Droplet Microfluidic-Based In Situ Analyzer for Monitoring Free Nitrate in Soil.

Monitoring nutrients in the soil can provide valuable information for understanding their spatiotemporal variability and informing precise soil management. Here, we describe an autonomous in situ analyzer for the real-time monitoring of nitrate in soil. The analyzer can sample soil nitrate using either microdialysis or ultrafiltration probes placed within the soil and quantify soil nitrate using droplet microfluidics and colorimetric measurement. Compared with traditional manual sampling and lab analysis, the analyzer features low reagent consumption (96 µL per measurement), low maintenance requirement (monthly), and high measurement frequency (2 or 4 measurements per day), providing nondrifting lab-quality data with errors of less than 10% using a microdialysis probe and 2-3% for ultrafiltration. The analyzer was deployed at both the campus garden and forest for different periods of time, being able to capture changes in free nitrate levels in response to manual perturbation by the addition of nitrate standard solutions and natural perturbation by rainfall events.

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.

Projected Increases in Precipitation Are Expected To Reduce Nitrogen Use Efficiency and Alter Optimal Fertilization Timings in Agriculture in the South East of England.

Nitrogen fertilization is vital for productive agriculture and efficient land use. However, globally, approximately 50% of the nitrogen applied is lost to the environment, causing inefficiencies, pollution, and greenhouse gas emissions. Rainfall and its effect on soil moisture are the major components controlling nitrogen losses in agriculture. Thus, changing rainfall patterns could accelerate nitrogen inefficiencies. We used a mechanistic modeling platform to determine how precipitation-optimal nitrogen fertilization timings and resulting crop nitrogen uptake have changed historically (1950-2020) and how they are predicted to change under the RCP8.5 climate scenario (2021-2069) in the South East of England. We found that historically, neither precipitation-optimal fertilization timings nor resulting plant uptake changed significantly. However, there were large year-to-year variations in both. In the 2030s, where it is projected to get wetter, precipitation-optimal fertilization timings are predicted to be later in the season and the resulting plant uptake noticeably lower. After 2040, the precipitation-optimal uptakes are projected to increase with earlier precipitation-optimal timings closer to historical values, corresponding to the projected mean daily rainfall rates decreasing to the historical values in these growing seasons. It seems that the interannual variation in precipitation-optimal uptake is projected to increase. Ultimately, projected changes in precipitation patterns will affect nitrogen uptake and precipitation-optimal fertilization timings. We argue that the use of bespoke fertilization timings in each year can help recuperate the reduced N uptake due to changing precipitation.

Modelling of stress transfer in root-reinforced soils informed by four-dimensional X-ray computed tomography and digital volume correlation data.

Vegetation enhances soil shearing resistance through water uptake and root reinforcement. Analytical models for soils reinforced with roots rely on input parameters that are difficult to measure, leading to widely varying predictions of behaviour. The opaque heterogeneous nature of rooted soils results in complex soil-root interaction mechanisms that cannot easily be quantified. The authors measured, for the first time, the shear resistance and deformations of fallow, willow-rooted and gorse-rooted soils during direct shear using X-ray computed tomography and digital volume correlation. Both species caused an increase in shear zone thickness, both initially and as shear progressed. Shear zone thickness peaked at up to 35 mm, often close to the thickest roots and towards the centre of the column. Root extension during shear was 10-30% less than the tri-linear root profile assumed in a Waldron-type model, owing to root curvature. Root analogues used to explore the root-soil interface behaviour suggested that root lateral branches play an important role in anchoring the roots. The Waldron-type model was modified to incorporate non-uniform shear zone thickness and growth, and accurately predicted the observed, up to sevenfold, increase in shear resistance of root-reinforced soil.

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.

Space and time-resolved monitoring of phosphorus release from a fertilizer pellet and its mobility in soil using microdialysis and X-ray computed tomography.

Phosphorus is an essential nutrient for crops. Precise spatiotemporal application of P fertilizer can improve plant P acquisition and reduce run-off losses of P. Optimizing application would benefit from understanding the dynamics of P release from a fertilizer pellet into bulk soil, which requires space- and time-resolved measurements of P concentration in soil solutions. In this study, we combined microdialysis and X-ray computed tomography to investigate P transport in soil. Microdialysis probes enabled repeated solute sampling from one location with minimal physical disturbance, and their small dimensions permitted spatially resolved monitoring. We observed a rapid initial release of P from the source, producing high dissolved P concentrations within the first 24 h, followed by a decrease in dissolved P over time compatible with adsorption onto soil particles. Soils with greater bulk density (i.e., reduced soil porosity) impeded the P pulse movement, which resulted in a less homogeneous distribution of total P in the soil column at the end of the experiment. The model fit to the data showed that the observed phenomena can be explained by diffusion and adsorption. The results showed that compared with conventional measurement techniques (e.g., suction cups), microdialysis measurements present a less invasive alternative. The time-resolved measurements ultimately highlighted rapid P dynamics that require more attention for improving P use efficiency.

