Geometrical characterization of undisturbed soil samples using X-ray computed tomography image analysis. Effect of soil management on soil structure

El estudio de la estructura del suelo es de vital importancia en diferentes campos de la ciencia y la tecnología. La estructura del suelo controla procesos físicos y biológicos importantes en los sistemas suelo-planta-microorganismos. Estos procesos están dominados por la geometría de la estructura del suelo, y una caracterización cuantitativa de la heterogeneidad de la geometría del espacio poroso es beneficiosa para la predicción de propiedades físicas del suelo. La tecnología de la tomografía computerizada de rayos-X (CT) nos permite obtener imágenes digitales tridimensionales del interior de una muestra de suelo, proporcionando información de la geometría de los poros del suelo y permitiendo el estudio de los poros sin destruir las muestras. Las técnicas de la geometría fractal y de la morfología matemática se han propuesto como una poderosa herramienta para analizar y cuantificar características geométricas. Las dimensiones fractales del espacio poroso, de la interfaz poro-sólido y de la distribución de tamaños de poros son indicadores de la complejidad de la estructura del suelo. Los funcionales de Minkowski y las funciones morfológicas proporcionan medios para medir características geométricas fundamentales de los objetos geométricos tridimensionales. Esto es, volumen, superficie, curvatura media de la superficie y conectividad. Las características del suelo como la distribución de tamaños de poros, el volumen del espacio poroso o la superficie poro-solido pueden ser alteradas por diferentes practicas de manejo de suelo. En este trabajo analizamos imágenes tomográficas de muestras de suelo de dos zonas cercanas con practicas de manejo diferentes. Obtenemos un conjunto de medidas geométricas, para evaluar y cuantificar posibles diferencias que el laboreo pueda haber causado en el suelo. ABSTRACT The study of soil structure is of vital importance in different fields of science and technology. Soil structure controls important physical and biological processes in soil-plant-microbial systems. Those processes are dominated by the geometry of soil pore structure, and a quantitative characterization of the spatial heterogeneity of the pore space geometry is beneficial for prediction of soil physical properties. The technology of X-ray computed tomography (CT) allows us to obtain three-dimensional digital images of the inside of a soil sample providing information on soil pore geometry and enabling the study of the pores without disturbing the samples. Fractal geometry and mathematical morphological techniques have been proposed as powerful tools to analyze and quantify geometrical features. Fractal dimensions of pore space, pore-solid interface and pore size distribution are indicators of soil structure complexity. Minkowski functionals and morphological functions provide means to measure fundamental geometrical features of three-dimensional geometrical objects, that is, volume, boundary surface, mean boundary surface curvature, and connectivity. Soil features such as pore-size distribution, pore space volume or pore-solid surface can be altered by different soil management practices. In this work we analyze CT images of soil samples from two nearby areas with contrasting management practices. We performed a set of geometrical measures, some of them from mathematical morphology, to assess and quantify any possible difference that tillage may have caused on the soil.

Efficient PGD-based dynamic calculation of non-linear soil behavior

Non-linear behavior of soils during a seismic event has a predominant role in current site response analysis. Soil response analysis consistently indicates that the stress-strain relationship of soils is nonlinear and shows hysteresis. When focusing in forced response simulations, time integrations based on modal analysis are widely considered, however parametric analysis, non-linear behavior and complex damping functions make difficult the online use of standard discretization strategies, e.g. those based on the use of finite element. In this paper we propose a new harmonic analysis formulation, able to address forced response simulation of soils exhibiting their characteristic nonlinear behavior. The solution can be evaluated in real-time from the offline construction of a parametric solution of the associated linearized problem within the Proper Generalized Decomposition framework.

