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Modelling carbon mineralisation in natural soils is a major topic in soil and climate research. Current models need to be improved to include soil structure as an influencing factor to better predict C fluxes between pedosphere and atmosphere and to estimate carbon sequestration potentials. Geometry-based mechanistic modelling approaches have recently been developed to systematically study the effect of soil structure on carbon decomposition. Such models require spatially explicit input parameters describing the architecture of the pore space and the heterogeneous distribution of microbes and organic matter as decomposable substrate. The latter is very difficult to determine in situ, resulting in increased uncertainty in the models. To obtain more realistic input data, we have developed a novel approach to locate soil organic matter (SOM) in undisturbed aggregates of soil using a combination of synchrotron-based X-ray microtomography and osmium as a staining agent for SOM. Here, we present the first results using 5 mm sized soil aggregate samples with contrasting C-contents in which we obtained maps of organic matter distributions in relation to the pore networks at the aggregate scale. [ABSTRACT FROM AUTHOR]

Abstract: The study aim was to investigate the vacuum impregnation (VI) technique for apple enrichment with quercetin glycosides from apple peel. Beside the determination of the quercetin content, structural effects on the apple parenchyma were analyzed by computerized microtomography (μCT). VI was an efficient method to enrich apples with quercetin derivatives which was affected by the apple cultivar, the vacuum pressure, the soluble solid concentration (SSC) and the viscosity of VI solution. After VI of 13 apple cultivars the quercetin content varied between 368 and 604μg/g dry mass and correlated with the firmness of the native apple and the increased apple weight. The use of low SSC solution resulted in increased quercetin enrichment in contrast to apple pectin solutions with elevated viscosity. The μCT analyses demonstrate that VI was more effective in the inner apple sections than in the outer parts. The study indicates that differences of pore size and microstructure within the apple cortex substantially affected the enrichment process. [Copyright &y& Elsevier]

Analysis of the spatial variability of soil properties is important to interpret the site-specific ecosystems not only with respect to process investigations but also to model upscaling. This paper aims to study the effects of the grazing intensity on soil physical and mechanical properties and their interactions in a Leymus chinensis steppe of the Xilin River Basin, Inner Mongolia, China. The investigated sites were subjected to five grazing intensities (ungrazed since 1979, ungrazed since 1999, winter grazing, continuous grazing and heavy grazing). Soil water content (SWC), hydraulic conductivity (K), water drop penetration time (WDPT), shear strength (SS), soil organic carbon (SOC) concentration, bulk density (BD), and soil texture were measured at a grid with 15m sampling distance on the surface soil during the period of 2004–2005. The data were analyzed using descriptive statistics and geostatistics. The correlation and interaction between soil properties were analyzed by the methods of Pearson correlation, partial correlation and multiple regression analysis. The results showed that spatial distributions of soil properties could be well described by spherical or exponential models. The ranges of spatial dependence were the highest for WDPT and the lowest for SS. Grazing decreased SWC, SOC and WDPT but increased BD and SS. Multiple regression analysis showed significant correlations among SWC, K, WDPT, SOC and BD; as well as between SS and silt content. Soil compaction induced by sheep trampling, especially in the heavily grazed site, inclined to a homogenous spatial distribution of soil properties, which will possibly enhance soil vulnerability to water and nutrient loss, and consequently reduce the plant available water and thus grassland productivity. [Copyright &y& Elsevier]

