Estimating root–soil contact from 3D X‐ray microtomographs

Adequate contact with the soil is essential for water and nutrient adsorption by plant roots, but the determination of root–soil contact is a challenging task because it is difficult to visualize roots in situ and quantify their interactions with the soil at the scale of micrometres. A method to determine root–soil contact using X‐ray microtomography was developed. Contact areas were determined from 3D volumetric images using segmentation and iso‐surface determination tools. The accuracy of the method was tested with physical model systems of contact between two objects (phantoms). Volumes, surface areas and contact areas calculated from the measured phantoms were compared with those estimated from image analysis. The volume was accurate to within 0.3%, the surface area to within 2–4%, and the contact area to within 2.5%. Maize and lupin roots were grown in soil (<2 mm) and vermiculite at matric potentials of ?0.03 and ?1.6 MPa and in aggregate fractions of 4–2, 2–1, 1–0.5 and < 0.5 mm at a matric potential of ?0.03 MPa. The contact of the roots with their growth medium was determined from 3D volumetric images. Macroporosity (>70 µm) of the soil sieved to different aggregate fractions was calculated from binarized data. Root‐soil contact was greater in soil than in vermiculite and increased with decreasing aggregate or particle size. The differences in root–soil contact could not be explained solely by the decrease in porosity with decreasing aggregate size but may also result from changes in particle and aggregate packing around the root.     

Mapping soil clay contents in Dutch marine districts using gamma‐ray spectrometry

Conventional soil sampling methods to obtain high‐resolution soil data are labour intensive and costly. Recently, gamma ray spectrometry has emerged as a promising technique to overcome these obstacles. The objective of our study was to investigate the prediction of soil clay contents using gamma‐ray spectrometry in three marine clay districts in the Netherlands: the southwestern marine district (SMD), the IJsselmeerpolder district (IJPD) and the northern marine district (NMD). The performance of linear regression models was investigated at field (<1 km²), regional (1–1000 km²) and district (>1000 km²) scales and for all the Dutch marine districts together. For this study, a database was available with 1371 gamma‐ray spectra measured on arable fields in marine clay districts during the period 2005–2008 and these were all linked to laboratory analyses of clay contents. At the field scale, linear regression models based on ⁴⁰K, ²³²Th, or a combination of these revealed much smaller root mean squared error (RMSE) values (2–3%) compared with a model based on the field mean (8–10%). At the district scale, the regression models for the SMD and IJPD, which have comparable sediments, performed better than for the NMD. This indicates that the prediction of clay contents in late Holocene marine sediments may be made with gamma‐ray spectrometry provided that the origin of the parent material results in a unique fingerprint. Because of the heterogeneous parent material of all marine districts taken together, our study shows that no unique and precise fingerprint exists, and the RMSE of 6% between clay contents and gamma‐ray spectra is not much different from the RMSE of 7% when using the overall mean as a predictor.     

Effects of tillage and liming on macropore networks derived from X‐ray tomography images of a silty clay soil

Soil structure influences water infiltration, aeration and root growth and, thereby, also the conditions for sustainable crop production. Our objective was to quantify the effects of different soil management methods and land uses on the topsoil structure of a silty clay soil. We sampled 32 intact soil columns (18 cm high, 12.7 cm diameter) from an experimental silty clay field with four treatments: conventional tillage (CT ), conventional tillage followed by liming (CTL ), reduced tillage (RT ) and unfertilized fallow (UF ). The columns were analysed using 3‐D X‐ray tomography. The samples were taken in autumn after harvest, 7 yr after quick lime was applied to the CTL plots. Despite a relatively large number of replicates per treatment (8, 8, 8 and 6 (two UF samples were excluded), respectively), there were no significant differences between any of the investigated macropore network properties related to tilled treatments. The UF treatment, in contrast, exhibited more vertically oriented macropores, which were also better connected compared to the other treatments. This confirms previous findings that tillage may disrupt the vertical continuity of macropore clusters. The impact of liming on soil pore network properties may have been limited to pores smaller than the resolution in our X‐ray images. It is also possible that the effects of lime on soil structure were limited to a few years which means that any effect would have diminished by the time of this study. These matters should be further investigated in follow‐up studies to understand better the potential of lime amendments to clay soil.     

