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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

Geophysical surveys are now commonly used in agriculture for mapping applications. High‐throughput collection of geophysical properties such as electrical conductivity (inverse of resistivity) can be used as a proxy for soil properties of interest (e.g., moisture, texture, salinity). Most applications only rely on a single geophysical survey at a given time. However, time‐lapse geophysical surveys have greater capabilities to characterize the dynamics of the system, which is the focus of this work. Assessing the impact of agricultural practices through the growth season can reveal important information for the crop production. In this work, we demonstrate the use of time‐lapse electrical resistivity tomography (ERT) and electromagnetic induction (EMI) surveys through a series of three case studies illustrating common agricultural practices (cover crops, compaction with irrigation, and tillage with N fertilization). In the first case study, time‐lapse EMI reveals the initial effect of cover crops on soil drying and the absence of effect on the subsequent main crop. In the second case study, compaction leading to a shallower drying depth for potatoes (Solanum tuberosum L.) was imaged by time‐lapse ERT. In the third case study, larger changes in electrical conductivity over time were observed in conventional tillage compared with direct drill using time‐lapse EMI. In addition, different N application rates had a significant effect on the yield and leaf area index but only ephemeral effects on the dynamics of electrical conductivity, mainly after the first application. Overall, time‐lapse geophysical surveys show great potential for monitoring the impact of different agricultural practices that can influence crop yield. [ABSTRACT FROM AUTHOR]

Roots naturally exert axial and radial pressures during growth, which alter the structural arrangement of soil at the root–soil interface. However, empirical models suggest soil densification, which can have negative impacts on water and nutrient uptake, occurs at the immediate root surface with decreasing distance from the root. Here, we spatially map structural gradients in the soil surrounding roots using non‐invasive imaging, to ascertain the role of root growth in early stage formation of soil structure. X‐ray computed tomography provided a means not only to visualize a root system in situ and in 3‐D but also to assess the precise root‐induced alterations to soil structure close to, and at selected distances away from the root–soil interface. We spatially quantified the changes in soil structure generated by three common but contrasting plant species (pea, tomato, and wheat) under different soil texture and compaction treatments. Across the three plant types, significant increases in porosity at the immediate root surface were found in both clay loam and loamy sand soils and not soil densification, the currently assumed norm. Densification of the soil was recorded, at some distance away from the root, dependent on soil texture and plant type. There was a significant soil texture × bulk density × plant species interaction for the root convex hull, a measure of the extent to which root systems explore the soil, which suggested pea and wheat grew better in the clay soil when at a high bulk density, compared with tomato, which preferred lower bulk density soils. These results, only revealed by high resolution non‐destructive imagery, show that although the root penetration mechanisms can lead to soil densification (which could have a negative impact on growth), the immediate root–soil interface is actually a zone of high porosity, which is very important for several key rhizosphere processes occurring at this scale including water and nutrient uptake and gaseous diffusion. By high resolution imagery, we observed across the three plant types significant increases in porosity at the immediate root surface, irrespective of soil texture and bulk density, and not soil densification, the currently assumed norm. This has profound implication for several key rhizosphere processes occurring at this scale including water and nutrient uptake and gaseous diffusion that should be considered in plant breeding efforts. [ABSTRACT FROM AUTHOR]

There has been recent interest in the use of surface-deployed geophysical methods to estimate soil moisture profiles. In this study, we applied multi-coil, frequency domain, electromagnetic induction (EMI) geophysical surveys to determine electrical conductivity (σ) profiles of the root zone of four winter wheat (Triticum aestivum L.) genotypes grown in a randomized block experiment with four replicates. Field measurements of apparent electrical conductivity (σa) were obtained at sites with two different soil textures. We used the cumulative sensitivity model to predict EMI conductivity data from the conductivity profile measured with electrical resistivity tomography (ERT) on a subset of the plots we investigated. During the inversion of the EMI data, conductivities were adjusted on all plots so that they were consistent with the ERT data. Changes in electrical conductivity of field soil, with depth computed from inversion of the EMI data, during the growth period were compared with measured changes in soil water content. Laboratory measurements confirmed a positive correlation between electrical conductivity and soil water content. Between crop emergence and maturity, water extraction by the different wheat genotypes reduced the water content by up to 30% Comparing changes in electrical conductivity between reference profiles determined shortly after crop emergence and electrical conductivity profiles at later dates as the crop matured, we were able to use EMI to remotely monitor moisture extraction by the roots of different wheat genotypes with depth and time. [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]

ABSTRACT Understanding how root system architecture (RSA) adapts to changing nitrogen and water availability is important for improving acquisition. A sand rhizotron system was developed to study RSA in a porous substrate under tightly regulated nutrient supply. The RSA of Arabidopsis seedlings under differing nitrate (NO3-) and water supplies in agar and sand was described. The hydraulic conductivity of the root environment was manipulated by using altered sand particle size and matric potentials. Ion-selective microelectrodes were used to quantify NO3- at the surface of growing primary roots in sands of different particle sizes. Differences in RSA were observed between seedlings grown on agar and sand, and the influence of NO3- (0.1-10.0 m m) and water on RSA was determined. Primary root length (PRL) was a function of water flux and independent of NO3-. The percentage of roots with laterals correlated with water flux, whereas NO3- supply was important for basal root (BR) growth. In agar and sand, the NO3- activities at the root surface were higher than those supplied in the nutrient solution. The sand rhizotron system is a useful tool for the study of RSA, providing a porous growth environment that can be used to simulate the effects of hydraulic conductivity on growth. [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]

