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  • Soil
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  • 1
    Language: English
    In: Ecological Modelling, 2011, Vol.222(12), pp.1998-2010
    Description: ► The individual-based INDISIM-SOM model is far more sensitive to some parameters than to others. ► Key parameters for the evolution of C and N are microbial maintenance, energy, and death probability. ► The nitrification rate, in particular, appears highly affected by the death probability. ► The sensitivity analysis indicates what simplification of the model is possible. ► It also shows which parameters need to be evaluated with more accuracy than is currently achievable. The fate of soil carbon and nitrogen compounds in soils in response to climate change is currently the object of significant research. In particular, there is much interest in the development of a new generation of micro-scale models of soil ecosystems processes. Crucial to the elaboration of such models is the ability to describe the growth and metabolism of small numbers of individual microorganisms, distributed in a highly heterogeneous environment. In this context, the key objective of the research described in this article was to further develop an individual-based soil organic matter model, INDISIM-SOM, first proposed a few years ago, and to assess its performance with a broader experimental data set than previously considered. INDISIM-SOM models the dynamics and evolution of carbon and nitrogen associated with organic matter in soils. The model involves a number of state variables and parameters related to soil organic matter and microbial activity, including growth and decay of microbial biomass, temporal evolutions of easily hydrolysable N, mineral N in ammonium and nitrate, CO and O . The present article concentrates on the biotic components of the model. Simulation results demonstrate that the model can be calibrated to provide good fit to experimental data from laboratory incubation experiments performed on three different types of Mediterranean soils. In addition, analysis of the sensitivity toward its biotic parameters shows that the model is far more sensitive to some parameters, i.e., the microbial maintenance energy and the probability of random microbial death, than to others. These results suggest that, in the future, research should focus on securing better measurements of these parameters, on environmental determinants of the switch from active to dormant states, and on the causes of random cell death in soil ecosystems.
    Keywords: Individual-Based Model ; Soil Microbial Activity ; Soil Organic Matter ; C and N Mineralization ; Microbial Parameters ; Environmental Sciences ; Ecology
    ISSN: 0304-3800
    E-ISSN: 1872-7026
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  • 2
    Language: English
    In: Journal of Hazardous Materials, 21 March 2015, Vol.285, pp.137-139
    Description: In recent years, several authors have suggested repeatedly that visible and near-infrared reflectance spectroscopy (VNIRS) could be an advantageous alternative to traditional wet-laboratory methods for the measurement of heavy metal concentrations in soils. In this comment, we argue that, on the contrary, VNIRS is of limited practical use in such a context and should not serve as an excuse to get rid of direly needed laboratory facilities. The key reasons are that VNIRS spectra are irremediably insensitive to the presence of heavy metals, that the effect of soil moisture and surface rugosity on VNIR sensing still has to be satisfactorily accounted for, and finally that VNIRS probes an extremely thin layer of soil at the surface, which is generally irrelevant in terms of plant growth. Given these intrinsic limitations, it seems indicated to put the persistent VNIRS myth to rest, and to explore other measurement techniques that may have more potential.
