Image-based modelling of nutrient movement in and around the rhizosphere

The effect of root hairs on root water uptake is determined by root-soil contact and root hair shrinkage

The effect of root hairs on water uptake remains controversial. In particular, the key root hair and soil parameters that determine their importance have been elusive. We grew maize plants (Zea mays) in microcosms and scanned them using synchrotron-based X-ray computed microtomography. By means of image-based modelling, we investigated the parameters determining the effectiveness of root hairs in root water uptake. We explicitly accounted for rhizosphere features (e.g. root-soil contact and pore structure) and took root hair shrinkage of dehydrated root hairs into consideration. Our model suggests that > 85% of the variance in root water uptake is explained by the hair-induced increase in root-soil contact. In dry soil conditions, root hair shrinkage reduces the impact of hairs substantially. We conclude that the effectiveness of root hairs on root water uptake is determined by the hair-induced increase in root-soil contact and root hair shrinkage. Although the latter clearly reduces the effect of hairs on water uptake, our model still indicated facilitation of water uptake by root hairs at soil matric potentials from -1 to -0.1 MPa. Our findings provide new avenues towards a mechanistic understanding of the role of root hairs on water uptake.

Statistical Effective Diffusivity Estimation in Porous Media Using an Integrated On-site Imaging Workflow for Synchrotron Users

Transport in porous media plays an essential role for many physical, engineering, biological and environmental processes. Novel synchrotron imaging techniques and image-based models have enabled more robust quantification of geometric structures that influence transport through the pore space. However, image-based modelling is computationally expensive, and end users often require, while conducting imaging campaign, fast and agile bulk-scale effective parameter estimates that account for the pore-scale details. In this manuscript we enhance a pre-existing image-based model solver known as OpenImpala to estimate bulk-scale effective transport parameters. In particular, the boundary conditions and equations in OpenImpala were modified in order to estimate the effective diffusivity in an imaged system/geometry via a formal multi-scale homogenisation expansion. Estimates of effective pore space diffusivity were generated for a range of elementary volume sizes to estimate when the effective diffusivity values begin to converge to a single value. Results from OpenImpala were validated against a commercial finite element method package COMSOL Multiphysics (abbreviated as COMSOL). Results showed that the effective diffusivity values determined with OpenImpala were similar to those estimated by COMSOL. Tests on larger domains comparing a full image-based model to a homogenised (geometrically uniform) domain that used the effective diffusivity parameters showed differences below 2 % error, thus verifying the accuracy of the effective diffusivity estimates. Finally, we compared OpenImpala's parallel computing speeds to COMSOL. OpenImpala consistently ran simulations within fractions of minutes, which was two orders of magnitude faster than COMSOL providing identical supercomputing specifications. In conclusion, we demonstrated OpenImpala's utility as part of an on-site tomography processing pipeline allowing for fast and agile assessment of porous media processes and to guide imaging campaigns while they are happening at synchrotron beamlines.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11242-023-01993-7.

Multimodal correlative imaging and modelling of phosphorus uptake from soil by hyphae of mycorrhizal fungi

Phosphorus (P) is essential for plant growth. Arbuscular mycorrhizal fungi (AMF) aid its uptake by acquiring P from sources distant from roots in return for carbon. Little is known about how AMF colonise soil pore-space, and models of AMF-enhanced P-uptake are poorly validated. We used synchrotron X-ray computed tomography to visualize mycorrhizas in soil and synchrotron X-ray fluorescence/X-ray absorption near edge structure (XRF/XANES) elemental mapping for P, sulphur (S) and aluminium (Al) in combination with modelling. We found that AMF inoculation had a suppressive effect on colonisation by other soil fungi and identified differences in structure and growth rate between hyphae of AMF and nonmycorrhizal fungi. Our results showed that AMF co-locate with areas of high P and low Al, and preferentially associate with organic-type P species over Al-rich inorganic P. We discovered that AMF avoid Al-rich areas as a source of P. Sulphur-rich regions were found to be correlated with higher hyphal density and an increased organic-associated P-pool, whilst oxidized S-species were found close to AMF hyphae. Increased S oxidation close to AMF suggested the observed changes were microbiome-related. Our experimentally-validated model led to an estimate of P-uptake by AMF hyphae that is an order of magnitude lower than rates previously estimated - a result with significant implications for the modelling of plant-soil-AMF interactions.

