Variable selection in near infrared spectra for the biological characterization of soil and earthworm casts

International audienceNear infrared reflectance spectroscopy (NIRS) was used to predict six biological properties of soil and earthworm casts including extracellular soil enzymes, microbial carbon, potential nitrification and denitrification. Partial least squares regression (PLSR) models were developed with a selection of the most important near infrared wavelengths. They reached coefficients of determination ranging from 0.81 to 0.91 and ratios of performance-to-deviation above 2.3. Variable selection with the variable importance in the projection (VIP) method increased dramatically the prediction performance of all models with an important contribution from the 1750–2500 nm region. We discuss whether selected wavelengths can be attributed to macronutrient availability or to microbial biomass. Wavelength selection in NIR spectra is recommended for improving PLSR models in soil research

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 days 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 parameterised 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 visualised 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

Patterns of soil water repellency change with wetting and drying: the influence of cracks, roots and drainage conditions

The influence of simulated cracks and roots on soil water repellency (SWR) dynamics with and without basal drainage impedance in wetting–drying cycles was investigated in the laboratory experiments. Observations and measurements were taken following water application equivalent to 9.2-mm rainfall and then periodically during 80 h of drying. In total, 180 experiments were carried out using 60 samples of three homogeneous, reconstituted soils with different organic matter contents and textures, but of similar initial severity of SWR [18% molarity of an ethanol droplet (MED)]. Water flowing down the cracks and roots left the soil matrix largely dry and water repellent except for vertical zones adjacent to them and a shallow surface layer. A hydrophilic shallow basal layer was produced in experiments where basal drainage was impeded. During drying, changes in SWR were largely confined to the zones that had been wetted. Soil that had remained dry retained the initial severity of SWR, while wetted soil re-established either the same or slightly lower severity of SWR. In organic-rich soil, the scale of recovery to pre-wetting MED levels was much higher, perhaps associated with temporarily raised levels (up to 36% MED) of SWR recorded during drying of these soils. With all three soils, the re-establishment of the original SWR level was less widespread for surface than subsurface soil and with impeded than unimpeded basal drainage.Key findings are that as follows: (1) with unimpeded basal drainage, the soils remained at pre-wetting repellency levels except for a wettable thin surface layer and zones close to roots and cracks, (2) basal drainage impedance produced hydrophilic basal and surface layers, (3) thorough wetting delayed a return to water-repellent conditions on drying, and (4) temporarily enhanced SWR occurred in organic-rich soils at intermediate moisture levels during drying. Hydrological implications are discussed, and the roles of cracks and roots are placed into context with other influences on preferential flow and SWR under field conditions

Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis

The morphology of roots and root systems influences the efficiency by which plants acquire nutrients and water, anchor themselves and provide stability to the surrounding soil. Plant genotype and the biotic and abiotic environment significantly influence root morphology, growth and ultimately crop yield. The challenge for researchers interested in phenotyping root systems is, therefore, not just to measure roots and link their phenotype to the plant genotype, but also to understand how the growth of roots is influenced by their environment. This review discusses progress in quantifying root system parameters (e.g. in terms of size, shape and dynamics) using imaging and image analysis technologies and also discusses their potential for providing a better understanding of root:soil interactions. Significant progress has been made in image acquisition techniques, however trade-offs exist between sample throughput, sample size, image resolution and information gained. All of these factors impact on downstream image analysis processes. While there have been significant advances in computation power, limitations still exist in statistical processes involved in image analysis. Utilizing and combining different imaging systems, integrating measurements and image analysis where possible, and amalgamating data will allow researchers to gain a better understanding of root:soil interactions

Rhizosphere-scale quantification of hydraulic and mechanical properties of soil impacted by root and seed exudates

Using rhizosphere-scale physical measurements we test the hypothesis that plant exudates gel together soil particles and on drying they enhance soil water repellency. Barley and maize root exudates were compared with chia seed exudate, a commonly used root exudate analogue. Sandy loam and clay loam soils were treated with root exudates at 0.46 and 4.6 mg exudate g-1 dry soil, and chia seed exudate at 0.046, 0.46, 0.92, 2.3 and 4.6 mg exudate g-1 dry soil. Soil hardness and modulus of elasticity were measured at -10 kPa matric potential using a 3 mm diameter spherical indenter. Water sorptivity and repellency index of air-dry soil were measured using a miniaturized infiltrometer device with a 1 mm tip radius. Soil hardness increased by 28% for barley root exudate, 62% for maize root exudate, and 86% for chia seed exudate at 4.6 mg g-1 concentration for sandy loam soil. For a clay loam soil, root exudates did not affect soil hardness, whereas chia seed exudate increased soil hardness by 48% at 4.6 mg g-1concentration. Soil water repellency increased by 48% for chia seed exudate and 23% for maize root exudate, but not for barley root exudate at 4.6 mg g-1 concentration for sandy loam soil. For clay loam soil, chia seed exudate increased water repellency by 45%, whereas root exudates did not affect water repellency at 4.6 mg g-1concentration. Water sorptivity and repellency were both correlated with hardness, presumably due to the combined influence of exudates on hydrological and mechanical properties of soils

