Analysis of Tomographic Images of the Soil Pore Space Structure by Integral Geometry Methods

The technique of numerical analysis of three-dimensional tomographic images of the pore space of soil objects has been used in this paper. It applies methods of integral geometry, topology and morphological analysis. To characterize quantitatively the transformation of the pore space structure, tomographic images of four undisturbed soils were analyzed, i.e., heavy loamy agro-gray soil (Retic Phaeozem), agromineral (Sapric Rheic Mineralic Histosols), and hypnum (brown moss Sapric Rheic Histosols) peat soils in dry and wet conditions. For samples of the subplow horizon in agro-gray soil, a decrease in both Betty numbers was observed on wetting, where the zero number (b0) stands for the amount of topologically simple closed pores, and the first number (b1) indicates a decrease in pore connectivity, which varies in a narrower range of pore sizes as compared to b0. When a sample of agromineral peat soil is moistened, the Euler–Poincaré characteristic is negative ​in the pore range of 0.1–0.16 mm, which points to the predominating complicated branched structure of the pore space and high pore connectivity. When hypnum moss is saturated, a lot of tunnel pores get narrower (“collapse”), and the connectivity decreases due to the structural specifics of long-stemmed plant residues. The number of pores and connections between them in peat soils is an order of magnitude higher than those in the subplow horizon A of the agro-gray soil. The provided quantitative changes in the considered parameters of tomographic images of the soil pore space confirm the possibility of applying them for estimating the transformation of the pore space in soils.

No Tillage Improved Soil Pore Space Indices under Cover Crop and Crop Rotation

Assessment of the effects of crop management practices on soil physical properties is largely limited to soil moisture content, air content or bulk density, which can take considerable time to change. However, soil pore space indices evolve rapidly and could quickly detect changes in soil properties resulting from crop management practices, but they are not often measured. The objective of this study was to investigate how soil pore space indices—relative gas diffusion coefficient (Ds/Do) and pore tortuosity factor (τ)—are affected by tillage system (TL), cover crop (CC) and crop rotation (CR). A study was conducted on silt loam soil at Freeman farm, Lincoln University of Missouri during the 2011 to 2013 growing seasons. The experiment design was a randomized complete block with two tillage systems (no tillage or no-till vs conventional tillage), two cover crops (no rye vs cereal rye (Secale cereale L.)) and four crop rotations (continuous corn (Zea mays L.), continuous soybean (Glycine max L.), corn–soybean and soybean–corn successions). All the treatments were replicated three times for a total of 48 experimental units. Soils were collected from two sampling depths (SD), 0–10 and 10–20 cm, in each treatment and soil physical properties, including bulk density (BD), air-filled porosity (AFP, fa) and total pore space (TPS, Φ), were calculated. Gas diffusivity models following AFP and/or TPS were used to predict Ds/Do and τ values. Results showed that, overall, Ds/Do was significantly increased in no-tilled plots planted to cereal rye in 2012 (p = 0.001) and in 2013 (p = 0.05). No-tilled continuous corn, followed by continuous soybean and no-tilled soybean–corn rotations had the highest Ds/Do values, respectively. In magnitude, Ds/Do was also increased in no-till plots at the lower depth (10–20 cm). No-tilled plots planted with cereal rye significantly reduced τ in 2012 (p = 0.001) and in 2013 (p = 0.05). Finally, at the upper depth (0–10 cm), the no-tilled corn–soybean rotation and the tilled soybean–corn rotation had the lowest τ. However, at the lower depth (10–20 cm), the four crop rotations were not significantly different in their τ values. These results can be useful to quickly assess the changes in soil physical properties because of crop management practices and make necessary changes to enhance agricultural resilience.