Significance of root hairs in developing stress-resilient plants for sustainable crop production

Root hairs represent a beneficial agronomic trait to potentially reduce fertilizer and irrigation inputs. Over the past decades, research in the plant model Arabidopsis thaliana has provided insights into root hair development, the underlying genetic framework and the integration of environmental cues within this framework. Recent years have seen a paradigm shift, where studies are now highlighting conservation and diversification of root hair developmental programs in other plant species and the agronomic relevance of root hairs in a wider ecological context. In this review, we specifically discuss the molecular evolution of the RSL (RHD Six-Like) pathway that controls root hair development and growth in land plants. We also discuss how root hairs contribute to plant performance as an active physiological rooting structure by performing resource acquisition, providing anchorage and constructing the rhizosphere with desirable physical, chemical and biological properties. Finally, we outline future research directions that can help achieve the potential of root hairs in developing sustainable agroecosystems.

A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements

In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I-VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers' views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.

A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements

In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I-VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers' views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.

Bridging Microbial Functional Traits With Localized Process Rates at Soil Interfaces

In this review, we introduce microbially-mediated soil processes, players, their functional traits, and their links to processes at biogeochemical interfaces [e.g., rhizosphere, detritusphere, (bio)-pores, and aggregate surfaces]. A conceptual view emphasizes the central role of the rhizosphere in interactions with other biogeochemical interfaces, considering biotic and abiotic dynamic drivers. We discuss the applicability of three groups of traits based on microbial physiology, activity state, and genomic functional traits to reflect microbial growth in soil. The sensitivity and credibility of modern molecular approaches to estimate microbial-specific growth rates require further development. A link between functional traits determined by physiological (e.g., respiration, biomarkers) and genomic (e.g., genome size, number of ribosomal gene copies per genome, expression of catabolic versus biosynthetic genes) approaches is strongly affected by environmental conditions such as carbon, nutrient availability, and ecosystem type. Therefore, we address the role of soil physico-chemical conditions and trophic interactions as drivers of microbially-mediated soil processes at relevant scales for process localization. The strengths and weaknesses of current approaches (destructive, non-destructive, and predictive) for assessing process localization and the corresponding estimates of process rates are linked to the challenges for modeling microbially-mediated processes in heterogeneous soil microhabitats. Finally, we introduce a conceptual self-regulatory mechanism based on the flexible structure of active microbial communities. Microbial taxa best suited to each successional stage of substrate decomposition become dominant and alter the community structure. The rates of decomposition of organic compounds, therefore, are dependent on the functional traits of dominant taxa and microbial strategies, which are selected and driven by the local environment.

Rhizosphere Microbiome Cooperations: Strategies for Sustainable Crop Production

Interactions between microorganisms and host plants determine the growth and development as well as the health of the host plant. Various microbial groups inhabit the rhizosphere, each with its peculiar function. The survival of each microbial group depends to a large extent on its ability to colonize the plant root and outcompete the native organisms. The role of the rhizospheric microbiome in enhancing plant growth has not been fully maximized. An understanding of the complexities of microbial interactions and factors affecting their assembly in the community is necessary to benefit maximally from the cooperations of various microbial communities for sustainable crop production. In this review, we outline the various organisms associated with the plant rhizosphere with emphasis on their interactions and mechanisms used in plant growth promotion.

Developing a system for in vivo imaging of maize roots containing iodinated contrast media in soil using synchrotron XCT and XRF

AIMS

We sought to develop a novel experimental system which enabled application of iodinated contrast media to in vivo plant roots intact in soil and was compatible with time-resolved synchrotron X-ray computed tomography imaging. The system was developed to overcome issues of low contrast to noise within X-ray computed tomography images of plant roots and soil environments, the latter of which can complicate image processing and result in the loss of anatomical information.

METHODS

To demonstrate the efficacy of the system we employ the novel use of both synchrotron X-ray computed tomography and synchrotron X-ray fluorescence mapping to capture the translocation of the contrast media through root vasculature into the leaves.

RESULTS

With the application of contrast media we identify fluid flow in root vasculature and visualise anatomical features, which are otherwise often only observable in ex vivo microscopy, including: the xylem, metaxylem, pith, fibres in aerenchyma and leaf venation. We are also able to observe interactions between aerenchyma cross sectional area and solute transport in the root vasculature with depth.

CONCLUSIONS

Our novel system was capable of successfully delivering sufficient contrast media into root and leaf tissues such that anatomical features could be visualised and internal fluid transport observed. We propose that our system could be used in future to study internal plant transport mechanisms and parameterise models for fluid flow in plants.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11104-020-04784-x.