X-ray computed tomography (CT) combined with a quantitative analysis of the resulting volume images is a fruitful technique in soil science. However, the variations in X-ray attenuation due to different soil components keep the segmentation of single components within these highly heterogeneous samples a challenging problem. Particularly demanding are bio-pores due to their elongated shape and the low gray value difference to the surrounding soil structure. Recently, variational models in connection with algorithms from convex optimization were successfully applied for image segmentation. In this paper we apply these methods for the first time for the segmentation of bio-pores in CT images of soil samples. We introduce a novel convex model which enforces smooth boundaries of bio-pores and takes the varying attenuation values in the depth into account. Segmentation results are reported for different real-world 3D data sets as well as for simulated data. These results are compared with two gray value thresholding methods, namely indicator kriging and a global thresholding procedure, and with a morphological approach. Pros and cons of the methods are assessed by considering geometric features of the segmented bio-pore systems. The variational approach features well-connected smooth pores while not detecting smaller or shallower pores. This is an advantage in cases where the main bio-pores network is of interest and where infillings, e.g., excrements of earthworms, would result in losing pore connections as observed for the other thresholding methods. [ABSTRACT FROM AUTHOR]

Roots and the associated soil directly affected by root activity, termed the rhizosphere, have both been extensively studied and recognized for their crucial role in soil functioning. The formation of the rhizosphere is primarily driven by the effect of roots on shaping the physical structure of the soil, which in turn has direct feedbacks on the interactions between physical, biological and chemical processes. As a result, the rhizosphere is a hot spot for microbial activity, cycling of nutrients and turnover of organic matter. Despite the pivotal role of soil structure in controlling rhizosphere processes, we still lack a quantitative description and understanding of the interrelationships of root-systems and soil in the creation and stabilization of soil structure. We provide a comprehensive review of current knowledge and novel insights into processes that drive the formation and stabilization of soil structure in the rhizosphere. These processes are regulated by multiple indirect and direct pathways, involving root growth, the production of rhizodeposits and root hairs, as well as the activity of soil microorganisms and fauna. Further, we highlight that rhizosphere processes may persist and evolve after root death to an extent currently largely unknown. Finally, we identify five pertinent challenges that should be addressed to fully apprehend rhizosphere processes and thus harness the potential resilience of plant-soil interactions. These challenges include refining structural assessment and sampling of rhizosheaths, examining the rhizosphere in-situ and bridging the gap between solid phase and pore scale research. In our view, overcoming these obstacles can be accomplished by combining the power of imaging and isotopic approaches, especially at the field scale, encompassing diverse soils and plant species. The ultimate objective of future research should be to upscale rhizosphere processes by conducting more field experiments in concert with modeling efforts, under the umbrella of collaborative interdisciplinary research. • Plant roots are inherently bound to soil structure dynamics through rhizosphere processes. • Rhizodeposits and root hairs trigger rhizosheath formation through multiple routes. • Roots foster formation of unique habitat by affecting soil porosity and aggregation. • Soil fauna and legacy of dead roots are overlooked factors for rhizosphere structure formation and stability. • Bridging solid phase and pore scale research needed to advance rhizosphere research. [ABSTRACT FROM AUTHOR]

Abstract: Rheology is regarded as the science of flow behaviour, where, based on isothermic equations, the deformation of fluids and plastic bodies subjected to external stresses may be described. Hooke''s law of elasticity, Newton''s law for ideal fluids (viscosity), Mohr-Coulomb''s equation, and finally, Bingham''s yielding are well known relationships and parameters in the field of rheology. Rheometry is a well established measurement technique to determine the specific rheological properties of fluid and plastic bodies. However, the application of this technique in soil mechanical investigations is yet relatively uncommon. In order to explain point contact processes and strength an extrapolation of such findings to data of triaxial, direct shear or oedometer tests is still missing. Thus, this paper aims to introduce rheometry as a suitable method to determine the mechanical behaviour of soils and mineral suspensions when subjected to external stresses. To do this a Na-bentonite, Ibeco Seal-80 (IS-80) has been used as a testing material, and the suspensions were equilibrated with NaCl solutions in different concentrations in order to determine the ionic strength effects on interparticle strength and changes in mechanical properties. Furthermore a vertisol, a clayey oxisol, both from Brazil, and loess material from Israel, saturated with NaCl in several concentrations were analysed. A parallel-plate-rheometer MCR 300 (Modular Compact Rheometer, Paar Physica, Ostfildern, Germany) has been used to conduct oscillatory tests. From the stress–strain relationship parameters and specific characteristics as thixotropy, storage modulus G′ and loss modulus G″, viscosity η, yield stress τ y and the linear viscoelastic deformation (LVE) range including a limiting value γ L were determined and calculated, respectively. With aspect to salt effects, amplitude sweep tests on CaCO3 rich Avdat loess show an increasing stability due to higher NaCl concentrations. In a comparative test of Avdat loess and Ibeco Seal-80, turbulent versus sliding shear behaviour could be illustrated. To demonstrate clay mineralogy effects or textural effects clay rich substrates from Brazil, a smectitic vertisol and a kaolinitic oxisol were compared, showing a higher level of stored elasticity (stability) in case of smectites and a lower value in regard to kaolinites. These preliminary results of amplitude sweep tests show that rheometry is a potential method of investigating microstructural characteristics of mineral suspensions and of clayey or silty soils. [Copyright &y& Elsevier]