Combining global and local scaling (3D) methods to detect pore spaces in CT soil images

<p>The characterization of the spatial distribution of soil pore structures is essential to obtain different parameters that will be useful in developing predictive models for a range of physical, chemical, and biological processes in soils. Over the last decade, major technological advances in X-ray computed tomography (CT) have allowed for the investigation and reconstruction of natural porous soils at very fine scales. Delimiting the pore structure (pore space) from the CT soil images applying image segmentation methods is crucial when attempting to extract complex pore space geometry information.</p><p>Different segmentation methods can result in different spatial distributions of pores influencing the parameters used in the models [1]. A new combined global & local segmentation (2D) method called “Combining Singularity-CA method” was successfully applied [2]. This method combines a local scaling method (Singularity-CA method) with a global one (Maximum Entropy method). The Singularity-CA method, based on fractal concepts, creates singularity maps, and the CA (Concentration Area) method is used to define local thresholds that can be applied to binarize CT images [3]. Comparing Singularity-CA method with classical methods, such as Otsu and Maximum Entropy, we observed that more pores can be detected mainly due to its ability to amplify anomalous concentrations. However, some small pores were detected incorrectly. Combining Singularity-CA (2D) method gives better pore detection performance than the Singularity-CA and the Maximum Entropy method applied individually to the images.</p><p>The Combining Singularity-CV (3D) method is presented in this work. It combines the Singularity – CV (Concentration Volume) method [4] and a global one to improve 3D pore space detection.</p><p> </p><p>References:</p><p>[1] Zhang, Y.J. (2001). A review of recent evaluation methods for image segmentation: International symposium on signal processing and its applications. Kuala Lumpur, Malaysia, 13–16, pp. 148–151.</p><p>[2] Martín-Sotoca, J.J., Saa-Requejo, A., Grau, J.B., Paz-González, A., and Tarquis, A.M. (2018). Combining global and local scaling methods to detect soil pore space. J. of Geo. Exploration, vol. 189, June 2018, pp 72-84.</p><p>[3] Martín-Sotoca, J.J., Saa-Requejo, A., Grau, J.B. and Tarquis, A.M. (2017). New segmentation method based on fractal properties using singularity maps. Geoderma, vol. 287, February 2017, pp 40-53. http://dx.doi.org/10.1016/j.geoderma.2016.09.005.</p><p>[4] Martín-Sotoca, J.J., Saa-Requejo, A., Grau, J.B. and Tarquis, A.M. (2018). Local 3D segmentation of soil pore space based on fractal properties using singularity maps. Geoderma, vol. 311, February 2018, pp 175-188. http://dx.doi.org/10.1016/j.geoderma.2016.11.029.</p><p> </p><p>Acknowledgements:</p><p>The authors acknowledge support from Project No. PGC2018-093854-B-I00 of the Spanish Ministerio de Ciencia Innovación y Universidades of Spain and the funding from the Comunidad de Madrid (Spain), Structural Funds 2014-2020 512 (ERDF and ESF), through project AGRISOST-CM S2018/BAA-4330.</p>

Fungi as Ecosystem Engineers in the Soil Pore Space

<p>Soils are characterized by their largely varying microhabitats that determine their microbial communities and functions such as nutrient cycling. Microbes, and especially fungi, do not only react to those microhabitats but also contribute to shaping them.</p><p>We used transparent, microstructured chips simulating the internal pore space of soils, to microscopically study fungal mycelia at the hyphal scale. We investigated the variety of fungal morphologies in maze structures, and hyphal interactions with their biotic and abiotic microenvironments. We studied both a variety of laboratory strains including an arbuscular mycorrhizal fungus and natural soil inocula, and we quantified their growth strategies in different microstructures and their interactions with bacteria, protists and soil mineral particles.</p><p>We could observe how the rigid hyphae of fungi opened up passages through chip- or soil solids and aggregates, increasing the spatial availability of the pore space. They, on the other hand, also filled up pores and pore necks with their biomass, creatingbarriers for both organisms, flow of water and sedimentation of matter, and thus changing the pore size distribution and -connectivity. Hyphae also increased the wettability of pores, which led to a higher connectivity of water films across air pockets and thus benefiting the dispersal of water-dwelling microorganisms, a phenomenon earlier termed “fungal highways”. We found the abundance of both bacteria and protists strongly increased in pore spaces containing hyphae in comparison to those without, dispersal events via fungal hyphae that happened frequently and were quantifiable in the high internal replication of our chip’s pore space channels. This allowed us to conclude on a high relevance of this mode of dispersal in soils with intermediate moisture. Fungal hyphae had thus a strong and obvious effect on their surrounding microenvironments and organisms.</p><p>We consider the study of microbial behaviour and interactions at the cellular scale in microhabitats to be essential for a better understanding of soil functions, and to gain mechanistic insight into phenomena observable at macroscale.</p><p> </p>