Acid‐extractable potassium in agricultural soils: Source minerals assessed by differential and quantitative X‐ray diffraction

Different extraction methods are used world‐wide in routine soil analysis to estimate long‐term potassium (K) reserves for plants. In Sweden, K extracted with 2 M HCl at 100°C (K_HCl) is frequently used, although with limited understanding of the phases extracted. In the present study, we quantified the effects of this extraction on soil minerals in particle size fractions ranging from clay to sand, and estimated their relative contribution to K_HCl. The study included three Swedish long‐term agricultural field experiments with texture ranging from loamy sand to silty clay, as well as mineral specimens of K feldspar. Total weight loss of particle size fractions was determined, and quantitative and differential X‐ray powder diffraction (QXRD, DXRD), applied on solids before and after extraction, was used to quantify the dissolution of individual mineral phases. QXRD and DXRD included spray‐drying of samples, addition of an internal standard and full pattern fitting, where a combination of mineral‐standard XRD traces was matched with the experimental one. Our results show that K_HCl was primarily associated with clay minerals concentrated in the two finest fractions (2–20 and < 2 μm). Highly expandable and mixed‐layer phyllosilicates were quantitatively the most important minerals dissolved. The K was released from micaceous layers in mixed‐layer phyllosilicates with a vermiculitic character. Whether di‐ or trioctahedral, a shared property of the dissolved phases was that they were rich in Fe. In the loamy sand, the coarser fractions (20–2000 μm), where feldspars were prominent, accounted for 35% of K_HCl. According to DXRD, there was no significant decrease in K feldspars in any of the samples, and K_HCl data for the feldspar specimens suggest that clay minerals contributed at least 70% of K_HCl also in the loamy sand. Our study provides insights about the soil minerals that contribute to the long‐term K delivery capacity of soils and an explanation for the prior observation that K_HCl is a dynamic fraction that can be affected by management.     

Biogeochemical processes and arsenic enrichment around rice roots in paddy soil: results from micro‐focused X‐ray spectroscopy

The spatial distribution and speciation of iron (Fe), manganese (Mn) and arsenic (As) around rice roots grown in an As‐affected paddy field in Bangladesh were investigated on soil sampled after rice harvest. Synchrotron micro‐X‐ray fluorescence spectrometry on soil thin sections revealed that roots influence soil Fe, Mn and As distribution up to 1 mm away from the root–soil interface. Around thick roots (diameter around 500 µm), Mn was concentrated in discrete enrichments close to the root surface without associated As, whereas concentric Fe accumulations formed farther away and were closely correlated with As accumulations. Near thin roots (diameter < 100 µm), in contrast, a pronounced enrichment of Fe and As next to the root surface and a lack of Mn enrichments was observed. X‐ray absorption fine structure spectroscopy suggested that (i) accumulated Fe was mainly contained in a two‐line ferrihydrite‐like phase, (ii) associated As was mostly As(V) and (iii) Mn enrichments consisted of Mn(III/IV) oxyhydroxides. The distinct enrichment patterns can be related to the extent of O₂ release from primary and lateral rice roots and the thermodynamics and kinetics of Fe, Mn and As redox transformations. Our results suggest that in addition to Fe(III) plaque at the root surface, element accumulation and speciation in the surrounding rhizosphere soil must be taken into account when addressing the transfer of nutrients or contaminants into rice roots.     

