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Rhizosphere soil has distinct physical and chemical properties from bulk soil. However, besides root-induced physical changes, chemical changes have not been extensively measured in situ on the pore scale. In this study, we couple structural information, previously obtained using synchrotron X-ray computed tomography (XCT), with synchrotron X-ray fluorescence microscopy (XRF) and X-ray absorption near-edge structure (XANES) to unravel chemical changes induced by plant roots. Our results suggest that iron (Fe) and sulfur (S) increase notably in the direct vicinity of the root via solubilization and microbial activity. XANES further shows that Fe is slightly reduced, S is increasingly transformed into sulfate (SO 4 2- ) and phosphorus (P) is increasingly adsorbed to humic substances in this enrichment zone. In addition, the ferrihydrite fraction decreases drastically, suggesting the preferential dissolution and the formation of more stable Fe oxides. Additionally, the increased transformation of organic S to sulfate indicates that the microbial activity in this zone is increased. These changes in soil chemistry correspond to the soil compaction zone as previously measured via XCT. The fact that these changes are colocated near the root and the compaction zone suggests that decreased permeability as a result of soil structural changes acts as a barrier creating a zone with increased rhizosphere chemical interactions via surface-mediated processes, microbial activity and acidification., (© 2019 The Authors. New Phytologist © 2019 New Phytologist Trust.)

The growth of rice in submerged soils depends on its ability to form continuous gas channels-aerenchyma-through which oxygen (O 2 ) diffuses from the shoots to aerate the roots. Less well understood is the extent to which aerenchyma permits venting of respiratory carbon dioxide (CO 2 ) in the opposite direction. Large, potentially toxic concentrations of dissolved CO 2 develop in submerged rice soils. We show using X-ray computed tomography and image-based mathematical modelling that CO 2 venting through rice roots is far greater than thought hitherto. We found rates of venting equivalent to a third of the daily CO 2 fixation in photosynthesis. Without this venting through the roots, the concentrations of CO 2 and associated bicarbonate (HCO 3 - ) in root cells would have been well above levels known to be toxic to roots. Removal of CO 2 and hence carbonic acid (H 2 CO 3 ) from the soil was sufficient to increase the pH in the rhizosphere close to the roots by 0.7 units, which is sufficient to solubilize or immobilize various nutrients and toxicants. A sensitivity analysis of the model showed that such changes are expected for a wide range of plant and soil conditions., (© 2019 The Authors. Plant, Cell & Environment published by John Wiley & Sons Ltd.)

Soil adjacent to roots has distinct structural and physical properties from bulk soil, affecting water and solute acquisition by plants. Detailed knowledge on how root activity and traits such as root hairs affect the three-dimensional pore structure at a fine scale is scarce and often contradictory. Roots of hairless barley (Hordeum vulgare L. cv Optic) mutant (NRH) and its wildtype (WT) parent were grown in tubes of sieved (<250 μm) sandy loam soil under two different water regimes. The tubes were scanned by synchrotron-based X-ray computed tomography to visualise pore structure at the soil-root interface. Pore volume fraction and pore size distribution were analysed vs distance within 1 mm of the root surface. Less dense packing of particles at the root surface was hypothesised to cause the observed increased pore volume fraction immediately next to the epidermis. The pore size distribution was narrower due to a decreased fraction of larger pores. There were no statistically significant differences in pore structure between genotypes or moisture conditions. A model is proposed that describes the variation in porosity near roots taking into account soil compaction and the surface effect at the root surface., (© 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.)

Spatially averaged models of root-soil interactions are often used to calculate plant water uptake. Using a combination of X-ray computed tomography (CT) and image-based modelling, we tested the accuracy of this spatial averaging by directly calculating plant water uptake for young wheat plants in two soil types. The root system was imaged using X-ray CT at 2, 4, 6, 8 and 12 d after transplanting. The roots were segmented using semi-automated root tracking for speed and reproducibility. The segmented geometries were converted to a mesh suitable for the numerical solution of Richards' equation. Richards' equation was parameterized using existing pore scale studies of soil hydraulic properties in the rhizosphere of wheat plants. Image-based modelling allows the spatial distribution of water around the root to be visualized and the fluxes into the root to be calculated. By comparing the results obtained through image-based modelling to spatially averaged models, the impact of root architecture and geometry in water uptake was quantified. We observed that the spatially averaged models performed well in comparison to the image-based models with <2% difference in uptake. However, the spatial averaging loses important information regarding the spatial distribution of water near the root system., (© 2017 John Wiley & Sons Ltd.)