Whole plant-environment microscopy reveals how Bacillus subtilis utilises the soil pore space to colonise plant roots

Plant growth is supported by complex interactions with many biophysical elements of their environment including microorganisms, geochemicals, water and gas, all within the otherwise complex and heterogeneous soils’ physical environment. Our understanding of plant-environment interactions in soil are limited by the difficulty of observing such interactions at the microscopic scale which occur throughout the large volume of influence of the plant. Here, we present the development of 3D live microscopy approaches for resolving plant-microbe interactions across the environment of an entire seedling root growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A dual-illumination light-sheet system was used to acquire scattering signals from the plant whilst fluorescence signals were captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm3 in size with as good as 5 μm resolution at a rate of up to one scan every 30 minutes. The system can track the movement of Bacillus subtilis populations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favoured small pore spaces over the surface of soil particles, colonising the root in a pulsatile manner. Migrations appeared to be directed first towards the root cap as the point “first contact”, before subsequent colonisation of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand life in soils.SignificanceBetter knowledge of microbial movement and interaction with plant roots is essential to understanding soil ecosystems. However, the lack of a suitable approach for observing biological activity in such environments severely impedes advances in this field of research. Here, we overcome this major limitation by combining the use of transparent soil with cutting edge live microscopy techniques. We performed a detailed analysis of the movements of Bacillus subtilis and revealed how the soil pore structure influences the behaviour of the bacteria, both before and during the formation of biofilms on the root surface. This work sheds light on previously unseen phenomenon, and accelerates our understanding of soil dwelling organisms which were, before now, unobserved in their native environment.

Fungal foraging behaviour and hyphal space exploration in micro-structured Soil Chips

How do fungi navigate through the complex microscopic maze-like structures found in the soil? Fungal behaviour, especially at the hyphal scale, is largely unknown and challenging to study in natural habitats such as the opaque soil matrix. We monitored hyphal growth behaviour and strategies of seven Basidiomycete litter decomposing species in a micro-fabricated “Soil Chip” system that simulates principal aspects of the soil pore space and its micro-spatial heterogeneity. The hyphae were faced with micrometre constrictions, sharp turns and protruding obstacles, and the species examined were found to have profoundly different responses in terms of foraging range and persistence, spatial exploration and ability to pass obstacles. Hyphal behaviour was not predictable solely based on ecological assumptions, and our results obtained a level of trait information at the hyphal scale that cannot be fully explained using classical concepts of space exploration and exploitation such as the phalanx/guerrilla strategies. Instead, we propose a multivariate trait analysis, acknowledging the complex trade-offs and microscale strategies that fungal mycelia exhibit. Our results provide novel insights about hyphal behaviour, as well as an additional understanding of fungal habitat colonisation, their foraging strategies and niche partitioning in the soil environment.

Experimental Investigation of Cement/Soda Residue for Solidification/Stabilization of Cr-Contaminated Soils