X‐ray Image Analysis to Detect Infestations Caused by Insects in Grain

Insect infestations in stored wheat affect the chemical characteristics and baking qualities of wheat flour, and insect‐infested flours are unacceptable in the baking industry. The efficiency of the soft X‐ray method to detect infestations caused by Cryptolestes ferrugineus (Stephens), Tribolium castaneum (Herbst), Plodia interpunctella (Hübner), Sitophilus oryzae (L.), and Rhyzopertha dominica (F.) in wheat kernels was determined in this study. Wheat kernels infested by different insects were prepared by artificial implantation of insect eggs or by introducing adult insects in wheat samples. Kernels infested by different stages of the insects were X‐rayed until the adults emerged from the kernels. A total of 57 features using histogram groups, histogram and shape moments, and textural features were extracted from the X‐ray images and a linear‐function parametric classifier was used to identify the insect‐infested kernels. The parametric classifier identified more than 84% of infestations due to C. ferrugineus and T. castaneum larvae. The infestations by C. ferrugineus pupae‐adults and P. interpunctella larvae were identified with >96% accuracy. Kernels infested by different stages of S. oryzae and R. dominica larvae were identified with >98% accuracy. Using the Berlese funnel method, 67, 51, and 81% of first, second, and third instars of C. ferrugineus, respectively, were extracted in 6 hr. The same infested kernels were all categorized as infested by the parametric classifier. When kernels infested by different insects were pooled together, the parametric classifier correctly identified 74% of uninfested and 94% of infested kernels by the internal and external grain feeders. The 26% false positives identified from the independent test was caused by one sample infested by T. castaneum. When that sample was removed from the training set, the false positives were reduced to 16%, and 92.7% of infested kernels by different insects were correctly identified.     

Applications of X‐ray computed tomography for examining biophysical interactions and structural development in soil systems: a review

Soil systems are characterized by the spatial and temporal distribution of organic and mineral particles, water and air within a soil profile. Investigations into the complex interactions between soil constituents have greatly benefited from the advent of non‐invasive techniques for structural analysis. In this paper we present a review of the application of one such technique, X‐ray computed tomography (CT), for studies of undisturbed soil systems, focusing on research during the last 10 years in particular. The ability to undertake three‐dimensional imaging has provided valuable insights regarding the quantitative assessment of soil features, in a way previously unachievable because of the opaque nature of soil. A dynamic approach to the evaluation of soil pore networks, hydro‐physical characteristics and soil faunal behaviour has seen numerous scanning methodologies employed and a diverse range of image analysis protocols used. This has shed light on functional processes across multiple scales whilst also bringing its own challenges. In particular, much work has been carried out to link a soil's porous architecture with hydraulic function, although new technical improvements allowing the characterization of organic matter and the influence of soil biota on structural development are showing great promise. Here we summarize the development of X‐ray CT in soil science, highlight the major issues relating to its use, outline some of the applications for overcoming these challenges and describe the potential of future technological advances for non‐invasive soil characterization through integration with other complementary techniques.     

Mobilization of X‐ray amorphous and crystalline aluminum and iron phosphates by common soil extraction procedures

Soil extraction with 0.1 M NaOH completely dissolves X‐ray amorphous as well as crystalline AlPO₄ and FePO₄. Extraction with acidic NH₄ oxalate completely mobilizes X‐ray amorphous AlPO₄ and FePO₄ in addition to phosphate adsorbed to poorly‐crystallized Al and Fe minerals, but only a minor portion of crystalline AlPO₄ and FePO₄. Extraction with dithionite‐citrate‐bicarbonate mobilizes X‐ray amorphous AlPO₄ and FePO₄ as well as crystalline FePO₄, but only a minor portion of crystalline AlPO₄.     

Characterization of structural disturbances in peats by X‐ray CT‐based density determinations

Bulk density was determined indirectly in peat samples by X‐ray computed tomography (X‐ray CT) and compared with density values obtained by standard laboratory methods. Five Histosols were collected in the same cut‐over peatland, representing various degrees of disturbance related to the process of peat extraction. Soil cores were fully imaged by X‐ray CT with a voxel size of about 0.25 mm. Each one of these five attenuation profiles was analysed and compared with direct density measurements. A linear relationship, to convert attenuation values into density values, is proposed to determine the variation in bulk density with a spatial resolution clearly greater than standard laboratory determinations. It is also shown that X‐ray‐based density values can be effectively used to characterize the structure of peat soils and the possible consequences of disturbances after drainage and peat mining. Under the accepted limitations of the method, X‐ray CT opens up new opportunities to determine the structural quality of peat and to monitor its modifications with time. This indirect diagnostic could be particularly useful to study peatlands' hydraulic systems or evaluate the effectiveness of restoration measures.     