The rhizosphere is a zone of fundamental importance for understanding the dynamics of nutrient acquisition by plant roots. The canonical difficulty of experimentally investigating the rhizosphere led long ago to the adoption of mathematical models, the most sophisticated of which now incorporate explicit representations of root hairs and rhizosphere soil. Mathematical upscaling regimes, such as homogenisation, offer the possibility of incorporating into larger-scale models the important mechanistic processes occurring at the rhizosphere scale. However, we lack concrete descriptions of all the features required to fully parameterise models at the rhizosphere scale. By combining synchrotron X-ray computed tomography (SRXCT) and a novel root growth assay, we derive a three-dimensional description of rhizosphere soil structure suitable for use in multi-scale modelling frameworks. We describe an approach to mitigate sub-optimal root hair detection via structural root hair growth modelling. The growth model is explicitly parameterised with SRXCT data and simulates three-dimensional root hair ideotypes in silico, which are suitable for both ideotypic analysis and parameterisation of 3D geometry in mathematical models. The study considers different hypothetical conditions governing root hair interactions with soil matrices, with their respective effects on hair morphology being compared between idealised and image-derived soil/root geometries. The studies in idealised geometries suggest that packing arrangement of soil affects hair tortuosity more than the particle diameter. Results in field-derived soil suggest that hair access to poorly mobile nutrients is particularly sensitive to the physical interaction between the growing hairs and the phase of the soil in which soil water is present (i.e. the hydrated textural phase). The general trends in fluid-coincident hair length with distance from the root, and their dependence on hair/soil interaction mechanisms, are conserved across Cartesian and cylindrical geometries.

This study applied time lapse (four-dimensional) synchrotron X-ray computed tomography to observe micro-scale interactions between plant roots and soil. Functionally contrasting maize root tips were repeatedly imaged during ingress into soil columns of varying water content and compaction. This yielded sequences of three-dimensional densiometric data, representing time-resolved geometric soil and root configurations at the micronmetre scale. These data were used as inputs for two full-field kinematic quantification methods, which enabled the analysis of three-dimensional soil deformation around elongating roots. Discrete object tracking was used to track rigid mineral grains, while continuum digital volume correlation was used to track grey-level patterns within local sub-volumes. These techniques both allowed full-field soil displacements to be quantified at an intra-rhizosphere spatial sampling scale of less than 300 µm. Significant differences in deformation mechanisms were identified around different phenotypes under different soil conditions. A uniquely strong contrast was observed between intact and de-capped roots grown in dry, compacted soil. This provides evidence that functional traits of the root cap significantly reduce the amount of soil disturbance per unit of root elongation, with this effect being particularly significant in drier soil., (© 2017 The Author(s).)

In this paper, we provide direct evidence of the importance of root hairs on pore structure development at the root-soil interface during the early stage of crop establishment. This was achieved by use of high-resolution (c. 5 μm) synchrotron radiation computed tomography (SRCT) to visualise both the structure of root hairs and the soil pore structure in plant-soil microcosms. Two contrasting genotypes of barley (Hordeum vulgare), with and without root hairs, were grown for 8 d in microcosms packed with sandy loam soil at 1.2 g cm -3 dry bulk density. Root hairs were visualised within air-filled pore spaces, but not in the fine-textured soil regions. We found that the genotype with root hairs significantly altered the porosity and connectivity of the detectable pore space (> 5 μm) in the rhizosphere, as compared with the no-hair mutants. Both genotypes showed decreasing pore space between 0.8 and 0.1 mm from the root surface. Interestingly the root-hair-bearing genotype had a significantly greater soil pore volume-fraction at the root-soil interface. Effects of pore structure on diffusion and permeability were estimated to be functionally insignificant under saturated conditions when simulated using image-based modelling., (© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.)

