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The soil water release characteristic is controlled by the soil pores and so alteration of the pore system will have an effect. We sought to examine the effects of various pore deformations in a range of arable and grassland soils from the UK. Sieved topsoil materials were compressed to 50 or 200 kPa, or remolded to simulate shear deformation at the plastic limit. They were then subjected to matric potentials from 0 to-1500 kPa using conventional tension and pressure plate apparatus. Volume changes were monitored to assess shrinkage. Further samples in the compressed state were subjected to x-ray computed tomography scanning to nondestructively characterize the soil pore system. Increasing the compression from 50 to 200 kPa mainly affected the >30-[micro]m pores, changing a dual porous system of inter-and intraaggregate pores to one mainly dominated by intraaggregate pores, as confirmed by gravimetric water release characteristic data and the scans. Shear-deformed soils retained more water than the compressed soil and shrank more, such that they remained tension saturated at low (negative) matric potentials. We developed a function to predict the soil saturation state as a function of matric potential and porosity. This explained 28 to 63% of the variance, irrespective of the initial structural state, but up to 94% of the variation when one of the fitted parameters was allowed to vary for the different initial states. This was sufficiently systematic to suggest that a general model of the effects of soil deformation and shrinkage on the water release characteristic may be possible. doi: 10.2136/sssa12009.0278

To understand the hydraulic properties of soils, accurate prediction of the unsaturated hydraulic conductivity is needed, which is commonly derived from the soil water release characteristic. In fine-textured soils, the modified Mualem--van Genuchten (MMVG) function has been used extensively to predict the change in relative conductivity with changes in matric potential, but this assumes that the soil is rigid with a constant porosity (CP), which is unrealistic for shrinking soils. We used a triaxial cell apparatus to accurately monitor soil volume changes during water release in a clay soil. From this we derived relative hydraulic conductivity functions based on either MMVG (CP), or based on geometrically similar shrinkage (GSS) of all pore sizes by a constant factor as calculated from the measured shrinking porosity (SP). The MMVG (CP) function predicted a decline in relative conductivity of up to three orders of magnitude from 0 to -400 kPa matric potential. This was similar to published data on the response of conductivity in the same soil to consolidation of larger pores. Based on SP, however, the soil remained effectively tension saturated (>0.97) down to a matric potential of -85 kPa due to normal shrinkage. The corresponding GSS (SP) function predicted only a modest decrease in relative conductivity from 1 to 0.85 across this range. In this case the larger pores, although reduced in size, are assumed to be still water filled and conducting. The GSS function was probably the most realistic portrayal of hydraulic functioning in a tension-saturated shrinking clay soil. doi: 10.2136/sssaj2009.0356

Rationale: Isotopic signatures of N2O can help distinguish between two sources (fertiliser N or endogenous soil N) of N2O emissions. The contribution of each source to N2O emissions after N‐application is difficult to determine. Here, isotopologue signatures of emitted N2O are used in an improved isotopic model based on Rayleigh‐type equations. Methods: The effects of a partial (33% of surface area, treatment 1c) or total (100% of surface area, treatment 3c) dispersal of N and C on gaseous emissions from denitrification were measured in a laboratory incubation system (DENIS) allowing simultaneous measurements of NO, N2O, N2 and CO2 over a 12‐day incubation period. To determine the source of N2O emissions those results were combined with both the isotope ratio mass spectrometry analysis of the isotopocules of emitted N2O and those from the 15N‐tracing technique. Results: The spatial dispersal of N and C significantly affected the quantity, but not the timing, of gas fluxes. Cumulative emissions are larger for treatment 3c than treatment 1c. The 15N‐enrichment analysis shows that initially ~70% of the emitted N2O derived from the applied amendment followed by a constant decrease. The decrease in contribution of the fertiliser N‐pool after an initial increase is sooner and larger for treatment 1c. The Rayleigh‐type model applied to N2O isotopocules data (δ15Nbulk‐N2O values) shows poor agreement with the measurements for the original one‐pool model for treatment 1c; the two‐pool models gives better results when using a third‐order polynomial equation. In contrast, in treatment 3c little difference is observed between the two modelling approaches. Conclusions: The importance of N2O emissions from different N‐pools in soil for the interpretation of N2O isotopocules data was demonstrated using a Rayleigh‐type model. Earlier statements concerning exponential increase in native soil nitrate pool activity highlighted in previous studies should be replaced with a polynomial increase with dependency on both N‐pool sizes. [ABSTRACT FROM AUTHOR]

