Assessing the influence of the rhizosphere on soil hydraulic properties using X-ray computed tomography and numerical modelling

© 2015 © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. Understanding the dynamics of water distribution in soil is crucial for enhancing our knowledge of managing soil and water resources. The application of X-ray computed tomography (CT) to the plant and soil sciences is now well established. However, few studies have utilized the technique for visualizing water in soil pore spaces. Here this method is utilized to visualize the water in soil in situ and in three-dimensions at successive reductive matric potentials in bulk and rhizosphere soil. The measurements are combined with numerical modelling to determine the unsaturated hydraulic conductivity, providing a complete picture of the hydraulic properties of the soil. The technique was performed on soil cores that were sampled adjacent to established roots (rhizosphere soil) and from soil that had not been influenced by roots (bulk soil). A water release curve was obtained for the different soil types using measurements of their pore geometries derived from CT imaging and verified using conventional methods, such as pressure plates. The water, soil, and air phases from the images were segmented and quantified using image analysis. The water release characteristics obtained for the contrasting soils showed clear differences in hydraulic properties between rhizosphere and bulk soil, especially in clay soil. The data suggest that soils influenced by roots (rhizosphere soil) are less porous due to increased aggregation when compared with bulk soil. The information and insights obtained on the hydraulic properties of rhizosphere and bulk soil will enhance our understanding of rhizosphere biophysics and improve current water uptake models

Effects of X-ray dose on rhizosphere studies using X-ray computed tomography

X-ray Computed Tomography (CT) is a non-destructive imaging technique originally designed for diagnostic medicine, which was adopted for rhizosphere and soil science applications in the early 1980s. X-ray CT enables researchers to simultaneously visualise and quantify the heterogeneous soil matrix of mineral grains, organic matter, air-filled pores and water-filled pores. Additionally, X-ray CT allows visualisation of plant roots in situ without the need for traditional invasive methods such as root washing. However, one routinely unreported aspect of X-ray CT is the potential effect of X-ray dose on the soil-borne microorganisms and plants in rhizosphere investigations. Here we aimed to i) highlight the need for more consistent reporting of X-ray CT parameters for dose to sample, ii) to provide an overview of previously reported impacts of X-rays on soil microorganisms and plant roots and iii) present new data investigating the response of plant roots and microbial communities to X-ray exposure. Fewer than 5% of the 126 publications included in the literature review contained sufficient information to calculate dose and only 2.4% of the publications explicitly state an estimate of dose received by each sample. We conducted a study involving rice roots growing in soil, observing no significant difference between the numbers of root tips, root volume and total root length in scanned versus unscanned samples. In parallel, a soil microbe experiment scanning samples over a total of 24 weeks observed no significant difference between the scanned and unscanned microbial biomass values. We conclude from the literature review and our own experiments that X-ray CT does not impact plant growth or soil microbial populations when employing a low level of dose (<30 Gy). However, the call for higher throughput X-ray CT means that doses that biological samples receive are likely to increase and thus should be closely monitored

Sward composition and soil moisture conditions affect nitrous oxide emissions and soil nitrogen dynamics following urea-nitrogen application

peer-reviewedIncreased emissions of N2O, a potent greenhouse gas (GHG), from agricultural soils is a major concern for the sustainability of grassland agriculture. Emissions of N2O are closely associated with the rates and forms of N fertilisers applied as well as prevailing weather and soil conditions. Evidence suggests that multispecies swards require less fertiliser N input, and may cycle N differently, thus reducing N loss to the environment. This study used a restricted simplex-centroid experimental design to investigate N2O emissions and soil N cycling following application of urea-N (40 kg N ha−1) to eight experimental swards (7.8 m2) with differing proportions of three plant functional groups (grass, legume, herb) represented by perennial ryegrass (PRG, Lolium perenne), white clover (WC, Trifolium repens) and ribwort plantain (PLAN, Plantago lanceolata), respectively. Swards were maintained under two contrasting soil moisture conditions to examine the balance between nitrification and denitrification. Two N2O peaks coincided with fertiliser application and heavy rainfall events; 13.4 and 17.7 g N2O-N ha−1 day−1 (ambient soil moisture) and 39.8 and 86.9 g N2O-N ha−1 day−1 (wet soil moisture). Overall, cumulative N2O emissions post-fertiliser application were higher under wet soil conditions. Increasing legume (WC) proportions from 0% to 60% in multispecies swards resulted in model predicted N2O emissions increasing from 22.3 to 96.2 g N2O-N ha−1 (ambient soil conditions) and from 59.0 to 219.3 g N2O-N ha−1 (wet soil conditions), after a uniform N application rate. Soil N dynamics support denitrification as the dominant source of N2O especially under wet soil conditions. Significant interactions of PRG or WC with PLAN on soil mineral N concentrations indicated that multispecies swards containing PLAN potentially inhibit nitrification and could be a useful mitigation strategy for N loss to the environment from grassland agriculture.Teagas

Three-dimensional quantification of soil hydraulic properties using X-ray computed tomography and image-based modeling

We demonstrate the application of a high-resolution X-ray Computed Tomography (CT) method to quantify water distribution in soil pores under successive reductive drying. We focus on the wet end of the water release characteristic (WRC) (0 to −75 kPa) to investigate changes in soil water distribution in contrasting soil textures (sand and clay) and structures (sieved and field structured) and to determine the impact of soil structure on hydraulic behavior. The 3-D structure of each soil was obtained from the CT images (at a 10 μm resolution). Stokes equations for flow were solved computationally for each measured structure to estimate hydraulic conductivity. The simulated values obtained compared extremely well with the measured saturated hydraulic conductivity values. By considering different sample sizes we were able to identify the smallest possible representative sample size which is required to determine a globally valid hydraulic conductivity