The mechanical impedance of soils inhibits the growth of plant roots, often being the most significant physical limitation to root system development. Non-invasive imaging techniques have recently been used to investigate the development of root system architecture over time, but the relationship with soil deformation is usually neglected. Correlative mapping approaches parameterised using 2D and 3D image data have recently gained prominence for quantifying physical deformation in composite materials including fibre-reinforced polymers and trabecular bone. Digital Image Correlation (DIC) and Digital Volume Correlation (DVC) are computational techniques which use the inherent material texture of surfaces and volumes, captured using imaging techniques, to map full-field deformation components in samples during physical loading. Here we develop an experimental assay and methodology for four-dimensional, in vivo X-ray Computed Tomography (XCT) and apply a Digital Volume Correlation (DVC) approach to the data to quantify deformation. The method is validated for a field-derived soil under conditions of uniaxial compression, and a calibration study is used to quantify thresholds of displacement and strain measurement. The validated and calibrated approach is then demonstrated for an in vivo test case in which an extending maize root in field-derived soil was imaged hourly using XCT over a growth period of 19h. This allowed full-field soil deformation data and 3D root tip dynamics to be quantified in parallel for the first time. This fusion of methods paves the way for comparative studies of contrasting soils and plant genotypes, improving our understanding of the fundamental mechanical processes which influence root system development., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

In this study, we developed a spatially explicit model for nutrient uptake by root hairs based on X-ray computed tomography images of the rhizosphere soil structure. This work extends our previous work to larger domains and hence is valid for longer times. Unlike the model used previously, which considered only a small region of soil about the root, we considered an effectively infinite volume of bulk soil about the rhizosphere. We asked the question: At what distance away from root surfaces do the specific structural features of root-hair and soil aggregate morphology not matter because average properties start dominating the nutrient transport? The resulting model was used to capture bulk and rhizosphere soil properties by considering representative volumes of soil far from the root and adjacent to the root, respectively. By increasing the size of the volumes that we considered, the diffusive impedance of the bulk soil and root uptake were seen to converge. We did this for two different values of water content. We found that the size of region for which the nutrient uptake properties converged to a fixed value was dependent on the water saturation. In the fully saturated case, the region of soil we needed to consider was only of radius 1.1mm for poorly soil-mobile species such as phosphate. However, in the case of a partially saturated medium (relative saturation 0.3), we found that a radius of 1.4mm was necessary. This suggests that, in addition to the geometrical properties of the rhizosphere, there is an additional effect of soil moisture properties, which extends further from the root and may relate to other chemical changes in the rhizosphere. The latter were not explicitly included in our model., (© The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.)

· Root hairs are known to be highly important for uptake of sparingly soluble nutrients, particularly in nutrient deficient soils. Development of increasingly sophisticated mathematical models has allowed uptake characteristics to be quantified. However, modelling has been constrained by a lack of methods for imaging live root hairs growing in real soils. · We developed a plant growth protocol and used Synchrotron Radiation X-ray Tomographic Microscopy (SRXTM) to uncover the three-dimensional (3D) interactions of root hairs in real soil. We developed a model of phosphate uptake by root hairs based directly on the geometry of hairs and associated soil pores as revealed by imaging. · Previous modelling studies found that root hairs dominate phosphate uptake. By contrast, our study suggests that hairs and roots contribute equally. We show that uptake by hairs is more localized than by roots and strongly dependent on root hair and aggregate orientation. · The ability to image hair-soil interactions enables a step change in modelling approaches, allowing a more realistic treatment of processes at the scale of individual root hairs in soil pores., (© 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.)

Rice (Oryza sativa L.) secretes far smaller amounts of metal-complexing phytosiderophores (PS) than other grasses. But there is increasing evidence that it relies on PS secretion for its zinc (Zn) uptake. After nitrogen, Zn deficiency is the most common nutrient disorder in rice, affecting up to 50% of lowland rice soils globally. We developed a mathematical model of PS secretion from roots and resulting solubilization and uptake of Zn, allowing for root growth, diurnal variation in secretion, decomposition of the PS in the soil, and the transport and interaction of the PS and Zn in the soil. A sensitivity analysis showed that with realistic parameter values for rice in submerged soil, the typically observed rates of PS secretion from rice are sufficient and necessary to explain observed rates of Zn uptake. There is little effect of diurnal variation in secretion on cumulative Zn uptake, irrespective of other model parameter values, indicating that the observed diurnal variation is not causally related to Zn uptake efficiency. Rooting density has a large effect on uptake per unit PS secretion as a result of overlap of the zones of influence of neighbouring roots. The effects of other complications in the rice rhizosphere are discussed., (© 2011 Blackwell Publishing Ltd.)

