifty years of organisational change in container shipping: regional shift and the role of family firms

Spectacular growth has marked the industry initiated by Malcolm McLean with the sailing of the Ideal-X in 1956. While the growth of container shipping has been typically seen in terms of technological advances, increasing vessel capacity, traffic growth, financial performance and competitiveness, it has been shaped also by organisational transformations. This paper provides an overview of the major companies that make up the container shipping industry, tracing the rapid adoption of containerisation by American carriers to its diffusion to Europe and then Asia. While several carriers belong to business conglomerates, the most dynamic in recent years have been those that are those that possess a family structure. About 12 of the present top 20 carriers are largely family controlled, including 4 out of the top 5. Unlike other capital intensive industries, where the power has shifted towards corporate governance, the container shipping industry retains a strong individualistic entrepreneurial character. At a time when North American ownership in container shipping is no more, the spirit of innovation began 50 years ago by an American visionary is still evident in the entrepreneurial dynamism of many of the industry leaders.     

Peierls dislocation modelling in perovskite (CaTiO<Subscript>3</Subscript>): comparison with tausonite (SrTiO<Subscript>3</Subscript>) and MgSiO<Subscript>3</Subscript> perovskite

We present here a numerical modelling study of dislocations in perovskite CaTiO₃. The dislocation core structures and properties are calculated through the Peierls–Nabarro model using the generalized stacking fault (GSF) results as a starting model. The GSF are determined from first-principles calculations using the VASP code. The dislocation properties such as collinear, planar core spreading and Peierls stresses are determined for the following slip systems: [100](010), [100](001), [010](100), [010](001), [001](100), [001](010), and All dislocations exhibit lattice friction, but glide appears to be easier for [100](010) and [010](100). [001](010) and [001](100) exhibit collinear dissociation. Comparing Peierls stresses among tausonite (SrTiO₃), perovskite (CaTiO₃) and MgSiO₃ perovskite demonstrates the strong influence of orthorhombic distortions on lattice friction. However, and despite some quantitative differences, CaTiO₃ appears to be a satisfactory analogue material for MgSiO₃ perovskite as far as dislocation glide is concerned.     

Stress Measurement by Overcoring at Shallow Depths in a Rock Slope: the Scattering of Input Data and Results

This paper describes a field experiment of stress measurement using the overcoring method performed in a rock slope, called Rochers de Valabres (located in France’s Southern Alps Region), a field laboratory site prone to rockfalls. Six measurements were conducted at shallow depths from the surface, moving deeper along a sub-horizontal borehole. The experiment was conducted in heterogeneous and anisotropic gneiss, with the overcored rock elastic properties, as evaluated by biaxial and uniaxial tests, being widely scattered. Since stress calculations are sensitive to all input data uncertainties, strain inversion was, thus, performed using an experimental device and Monte Carlo simulations. The experimental device allows the assessment of rather broad confidence intervals for both stress magnitude and orientation. The results indicate that the stress state in the surface area is quite heterogeneous and may be correlated with topography. The measurements show a nonlinear stress distribution with distance to the free surface, along with high values of principal stresses, despite the vicinity of the surface. Although influenced by local topography, orientations of the principal computed stresses are characterized by a high turnover due to local heterogeneities. The results are roughly in accordance to a 2D finite element model of the site.     

Line-of-Sight Observables Algorithms for the <Emphasis Type="Italic">Helioseismic and Magnetic Imager</Emphasis> (HMI) Instrument Tested with <Emphasis Type="Italic">Interferometric Bidimensional Spectrometer</Emphasis> (IBIS) Observations

The Helioseismic and Magnetic Imager (HMI) instrument onboard the Solar Dynamics Observatory produces line-of-sight (LOS) observables (Doppler velocity, magnetic-field strength, Fe i line width, line depth, and continuum intensity) as well as vector magnetic-field maps at the solar surface. The accuracy of LOS observables is dependent on the algorithm used to translate a sequence of HMI filtergrams into the corresponding observables. Using one hour of high-cadence imaging spectropolarimetric observations of a sunspot in the Fe i line at 6173 Å through the Interferometric Bidimensional Spectrometer installed at the Dunn Solar Telescope, and the Milne–Eddington inversion of the corresponding Stokes vectors, we test the accuracy of the observables algorithm currently implemented in the HMI data-analysis pipeline: the MDI-like algorithm. In an attempt to improve the accuracy of HMI observables, we also compare this algorithm to others that may be implemented in the future: a least-squares fit with a Gaussian profile, a least-squares fit with a Voigt profile, and the use of second Fourier coefficients in the MDI-like algorithm.     

Numerical Simulation of a Solar Active Region. I: Bastille Day Flare

We present three-dimensional unsteady modeling and numerical simulations of a coronal active region, carried out within the compressible single-fluid MHD approximation. We focus on AR 9077 on 14 July 2000, and the triggering of the X5.7 GOES X-ray class “Bastille Day” flare. We simulate only the lower corona, although we include a virtual photosphere and chromosphere below. The boundary conditions at the base of this layer are set using temperature maps from line intensities and line-of-sight magnetograms (SOHO/MDI). From the latter, we generate vector magnetograms using the force-free approximation; these vector magnetograms are then used to produce the boundary condition on the velocity field using a minimum energy principle (Longcope, Astrophys. J. 612, 1181, 2004). The reconnection process is modeled through a dynamical hyper-resistivity which is activated when the current exceeds a critical value (Klimas et al., J. Geophys. Res. 109, 2218, 2004). Comparing the time series of X-ray fluxes recorded by GOES with modeled time series of various mean physical variables such as current density, Poynting energy flux, or radiative loss inside the active region, we can demonstrate that the model properly captures the evolution of an active region over a day and, in particular, is able to explain the initiation of the flare at the observed time.