Field level digital mapping of soil mineralogy using proximal and remote‐sensed data

Primary (e.g., quartz) and secondary (clay) minerals are key factors determining the physical and chemical characteristics of soil. Understanding spatial distribution of minerals at the field scale would, therefore, be of potential benefit for soil management. However, current analysis requires time‐consuming laboratory procedures and computational quantification analysis (e.g., SIROQUANT). Furthermore, mineral composition (e.g., quartz, kaolinite, illite and expandable clay minerals) must sum to 100. We aimed to add value to laboratory data by developing multiple linear regression (MLR) relationships between mineralogy and ancillary data such as digital numbers (DNs) (i.e., Red [R], Green [G] and Blue [B]) acquired from remotely sensed air‐photographs and soil apparent electrical conductivity (EC_a – mS/m) measured from proximal sensing electromagnetic (EM) instruments (i.e., EM38 and EM31). To account for composition, we compare results from the MLR approach with those from additive log‐ratio (ALR) transformation of mineralogy prior to MLR modelling. This approach together with various ancillary data and trend surface parameters (i.e., scaled Easting and Northing) has greater precision and less bias of prediction than the MLR approach using untransformed data. Our approach also enables predictions to sum to 100. We conclude that the most useful ancillary data to predict the abundance of quartz, kaolinite and illite are B DNs and EM31, while expandable clays are best predicted with R DNs, EM38 and scaled Northing. The use of ancillary data to map mineralogical components combined with ALR‐MLR is an effective approach, with resulting maps providing insights into soil and water management issues consistent with farmer experience.     

生物炭碳固定于稳定性土壤团聚体中：土壤黏土矿物及其它土壤性质的作用

Aggregation and structure play key roles in water-holding capacity and stability of soils.In this study,the incorporation of carbon(C) from switchgrass biochar into stable aggregate size fractions was assessed in an Aridisol(from Colorado,USA) dominated by 2:1 clays and an Alfisol(from Virginia,USA) containing weathered mixed 1:1 and 2:1 mineralogy,to evaluate the effect of biochar addition on soil characteristics.The biochar was applied at 4 levels,0,25,50,and 100 g kg~(-1),to the soils grown with wheat in a growth chamber experiment.The changes in soil strength and water-holding capacity using water release curves were measured.In the Colorado soil,the proportion of soil occurring in large aggregates decreased,with concomitant increases in small size fractions.No changes in aggregate size fractions occurred in the Virginia soil.In the Colorado soil,C content increased from 3.3 to 16.8 g kg~(-1),whereas in the53 μm fraction C content increased from 5.7 to 22.6 g kg~(-1) with 100 g kg~(-1)biochar addition.In the Virginia soil,C content within aggregate size fractions increased for each size fraction,except the2 000 μm fraction.The greatest increase(from 6.2 to 22.0 g kg~(-1)) occurred in the 53–250 μm fraction.The results indicated that C was incorporated into larger aggregates in the Virginia soil,but remained largely unassociated to soil particles in the Colorado soil.Biochar addition had no significant effect on water-holding capacity or strength measurements.Adding biochar to more weathered soils with high native soil organic content may result in greater stabilization of incorporated C and result in less loss because of erosion and transport,compared with the soils dominated by 2:1 clays and low native soil organic content.     

Advances in characterization of soil structure

Soil structure is defined as “the spatial heterogeneity of the different components or properties of soil”. Aspects of soil structure which are important for plant development, soil water balance and soil workability are reviewed briefly. The different types of soil structure which occur on different size scales are placed in a hierarchical order. Different mechanisms give rise to the different hierarchical orders. Similarly, different physical/chemical/biological processes are involved in the stabilization of the different hierarchical orders.A number of methods for measuring soil structure are described. Preference is given to methods involving direct observation of structural features by scanning electron microscopy and by optical scanning of impregnated sections and fracture surfaces. These need to be supported by assessments of the stabilities of compound particles in water and of the mechanical strengths of compound particles as a function of water content.“Good” soil structure is described as one where all the hierarchical orders are well-developed and stable. The greatest lack of knowledge appears to be in the 2–100 μm size range which is too large to have been studied by colloid chemists and too small to be visible to the naked eye. It is suggested that more observations of soil structure should be made in this size range, as it may hold many important clues on how to manage soil structure in the field.     

