Muhammad Naveed

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

Summary 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.

Plant exudates may stabilize or weaken soil depending on species, origin and time

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

Correlating Gas Transport Parameters and X-Ray Computed Tomography Measurements in Porous Media

Abstract Gas transport parameters and X-ray computed tomography (CT) measurements in porous medium under controlled and identical conditions provide a useful methodology for studying the relationships among them, ultimately leading to a better understanding of subsurface gaseous transport and other soil physical processes. The objective of this study was to characterize the relationships between gas transport parameters and soil-pore geometry revealed by X-ray CT. Sands of different shapes with a mean particle diameter (d50) ranging from 0.19 to 1.51 mm were used as porous media under both air-dried and partially saturated conditions. Gas transport parameters including gas dispersivity (&agr;), diffusivity (DP/D0), and permeability (ka) were measured using a unified measurement system (UMS). The 3DMA-Rock computational package was used for analysis of three-dimensional CT data. A strong linear relationship was found between &agr; and tortuosity calculated from gas transport parameters ( ), indicating that gas dispersivity has a linear and inverse relationship with gas diffusivity. A linear relationship was also found between ka and d50/TUMS2, indicating a strong dependency of ka on mean particle size and direct correlation with gas diffusivity. Tortuosity (TMFX) and equivalent pore diameter (deq.MFX) analyzed from microfocus X-ray CT increased linearly with increasing d50 for both Granusil and Accusand and further showing no effect of particle shape. The TUMS values showed reasonably good agreement with TMFX values. The ka showed a strong relationship when plotted against deq.MFX/TMFX2, indicating its strong dependency on pore size distribution and tortuosity of pore space.

Biochar effects on soil aggregate properties under no-till maize.

Abstract Soil aggregates are useful indicators of soil structure and stability, and the impact on physical and mechanical aggregate properties is critical for the sustainable use of organic amendments in agricultural soil. In this work, we evaluated the short-term soil quality effects of applying biochar (0–10 kg m−2), in combination with swine manure (2.1 and 4.2 kg m−2), to a no-till maize (Zea mays L.) cropping system on a sandy loam soil in Denmark. Topsoil (0–20 cm) aggregates were analyzed for clay dispersibility, aggregate stability, tensile strength (TS), and specific rupture energy (SRE) using end-over-end shaking, a Yoder-type wet-sieving method, and an unconfined compression test in soil samples collected 7 and 19 months after final biochar application. The highest rates of biochar and swine manure application resulted in the highest aggregate stability and lowest clay dispersibility. Applying both amendments systematically increased TS and SRE for large aggregates (4–8 and 8–16 mm) but not for small aggregates (1–2 and 2–4 mm). Increased biochar application also decreased the friability index of soil aggregates. Based on X-ray visualization, it was found that aggregates containing larger amounts of biochar particles had higher TS and SRE probably because of bonding effects. Based on the improved soil aggregate properties, we suggest that biochar can be effective for increasing and sustaining overall soil quality, for example, related to minimizing the soil erosion potential.

Effects of Past Copper Contamination and Soil Structure on Copper Leaching from Soil

Copper contamination affects biological, chemical, and physical soil properties and associated ecological functions. Changes in soil pore organization as a result of Cu contamination can dramatically affect flow and contaminant transport in polluted soils. This study assessed the influence of soil structure on the movement of water and Cu in a long-term polluted soil. Undisturbed soil cores collected along a Cu gradient (from about 20 to about 3800 mg Cu kg soil) were scanned using X-ray computed tomography (CT). Leaching experiments were performed to analyze tracer transport, colloid leaching, and dissolved organic carbon (DOC) and Cu losses. The 5% arrival time () and apparent dispersivity (λ) for tracer breakthrough were calculated by fitting the experimental data to a nonparametric, double-lognormal probability density function. Soil bulk density, which did not follow the Cu gradient, was the main driver of preferential flow, while macroporosity determined by X-ray CT (for pores >180 μm) proved the best predictor of solute transport. Higher preferential flow due to the presence of well-aligned pores and small cracks controlled water movement in compacted soil. Transport of Cu was rapid during the first flush (≈1 pore volume) in association with the movement of colloid particles, followed by slower transport in association with the movement of DOC in the soil solution. The relative amount of Cu released was strongly correlated with macroporosity as determined by X-ray CT, indicating the promising potential of this visualization technique for predicting contaminant transport through soil.

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 6u2009μm 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.

Plant exudates improve the mechanical conditions for root penetration through compacted soils

Background and aimPlant exudates greatly affect the physical behaviour of soil, but measurements of the impact of exudates on compression characteristics are missing. Our aim is to provide these data and explore how plant exudates may enhance the restructuring of compacted soils following cycles of wetting and drying.MethodsTwo soils were amended with Chia (Salvia hispanica) seed exudate at 5 concentrations, compacted in cores to 200xa0kPa stress (equivalent to tractor stress), equilibrated to −50xa0kPa matric potential, and then compacted to 600xa0kPa (equivalent to axial root stress) followed by 3xa0cycles of wetting and drying and recompression to 600xa0kPa at −50xa0kPa matric potential. Penetration resistance (PR), compression index (CC) and pore characteristics were measured at various steps.ResultsPR decreased and CC increased with increasing exudate concentration. At 600xa0kPa compression, 1.85xa0mg exudate g−1 soil increased CC from 0.37 to 0.43 for sandy loam soil and from 0.50 to 0.54 for clay loam soil. After 3 wetting-drying cycles the clay loam was more resillient than the sandy loam soil, with resilience increasing with greater exudate concentration. Root growth modelled on PR data suggested plant exudates significantly eased root elongation in soil.ConclusionPlant exudates improve compression characteristics of soils, easing penetration and enhancing recovery of root induced soil compaction.

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 (<250xa0μm) 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 1xa0mm 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.

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

Dataset supports:nKoebernick, N.et al (2017). High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation. New Phytologist.