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.

Linking root structure to functionality: the impact of root system architecture on citrate-enhanced phosphate uptake.

Root citrate exudation is thought to be important for phosphate solubilization. Previous research has concluded that cluster-like roots benefit most from this exudation in terms of increased phosphate uptake, suggesting that root structure plays an important role in citrate-enhanced uptake (additional phosphate uptake due to citrate exudation). Time-resolved computed tomography images of wheat root systems were used as the geometry for 3D citrate-phosphate solubilization models. Citrate-enhanced uptake was correlated with morphological measures of the root systems to determine which had the most benefit. A large variation of citrate-enhanced uptake over 11 root structures was observed. Root surface area dominated absolute phosphate uptake, but did not explain citrate-enhanced uptake. Number of exuding root tips correlated well with citrate-enhanced uptake. Root tips in close proximity could collectively exude high amounts of citrate, resulting in a delayed spike in citrate-enhanced uptake. Root system architecture plays an important role in citrate-enhanced uptake. Singular morphological measurements of the root systems cannot entirely explain variations in citrate-enhanced uptake. Root systems with many tips would benefit greatly from citrate exudation. Quantifying citrate-enhanced uptake experimentally is difficult as variations in root surface area would overwhelm citrate benefits.

A four-compartment multiscale model of fluid and drug distribution in vascular tumours.

The subtle relationship between vascular network structure and mass transport is vital to predict and improve the efficacy of anticancer treatments. Here, mathematical homogenisation is used to derive a new multiscale continuum model of blood and chemotherapy transport in the vasculature and interstitium of a vascular tumour. This framework enables information at a range of vascular hierarchies to be fed into an effective description on the length scale of the tumour. The model behaviour is explored through a demonstrative case study of a simplified representation of a dorsal skinfold chamber, to examine the role of vascular network architecture in influencing fluid and drug perfusion on the length scale of the chamber. A single parameter, P, is identified that relates tumour-scale fluid perfusion to the permeability and density of the capillary bed. By fixing the topological and physiological properties of the arteriole and venule networks, an optimal value for P is identified, which maximises tumour fluid transport and is thus hypothesised to benefit chemotherapy delivery. We calculate the values for P for eight explicit network structures; in each case, vascular intervention by either decreasing the permeability or increasing the density of the capillary network would increase fluid perfusion through the cancerous tissue. Chemotherapeutic strategies are compared and indicate that single injection is consistently more successful compared with constant perfusion, and the model predicts optimal timing of a second dose. These results highlight the potential of computational modelling to elucidate the link between vascular architecture and fluid, drug distribution in tumours.

Root-induced soil deformation influences Fe, S and P: rhizosphere chemistry investigated using synchrotron XRF and XANES.

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 (SO42- ) 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.

Stabilizing gold nanoparticles for use in X-ray computed tomography imaging of soil systems.

This investigation establishes a system of gold nanoparticles that show good colloidal stability as an X-ray computed tomography (XCT) contrast agent under soil conditions. Gold nanoparticles offer numerous beneficial traits for experiments in biology including: comparatively minimal phytotoxicity, X-ray attenuation of the material and the capacity for functionalization. However, soil salinity, acidity and surface charges can induce aggregation and destabilize gold nanoparticles, hence in biomedical applications polymer coatings are commonly applied to gold nanoparticles to enhance stability in the in vivo environment. Here we first demonstrate non-coated nanoparticles aggregate in soil-water solutions. We then show coating with a polyethylene glycol (PEG) layer prevents this aggregation. To demonstrate this, PEG-coated nanoparticles were drawn through flow columns containing soil and were shown to be stable; this is in contrast with control experiments using silica and alumina-packed columns. We further determined that a suspension of coated gold nanoparticles which fully saturated soil maintained stability over at least 5 days. Finally, we used time resolved XCT imaging and image based models to approximate nanoparticle diffusion as similar to that of other typical plant nutrients diffusing in water. Together, these results establish the PEGylated gold nanoparticles as potential contrast agents for XCT imaging in soil.

Multiple Scale Homogenisation of Nutrient Movement and Crop Growth in Partially Saturated Soil.

In this paper, we use multiple scale homogenisation to derive a set of averaged macroscale equations that describe the movement of nutrients in partially saturated soil that contains growing potato tubers. The soil is modelled as a poroelastic material, which is deformed by the growth of the tubers, where the growth of each tuber is dependent on the uptake of nutrients via a sink term within the soil representing root nutrient uptake. Special attention is paid to the reduction in void space, resulting change in local water content and the impact on nutrient diffusion within the soil as the tubers increase in size. To validate the multiple scale homogenisation procedure, we compare the system of homogenised equations to the original set of equations and find that the solutions between the two models differ by [Formula: see text]. However, we find that the computation time between the two sets of equations differs by several orders of magnitude. This is due to the combined effects of the complex three-dimensional geometry and the implementation of a moving boundary condition to capture tuber growth.