Non-destructive determination of floral staging in cereals using X-ray micro computed tomography (µCT)

Background Accurate floral staging is required to aid research into pollen and flower development, in particular male development. Pollen development is highly sensitive to stress and is critical for crop yields. Research into male development under environmental change is important to help target increased yields. This is hindered in monocots as the flower develops internally in the pseudostem. Floral staging studies therefore typically rely on destructive analysis, such as removal from the plant, fixation, staining and sectioning. This time-consuming analysis therefore prevents follow up studies and analysis past the point of the floral staging. Results This study focuses on using X-ray µCT scanning to allow quick and detailed non-destructive internal 3D phenotypic information to allow accurate staging of Arabidopsis thaliana L. and Barley (Hordeum vulgare L.) flowers. X-ray µCT has previously relied on fixation methods for above ground tissue, therefore two contrast agents (Lugol’s iodine and Bismuth) were observed in Arabidopsis and Barley in planta to circumvent this step. 3D models and 2D slices were generated from the X-ray µCT images providing insightful information normally only available through destructive time-consuming processes such as sectioning and microscopy. Barley growth and development was also monitored over three weeks by X-ray µCT to observe flower development in situ. By measuring spike size in the developing tillers accurate non-destructive staging at the flower and anther stages could be performed; this staging was confirmed using traditional destructive microscopic analysis. Conclusion The use of X-ray micro computed tomography (µCT) scanning of living plant tissue offers immense benefits for plant phenotyping, for successive developmental measurements and for accurate developmental timing for scientific measurements. Nevertheless, X-ray µCT remains underused in plant sciences, especially in above-ground organs, despite its unique potential in delivering detailed non-destructive internal 3D phenotypic information. This work represents a novel application of X-ray µCT that could enhance research undertaken in monocot species to enable effective non-destructive staging and developmental analysis for molecular genetic studies and to determine effects of stresses at particular growth stages

Introduction to The Plant Phenome Journal special section on belowground phenotyping

Abstract The Plant Phenome Journal is excited to present 10 papers that were submitted in a special section on belowground phenotyping. Plant roots and their environment are important for crop resilience and resource efficiency. To meet growing productivity challenges, breeders will benefit from tools that are developed to optimize belowground traits

Using X-ray computed tomography to explore the role of abscisic acid in moderating the impact of soil compaction on root system architecture

Background and Airns: Understanding how soil compaction affects root system architecture (RSA) and root deployment within soil is critical to maximise crop growth. This study examined the role of abscisic acid (ABA) in mediating root responses to soil compaction using tomato genotypes with differing endogenous ABA concentrations. Methods: Plants of the wild-type tomato genotype (Solanum lycopersicum L. cv. Ailsa Craig) and its ABA-deficient mutant notabilis, of uniform developmental stage, were transplanted to columns containing a loamy sand soil at bulk densities of 1.2, 1.4 and 1.6 Mg m(-3). Fourteen days after transplanting (DAT), an X-ray mu CT scanner acquired non-destructive 3-D images of RSA. Destructive analysis of RSA was undertaken using WinRHIZO((R)) 2-D scanning equipment. Key results: Increased bulk density decreased root volume, surface area, rooting depth and lateral root number (P<0.05), which adversely affected RSA and the subsequent volume of soil explored. The ABA-deficient mutant notabilis displayed a poor rooting phenotype with reduced root volume, surface area and lateral roots at all bulk densities. Conclusions: The response of RSA to soil compaction in situ differed between the ABA-deficient mutant genotypes of tomato. The differences in rooting phenotype between genotypes suggest that endogenous ABA concentration has a positive influence on RSA when roots encounter compacted soil. (C) 2014 Elsevier B.V. All rights reserved

Crop Improvement from Phenotyping Roots: Highlights Reveal Expanding Opportunities

Root systems determine the water and nutrients for photosynthesis and harvested products, underpinning agricultural productivity. We highlight 11 programs that integrated root traits into germplasm for breeding, relying on phenotyping. Progress was successful but slow. Today’s phenotyping technologies will speed up root trait improvement. They combine multiple new alleles in germplasm for target environments, in parallel. Roots and shoots are detected simultaneously and nondestructively, seed to seed measures are automated, and field and laboratory technologies are increasingly linked. Available simulation models can aid all phenotyping decisions. This century will see a shift from single root traits to rhizosphere selections that can be managed dynamically on farms and a shift to phenotype-based improvement to accommodate the dynamic complexity of whole crop systems

Three-dimensional quantification of soil hydraulic properties using X-ray computed tomography and image-based modeling

We demonstrate the application of a high-resolution X-ray Computed Tomography (CT) method to quantify water distribution in soil pores under successive reductive drying. We focus on the wet end of the water release characteristic (WRC) (0 to −75 kPa) to investigate changes in soil water distribution in contrasting soil textures (sand and clay) and structures (sieved and field structured) and to determine the impact of soil structure on hydraulic behavior. The 3-D structure of each soil was obtained from the CT images (at a 10 μm resolution). Stokes equations for flow were solved computationally for each measured structure to estimate hydraulic conductivity. The simulated values obtained compared extremely well with the measured saturated hydraulic conductivity values. By considering different sample sizes we were able to identify the smallest possible representative sample size which is required to determine a globally valid hydraulic conductivity

X-ray dose in plant and soil studies.

<p>Dose was calculated in Rad Pro with X-ray parameters derived from literature. Most studies involve doses below the 33Gy threshold noted by Johnson <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067250#pone.0067250-Johnson1" target="_blank">[14]</a>, below which she did not observe visible alteration of post-germination plant growth after X-ray exposure. Note the reduction in published studies between 1940 and 1980 and the clear rise in the 1990s.</p