Ca-amendement and tillage: medium term synergies for improving key soil properties of acid soils. Soil and tillage research, 134: 195-206

Ca-amendments are routinely applied to improve acid soils, whilst no-tillage (NT) has been widely recommended in soils where traditional tillage (TT) has led to losses of organic matter. However, the potential interactions between the two treatments are only partially known. Our study was conducted on an annual forage crop agrosystem with a degraded Palexerult soil located in SW Spain, in order to assess if the combination of NT plus a Ca-amendment provides additional benefits to those of their separate use. To this end we analysed the effects of four different combinations of tillage and Ca-amendment on selected key soil properties, focusing on their relationships. The experimental design was a split-plot with four replicates. The main factor was tillage (NT versus TT) and the second factor was the application or not of a Ca-amendment, consisting of a mixture of sugar foam (SF) and red gypsum (RG). Soil samples were collected from 3 soil layers down to 50 cm after four years of treatment (2009). The use of the Ca-amendment improved pH and Al-toxicity down to 25 cm and increased exchangeable Ca2+ down to 50 cm, even under NT due to the combined effect of SF and RG. Both NT and the Ca-amendment had a beneficial effect on total organic carbon (TOC), especially on particulate organic carbon (POC), in the 0–5 cm layer, with the highest contents observed when both practices were combined. Unlike NT, the Ca-amendment failed to improve soil aggregation in spite of the carbon supplied. This carbon was not protected within the stable aggregates in the medium term, making it more susceptible to mineralization. We suggest that the fraction of Al extracted by oxalate from solid phase (AlOxa-Cu-K) and the glomalin-related soil proteins (GRSPs) are involved in the accumulation of carbon within water stable aggregates, probably through the formation of non-toxic stable Al-OM compounds, including those formed with GRSPs. NT alone decreased AlK in the 0–5 cm soil layer, possibly by increasing POC, TOC and GRSPs, which were observed to play a role in reducing Al toxicity. From our findings, the combination of NT and Ca-amendment appears to be the best management practice to improve chemical and physical characteristics of acid soils degraded by tillage.

Soil aggregate geometry: Measurements and morphology

Aggregates provide physical microenvironments for microorganisms, the vital actors of soil systems, and thus play a major role as both, an arena and a product of soil carbon stabilization and dynamics. The surface of an aggregate is what enables exchange of the materials and air and water fluxes between aggregate exterior and interior regions. We made use of 3D images from X-ray CT of aggregates and mathematical morphology to provide an exhaustive quantitative description of soil aggregate morphology that includes both intra-aggregate pore space structure and aggregate surface features. First, the evolution of Minkowski functionals (i.e. volume, boundary surface, curvature and connectivity) for successive dilations of the solid part of aggregates was investigated to quantify its 3D geometrical features. Second, the inner pore space was considered as the object of interest. We devised procedures (a) to define the ends of the accessible pores that are connected to the aggregate surface and (b) to separate accessible and inaccessible porosity. Geometrical Minkowski functionals of the intra-aggregate pore space provide the exhaustive characterization of the inner structure of the aggregates. Aggregates collected from two different soil treatments were analyzed to explore the utility of these morphological tools in capturing the impact on their morphology of two different soil managements, i.e. conventional tillage management, and native succession vegetation treatment. The quantitative tools of mathematical morphology distinguished differences in patterns of aggregate structure associated to the different soil managements.

Occurrence and analysis of selected pharmaceutical compounds in soil from Spanish agricultural fields

This work describes the analysis of 15 pharmaceutical compounds, belonging to different therapeutic classes (anti-inflammatory/analgesics, lipid regulators, antiepileptics, ?-blockers and antidepressants) and with diverse physical?chemical properties, in Spanish soils with different farmland uses. The studied compounds were extracted from soil by ultrasound-assisted extraction (UAE) and determined, after derivatization, by gas chromatography with mass spectrometric detection (GC?MS). The limits of detection (LODs) ranged from 0.14 ng g?1 (naproxen) to 0.65 ng g?1 (amitriptyline). At least two compounds where detected in all samples, being ibuprofen, salicylic acid, and paracetamol, the most frequently detected compounds. The highest levels found in soil were 47 ng g?1 for allopurinol and 37 ng g?1 for salicylic acid. The influence of the type of crop and the sampling area on the levels of pharmaceuticals in soil, as well as their relationship with soil physical?chemical properties, was studied. The frequent and widespread detection of some of these compounds in agricultural soils show a diffuse contamination, although the low levels found do not pose a risk to the environment or the human health.