Soil carbon dioxide venting through rice roots.

The growth of rice in submerged soils depends on its ability to form continuous gas channels-aerenchyma-through which oxygen (O2 ) diffuses from the shoots to aerate the roots. Less well understood is the extent to which aerenchyma permits venting of respiratory carbon dioxide (CO2 ) in the opposite direction. Large, potentially toxic concentrations of dissolved CO2 develop in submerged rice soils. We show using X-ray computed tomography and image-based mathematical modelling that CO2 venting through rice roots is far greater than thought hitherto. We found rates of venting equivalent to a third of the daily CO2 fixation in photosynthesis. Without this venting through the roots, the concentrations of CO2 and associated bicarbonate (HCO3- ) in root cells would have been well above levels known to be toxic to roots. Removal of CO2 and hence carbonic acid (H2 CO3 ) 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.

Correlative 3D Imaging and Microfluidic Modelling of Human Pulmonary Lymphatics using Immunohistochemistry and High-resolution µCT.

Lung lymphatics maintain fluid homoeostasis by providing a drainage system that returns fluid, cells and metabolites to the circulatory system. The 3D structure of the human pulmonary lymphatic network is essential to lung function, but it is poorly characterised. Image-based 3D mathematical modelling of pulmonary lymphatic microfluidics has been limited by the lack of accurate and representative image geometries. This is due to the microstructural similarity of the lymphatics to the blood vessel network, the lack of lymphatic-specific biomarkers, the technical limitations associated with image resolution in 3D, and sectioning artefacts present in 2D techniques. We present a method that combines lymphatic specific (D240 antibody) immunohistochemistry (IHC), optimised high-resolution X-ray microfocus computed tomography (µCT) and finite-element mathematical modelling to assess the function of human peripheral lung tissue. The initial results identify lymphatic heterogeneity within and between lung tissue. Lymphatic vessel volume fraction and fractal dimension significantly decreases away from the lung pleural surface (p < 0.001, n = 25 and p < 0.01, n = 20, respectively). Microfluidic modelling successfully shows that in lung tissue the fluid derived from the blood vessels drains through the interstitium into the lymphatic vessel network and this drainage is different in the subpleural space compared to the intralobular space. When comparing lung tissue from health and disease, human pulmonary lymphatics were significantly different across five morphometric measures used in this study (p ≤ 0.0001). This proof of principle study establishes a new engineering technology and workflow for further studies of pulmonary lymphatics and demonstrates for the first time the combination of correlative µCT and IHC to enable 3D mathematical modelling of human lung microfluidics at micrometre resolution.

Can VEGFC Form Turing Patterns in the Zebrafish Embryo?

This paper is concerned with a late stage of lymphangiogenesis in the trunk of the zebrafish embryo. At 48 hours post-fertilisation (HPF), a pool of parachordal lymphangioblasts (PLs) lies in the horizontal myoseptum. Between 48 and 168 HPF, the PLs spread from the horizontal myoseptum to form the thoracic duct, dorsal longitudinal lymphatic vessel, and parachordal lymphatic vessel. This paper deals with the potential of vascular endothelial growth factor C (VEGFC) to guide the differentiation of PLs into the mature lymphatic endothelial cells that form the vessels. We built a mathematical model to describe the biochemical interactions between VEGFC, collagen I, and matrix metalloproteinase 2 (MMP2). We also carried out a linear stability analysis of the model and computer simulations of VEGFC patterning. The results suggest that VEGFC can form Turing patterns due to its relations with MMP2 and collagen I, but the zebrafish embryo needs a separate control mechanism to create the right physiological conditions. Furthermore, this control mechanism must ensure that the VEGFC patterns are useful for lymphangiogenesis: stationary, steep gradients, and reasonably fast forming. Generally, the combination of a patterning species, a matrix protein, and a remodelling species is a new patterning mechanism.

Imaging microstructure of the barley rhizosphere: particle packing and root hair influences.

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.

A Model of Uranium Uptake by Plant Roots Allowing for Root-Induced Changes in the soil.

We develop a model with which to study the poorly understood mechanisms of uranium (U) uptake by plants. The model is based on equations for transport and reaction of U and acids and bases in the rhizosphere around cylindrical plant roots. It allows for the speciation of U with hydroxyl, carbonate, and organic ligands in the soil solution; the nature and kinetics of sorption reactions with the soil solid; and the effects of root-induced changes in rhizosphere pH. A sensitivity analysis showed the importance of soil sorption and speciation parameters as influenced by pH and CO2 pressure; and of root geometry and root-induced acid-base changes linked to the form of nitrogen taken up by the root. The root absorbing coefficient for U, relating influx to the concentration of U species in solution at the root surface, was also important. Simplified empirical models of U uptake by different plant species and soil types need to account for these effects.

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.

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.