    Keywords: Engineering ; Law
    ISSN: 0304-3894
    E-ISSN: 1873-3336
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  • 3
    Language: English
    In: PLoS ONE, 01 January 2015, Vol.10(9), p.e0137205
    Description: There is currently a significant need to improve our understanding of the factors that control a number of critical soil processes by integrating physical, chemical and biological measurements on soils at microscopic scales to help produce 3D maps of the related properties. Because of technological limitations, most chemical and biological measurements can be carried out only on exposed soil surfaces or 2-dimensional cuts through soil samples. Methods need to be developed to produce 3D maps of soil properties based on spatial sequences of 2D maps. In this general context, the objective of the research described here was to develop a method to generate 3D maps of soil chemical properties at the microscale by combining 2D SEM-EDX data with 3D X-ray computed tomography images. A statistical approach using the regression tree method and ordinary kriging applied to the residuals was developed and applied to predict the 3D spatial distribution of carbon, silicon, iron, and oxygen at the microscale. The spatial correlation between the X-ray grayscale intensities and the chemical maps made it possible to use a regression-tree model as an initial step to predict the 3D chemical composition. For chemical elements, e.g., iron, that are sparsely distributed in a soil sample, the regression-tree model provides a good prediction, explaining as much as 90% of the variability in some of the data. However, for chemical elements that are more homogenously distributed, such as carbon, silicon, or oxygen, the additional kriging of the regression tree residuals improved significantly the prediction with an increase in the R2 value from 0.221 to 0.324 for carbon, 0.312 to 0.423 for silicon, and 0.218 to 0.374 for oxygen, respectively. The present research develops for the first time an integrated experimental and theoretical framework, which combines geostatistical methods with imaging techniques to unveil the 3-D chemical structure of soil at very fine scales. The methodology presented in this study can be easily adapted and applied to other types of data such as bacterial or fungal population densities for the 3D characterization of microbial distribution.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 4
    Language: English
    In: Science of the Total Environment, 15 July 2018, Vol.630, pp.146-153
    Description: Thallium (Tl) is a toxic trace metal, whose geochemical behavior and biological effects are closely controlled by its chemical speciation in the environment. However, little tends to be known about this speciation of Tl in soil and plant systems that directly affect the safety of food supplies. In this context, the objective of the present study was to elaborate an efficient method to separate and detect Tl(I) and Tl(III) species for soil and plant samples. This method involves the selective adsorption of Tl(I) on microcolumns filled with immobilized oxine, in the presence of DTPA (diethylenetriaminepentaacetic acid), followed by DTPA-enhanced ultrasonic and heating-induced extraction, coupled with ICP-MS detection. The method was characterized by a LOD of 0.037 μg/L for Tl(I) and 0.18 μg/L for Tl(III) in 10  mL samples. With this method, a second objective of the research was to assess the speciation of Tl in pot and field soils and in green cabbage crops. Experimental results suggest that DTPA extracted Tl was mainly present as Tl(I) in soils (〉95%). Tl in hyperaccumulator plant green cabbage was also mainly present as Tl(I) (〉90%). With respect to Tl uptake in plants, this study provides direct evidence that green cabbage mainly takes up Tl(I) from soil, and transports it into the aboveground organs. In soils, Tl(III) is reduced to Tl(I) even at the surface where the chemical environment promotes oxidation. This observation is conducive to understanding the mechanisms of Tl isotope fractionation in the soil-plant system. Based on geochemical fraction studies, the reducible fraction was the main source of Tl getting accumulated by plants. These results indicate that the improved analytical method presented in this study offers an economical, simple, fast, and sensitive approach for the separation of Tl species present in soils at trace levels.
    Keywords: Tl Speciation ; Extraction ; Soil ; Green Cabbage ; Geochemical Fraction ; Tl Bioavailability ; Environmental Sciences ; Biology ; Public Health
    ISSN: 0048-9697
    E-ISSN: 1879-1026
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  • 5
    Language: English
    In: Soil Science Society of America Journal, Jan, 2013, Vol.77(1), p.54(6)
    Description: Until recently, the custom manufacture of equipment for laboratory or field experiments in soil science required appreciable know-how, and was extremely time-consuming. Technological advances in rapid prototyping and o3-D printingo in the last decade afford significant, and as yet untapped, opportunities to manufacture equipment in a very different way. In the present note, we demonstrate with two concrete examples that 3-D printing is not only a very effective and versatile technique to produce laboratory or field equipment. It also alleviates some of the restrictive technical constraints imposed by lathes and molding processes used traditionally, and it permits a much more efficient sharing of information among researchers. Given the tremendous advances in 3-D printing unfolding at the moment, it is anticipated that this technology will revolutionize the way we design, and especially replicate, experiments in soil science.
