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Summary: We compared water and solute movement between a ridge and furrow geometry and that of flat soil with a mathematical model. We focused on the effects of two physical processes: root water uptake and pond formation on the soil surface. The mathematical model describes the interaction between solute transport, water movement and surface pond depth. Numerical simulations were used to determine how solutes of varying mobility and rates of degradation penetrated into the two soil geometries over a growing season. Both the ridge and furrow or flat soil geometries could reduce solute leaching, but this depended on several factors. Rain immediately after a solute application was a key factor in determining solute penetration into soil. In cases with delayed rain after a solute application, solutes in ridge and furrow geometries collected adjacent to the root system, resulting in reduced solute penetration compared to the flat soil geometry. In contrast, substantial rain immediately after a solute application resulted in ponding where water infiltration acted as the dominant transport mechanism. This resulted in increased solute penetration in the ridge and furrow geometry compared to the flat soil geometry. Highlights: We studied solute movement controlled by ponding in ridge and furrow and flat fields.We found the ridged soil could impede or increase leaching compared to the flat soil.Solute hot‐spots formed in ridge and furrow soil because of root water uptake.Time between solute application and rainfall is a key factor for solute penetration. [ABSTRACT FROM AUTHOR]

We present a mathematical model that describes the movement of water and solutes in a ridge and furrow geometry. We focus on the effects of two physical processes: root water uptake and pond formation in the furrows. Special attention is paid to the physical description of ponding as an effect of transient rain events. We focus on phenomena taking place in the furrow cross‐section, not on the drainage along the furrow. The resulting model comprises a coupled system of partial and ordinary differential equations that describe the mathematical interplay between solute transport, water movement and furrow pond depth. The system of equations is solved numerically using finite element techniques. We conducted numerical simulations to determine how mobile solutes with low buffer powers penetrate into the soil. We considered two cases: low rainfall, in which pond formation does not occur, and high rainfall, in which significant ponding is observed in the furrows. We found, in the presence of roots, that mobile solutes collected into a concentrated spot adjacent to the root system independent of rainfall intensity. In the absence of roots, however, we observed that water infiltration from ponding acted as the dominant transport mechanism for mobile solutes. This resulted in deep solute penetration into the soil when compared with non‐ponded furrows. Highlights: Effect of furrow ponding and plant water uptake on solute movement in ridged fields. We developed a mathematical model that describes ponding in furrows from rainfall events. Solute ‘hot spots’ formed in soil from surface ponding and root water uptake. We estimate reduced risk to solute leaching under the effects of ponding when roots are present in soil. [ABSTRACT FROM AUTHOR]

Core Ideas: We hypothesized that plant exudates gel soil particles and on drying enhance water repellency.This has been carried out using rhizosphere‐scale mechanical and hydraulic measurements.Plant exudates enhanced soil hardness and modulus of elasticity as chia seed > maize root > barley root.Plant exudates caused measureable decreases in soil wetting rates through water repellency. Using rhizosphere‐scale physical measurements, we tested the hypothesis that plant exudates gel together soil particles and, on drying, enhance soil water repellency. Barley (Hordeum vulgare L. cv. Optic) and maize (Zea mays L. cv. Freya) root exudates were compared with chia (Salvia hispanica L.) seed exudate, a commonly used root exudate analog. Sandy loam and clay loam soils were treated with root exudates at 0.46 and 4.6 mg exudate g−1 dry soil and chia seed exudate at 0.046, 0.46, 0.92, 2.3 and 4.6 mg exudate g−1 dry soil. Soil hardness and modulus of elasticity were measured at −10 kPa matric potential using a 3‐mm‐diameter spherical indenter. The water sorptivity and repellency index of air‐dry soil were measured using a miniaturized infiltrometer device with a 1‐mm tip radius. Soil hardness increased by 28% for barley root exudate, 62% for maize root exudate, and 86% for chia seed exudate at 4.6 mg g−1 concentration in the sandy loam soil. For the clay loam soil, root exudates did not affect soil hardness, whereas chia seed exudate increased soil hardness by 48% at 4.6 mg g−1 concentration. Soil water repellency increased by 48% for chia seed exudate and 23% for maize root exudate but not for barley root exudate at 4.6 mg g−1 concentration in the sandy loam soil. For the clay loam soil, chia seed exudate increased water repellency by 45%, whereas root exudates did not affect water repellency at 4.6 mg g−1 concentration. Water sorptivity and repellency were both correlated with hardness, presumably due to the combined influence of exudates on the hydrological and mechanical properties of the soils. [ABSTRACT FROM AUTHOR]