Abstract Soil membrane zymography enables 2D mapping of enzyme activities on the surface of soil samples. The method is based on diffusion of components of enzymatically-mediated reactions to/from membrane, and, thus, reflects the distribution of enzyme activities at the intact soil surface. Zymography has been already successfully implemented in numerous soil ecology applications. Here we identify two methodological aspects for further improvement and expansion of the method at micro and macro scales: first, accounting for the area of contact between the soil surface and the zymography membranes and, second, accounting for diffusion effects during the zymography procedure. We tested three methods, namely, laser-scanning, staining with a fluorescent product (e.g. MUF: 4-methylumbelliferone), and X-ray computed micro-tomography, for assessing the area of the soil surface in contact with the membranes. We quantified diffusion of MUF, enzymes and substrate between the substrate-saturated membrane and soil as well as diffusion processes during membrane zymography via HP2 software. Diffusion of the substrate from the membrane and of the MUF-product to the membrane was detected, while there were no clear evidence of enzyme diffusion to/in the membrane. According to the model simulations, the enzyme activities detected via 2D zymography probably represent only a small portion, about 20%, of the actual reactions within the soil volume that is in both direct contact and in hydrological contact with zymography membranes. This is a result of omnidirectional diffusion of reaction products. The membrane contact with the soil surface estimated by three methods ranged from 3.4 to 36.5% further signifying that only a fraction of enzymes activity is detectable in a course of 2D soil zymography. Highlights • We studied processes occurring in the soil and the membrane during 2D soil zymography. • We modeled product and substrate diffusion in the soil/membrane. • Zymography underestimates enzyme activity due to product diffusion losses in soil. • Interpretation of 2D zymography requires measurements to be combined with modeling. [ABSTRACT FROM AUTHOR]

Abstract Soil inoculation with cyanobacteria to promote the formation of biocrusts is considered a potential eco-friendly method to counteract desertification spread in drylands. Research is needed to increase the number of proficient cyanobacterial strains, selected for their capability to survive in harsh conditions and to form stable biocrusts quickly. We hereby present a microcosm study to assess the capability of Leptolyngbya ohadii , native to the Negev Desert, to form biocrusts on sand collected in the same environment, during a three-month incubation period. Inoculation was carried out in sand-filled microcosms without nutrient addition and a limited water supply (equivalent to desert dew input). Parameters related to biocrusts growth and to their physico-chemical attributes were measured, and the exopolysaccharides (EPS) synthesized by the strain during biocrust formation were quantified and characterized. After 15 days of incubation, L. ohadii was able to form biocrusts with a thickness and a physical stability superior to other test strains of cyanobacteria, and typical of much older natural biocrusts. Biocrust characteristics were dependent on the synthesis of EPS, and on the capability to migrate in the sand, stabilizing sand aggregates at different locations within the microcosms. In contrast to other tested strains, L. ohadii produced compositionally complex EPS during the entire incubation period despite the lack of nutrients, producing biocrusts with an amphiphilic extracellular matrix, a character effective in conferring stability to sand aggregates, chelating nutrients and maintaining hydration. Overall, this study shows that L. ohadii is a promising inoculant that may be considered to promote the formation of biocrusts in natural desert settings. Highlights • Leptolynbya ohadii inoculation produces very thick and stable biocrusts on a sandy oligotrophic substrate. • Inoculation procedure does not need any support treatment (e.g., pre-stabilization of the substrate or nutrient addition). • Biocrusts formation happens with a very limited water provision. • The performance as inoculant benefits from exopolysaccharide synthesis and filament gliding in the sand. • Exopolysaccharide productivity and characteristics are affected by variations in water availability. [ABSTRACT FROM AUTHOR]