Comprehensive assessment of growth parameters for screening endophytic bacterial strains in Solanum lycopersicum (Tomato)

Conventional agricultural practices demand application of pesticides for better yield, yet their uncontrolled use for longer duration exhibit deleterious effects on the soil health and subsequent plant productivity. These circumstances have displayed alarming effects on food security in the modern world. Therefore, biological solutions to the crisis can be practiced in consideration to their environmental benefits. Bacterial endophytes are ubiquitous in the phytosystem and beneficial for the plant growth and productivity. The present study aimed to obtain endophytic bacterial strains that can be developed as effective plant growth promoters. For this purpose twelve strains of bacterial endophytes were isolated from different plant sources and their putative plant growth promoting attributes were analyzed by morphological and biochemical studies. Subsequently these isolates were inoculated in the Solanum lycopersicum (Tomato) and the factors like germination percentage, seedling length, biomass production, and leaf variables were analyzed. However, the vigour index was considered as the prime parameter for determining plant growth. In essence, RR2 and RR4 strains were observed as effective growth promoter, hence in future they can be utilized as effective biofertilizers.

Analytical solutions of citrate–phosphate coupled model of rice (Oryza sativa L.) roots

The citrate secreted by the rice (Oryza sativa L.) roots will promote the absorption of phosphate, and this process is described by the Kirk model. In our work, the Kirk model is divided into citrate sub-model and phosphate sub-model. In the citrate sub-model, we obtain the analytical solution of citrate with the Laplace transform, inverse Laplace transform and convolution theorem. The citrate solution is substituted into the phosphate sub-model, and the analytical solution of phosphate is obtained by the separation variable method. The existence of the solutions can be proved by the comparison test, the Weierstrass M-test and the Abel discriminating method.

Image-based quantification of soil microbial dead zones induced by nitrogen fertilization

Microbial communities in agricultural soils underpin many ecosystem services including the maintenance of soil structure, food production, water purification and carbon storage. However, the impact of fertilization on the health of microbial communities is not well understood. This study investigates the spatial and temporal dynamics of nitrogen (N) transport away from a fertilizer granule with pore scale resolution. Specifically, we examined how soil structure and moisture content influence fertilizer derived N movement through the soil pore network and the subsequent impact of on soil microbial communities. We develop a mathematical model to describe N transport and reactions in soil at the pore-scale. Using X-ray Computed Tomography scans, we reconstructed a microscale description of a soil-pore geometry as a computational mesh. Solving two-phase water/air model produced pore-scale water distributions at 15, 30 and 70% water-filled pore volume. The N-speciation model considered ammonium (NH₄⁺), nitrate (NO₃^-) and dissolved organic N (DON), and included N immobilization, ammonification and nitrification processes, as well as diffusion in soil solution. We simulated the dissolution of a fertilizer pellet and a pore scale N cycle at three different water saturations. To aid interpretation of the model results, microbial activity at a range of N concentrations was measured. The model showed that the diffusion and concentration of N in water films is critically dependent upon soil moisture and N species. We predict that the maximum NH₄⁺ and NO₃^- concentrations in soil solution around the pellet under dry conditions are in the order of 1 × 10³ and 1 × 10⁴ mol m^-3 respectively, and under wet conditions 2 × 10² and 1 × 10³ mol m^-3, respectively. Supporting experimental evidence suggests that these concentrations would be sufficient to reduce microbial activity in the short-term in the zone immediately around the fertilizer pellet (ranging from 0.9 to 3.8 mm), causing a major loss of soil biological functioning. This model demonstrates the importance of pore-scale processes in regulating N movement and their interactions with the soil microbiome.

Significance of root hairs at the field scale - modelling root water and phosphorus uptake under different field conditions

ABSTRACT

BACKGROUND AND AIMS

Root hairs play a significant role in phosphorus (P) extraction at the pore scale. However, their importance at the field scale remains poorly understood.

METHODS

This study uses a continuum model to explore the impact of root hairs on the large-scale uptake of P, comparing root hair influence under different agricultural scenarios. High vs low and constant vs decaying P concentrations down the soil profile are considered, along with early vs late precipitation scenarios.

RESULTS

Simulation results suggest root hairs accounted for 50% of total P uptake by plants. Furthermore, a delayed initiation time of precipitation potentially limits the P uptake rate by over 50% depending on the growth period. Despite the large differences in the uptake rate, changes in the soil P concentration in the domain due to root solute uptake remains marginal when considering a single growth season. However, over the duration of 6 years, simulation results showed that noticeable differences arise over time.

CONCLUSION

Root hairs are critical to P capture, with uptake efficiency potentially enhanced by coordinating irrigation with P application during earlier growth stages of crops.