We hypothesized that plant exudates could either gel or disperse soil depending on their chemical characteristics. Barley ( Hordeum vulgare L. cv. Optic) and maize ( Zea mays L. cv. Freya) root exudates were collected using an aerated hydroponic method and compared with chia ( Salvia hispanica L.) seed exudate, a commonly used root exudate analogue. Sandy loam soil was passed through a 500 -μm mesh and treated with each exudate at a concentration of 4.6 mg exudate g−1 dry soil. Two sets of soil samples were prepared. One set of treated soil samples was maintained at 4°C to suppress microbial processes. To characterize the effect of decomposition, the second set of samples was incubated at 16°C for 2 weeks at −30 kPa matric potential. Gas chromatography-mass spectrometry ( GC- MS) analysis of the exudates showed that barley had the largest organic acid content and chia the largest content of sugars (polysaccharide-derived or free), and maize was in between barley and chia. Yield stress of amended soil samples was measured by an oscillatory strain sweep test with a cone plate rheometer. When microbial decomposition was suppressed at 4°C, yield stress increased 20-fold for chia seed exudate and twofold for maize root exudate compared with the control, whereas for barley root exudate decreased to half. The yield stress after 2 weeks of incubation compared with soil with suppressed microbial decomposition increased by 85% for barley root exudate, but for chia and maize it decreased by 87 and 54%, respectively. Barley root exudation might therefore disperse soil and this could facilitate nutrient release. The maize root and chia seed exudates gelled soil, which could create a more stable soil structure around roots or seeds. Highlights Rheological measurements quantified physical behaviour of plant exudates and effect on soil stabilization., Barley root exudates dispersed soil, which could release nutrients and carbon., Maize root and chia seed exudates had a stabilizing effect on soil., Physical engineering of soil in contact with plant roots depends on the nature and origin of exudates. [ABSTRACT FROM AUTHOR]

Muscle spindles are skeletal muscle sensory organs involved in the sensation of position and movement of the body. We have explored the capability of phase contrast computed tomography to visualise muscle spindles in murine skeletal muscle. In particular, we have validated the visualisation of nerve fibres through phase contrast computed tomography using light microscopy on stained histological sections. We further present the first three-dimensional visualisation of muscle spindles in mouse soleus skeletal muscle in conjunction with the neurovascular bundle associated with it. [ABSTRACT FROM AUTHOR]

Conventional models of solute transport in soil consider only soil volumes large enough to average over microscale heterogeneities, and it is assumed that microscale variations are unimportant at the macroscale. In this research we test this assumption for cases in which the microscale distribution of solute-sorbing sites is patchy. We obtain a set of equations at the macroscale that allow for the effect of the microscale distribution with the mathematical technique of homogenization. We combine these equations with an image-based model that describes the true microscale pore geometry in a real, structured soil measured with X-ray computed tomography. The resulting models are used to test the microscale averaging assumptions inherent in conventional models. We show that, in general, macroscale diffusion is little affected by microscale variation in the distribution of sorption sites. Therefore, for most purposes the assumption of microscale averaging used in conventional models is justified. The effects of microscale heterogeneity are noticeable only when (i) the rate of sorption is slow compared with diffusion, but still fast enough to affect macroscale transport and (ii) the defined macroscale volume approaches the microscale. We discuss the effects when these conditions are met. Highlights When does microscale variation need to be allowed for in macroscale transport and reaction models?, We use image-based modelling and homogenization to answer this., We find macroscale transport is generally little affected by microscale patchiness of sorption sites., The microscale averaging implicit in conventional models is justified in most cases. [ABSTRACT FROM AUTHOR]