Biological soil crusts (biocrusts) are considered key players in hydrological cycles of many arid environments. The phototrophic organisms in these crusts excrete extracellular polymeric substances (EPSs), which bind soil particles together, thereby stabilizing the soil surface. In a previous work, the non-invasive extraction of EPSs in biocrusts resulted in a change of their hydrological behavior. As this was suspected to be the effect of a change in their pore structure, we employed high resolution X-ray micro-tomography to investigate structural changes of biocrusts after EPS-extraction. We studied biocrusts from four different study sites in Svalbard, Germany, Israel and South Africa. Two different fractions of EPSs (tightly bound and colloidal) were extracted, using the same extraction method with two different solvents. Our results suggest that the extraction of EPSs did not result in structural differences at a resolution of 7 μm. We therefore conclude that the previously observed change in hydrological behavior is likely to be the result of a change of the physico-chemical properties of the very surface of the crust, rather than of its inner structure. [ABSTRACT FROM AUTHOR]

Soils are faced with man-made chemical stress factors, such as the input of organic or metal-containing pesticides, in combination with non-chemical stressors like soil compaction and natural disturbance like drought. Although multiple stress factors are typically co-occurring in soil ecosystems, research in soil sciences on this aspect is limited and focuses mostly on single structural or functional endpoints. A mechanistic understanding of the reaction of soils to multiple stressors is currently lacking. Based on a review of resilience theory, we introduce a new concept for research on the ability of polluted soil (xenobiotics or other chemical pollutants as one stressor) to resist further natural or anthropogenic stress and to retain its functions and structure. There is strong indication that pollution as a primary stressor will change the system reaction of soil, i.e., its resilience, stability and resistance. It can be expected that pollution affects the physiological adaption of organisms and the functional redundancy of the soil to further stress. We hypothesize that the recovery of organisms and chemical-physical properties after impact of a follow-up stressor is faster in polluted soil than in non-polluted soil, i.e., polluted soil has a higher dynamical stability (dynamical stability = 1 / recovery time), whereas resilience of the contaminated soil is lower compared to that of not or less contaminated soil. Thus, a polluted soil might be more prone to change into another system regime after occurrence of further stress. We highlight this issue by compiling the literature exemplarily for the effects of Cu contamination and compaction on soil functions and structure. We propose to intensify research on effects of combined stresses involving a multidisciplinary team of experts and provide suggestions for corresponding experiments. Our concept offers thus a framework for system level analysis of soils paving the way to enhance ecological theory. [ABSTRACT FROM AUTHOR]