• The importance of root hairs in the uptake of sparingly soluble nutrients is understood qualitatively, but not quantitatively, and this limits efforts to breed plants tolerant of nutrient-deficient soils. • Here, we develop a mathematical model of nutrient uptake by root hairs allowing for hair geometry and the details of nutrient transport through soil, including diffusion within and between soil particles. We give illustrative results for phosphate uptake. • Compared with conventional 'single porosity' models, this 'dual porosity' model predicts greater root uptake because more nutrient is available by slow release from within soil particles. Also the effect of soil moisture is less important with the dual porosity model because the effective volume available for diffusion in the soil is larger, and the predicted effects of hair length and density are different. • Consistent with experimental observations, with the dual porosity model, increases in hair length give greater increases in uptake than increases in hair density per unit main root length. The effect of hair density is less in dry soil because the minimum concentration in solution for net influx is reached more rapidly. The effect of hair length is much less sensitive to soil moisture., (© 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.)

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.

This article deals with modelling the simultaneous uptake of water and highly buffered nutrient, such as phosphate, by root branching structures from partially saturated soil. We use the simultaneous water and nutrient uptake model to investigate the effect that water movement has on nutrient uptake. With the aid of this model we are also able to show that the previous models by Barber and Tinker and Nye systematically underestimated the phosphate uptake, due to the oversimplified approach in dealing with root branching structure. In this article we show how this discrepancy can be remedied and the root branching structure included in the models of plant nutrient uptake. We will also discuss the differences in the results for continuous and spot fertilization combined with variable rainfall.

We present a model for water uptake by plant roots from unsaturated soil. The model includes the simultaneous flow of water inside the root network and in the soil. It is constructed by considering first the water uptake by a single root, and then using the parameterized results thereby obtained to build a model for water uptake by the developing root network. We focus our model on annual plants, in particular the model will be applicable to commercial monocultures like maize, wheat, etc. The model is solved numerically, and the results are compared with approximate analytic solutions. The model predicts that as a result of water uptake by plant roots, dry and wet zones will develop in the soil. The wet zone is located near the surface of the soil and the depth of it is determined by a balance between rainfall and the rate of water uptake. The dry zone develops directly beneath the wet zone because the influence of the rainfall at the soil surface does not reach this region, due to the nonlinear nature of the water flow in the partially saturated soil. We develop approximate analytic expressions for the depth of the wet zone and discuss briefly its ecological significance for the plant. Using this model we also address the question of where water uptake sites are concentrated in the root system. The model indicates that the regions near the base of the root system (i.e. close to the ground surface) and near the root tips will take up more water than the middle region of the root system, again due to the highly nonlinear nature of water flow in the soil.

The classical model of plant root nutrient uptake due to Nye. Tinker and Barber is developed and extended. We provide an explicit closed formula for the uptake by a single cylindrical root for all cases of practical interest by solving the absorption-diffusion equation for the soil nutrient concentration asymptotically in the limit of large time. We then use this single root model as a building block to construct a model which allows for root size distribution in a more realistic plant root system, and we include the effects of root branching and growth. The results are compared with previous theoretical and experimental studies.