Impact of Spatial Soil and Climate Input Data Aggregation on Regional Yield Simulations

This work was financially supported by the German Federal Ministry of Food and Agriculture (BMEL) through the Federal Office for Agriculture and Food (BLE), (2851ERA01J). FT and RPR were supported by FACCE MACSUR (3200009600) through the Finnish Ministry of Agriculture and Forestry (MMM). EC, HE and EL were supported by The Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (220-2007-1218) and by the strategic funding ‘Soil-Water-Landscape’ from the faculty of Natural Resources and Agricultural Sciences (Swedish University of Agricultural Sciences) and thank professor P-E Jansson (Royal Institute of Technology, Stockholm) for support. JC, HR and DW thank the INRA ACCAF metaprogramm for funding and Eric Casellas from UR MIAT INRA for support. CB was funded by the Helmholtz project “REKLIM—Regional Climate Change”. CK was funded by the HGF Alliance “Remote Sensing and Earth System Dynamics” (EDA). FH was funded by the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) under the Grant FOR1695. FE and SS acknowledge support by the German Science Foundation (project EW 119/5-1). HH, GZ, SS, TG and FE thank Andreas Enders and Gunther Krauss (INRES, University of Bonn) for support. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Effects of hydrocarbon contamination on soil microbial community and enzyme activity

Acknowledgment I would like to gratefully acknowledge the government of Saudi Arabia for the scholarship and financial support.

The impact of soil salinity on the yield, composition and physiology of the bioenergy grass Miscanthus × giganteus

Funded by OPTIMA Biotechnology & Biological Sciences Research Council (BBSRC) Institute Strategic Programme Energy Grasses & Biorefining. Grant Number: BBS/E/W/10963A01 Defra GIANT LINK

Isolation of 'Candidatus Nitrosocosmicus franklandus', a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration

Acknowledgements. The authors would like to thank Mr Kevin Mackenzie and Mrs Gillian Milne (University of Aberdeen) for technical support with scanning electron microscopy, and Dr Robin Walker for access to the Woodlands Field experimental plots at the SRUC,Craibstone Estate, Aberdeen. This work was financially supported by Natural Environmental Research Council (standard grants NE/I027835/1 and NE/L006286/1 and fellowship NE/J019151/1), EC Marie Curie ITN NORA, Grant Agreement No. 316472, the AXA Research Fund and the Centre for Genome Enabled Biology and Medicine, University of Aberdeen.

Plant regeneration functional groups modulate the response to fire of soil enzyme activities in a Mediterranean shrubland

Soil enzymes are critical to soil nutrient cycling function but knowledge on the factors that control their response to major disturbances such as wildfires remains very limited. We evaluated the effect of fire-related plant functional traits (resprouting and seeding) on the resistance and resilience to fire of two soil enzyme activities involved in phosphorus and carbon cycling (acid phosphatase and β-glucosidase) in a Mediterranean shrublands in SE Spain. Using experimental fires, we compared four types of shrubland microsites: SS (vegetation patches dominated by seeder species), RR (patches dominated by resprouter species), SR (patches co-dominated by seeder and resprouter species), and IP (shrub interpatches). We assessed pre- and post-fire activities of the target soil enzymes, available P, soil organic C, and plant cover dynamics over three years after the fire. Post-fire regeneration functional groups (resprouter, seeder) modulated both pre- and post-fire activity of acid phosphatase and β-glucosidase, with higher activity in RR and SR patches than in SS patches and IP. However, we found no major differences in enzyme resistance and resilience between microsite types, except for a trend towards less resilience in SS patches. Fire similarly reduced the activity of both enzymes. However, acid phosphatase and β-glucosidase showed contrasting post-fire dynamics. While β-glucosidase proved to be rather resilient to fire, fully recovering three years after fire, acid phosphatase showed no signs of recovery in that period. Overall, the results indicate a positive influence of resprouter species on soil enzyme activity that is very resistant to fire. Long-lasting decrease in acid phosphatase activity probably resulted from the combined effect of P availability and post-fire drought. Our results provide insights on how plant functional traits modulate soil biochemical and microbiological response to fire in Mediterranean fire-prone shrublands.