The readily available global rock phosphate ( P) reserves may run out within the next 50-130 years, causing soils to have a reduced P concentration which will affect plant P uptake. Using a combination of mathematical modelling and experimental data, we investigated potential plant-based options for optimizing crop P uptake in reduced soil P environments. By varying the P concentration within a well-mixed agricultural soil, for high and low P (35.5-12.5 mg L−1 respectively using Olsen's P index), we investigated branching distributions within a wheat root system that maximize P uptake. Changing the root branching distribution from linear (evenly spaced branches) to strongly exponential (a greater number of branches at the top of the soil) improves P uptake by 142% for low- P soils when root mass is kept constant between simulations. This causes the roots to emerge earlier and mimics topsoil foraging. Manipulating root branching patterns, to maximize P uptake, is not enough on its own to overcome the drop in soil P from high to low P. Further mechanisms have to be considered to fully understand the impact of P reduction on plant development. [ABSTRACT FROM AUTHOR]

Soil structure is known to govern aspects of hydration, aeration, faunal activity and root growth, which influence plant development. Industrial X-ray computed tomography ( μCT) has been used for over 15 years for the elucidation of soil structure, leading to a number of valuable insights. However, there is evidence of a need for more robust, repeatable methods for segmentation of significant structural features, which are essentially free from operator interference. We develop in this paper an automatable approach using a seeded region growth (SRG) algorithm for segmentation of the connected, macroporous domain of homogenized, real soils. Furthermore, we demonstrate methods for user-independent selection of seed point and tolerance values, leading to a fully automated segmentation regime. The stability of this approach to different seed locations has been assessed, as well as the impact of X-ray target and filter choice upon mitigation of artifacts, which are particularly detrimental to accuracy of SRG methods. Estimated porosity derived using this method has been compared with values from a gravimetric protocol and histogram thresholding approaches. It is seen that substantial differences exist in porosity quantified by such methods, with these differences probably the result of varying categorization of different porosity domains. [ABSTRACT FROM AUTHOR]

Summary [ABSTRACT FROM AUTHOR]

The functional role of organic acid anions in soil has been intensively investigated, with special focus on (i) microbial respiration and soil carbon dynamics, (ii) nutrient solubilization or (iii) metal detoxification and reduction of plant metal uptake. Little is known about the interaction dynamics of organic acid anions with the soil matrix and the potential impact of adsorption and desorption processes on the functional significance of these effects. The aim of this study was to characterize experimentally the adsorption and desorption dynamics of organic acid anions in five agricultural soils differing in iron and aluminium oxide contents and using citrate as a model carboxylate. Results showed that both adsorption and desorption processes were fast in all soils, reaching a steady state within approximately 1 hour. However, for a given total soil citrate concentration ( ct) the steady state was critically dependent on the starting conditions of the experiment, whether most of the citrate was initially present in solution ( cl) or held on the solid phase ( cs). Specifically, desorption-led processes resulted in significantly smaller steady-state solution concentrations than adsorption-led processes, indicating that hysteresis occurred. As it is not possible to distinguish between different adsorption and desorption pools in soil experimentally, a new dynamic hysteresis model that relies only on measured soil solution concentrations was developed. The model satisfactorily explained experimental data and was able to predict dynamic adsorption and desorption behaviour. To demonstrate its use, we applied the model to two relevant situations involving exudation and microbial degradation. The study highlighted the complex nature of citrate adsorption and desorption dynamics in soil. We conclude that existing models need to incorporate both temporal and hysteresis components to describe realistically the role and fate of organic acids in soil processes. [ABSTRACT FROM AUTHOR]

We use homogenization techniques to derive a dual (or double) porosity model of solute diffusion and reaction in soil, allowing for slow access to sorption sites within micro-aggregates and time-dependent sorption reactions. We give a means for determining the conditions in which micro-scale concentration gradients affect macro-scale gradients and fluxes. We present equations for a unit volume of soil represented as a series of uniformly-spaced, porous spherical particles, containing and surrounded by solution through which solutes diffuse. The methods we use can, in principle, be applied to more complex geometries. We compare the model's predictions with those of the equivalent single porosity model for commonly used boundary conditions. We show that failure to allow for slow access to reaction sites can lead to seriously erroneous results. Slow access has the effect of decreasing the sorption of solute into soil from a source or desorption from soil to a sink. As a result of slow access, the diffusion coefficients of strongly-sorbed solutes measured at the macro-scale will be time-dependent and will depend on the method of measurement. We also show that slow access is more often likely to limit macro-scale diffusion than rates of slow chemical reactions per se. In principle, the unimportance of slow reactions except at periods longer than several weeks of diffusion simplifies modelling because, if slow access is correctly allowed for, sorption can be described with equilibrium relations with an understanding of speciation and rapid sorption-desorption reactions. [ABSTRACT FROM AUTHOR]