RATIONALE This study aimed (i) to determine the isotopic fractionation factors associated with N2O production and reduction during soil denitrification and (ii) to help specify the factors controlling the magnitude of the isotope effects. For the first time the isotope effects of denitrification were determined in an experiment under oxic atmosphere and using a novel approach where N2O production and reduction occurred simultaneously. METHODS Soil incubations were performed under a He/O2 atmosphere and the denitrification product ratio [N2O/(N2 + N2O)] was determined by direct measurement of N2 and N2O fluxes. N2O isotopocules were analyzed by mass spectrometry to determine δ18O, δ15N and 15 N site preference within the linear N2O molecule (SP). An isotopic model was applied for the simultaneous determination of net isotope effects (η) of both N2O production and reduction, taking into account emissions from two distinct soil pools. RESULTS A clear relationship was observed between 15 N and 18O isotope effects during N2O production and denitrification rates. For N2O reduction, diverse isotope effects were observed for the two distinct soil pools characterized by different product ratios. For moderate product ratios (from 0.1 to 1.0) the range of isotope effects given by previous studies was confirmed and refined, whereas for very low product ratios (below 0.1) the net isotope effects were much smaller. CONCLUSIONS The fractionation factors associated with denitrification, determined under oxic incubation, are similar to the factors previously determined under anoxic conditions, hence potentially applicable for field studies. However, it was shown that the η18O/η15N ratios, previously accepted as typical for N2O reduction processes (i.e., higher than 2), are not valid for all conditions. Copyright © 2014 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

In nuclear graphite, the wide range of void sizes precludes a full characterisation of pore volume by means of a single technique. A novel multi-technique approach, consisting of pycnometry, low pressure gas adsorption and mercury porosimetry is presented. The approach is validated for two nuclear-grade graphites designed for use in Generation IV nuclear reactors, namely IG-110 and IG-430. Damage and deformation caused to the structure of the graphite by mercury intrusion is estimated by consecutive intrusion experiments. The damage is assumed to be caused by the highest applied pressures of mercury. It is compensated by substituting that part of the percolation curve with one derived from adsorption measurements. The various measurements are inverse modelled in a way which intelligently bridges the size gap between the techniques. The resulting complete non-hierarchical pore structure covers sizes spanning 4 orders of magnitude. The new approach resolves the long standing issues associated with performing porosimetry on graphitic samples, and fills the gap in knowledge for the assessment of multilevel porosity within graphite. As an example of the possible applications of the resulting void network structure, we calculated the air network flow capacity, related to absolute permeability, for the two graphite samples. [ABSTRACT FROM AUTHOR]

Presents the Molecular Dynamics Simulator, a computer software package that provides a display of molecular motion in a solid, liquid or gas. Calculation processing; Molecular motion displays as tracks or as spheres.

Agricultural soils are a major source of nitric oxide (NO) and nitrous oxide (N 2 O), which are produced and consumed by biotic and abiotic soil processes. The dominant sources of NO and N 2 O are microbial nitrification and denitrification. While N 2 O emissions have been attributed to both processes, depending on the environmental conditions such as substrate availability, pH and water filled pore space (WFPS), NO emissions are thought to predominantly derive from nitrification. Although attributing gaseous emissions to specific processes is still difficult, recent findings challenge the latter of those assumptions. Using the gas-flow-soil-core method, i.e soil cores incubated under a He/O 2 atmosphere at constant surface gas flow, combined with 15 N labelled isotopic techniques, the present study investigated the role of denitrification on NO, N 2 O and N 2 emissions in a UK grassland soil under high soil moisture and an aerobic headspace atmosphere. With the application of KNO3 and glucose to support denitrification, denitrification was the source of N loss of between 0.61 and 0.67% of the added N via NO emissions, 1.60–1.68% via N 2 O and 0.03–0.05% via N 2 emissions. Overall, our study showed that denitrification has been overlooked as a source of NO emissions. [ABSTRACT FROM AUTHOR]