Improved root water and nutrient acquisition can increase fertiliser use efficiency and is important for securing food production. Root nutrient acquisition includes proliferation, transporter function, exudation, symbioses, and the delivery of dissolved nutrients from the bulk soil to the root surface via mass flow and diffusion. The widespread adoption of simplified experimental systems has restricted consideration of the influence of soil symbiotic organisms and physical properties on root acquisition. The soil physical properties can directly influence root growth and explain some of the disparities obtained from different experimental systems. Turning this to an advantage, comparing results obtained with the same model plant Arabidopsis (Arabidopsis thaliana) in different systems, we can tease apart the specific effects of soil physical properties. [Copyright &y& Elsevier]

Arsenic is a known human carcinogen, whereas Se is essential to human health and human Se intake in some European countries has decreased in recent decades. There have been few reports on the potential effect of soil physical conditions on the uptake of Se and As by food crops. Field experiments were conducted to evaluate the effects of soil compaction and irrigation on Se and As concentrations in wheat grains in two seasons. Grain Se concentration varied from 10 to 115 μg kg−1, whereas the concentration of As in grain was low (<20 μg kg−1). Irrigation significantly decreased grain Se concentration by 30–75%, and the effect was likely due to a dilution as a result of increased grain yield, a competition of sulfate added in the irrigation water on Se uptake and increased leaching losses. Soil compaction significantly decreased grain Se concentration in one season. In contrast, soil compaction increased grain As concentration significantly when the crop was irrigated. The contrasting effects of soil compaction on As and Se uptake are explained by the difference in their mobility in soil and the pathway of ion transport to roots. The observed effect on grain Se is significant for human and animal nutrition, because the concentration varied from sufficient to very low levels in response to the alternation of soil physical conditions in the field. Soil physical conditions have to be taken into account when assessing the bioavailability of the contaminant As or the essential nutrient Se. [Copyright &y& Elsevier]

Biogeochemical reactions occurring in soil pore space underpin gaseous emissions measured at macroscopic scales but are difficult to quantify due to their complexity and heterogeneity. We develop a volumetric-average method to calculate aerobic respiration rates analytically from soil with microscopic soil structure represented explicitly. Soil water content in the model is the result of the volumetric-average of the microscopic processes, and it is nonlinearly coupled with temperature and other factors. Since many biogeochemical reactions are driven by oxygen (O 2 ) which must overcome various resistances before reaching reactive microsites from the atmosphere, the volumetric-average results in negative feedback between temperature and soil respiration, with the magnitude of the feedback increasing with soil water content and substrate quality. Comparisons with various experiments show the model reproduces the variation of carbon dioxide emission from soils under different water content and temperature gradients, indicating that it captures the key microscopic processes underpinning soil respiration. We show that alongside thermal microbial adaptation, substrate heterogeneity and microbial turnover and carbon use efficiency, O 2 dissolution and diffusion in water associated with soil pore space is another key explanation for the attenuated temperature response of soil respiration and should be considered in developing soil organic carbon models.

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.)

We report on the evaluation of a novel grass hybrid that provides efficient forage production and could help mitigate flooding. Perennial ryegrass (Lolium perenne) is the grass species of choice for most farmers, but lacks resilience against extremes of climate. We hybridised L. perenne onto a closely related and more stress-resistant grass species, meadow fescue Festuca pratensis. We demonstrate that the L. perenne × F. pratensis cultivar can reduce runoff during the events by 51% compared to a leading UK nationally recommended L. perenne cultivar and by 43% compared to F. pratensis over a two year field experiment. We present evidence that the reduced runoff from this Festulolium cultivar was due to intense initial root growth followed by rapid senescence, especially at depth. Hybrid grasses of this type show potential for reducing the likelihood of flooding, whilst providing food production under conditions of changing climate.

Carbon sequestration, infrastructure rehabilitation, brownfields clean-up, hazardous waste disposal, water resources protection and global warming-these twenty-first century challenges can neither be solved by the high-energy consumptive practices that hallmark industry today, nor by minor tweaking or optimization of these processes. A more radical, holistic approach is required to develop the sustainable solutions society needs. Most of the above challenges occur within, are supported on, are enabled by or grown from soil. Soil, contrary to conventional civil engineering thought, is a living system host to multiple simultaneous processes. It is proposed herein that 'soil engineering in vivo', wherein the natural capacity of soil as a living ecosystem is used to provide multiple solutions simultaneously, may provide new, innovative, sustainable solutions to some of these great challenges of the twenty-first century. This requires a multi-disciplinary perspective that embraces the science of biology, chemistry and physics and applies this knowledge to provide multi-functional civil and environmental engineering designs for the soil environment. For example, can native soil bacterial species moderate the carbonate cycle in soils to simultaneously solidify liquefiable soil, immobilize reactive heavy metals and sequester carbon-effectively providing civil engineering functionality while clarifying the ground water and removing carbon from the atmosphere? Exploration of these ideas has begun in earnest in recent years. This paper explores the potential, challenges and opportunities of this new field, and highlights one biogeochemical function of soil that has shown promise and is developing rapidly as a new technology. The example is used to propose a generalized approach in which the potential of this new field can be fully realized.