Phosphorus (P) is a key yield-limiting nutrient for crops, but the main source of P fertiliser is finite. Therefore, efficient fertilisation is crucial. Optimal P application requires understanding of the dynamic processes affecting P availability to plants, including fertiliser dissolution rate and soil buffer power. However, standard soil testing methods sample at fixed time points, preventing a mechanistic understanding of P uptake variability. We used image-based modelling to investigate the effects of fertiliser dissolution rate and soil buffer power on P uptake by wheat roots imaged using X-ray CT. We modelled uptake based on 1-day, 1-week, and 14-week dissolution of a fixed quantity of total P for two common soil buffer powers. We found rapid fertiliser dissolution increased short-term root uptake, but total uptake from 1-week matched 1-day dissolution. We quantified the large effects root system architecture had on P uptake, finding that there were trade-offs between total P uptake and uptake per unit root length, representing a carbon investment/phosphorus uptake balance. These results provide a starting point for predictive modelling of uptake from different P fertilisers in different soils. With the addition of further X-ray CT image datasets and a wider range of conditions, our simulation approach could be developed further for rapid trialling of fertiliser-soil combinations to inform field-scale trials or management. [ABSTRACT FROM AUTHOR]

Background and Aims Previous laboratory studies have suggested selection for root hair traits in future crop breeding to improve resource use efficiency and stress tolerance. However, data on the interplay between root hairs and open-field systems, under contrasting soils and climate conditions, are limited. As such, this study aims to experimentally elucidate some of the impacts that root hairs have on plant performance on a field scale. Methods A field experiment was set up in Scotland for two consecutive years, under contrasting climate conditions and different soil textures (i.e. clay loam vs. sandy loam). Five barley (Hordeum vulgare) genotypes exhibiting variation in root hair length and density were used in the study. Root hair length, density and rhizosheath weight were measured at several growth stages, as well as shoot biomass, plant water status, shoot phosphorus (P) accumulation and grain yield. Key Results Measurements of root hair density, length and its correlation with rhizosheath weight highlighted trait robustness in the field under variable environmental conditions, although significant variations were found between soil textures as the growing season progressed. Root hairs did not confer a notable advantage to barley under optimal conditions, but under soil water deficit root hairs enhanced plant water status and stress tolerance resulting in a less negative leaf water potential and lower leaf abscisic acid concentration, while promoting shoot P accumulation. Furthermore, the presence of root hairs did not decrease yield under optimal conditions, while root hairs enhanced yield stability under drought. Conclusions Selecting for beneficial root hair traits can enhance yield stability without diminishing yield potential, overcoming the breeder's dilemma of trying to simultaneously enhance both productivity and resilience. Therefore, the maintenance or enhancement of root hairs can represent a key trait for breeding the next generation of crops for improved drought tolerance in relation to climate change. [ABSTRACT FROM AUTHOR]

Aims: Organic acid exudation by plant roots is thought to promote phosphate (P) solubilisation and bioavailability in soils with poorly available nutrients. Here we describe a new combined experimental (microdialysis) and modelling approach to quantify citrate-enhanced P desorption and its importance for root P uptake. Methods: To mimic the rhizosphere, microdialysis probes were placed in soil and perfused with citrate solutions (0.1, 1.0 and 10 mM) and the amount of P recovered from soil used to quantify rhizosphere P availability. Parameters in a mathematical model describing probe P uptake, citrate exudation, P movement and citrate-enhanced desorption were fit to the experimental data. These parameters were used in a model of a root which exuded citrate and absorbed P. The importance of soil citrate-P mobilisation for root P uptake was then quantified using this model. Results: A plant needs to exude citrate at a rate of 0.73 μmol cm−1 of root h−1 to see a significant increase in P absorption. Microdialysis probes with citrate in the perfusate were shown to absorb similar quantities of P to an exuding root. Conclusion: A single root exuding citrate at a typical rate (4.3 × 10−5 μmol m−1 of root h−1) did not contribute significantly to P uptake. Microdialysis probes show promise for measuring rhizosphere processes when calibration experiments and mathematical modelling are used to decouple microdialysis and rhizosphere mechanisms. [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]

We present a new numerical approach describing nutrient uptake in three dimensions. Dynamic boundary conditions are considered at the individual root surfaces within a root system. As an example, we compare the three-dimensional simulation results of phosphate uptake by a young maize root system to the corresponding effective solution. We show that the two solutions are similar concerning phosphate uptake and the size of the depletion zones. The presented approach makes it possible to verify simplifications that are made in the development of effective models. Furthermore, it is possible to extend existing models by including spatial heterogeneities that will increase our understanding of rhizosphere processes. [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 correction to the article "Verification and intercomparison of reactive transport codes to describe root-uptake" that was published in the October 30, 2007 issue is presented.