• Gibbsite, hematite/goethite ratio and biological activity influence the degree of microaggregation. • The microgranular structure promotes a better-connected pore system. • A better-connected pore system improves saturated hydraulic conductivity - K sat. • The 2D and 3D analyses are complementary in the study of the porous system. Structure and porous geometry are dynamic soil parameters that control several soil processes and functions. This study details the differences in the structure of typical Oxisols regarding the clay amount, biological activity, and mineralogy. Combining 2D and 3D image analysis can provide detailed information about the soil structure and porous system. The objectives of this study were: (i) to describe the soil microstructure and degree of microaggregation; (ii) to quantify porosity, soil pore types, and soil pore size distribution using 2D and 3D techniques; and (iii) to better understand the relationship between the porous system and the biological, chemical, mineralogical, and physical properties of the soil. The study considered four Oxisols: Xantic Kandiustox (P1), Rhodic Haplustox (P2), Anionic Acrustox (P3), and Typic Hapludox (P4). The results showed that all Oxisols have some degree of microaggregation. The Rhodic Haplustox (P2) had the most pronounced degree of microaggregation, which reflects the greater biological activity and gibbsite/kaolinite ratio, and lower hematite/(hematite + goethite) ratio compared to the other Oxisols. The pore types found by 2D analysis were complex pores in P1 and P2 and rounded pores in P3 and P4. The 3D analysis showed that P2 and P3 have a more connected porous system compared to the other Oxisols, evidenced by the lower value of the Euler number. The best connectivity values of the porous system were congruent to improved saturated hydraulic conductivity measured in a separate sample set. [ABSTRACT FROM AUTHOR]

Abstract: In arable farming systems, the term ‘subsoil’ refers to the soil beneath the tilled or formerly tilled soil horizon whereas the latter one is denoted as ‘topsoil’. To date, most agronomic and plant nutrition studies have widely neglected subsoil processes involved in nutrient acquisition by crop roots. Based on our current knowledge it can be assumed that subsoil properties such as comparatively high bulk density, low air permeability, and poverty of organic matter, nutrients and microbial biomass are obviously adverse for nutrient acquisition, and sometimes subsoils provide as little as less than 10% of annual nutrient uptake in fertilised arable fields. Nevertheless, there is also strong evidence indicating that subsoil can contribute to more than two-thirds of the plant nutrition of N, P and K, especially when the topsoil is dry or nutrient-depleted. Based on the existing literature, nutrient acquisition from arable subsoils may be conceptualised into three major process components: (I) mobilisation from the subsoil, (II) translocation to the shoot and long-term accumulation in the Ap horizon and (III) re-allocation to the subsoil. The quantitative estimation of nutrient acquisition from the subsoil requires the linking of field experiments with mathematical modelling approaches on different spatial scales including Process Based Models for the field scale and Functional–Structural Plant Models for the plant scale. Possibilities to modify subsoil properties by means of agronomic management are limited, but ‘subsoiling’ – i.e. deep mechanical loosening – as well as the promotion of biopore formation are two potential strategies for increasing access to subsoil resources for crop roots in arable soils. The quantitative role of biopores in the nutrient acquisition from the subsoil is still unclear, and more research is needed to determine the bioaccessibility of nutrients in subsoil horizons. [Copyright &y& Elsevier]

Abstract: Dry spells during the summer period affecting water uptake and plant growth in central Europe may occur more frequently in the future due to climate change. Improving the ability of crops to take up water from deeper soil layers is a potential strategy to secure water supply. The objective of this paper is to report on the effect of different preceding fodder crops on root growth and water uptake of spring wheat from the subsoil. Water extraction and root length density during grain filling of spring wheat were observed between anthesis and maturity in six different soil depths (0–15, 15–45, 45–60, 60–75, 75–90 and 90–105cm) and with four different preceding crops: 1 year of fescue (Fes1Y), 2 years of chicory (Chi2Y), 2 years of lucerne (Luc2Y) and 3 years of chicory (Chi3Y). While there was no difference in total water extraction by wheat in the four crop sequences, water extraction from the deepest layer (90–105cm) was significantly higher after 2 years of lucerne (Luc2Y). This was consistent with the root length densities measured in the 90–105 layer, which were 82, 89 and 112% higher in Luc2Y as compared to Fes1Y, Chi2Y and Chi3Y, respectively. Results suggest that lucerne as preceding crop supports deeper rooting and higher rooting density of following spring wheat enhancing access to water in deeper soil layers in response to prolonged dry spells. Effects facilitating root penetration like improved soil structure and higher nitrogen availability after lucerne are discussed. We conclude that suitable crop rotations with lucerne might be a cost-effective adaptation measure to overcome drought stress. [Copyright &y& Elsevier]