    Keywords: Rapid Prototyping -- Technology Application ; 3d Printing -- Technology Application ; Technological Innovations -- Usage
    ISSN: 0361-5995
    E-ISSN: 14350661
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  • 6
    Language: English
    In: Environmental Pollution, July 2018, Vol.238, pp.140-149
    Description: Soil contamination due to atmospheric deposition of metals originating from smelters is a global environmental problem. A common problem associated with this contamination is the discrimination between anthropic and natural contributions to soil metal concentrations: In this context, we investigated the characteristics of soil contamination in the surrounding area of a world class smelter. We attempted to combine several approaches in order to identify sources of metals in soils and to examine contamination characteristics, such as pollution level, range, and spatial distribution. Soil samples were collected at 100 sites during a field survey and total concentrations of As, Cd, Cr, Cu, Fe, Hg, Ni, Pb, and Zn were analyzed. We conducted a multivariate statistical analysis, and also examined the spatial distribution by 1) identifying the horizontal variation of metals according to particular wind directions and distance from the smelter and 2) drawing a distribution map by means of a GIS tool. As, Cd, Cu, Hg, Pb, and Zn in the soil were found to originate from smelter emissions, and As also originated from other sources such as abandoned mines and waste landfill. Among anthropogenic metals, the horizontal distribution of Cd, Hg, Pb, and Zn according to the downwind direction and distance from the smelter showed a typical feature of atmospheric deposition (regression model:  =   + αe ). Lithogenic Fe was used as an indicator, and it revealed the continuous input and accumulation of these four elements in the surrounding soils. Our approach was effective in clearly identifying the sources of metals and analyzing their contamination characteristics. We believe this study will provide useful information to future studies on soil pollution by metals around smelters.
    Keywords: Soil Contamination ; Smelter ; Metal ; Gis ; Atmospheric Deposition ; Engineering ; Environmental Sciences ; Anatomy & Physiology
    ISSN: 0269-7491
    E-ISSN: 1873-6424
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  • 7
    In: Soil Science, 2012, Vol.177(2), pp.111-119
    Description: ABSTRACT: Macroscopic measurements and observations in two-dimensional soil-thin sections indicate that fungal hyphae invade preferentially the larger, air-filled pores in soils. This suggests that the architecture of soils and the microscale distribution of water are likely to influence significantly the dynamics of fungal growth. Unfortunately, techniques are lacking at present to verify this hypothesis experimentally, and as a result, factors that control fungal growth in soils remain poorly understood. Nevertheless, to design appropriate experiments later on, it is useful to indirectly obtain estimates of the effects involved. Such estimates can be obtained via simulation, based on detailed micron-scale X-ray computed tomography information about the soil pore geometry. In this context, this article reports on a series of simulations resulting from the combination of an individual-based fungal growth model, describing in detail the physiological processes involved in fungal growth, and of a Lattice Boltzmann model used to predict the distribution of air-liquid interfaces in soils. Three soil samples with contrasting properties were used as test cases. Several quantitative parameters, including Minkowski functionals, were used to characterize the geometry of pores, air-water interfaces, and fungal hyphae. Simulation results show that the water distribution in the soils is affected more by the pore size distribution than by the porosity of the soils. The presence of water decreased the colonization efficiency of the fungi, as evinced by a decline in the magnitude of all fungal biomass functional measures, in all three samples. The architecture of the soils and water distribution had an effect on the general morphology of the hyphal network, with a “looped” configuration in one soil, due to growing around water droplets. These morphologic differences are satisfactorily discriminated by the Minkowski functionals, applied to the fungal biomass.
    Keywords: Agriculture;
    ISSN: 0038-075X
    E-ISSN: 15389243
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  • 8
    Language: English
    In: Frontiers in Microbiology, 01 July 2018, Vol.9
    Description: There is still no satisfactory understanding of the factors that enable soil microbial populations to be as highly biodiverse as they are. The present article explores in silico the hypothesis that the heterogeneous distribution of soil organic matter, in addition to the spatial connectivity of the soil moisture, might account for the observed microbial biodiversity in soils. A multi-species, individual-based, pore-scale model is developed and parameterized with data from 3 Arthrobacter sp. strains, known to be, respectively, competitive, versatile, and poorly competitive. In the simulations, bacteria of each strain are distributed in a 3D computed tomography (CT) image of a real soil and three water saturation levels (100, 50, and 25%) and spatial heterogeneity levels (high, intermediate, and low) in the distribution of the soil organic matter are considered. High and intermediate heterogeneity levels assume, respectively, an amount of particulate organic matter (POM) distributed in a single (high heterogeneity) or in four (intermediate heterogeneity) randomly placed fragments. POM is hydrolyzed at a constant rate following a first-order kinetic, and continuously delivers dissolved organic carbon (DOC) into the liquid phase, where it is then taken up by bacteria. The low heterogeneity level assumes that the food source is available from the start as DOC. Unlike the relative abundances of the 3 strains, the total bacterial biomass and respiration are similar under the high and intermediate resource heterogeneity schemes. The key result of the simulations is that spatial heterogeneity in the distribution of organic matter influences the maintenance of bacterial biodiversity. The least competing strain, which does not reach noticeable growth for the low and intermediate spatial heterogeneities of resource distribution, can grow appreciably and even become more abundant than the other strains in the absence of direct competition, if the placement of the resource is favorable. For geodesic distances exceeding 5 mm, microbial colonies cannot grow. These conclusions are conditioned by assumptions made in the model, yet they suggest that microscale factors need to be considered to better understand the root causes of the high biodiversity of soils.