Although the Park Grass Experiment is an important international reference soil for temperate grasslands, it still lacks the direct extraction of its metaproteome. The identification of these proteins can be crucial to our understanding of soil ecology and major biogeochemical processes. However, the extraction of protein from soil is a technically fraught process due to difficulties with co-extraction of humic material and lack of compatible databases to identify proteins. To address these issues, we combined two protein extraction techniques on Park Grass experiment soil, one based on humic acid removal, namely a modified freeze-dry, heat/thaw/phenol/chloroform (HTPC) method and another which co-extracts humic material, namely an established surfactant method. A broad range of proteins were identified by matching the mass spectra of extracted soil proteins against a tailored Park Grass proteome database. These were mainly in the categories of "protein metabolism", "membrane transport", "carbohydrate metabolism", "respiration" "ribosomal and nitrogen cycle" proteins, enabling reconstitution of specific processes in grassland soil. Protein annotation using NCBI and EBI databases inferred that the Park Grass soil is dominated by Proteobacteria , Actinobacteria , Acidobacteria and Firmicutes at phylum level and Bradyrhizobium , Rhizobium , Acidobacteria , Streptomyces and Pseudolabrys at genus level. Further functional enrichment analysis enabled us to connect protein identities to regulatory and signalling networks of key biogeochemical cycles, notably the nitrogen cycle. The newly identified Park Grass metaproteome thus provides a baseline on which future targeted studies of important soil processes and their control can be built. Identification of the Park Grass Experiment soil metaproteome using Complementary extraction methods. Soil samples processed by surfactant or modified heat thaw phenol chloroform (HTPC) methods, purified and applied to Gel Top. Proteins were then processed and identified using mass spectrometry and a compatible soil protein database. Protein identities were sorted into functional groups and linked to organism data through NCBI and EBI. Data is used to compare extraction processes and present an overall picture of the main processes in the Park Grass microbiome. These processes are linked to the Park Grass metadata repository. [Display omitted] • Complementary protein extraction methods identified 1266 proteins from Park Grass soil • Proteome enriched in ribosomal, respiratory and nitrogen cycle associated proteins • Identification of regulatory and signalling proteins in key biogeochemical cycles • Connects metaproteome to microbiome and biogeochemistry of Park Grass soil • Provides baseline metaproteome for future targeted studies [ABSTRACT FROM AUTHOR]

This work analyses the applicability of the Lucas–Washburn equation to experimental observations of imbibition into real network structures. The experimental pore structures used in this study are constructed from tablets of two finely ground calcium carbonates, with defined differences in particle size distribution. These are compressed under a range of different applied pressures to achieve a controlled series of porosities while maintaining the surface chemical, particulate and morphological pore characteristics constant. The porosities are determined by mercury intrusion porosimetry applying corrections for mercury compression and penetrometer expansion together with a correction for sample skeletal compression (Gane et al., J. Am. Chem. Soc., 35 (1996)). Imbibition studies are made by bringing each porous sample into contact with a supersource of liquid and the dynamic imbibition is recorded gravimetrically. Results follow a long timescale macroscopic absorption rate depending on the square root of time but show a failure to scale according to pore size in the Lucas–Washburn equation even though the constants of surface energy, contact angle and fluid viscosity have been maintained. Furthermore, values of average measured pore radius are shown to be finer than the Lucas–Washburn predicted equivalent hydraulic capillary radius. The predominance of a relevant pore size within a given pore size distribution forming a selective pathway filling based on inertial retardation of larger pores and short-term linear time wetting in finer pores is argued to account for the departure from simple pore size scaling. [Copyright &y& Elsevier]

Rationale: Isotopic signatures of N 2 O can help distinguish between two sources (fertiliser N or endogenous soil N) of N 2 O emissions. The contribution of each source to N 2 O emissions after N-application is difficult to determine. Here, isotopologue signatures of emitted N 2 O are used in an improved isotopic model based on Rayleigh-type equations., Methods: The effects of a partial (33% of surface area, treatment 1c) or total (100% of surface area, treatment 3c) dispersal of N and C on gaseous emissions from denitrification were measured in a laboratory incubation system (DENIS) allowing simultaneous measurements of NO, N 2 O, N 2 and CO 2 over a 12-day incubation period. To determine the source of N 2 O emissions those results were combined with both the isotope ratio mass spectrometry analysis of the isotopocules of emitted N 2 O and those from the 15 N-tracing technique., Results: The spatial dispersal of N and C significantly affected the quantity, but not the timing, of gas fluxes. Cumulative emissions are larger for treatment 3c than treatment 1c. The 15 N-enrichment analysis shows that initially ~70% of the emitted N 2 O derived from the applied amendment followed by a constant decrease. The decrease in contribution of the fertiliser N-pool after an initial increase is sooner and larger for treatment 1c. The Rayleigh-type model applied to N 2 O isotopocules data (δ 15 N bulk -N 2 O values) shows poor agreement with the measurements for the original one-pool model for treatment 1c; the two-pool models gives better results when using a third-order polynomial equation. In contrast, in treatment 3c little difference is observed between the two modelling approaches., Conclusions: The importance of N 2 O emissions from different N-pools in soil for the interpretation of N 2 O isotopocules data was demonstrated using a Rayleigh-type model. Earlier statements concerning exponential increase in native soil nitrate pool activity highlighted in previous studies should be replaced with a polynomial increase with dependency on both N-pool sizes., (© 2018 The Authors Rapid Communications in Mass Spectrometry Published by John Wiley & Sons, Ltd.)