•Root hairs are known to be important in the uptake of sparingly soluble nutrients by plants, but quantitative understanding of their role in this is weak. This limits, for example, the breeding of more nutrient-efficient crop genotypes. •We developed a mathematical model of nutrient transport and uptake in the root hair zone of single roots growing in soil or solution culture. Accounting for root hair geometry explicitly, we derived effective equations for the cumulative effect of root hair surfaces on uptake using the method of homogenization. •Analysis of the model shows that, depending on the morphological and physiological properties of the root hairs, one of three different effective models applies. They describe situations where: (1) a concentration gradient dynamically develops within the root hair zone; (2) the effect of root hair uptake is negligibly small; or (3) phosphate in the root hair zone is taken up instantaneously. Furthermore, we show that the influence of root hairs on rates of phosphate uptake is one order of magnitude greater in soil than solution culture. •The model provides a basis for quantifying the importance of root hair morphological and physiological properties in overall uptake, in order to design and interpret experiments in different circumstances. [ABSTRACT FROM AUTHOR]

The rhizosphere is a dynamic region where multiple interacting processes in the roots and surrounding soil take place, with dimensions set by the distance to which the zone of root influence spreads into the soil. Its complexity is such that some form of mathematical modelling is essential for understanding which of the various processes operating are important, and a minimal model of the rhizosphere must provide information on (a) the spatiotemporal concentration changes of mobile solutes in the root-influenced soil, and (b) the cumulative uptake of solutes per unit length of root over time. Both are unique for a given set of parameters and initial conditions and hence the model is fully deterministic. ‘Up-scaling’ to uptake by whole plants by integrating individual fluxes requires a measure of the growth and senescence of the root system. Root architecture models are increasingly successful in providing this. The spatio-temporal scales of the rhizosphere and roots are sufficiently different that they can be treated separately, and this greatly simplifies modelling. The minimal model has been successfully applied to the more-mobile nutrients in soil, such as nitrate or potassium, but much less successfully to less-soluble nutrients such as phosphorus, because other, undescribed processes become important. These include transfers from unavailable forms, heterogeneity of resource distribution, root competition, water redistribution and adaptive processes. Incorporating such processes into models can disrupt independent scaling. In general, scaling from the scale of the individual root to that of the whole plant does not pose insuperable problems. Paradoxically, the major challenge in introducing more complexity is that experimental corroboration of the model is required at the individual root scale. [ABSTRACT FROM AUTHOR]

A response by E. Oburger and colleagues to a letter to the editor about their article on the sorption behaviour of several anions is presented.

The remarkable complexity of soil and its importance to a wide range of ecosystem services presents major challenges to the modeling of soil processes. Although major progress in soil models has occurred in the last decades, models of soil processes remain disjointed between disciplines or ecosystem services, with considerable uncertainty remaining in the quality of predictions and several challenges that remain yet to be addressed. First, there is a need to improve exchange of knowledge and experience among the different disciplines in soil science and to reach out to other Earth science communities. Second, the community needs to develop a new generation of soil models based on a systemic approach comprising relevant physical, chemical, and biological processes to address critical knowledge gaps in our understanding of soil processes and their interactions. Overcoming these challenges will facilitate exchanges between soil modeling and climate, plant, and social science modeling communities. It will allow us to contribute to preserve and improve our assessment of ecosystem services and advance our understanding of climate-change feedback mechanisms, among others, thereby facilitating and strengthening communication among scientific disciplines and society. We review the role of modeling soil processes in quantifying key soil processes that shape ecosystem services, with a focus on provisioning and regulating services. We then identify key challenges in modeling soil processes, including the systematic incorporation of heterogeneity and uncertainty, the integration of data and models, and strategies for effective integration of knowledge on physical, chemical, and biological soil processes. We discuss how the soil modeling community could best interface with modern modeling activities in other disciplines, such as climate, ecology, and plant research, and how to weave novel observation and measurement techniques into soil models. We propose the establishment of an international soil modeling consortium to coherently advance soil modeling activities and foster communication with other Earth science disciplines. Such a consortium should promote soil modeling platforms and data repository for model development, calibration and intercomparison essential for addressing contemporary challenges. [ABSTRACT FROM AUTHOR]