Plant diversity and root traits benefit physical properties key to soil function in grasslands

Plant diversity loss impairs ecosystem functioning, including important effects on soil. Most studies that have explored plant diversity effects belowground, however, have largely focused on biological processes. As such, our understanding of how plant diversity impacts the soil physical environment remains limited, despite the fundamental role soil physical structure plays in ensuring soil function and ecosystem service provision. Here, in both a glasshouse and a long-term field study, we show that high plant diversity in grassland systems increases soil aggregate stability, a vital structural property of soil, and that root traits play a major role in determining diversity effects. We also reveal that the presence of particular plant species within mixed communities affects an even wider range of soil physical processes, including hydrology and soil strength regimes. Our results indicate that alongside well-documented effects on ecosystem functioning, plant diversity and root traits also benefit essential soil physical properties

Estimating soil aggregate size distribution from images using pattern spectra

A method for quantifying aggregate size distribution from the images of soil samples is introduced. Knowledge of soil aggregate size distribution can help to inform soil management practices for the sustainable growth of crops. While current in-field approaches are mostly subjective, obtaining quantifiable results in a laboratory is labour- and time-intensive. Our goal is to develop an imaging technique for quantitative analysis of soil aggregate size distribution, which could provide the basis of a tool for rapid assessment of soil structure. The prediction accuracy of pattern spectra descriptors based on hierarchical representations from attribute morphology are analysed, as well as the impact of using images of different quality and scales. The method is able to handle greater sample complexity than the previous approaches, while working with smaller samples sizes that are easier to handle. The results show promise for size analysis of soils with larger structures, and minimal sample preparation, as typical of soil assessment in agriculture

Effect of microbial activity on penetrometer resistance and elastic modulus of soil at different temperatures

We explore the effect of microbial activity stimulated by root exudates on the penetrometer resistance of soil and its elastic modulus. This is important because it is a measure of the mechanical strength of soil and it correlates closely with the rate of elongation of roots. A sandy soil was incubated with a synthetic root exudate at different temperatures, for different lengths of time and with selective suppression of either fungi or bacteria. The shape of the temperature response of penetrometer resistance in soil incubated with synthetic exudate was typical of a poikilothermic temperature response. Both penetrometer resistance and small strain shear modulus had maximum values between 25 and 30°C. At temperatures of 20°C and less, there was little effect of incubation with synthetic root exudate on the small strain shear modulus, although penetrometer resistance did increase with temperature over this range (4–20°C). This suggests that in this temperature range the increase in penetrometer resistance was related to a greater resistance to plastic deformation. At higher temperatures (> 25°C) penetrometer resistance decreased. Analysis of the DNA sequence data showed that at 25°C the number of Streptomyces (Gram‐positive bacteria) increased, but selective suppression of either fungi or bacteria suggested that fungi have the greater role with respect to penetrometer resistance

The emergent rhizosphere: imaging the development of the porous architecture at the root-soil interface

The rhizosphere is the zone of soil infuenced by a plant root and is critical for plant health and nutrient acquisition. All below ground resources must pass through this dynamic zone prior to their capture by plant roots. However, researching the undisturbed rhizosphere has proved very challenging. Here we compare the temporal changes to the intact rhizosphere pore structure during the emergence of a developing root system in diferent soils. High resolution X-ray Computed Tomography (CT) was used to quantify the impact of root development on soil structural change, at scales relevant to individual micro-pores and aggregates (µm). A comparison of micro-scale structural evolution in homogenously packed soils highlighted the impacts of a penetrating root system in changing the surrounding porous architecture and morphology. Results indicate the structural zone of infuence of a root can be more localised than previously reported (µm scale rather than mm scale). With time, growing roots signifcantly alter the soil physical environment in their immediate vicinity through reducing root-soil contact and crucially increasing porosity at the root-soil interface and not the converse as has often been postulated. This ‘rhizosphere pore structure’ and its impact on associated dynamics are discussed

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 (~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 L.), with and without root hairs, were grown for 8 days in microcosms packed with sandy loam soil at 1.2 g cm-3 36 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 (&gt; 5 μm) in the rhizosphere, as compared with the no-hair mutants. Both genotypes showed decreasing pore-space between 0.8 mm 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