Rationale: This study aimed (i) to determine the isotopic fractionation factors associated with N2O production and reduction during soil denitrification and (ii) to help specify the factors controlling the magnitude of the isotope effects. For the first time the isotope effects of denitrification were determined in an experiment under oxic atmosphere and using a novel approach where N2O production and reduction occurred simultaneously., Methods: Soil incubations were performed under a He/O2 atmosphere and the denitrification product ratio [N2O/(N2 + N2O)] was determined by direct measurement of N2 and N2O fluxes. N2O isotopocules were analyzed by mass spectrometry to determine δ(18)O, δ(15)N and (15)N site preference within the linear N2O molecule (SP). An isotopic model was applied for the simultaneous determination of net isotope effects (η) of both N2O production and reduction, taking into account emissions from two distinct soil pools., Results: A clear relationship was observed between (15)N and (18)O isotope effects during N2O production and denitrification rates. For N2O reduction, diverse isotope effects were observed for the two distinct soil pools characterized by different product ratios. For moderate product ratios (from 0.1 to 1.0) the range of isotope effects given by previous studies was confirmed and refined, whereas for very low product ratios (below 0.1) the net isotope effects were much smaller., Conclusions: The fractionation factors associated with denitrification, determined under oxic incubation, are similar to the factors previously determined under anoxic conditions, hence potentially applicable for field studies. However, it was shown that the η(18)O/η(15)N ratios, previously accepted as typical for N2O reduction processes (i.e., higher than 2), are not valid for all conditions., (Copyright © 2014 John Wiley & Sons, Ltd.)

The Pore-Cor void network model is used to construct stochastic realizations of the void structures of five sandstone samples of varying lithography. A close match was achieved to experimental porosity and mercury intrusion curves. The samples were resin impregnated and the fragments of voids revealed in thin sections photographed by backscatter electron microscopy at two magnifications. The sizes of these pore fragments matched those derived from a simulated microtoming of the network model much more closely than the sizes derived from the traditional capillary bundle approximation. Absolute permeabilities of the network were calculated by finding the flow capacity of the entire flow network, based on parametrized Navier Stokes equations with Klinkenberg correction, applied to each pore-throat-pore arc. A match to the experimental trend was obtained, although the network model considerably underestimated the experimental values. The results were also compared with the semiempirical equations of Thomson et al. and Kozeny and Carmen modified to accept thin section image analysis. Finally, the simulated pore and throat size distributions were compared to proton NMR transverse (T2) spin-echo relaxation times. Although the shapes of the distributions differed markedly, the mean values trended together. The capillary bundle approximation, however, gave a poor match to the NMR data.

The absorption (permeation) of alcohols into porous blocks of calcium carbonate has been studied experimentally and with a computer model. The experimental measurement was of change in apparent weight of a block with time after contact with liquid. The modeling used the previously developed 'Pore-Cor' model, based on unit cells of 1000 cubic pores connected by cylindrical throats. To gain some insight into absorption into voids of complex geometry, and to provide a representation of heterogeneities in surface interaction energy, the cylindrical throats were converted to double cones. Relative to cylinders, such geometries caused hold-ups of the percolation of nonwetting fluids with respect to increasing applied pressure, and a change in the rate of absorption of wetting fluids. Both the measured absorption of the alcohols and the simulated absorption of the alcohols and of water showed significant deviations from that predicted by an effective hydraulic radius approximation. The simulation demonstrated the development of a highly heterogeneous wetting front, and of preferred wetting pathways that were perturbed by inertial retardation. The findings are useful in the design of high-performance, low-waste pigments for paper coatings, and environmentally friendly printing inks, as well as in wider industrial, environmental, and geological contexts. Copyright 2001 Academic Press.