Methodological aspects of determining soil particle‐size distribution using the laser diffraction method

This paper presents the influence of selected methodological aspects on the results of particle‐size distribution (PSD) as measured by the laser diffraction method (LDM). The investigations were carried out using the Mastersizer 2000 with Hydro MU attachment (Malvern Ltd., UK). It was found that for the investigated soils: (1) optimal speed of pump and stirrer was 2500 rpm, (2) optimal measurement time was ≈ 1 min, (3) there are two, practically equivalent methods for soil‐sample dispersion: chemical (with the use of a solution of sodium hexametaphosphate) or physical (by means of ultrasound application for 4 min at a maximum power of 35W), (4) one must not use the chemical and physical dispersing methods simultaneously, because this can lead to aggregation (not dispersion) of soil particles, (5) the Fraunhofer theory (physical models) can be used to convert scattered‐light data to PSD. In the case of the Mie theory, the best results were obtained for a refractive index (RI) in the range of 1.5–1.6 and an absorption index (AI) of 1.0. It was also found that most of the discussed parameters depend on design of the measuring device and on the type and volume of the investigated suspensions. It is necessary, therefore, to explain how the data was obtained every time and to specify the details in the methodological part of the paper.     

Potassium release on drying of soil samples from a variety of weathering regimes and c clay mineralogy in China

Thirty two soil samples from China were analyzed for exchangeable K before and after drying. Most soil samples were higher in exchangeable K after air-drying and ovendrying (60°C) than when wet. Soil clay minerals, especially clay-size mica, affected K released in air-dry and oven-dry samples. According to composition of clay minerals of air-dried samples, five classes were recognized. Soil samples with high mica and montmorillonite have the highest exchangeable K. Samples that contained higher kaolinite than mica had lower exchangeable K. Samples with higher kaolinite than quartz and mica had still lower exchangeable K. Samples of sandy soils contained very low exchangeable K. When quartz was the main mineral, the samples that had kaolinite and gibbsite as the main clay minerals had very low exchangeable K. The degree of weathering (weathering mean) bore an inverse relationship to the amount of K released on drying in air or at 60°C. Udults and Udalfs (Red Earths) of southeastern China, because of their high K release on being dried, are inferred to have received fine mica from the Western Desert dust rainout, reported to Liu et al. (1981).     

Gamma‐ray spectrometry as versatile tool in soil science: A critical review

Gamma‐ray spectrometry is an established method in geo‐sciences. This article gives an overview on fundamentals of gamma‐ray spectrometry that are relevant to soil science including basic technical aspects, and discusses influencing factors, inconsistencies, limitations, and open questions related to the method. Gamma‐ray spectrometry relies on counting gamma quanta during radionuclide decay of ⁴⁰K, ²³⁸U, and ²³²Th, but secular equilibrium for the decay series of U and Th must be given as decays of their respective daughter radionuclides are used for determination. Secular equilibrium for U and Th decay series, however, is not always given leading to, e.g., anomalies in U concentration measurements. For soil science, gamma‐ray spectrometry is of specific value since it does not only detect a signal from the landscape surface, but integrates information over a certain volume. Besides, different spatial scales can be covered using either ground‐based or airborne sensing techniques. Together with other remote sensing methods, gamma signatures can provide completive information for understanding land forming processes and soil properties distributions. At first, signals depend on bedrock composition. The signals are in second order altered by weathering processes leading to more interpretation opportunities and challenges. Due to their physico‐chemical properties, radionuclides behave differently in soils and their properties can be distinguished via the resulting signatures. Hence, gamma signatures of soils are specific for local environments. Processes like soil erosion can superimpose gamma signals from in situ weathering. Soil mappings, available K and texture determination, or peat and soil erosion mapping are possible applications being discussed in this review.