Brackish groundwater desalination by reverse osmosis in southeastern Spain. Presence of emerging contaminants and potential impacts on soil-aquifer media

Desalinated brackish groundwater is becoming a new source of water supply to comply with growing water demands, especially in (semi-) arid countries. Recent publications show that some chemical compounds may persist in an unaltered form after the desalination processes and that there is an associated risk of mixing waters with different salinity for irrigation. At the university of Alicante campus (Spain), a mix of desalinated brackish groundwater and water from the existing aquifer is currently applied for landscape irrigation. The presence of 209 emerging compounds, surfactants, priority substances according to the 2008/105/EC Directive, 11 heavy metals and microbiological organisms in blended water and aquifer samples was investigated. Thirty-five compounds were detected (pesticides, pharmaceuticals and surfactants) among them two priority substances α-endosulfan and Ni were found above the permitted maximum concentration. Blended water used for landscape irrigation during the summer period is supersaturated with respect to carbonates, which may ultimately lead to mineral precipitation in the soil-aquifer media and changes in hydraulic parameters.

A PCR based method to detect Russula spp. in soil samples and Limodorum abortivum roots in Mediterranean environments

Aim of study. Orchidaceae has the largest number of species of any family in the plant kingdom. This family is subject to a high risk of extinction in natural environments, such as natural parks and protected areas. Recent studies have shown the prevalence of many species of orchids to be linked to fungal soil diversity, due to their myco-heterotrophic behaviour. Plant communities determine fungal soil diversity, and both generate optimal conditions for orchid development. Area of study. The work was carried out in n the two most important natural parks in Alicante (Font Roja and Sierra Mariola), in South-eastern of Spain. Material and Methods. We designed a molecular tool to monitor the presence of Russula spp. in soil and orchids roots, combined with phytosociological methods. Main results. Using a PCR-based method, we detected the presence in the soil and Limodorum abortivum orchid roots of the mycorrhizal fungi Russula spp. The species with highest coverage was Quercus rotundifolia in areas where the orchid was present. Research highlights. We present a useful tool based on PCR to detect the presence of Russula spp. in a natural environment. These results are consistent with those obtained in different studies that linked the presence of the mycorrhizal fungi Russula spp. in roots of the species Limodorum and the interaction between these fungal species and Quercus ilex trees in Mediterranean forest environments.

Comparison among monitoring strategies to assess water flow dynamic and soil hydraulic properties in agricultural soils

Irrigated agriculture is usually performed in semi-arid regions despite scarcity of water resources. Therefore, optimal irrigation management by monitoring the soil is essential, and assessing soil hydraulic properties and water flow dynamics is presented as a first measure. For this purpose, the control of volumetric water content, θ, and pressure head, h, is required. This study adopted two types of monitoring strategies in the same experimental plot to control θ and h in the vadose zone: i) non-automatic and more time-consuming; ii) automatic connected to a datalogger. Water flux was modelled with Hydrus-1D using the data collected from both acquisition strategies independently (3820 daily values for the automatic; less than 1000 for the non-automatic). Goodness-of-fit results reported a better adjustment in case of automatic sensors. Both model outputs adequately predicted the general trend of θ and h, but with slight differences in computed annual drainage (711 mm and 774 mm). Soil hydraulic properties were inversely estimated from both data acquisition systems. Major differences were obtained in the saturated volumetric water content, θs, and the n and α van Genuchten model shape parameters. Saturated hydraulic conductivity, Ks, shown lower variability with a coefficient of variation range from 0.13 to 0.24 for the soil layers defined. Soil hydraulic properties were better assessed through automatic data acquisition as data variability was lower and accuracy was higher.

Proceedings of the first Soil Microcommunities Conference : Syracuse, New York, October 18-20, 1971 /

On cover: Prepared for Atomic Energy Commission.