Approximate nutrient flux and concentration solutions of the Nye-Tinker-Barber model by the perturbation expansion method

The Nye-Tinker-Barber model is a basic and representative one for single-ion nutrient uptake by plant root from the soil and we aim to derive its approximate analytical solutions of flux and concentration. We divide the rhizosphere into the inner and the outer fields, match the inner and the outer solutions near the root surface, and then obtain the approximate analytical solutions of nutrient uptake flux at the root surface and global nutrient concentration of the diffusion or the convection-diffusion Nye-Tinker-Barber model. The analytical and numerical fluxes of K⁺ and [Formula: see text] decay quickly to 0 in less than 3 days while [Formula: see text] and Cd²⁺ gradually decrease in more than 15 days; the depletion profile spread of [Formula: see text] is apparently narrower than [Formula: see text] and K⁺ in 24 days. The different flux and concentration patterns of 4 nutrients result from their mobility and solubility in the rhizosphere. In comparison with the numerical simulations and the previous analytical results, we find that the analytical flux will overestimate the numerical flux of [Formula: see text] and Cd²⁺ while the analytical concentration can accurately predict the numerical concentration; the flux and the concentration solutions of the convection-diffusion Nye-Tinker-Barber model can be simplified to the diffusion versions by the Péclet number, and they can more widely describe the transport of nutrients of different attributes in soils of different textures with different levels of saturation, conductivity and permeability.

Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain

Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gasses. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale) that is commensurate with the habitat of many microorganisms. For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. With regard to the microbial aspects, although a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because of the scarcity of relevant experimental data. For significant progress to be made, it is crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead. Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future.

Measurement of micro-scale soil deformation around roots using four-dimensional synchrotron tomography and image correlation

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.

Determination of macro-scale soil properties from pore scale structures: image-based modelling of poroelastic structures

We show how a combination of X-ray computed tomography (X-CT) and image-based modelling can be used to calculate the effect of moisture content and compaction on the macroscopic structural properties of soil. Our method is based on the equations derived in Daly & Roose (2018 Proc. R. Soc. A474, 20170141. (doi:10.1098/rspa.2017.0141)), which we have extended so they can be directly applied to the segmented images obtained from X-CT. We assume that the soils are composed of air-filled pore space, solid mineral grains and a mixed phase composed of both clay particles and water. We considered three different initial soil treatments, composed of two different compaction levels and two different moisture contents. We found that the effective properties of the soils were unaffected by compaction over the range tested in this paper. However, changing the moisture content significantly altered the hydraulic and mechanical properties of the soils. A key strength of this method is that it enables the optimization or even design of soils composed from different constituents, with specific mechanical and hydraulic properties.

Determination of macro-scale soil properties from pore-scale structures: model derivation

In this paper, we use homogenization to derive a set of macro-scale poro-elastic equations for soils composed of rigid solid particles, air-filled pore space and a poro-elastic mixed phase. We consider the derivation in the limit of large deformation and show that by solving representative problems on the micro-scale we can parametrize the macro-scale equations. To validate the homogenization procedure, we compare the predictions of the homogenized equations with those of the full equations for a range of different geometries and material properties. We show that the results differ by [Formula: see text] for all cases considered. The success of the homogenization scheme means that it can be used to determine the macro-scale poro-elastic properties of soils from the underlying structure. Hence, it will prove a valuable tool in both characterization and optimization.

Quantification of root water uptake in soil using X-ray computed tomography and image-based modelling

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.

Fluid flow in porous media using image-based modelling to parametrize Richards' equation

The parameters in Richards' equation are usually calculated from experimentally measured values of the soil-water characteristic curve and saturated hydraulic conductivity. The complex pore structures that often occur in porous media complicate such parametrization due to hysteresis between wetting and drying and the effects of tortuosity. Rather than estimate the parameters in Richards' equation from these indirect measurements, image-based modelling is used to investigate the relationship between the pore structure and the parameters. A three-dimensional, X-ray computed tomography image stack of a soil sample with voxel resolution of 6 μm has been used to create a computational mesh. The Cahn-Hilliard-Stokes equations for two-fluid flow, in this case water and air, were applied to this mesh and solved using the finite-element method in COMSOL Multiphysics. The upscaled parameters in Richards' equation are then obtained via homogenization. The effect on the soil-water retention curve due to three different contact angles, 0°, 20° and 60°, was also investigated. The results show that the pore structure affects the properties of the flow on the large scale, and different contact angles can change the parameters for Richards' equation.

An Explicit Structural Model of Root Hair and Soil Interactions Parameterised by Synchrotron X-ray Computed Tomography

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.

High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation

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.