Abstract: Overgrazing increasingly affects large areas of Inner Mongolian semi-arid grasslands. Consequences for ecosystem functions and, in particular, for the decomposition as a key process of ecosystem carbon (C) and nitrogen (N) cycling are still unclear. We studied the effects of grazing on shoot and root decomposition with the litter bag method in a long-term grazing exclosure (UG79), a moderate winter grazed (WG) and a long-term heavily grazed site (HG). We separated the effects of local environmental factors and litter quality as altered by grazing. Growing seasons of average and very low precipitation allowed us to study the effect of inter annual rainfall variability on decomposition. Grazing-induced differences in environmental factors of the three studied grassland sites had no effect on decay rates of shoot and root dry mass. Also differences in litter quality among the grazing sites were not reflected by root decomposition dynamics. The accelerated shoot decay at site HG could not clearly be linked to litter quality parameters. Shoot decay rates were more or less constant, even under very dry conditions. This indicates the possibility of photodegradation (solar UV-B radiation) to control aboveground decomposition in this semi-arid ecosystem. By selecting the best predictors of root decomposition from regression analysis, we found that soil water content was the best parameter explaining the dynamics. Net N immobilization was generally not detected during the decay process of shoot and root. It is likely, when root decomposition is strongly reduced in dry periods, shoot decomposition becomes relatively more important for nutrient cycling. A separate analysis of shoot and root decay dynamics is required in order to describe C and N cycling in this semi-arid grassland. The grazing impact on C and N fluxes through decomposition of plant material likely exhibits a strong interaction with seasonal rainfall pattern. [Copyright &y& Elsevier]

Abstract: In this study the influence of X-ray computed tomography (XRCT) on the microbial community structure and function in soils has been investigated. Our results clearly indicate that XRCT of soil samples has a strong impact on microbial communities and changes structure and function significantly due to the death of selected microbial groups as a result of the treatment. [Copyright &y& Elsevier]

Wood harvesting is restricted to a system of permanent skid trails in order to minimize the soil disturbance and damage. Therefore, it is not the compaction of previously undisturbed forest soil, but the re-compaction of already existing skid trails that is of practical relevance when investigating machinery-induced wood harvest effects on soil properties. This study investigated the effects of machinery-induced re-compaction on soil physical, chemical, and microbiological properties of an old skid trail in a spruce forest by wheeling 8 times with a maximum total load of 32.2 Mg, using a genuine old skid trail as a control. Re-compaction significantly increased the bulk density and reduced the porosity, whereas the soil organic carbon (SOC) and total nitrogen (N) contents were not significantly affected. However, re-compaction reduced the SOC/total N ratio by 10%, suggesting considerable SOC mineralization after re-compaction. K 2 SO 4 extractable C contents were increased by 94% at 0–3 cm and 67% at 7–10 cm depth after re-compaction. This led to 20% and 90% increased microbial biomass C/soil organic C (MBC/SOC) ratios at 0–3 cm and at 7–10 cm depth, respectively. In contrast, the ergosterol/MBC ratio was significantly decreased by 10% at 0–3 cm and by about 30% at 7–10 cm depth by re-compaction, apparently due to the promotion of bacteria and mobilization of soil organic matter. • Re-compaction increased microbial biomass. • Re-compaction decreased SOC/total N and increased MBC/SOC ratios. • Re-compaction mobilized the extractable SOC fraction. • A part must be mineralizable directly after re-compaction. • At soil sampling, basal respiration was affected by re-compaction. [ABSTRACT FROM AUTHOR]