    Keywords: Soil ; Pore Scale ; Organic Matter ; Resource Allocation ; Bacteria ; Biodiversity ; Biology
    E-ISSN: 1664-302X
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  • 9
    In: Soil Science, 2010, Vol.175(8), pp.363-374
    Description: The need to predict with reasonable accuracy the fate of soil C and N compounds in soils in response to climate change is stimulating interest in a new generation of microscale models of soil ecosystem processes. Essential to the development of such models is the ability to describe the growth and metabolism of small numbers of individual microorganisms. In this context, the key objective of the research described in this article was to further develop an individual-based soil organic matter (SOM) model, INDISIM-SOM, first proposed a few years ago, and to assess its performance with a broader data set than previously considered. The INDISIM-SOM models the dynamics and evolution of C and N associated with organic matter in soils. The model involves a number of state variables and parameters related to SOM and microbial activity, including growth and decay of microbial biomass, temporal evolution of mineralized intermediate C and N, mineral N in ammonium and nitrate, carbon dioxide, and O2. Simulation results demonstrate good fit of the model to experimental data from laboratory incubation experiments performed on three different types of Mediterranean soils. A second objective was to determine the sensitivity of the model toward its various parameters. Sensitivity was small for several of the parameters, suggesting possible simplifications of the model for specific uses, but was significant particularly for the parameter associated with the fraction of the soil C present in the biomass. These results suggest that research should be focused on improving the measurement of this latter parameter.
    Keywords: Microorganisms ; Metabolism ; Climate Change ; Soil Microorganisms ; Soil Testing ; Evolution ; Simulation ; Biomass ; Carbon ; Nitrogen;
    ISSN: 0038-075X
    E-ISSN: 15389243
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  • 10
    Language: English
    In: Ecotoxicology and Environmental Safety, February 2015, Vol.112, pp.122-131
    Description: In various parts of the world, high cadmium (Cd) concentrations in environment are not related to anthropogenic contamination but have natural origins. Less is known about health risks that arise under these conditions. This study aimed to discuss the pollution of Cd with natural sources, and to investigate the concentration of Cd in food crops and the urine of inhabitants in an area of southwestern China. The results showed that the arable soils are moderately contaminated by Cd ( =1.51) relative to the local background, with a high ecological risk ( =218). The chemical fractions of Cd in soils with natural sources are probably controlled by parent materials and mostly in residual phase. The average Cd concentrations were 0.68 mg kg (fresh weight) in local vegetables, 0.04 mg kg in rice, and 0.14 μg L in water. Leafy vegetable tends to accumulate more Cd than the other crops. The calculated Target Hazard Quotient (THQ) had a much higher value (4.33) for Cd, suggesting that Cd represents a significant potential risk to the local population. The urinary Cd concentrations (mean at 3.92 μg L for male and 4.85 μg L for female) of inhabitants in the study area were significantly higher ( 〈0.05) than those from the control area (mean at 0.8 μg L for male and 0.42 μg L for female). Male and female test subjects had similar urinary Cd levels ( 〉0.05), but age seemed to lead to an increase in Cd in the urine. These findings show that naturally-occurring Cd in local soils is taken up appreciably by local food crops, and that dietary exposure of Cd through vegetable ingestion is a major exposure pathway for local populations, and a potential risk to public health in the study area.
    Keywords: Cadmium ; Pollution ; Food Crops ; Dietary Exposure ; Health Risk ; Ecology ; Public Health
    ISSN: 0147-6513
    E-ISSN: 1090-2414
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