Adopting more efficient and sustainable remediation materials is of great importance for the development of solidification and stabilization (S/S) technology. Among them, soda residue could be considered as a desirable binder due to its strong adsorption for heavy metals. For understanding of the performance of Cr-contaminated soils treated by cement/soda residue, the strength, leaching and microstructural characteristics, and the long-term effectiveness under wetting-drying cycles were comprehensively investigated in this study. The results showed that the unconfined compressive strength (UCS) increased and the leached Cr3+ concentration decreased with curing time, binder content, and binder ratio. Increasing the soda residue from C6S14 to C6S24 could improve soil strength and reduce leachability of Cr3+, while a reverse trend was presented with increasing initial Cr3+ concentration. With subsequent wetting-drying cycles, the UCS further increased and then decreased; inversely, the leached Cr3+ decreased, followed by an increase of Cr-contaminated soils. For the specimens of C6S14 and C6S24, the maximum UCS of 6.04 MPa and 6.48 MPa was reached; correspondingly, the minimum leached Cr3+ concentration of 2.78 mg/L and 1.93 mg/L was reached after 3 wetting-drying cycles, respectively. Microstructure analysis results found that reaction products like calcium silicate hydrate (C-S-H) and ettringite (AFt) increasingly occupied the soil pore space and caused a denser soil structure after 3 wetting-drying cycles, which indicated the long-term effectiveness of contaminated soils treated by cement/soda residue.

PEMANFAATAN PUPUK BOKASIH TERHADAP PENINGKATAN KESUBURAN FISIK DAN KIMIA TANAH PADA LAHAN PEMBUDIDAYAAN TANAMAN TOMAT (Lycopersicum esculentum MILL.)

This study aims to determine the effect of bokashi fertilizer dosage on the physical and chemical properties of soil on tomato plants and the optimum dose of bokashi fertilizer which can provide the best influence on the physical and chemical properties of the soil. The research design used was a randomized block design (RBD) with a single factor pattern consisting of five treatments namely B0 = 0 tons ha-1 bokashi fertilizer (control), B1 = 5 tons ha-1 bokashi fertilizer, B2 = 10 tons ha-1 bokashi fertilizer, B3 = 15 tons ha-1 bokashi fertilizer, B4 = 20 tons ha-1 bokashi fertilizer. The observation variables in this study were soil volume/bulk density (gr /cm3), total soil pore space (%), N- total soil, available P-soil, available K-soil, soil C-organic, and soil pH. The results showed that the administration of bokashi fertilizer was able to improve the physical properties of soil in tomato plants, namely the weight of the soil volume decreased by 1,120 gr / cm³, water holding capacity increased by 30.24%, and soil pore space increased by 57.74%, so that the soil aggregate became good Giving doses of bokashi fertilizer can improve soil chemical properties in tomato plants, namely C-organic 0.91% very low, N-total soil 0.32% medium, P-available 37.25 ppm very high, and K-available 425.64 ppm very high and soil pH to 6.81 neutral. The supply of 20 tons/ha of bokashi fertilizer can improve soil physical and chemical properties optimally in tomato plants.

Aridity-driven decoupling of δ13C between pedogenic carbonate and soil organic matter

Pedogenic carbonate is an invaluable archive for reconstructing continental paleoclimate and paleoecology. The δ13C of pedogenic carbonate (δ13Cc) has been widely used to document the rise and expansion of C4 plants over the Cenozoic. This application requires a fundamental presumption that in soil pores, soil-respired CO2 dominates over atmospheric CO2 during the formation of pedogenic carbonates. However, the decoupling between δ13Cc and δ13C of soil organic matter (δ13CSOM) have been observed, particularly in arid regions, suggesting that this presumption is not always valid. To evaluate the influence of atmospheric CO2 on soil δ13Cc, here we performed systematic δ13C analyses of paleosols across the Chinese Loess Plateau, with the sample ages spanning three intervals: the Holocene, the Late Pleistocene, and the mid-Pliocene warm period. Our paired δ13Cc and δ13CSOM data reveal broadly divergent trending patterns. Using a two-component CO2-mixing model, we show substantial incorporations of atmospheric CO2 (up to 60%) into soil pore space during carbonate precipitation. This result readily explains the enrichment of δ13Cc and its divergence from δ13CSOM. As a consequence, δ13C of pedogenic carbonates formed under semiarid and/or arid conditions are largely driven by regional aridity through its control on soil CO2 composition, and thus cannot be used to evaluate the relative abundance of C3 versus C4 plants. Nonetheless, these carbonates can be applied for atmospheric CO2 reconstructions, even for periods with low CO2 levels.