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  • Schlüter, Steffen  (29)
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  • 1
    Language: English
    In: PloS one, 2016, Vol.11(7), pp.e0159948
    Description: Matter turnover in soil is tightly linked to soil structure which governs the heterogeneous distribution of habitats, reaction sites and pathways in soil. Thereby, the temporal dynamics of soil structure alteration is deemed to be important for essential ecosystem functions of soil but very little is known about it. A major reason for this knowledge gap is the lack of methods to study soil structure turnover directly at microscopic scales. Here we devise a conceptual approach and an image processing workflow to study soil structure turnover by labeling some initial state of soil structure with small garnet particles and tracking their fate with X-ray microtomography. The particles adhere to aggregate boundaries at the beginning of the experiment but gradually change their position relative to the nearest pore as structure formation progresses and pores are destructed or newly formed. A new metric based on the contact distances between particles and pores is proposed that allows for a direct quantification of soil structure turnover rates. The methodology is tested for a case study about soil compaction of a silty loam soil during stepwise increase of bulk density (ρ = {1.1, 1.3, 1.5} g/cm3). We demonstrate that the analysis of mean contact distances provides genuinely new insights about changing diffusion pathways that cannot be inferred neither from conventional pore space attributes (porosity, mean pore size, pore connectivity) nor from deformation analysis with digital image correlation. This structure labeling approach to quantify soil structure turnover provides a direct analogy to stable isotope labeling for the analysis of matter turnover and can be readily combined with each other.
    Keywords: X-Ray Microtomography ; Soil -- Chemistry
    E-ISSN: 1932-6203
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  • 2
    Language: English
    In: Vadose Zone Journal, 01 March 2018, Vol.17(1)
    Description: X-ray radiography is a suitable approach to study water dynamics in undisturbed soil. However, beam hardening impairs the deduction of soil moisture changes from X-ray attenuation, especially when studying infiltration of water into cylindrical soil columns. We developed a calibration protocol to correct for beam hardening effects that enables the quantitative determination of changing average water content in two-dimensional projections. The method works for a broad range of materials and is easy to implement. Moreover, we studied the drift of X-ray attenuation values due to the detector latency and eliminated its contribution to the quantitative analysis. Finally we could visualize the dynamics of infiltrating water into undisturbed cylindrical soil samples.
    Keywords: Agriculture
    ISSN: 1539-1663
    E-ISSN: 1539-1663
    Source: Directory of Open Access Journals (DOAJ)
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  • 3
    Language: English
    In: Frontiers in Environmental Science, 01 April 2018, Vol.6
    Description: Soil-borne nitrous oxide (N2O) emissions have a high spatial and temporal variability which is commonly attributed to the occurrence of hotspots and hot moments for microbial activity in aggregated soil. Yet there is only limited information about the biophysical processes that regulate the production and consumption of N2O on microscopic scales in undisturbed soil. In this study, we introduce an experimental framework relying on simplified porous media that circumvents some of the complexities occuring in natural soils while fully accounting for physical constraints believed to control microbial activity in general and denitrification in particular. We used this framework to explore the impact of aggregate size and external oxygen concentration on the kinetics of O2 consumption, as well as CO2 and N2O production. Model aggregates of different sizes (3.5 vs. 7 mm diameter) composed of porous, sintered glass were saturated with a defined growth medium containing roughly 109 cells ml−1 of the facultative anaerobic, nosZ-deficient denitrifier Agrobacterium tumefaciens with N2O as final denitrification product and incubated at five different oxygen levels (0–13 vol-%). We demonstrate that the onset of denitrification depends on the amount of external oxygen and the size of aggregates. Smaller aggregates were better supplied with oxygen due to a larger surface-to-volume ratio, which resulted in faster growth and an earlier onset of denitrification. In larger aggregates, the onset of denitrification was more gradual, but with comparably higher N2O production rates once the anoxic aggregate centers were fully developed. The normalized electron flow from the reduced carbon substrate to N-oxyanions (edenit-/etotal- ratio) could be solely described as a function of initial oxygen concentration in the headspace with a simple, hyperbolic model, for which the two empirical parameters changed with aggregate size in a consistent way. These findings confirm the important role of soil structure on N2O emissions from denitrification by shaping the spatial patterns of microbial activity and anoxia in aggregated soil. Our dataset may serve as a benchmark for constraining or validating spatially explicit, biophysical models of denitrification in aggregated soil.
    Keywords: Greenhouse Gas Emissions ; Denitrification Kinetics ; Microbial Hotspots ; Microsites ; Anoxic Aggregate Centers ; Agrobacterium Tumefaciens ; Environmental Sciences
    E-ISSN: 2296-665X
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  • 4
    Language: English
    In: Frontiers in Microbiology, 2018, Vol.9, p.1929
    Description: Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the usual bulk, macroscopic parameters used to characterize soils (e.g., granulometry, pH, soil organic matter and biomass contents) provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gases. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale). For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. In terms of microbial aspects, whereas a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because relevant experimental data are extremely scarce. For the overall research to move forward, it will be crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead.Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future.
    Keywords: Life Sciences ; X-Ray Computed ; Upscaling ; Biodiversity ; Soil Microbiology ; Tomography ; Single-Cell Genomics ; Nanosims Imaging ; Biology
    ISSN: 1664-302X
    E-ISSN: 1664-302X
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  • 5
    Language: English
    In: Advances in Water Resources, 2011, Vol.34(2), pp.314-325
    Description: ► Stochastic reconstruction with a combination of multi-point statistics. ► Good rendition of connectivity with Minkowski functions and Chord length distributions. ► Transport behavior compares well between reference media and reconstructed media. ► Pressure field tends to bridge local discontinuities within highly conductive regions. Flow and transport in porous media is determined by its structure. Beside spatial correlation, especially the connectivity of heterogeneous conductivities is acknowledged to be a key factor. This has been demonstrated for well defined random fields having different topological properties. Yet, it remains an open question which morphological measures carry sufficient information to actually predict flow and transport in porous media. We analyze flow and transport in classical, two-dimensional random fields showing different topology and we determine a selection of structural characteristics including classical two-point statistics, chord-length distribution and Minkowski functions (four-point statistics) including the Euler number as a topological measure. Using the approach of simulated annealing for global optimization we generate analog random fields that are forced to reproduce one or several of theses structural characteristics. Finally we evaluate in how far the generated analogons reproduce the original flow and transport behavior as well as some more elaborate structural characteristics including percolation probabilities and the pair connectivity function. The results confirm that two-point statistics is insufficient to capture functional properties since it is not sensitive to connectivity. In contrast, the combination of Minkowski functions and chord length distributions carries sufficient information to reproduce the breakthrough curve of a conservative solute. Hence, global topology provided by the Euler number together with local clustering provided by the chord length distribution seems to be a powerful condensation of structural complexity with respect to functional properties.
    Keywords: Simulated Annealing ; Solute Transport ; Minkowski Functionals ; Chord Length Distribution ; Local Percolation Probability ; Pair Connectivity Function ; Engineering
    ISSN: 0309-1708
    E-ISSN: 1872-9657
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  • 6
    Language: English
    In: Advances in Water Resources, August 2012, Vol.44, pp.101-112
    Description: ► New averaging approach that conserves hydraulic non-equilibrium during rapid infiltration of water. ► New indicators to describe hydraulic non-equilibrium quantitatively. ► Direct link between front morphology and hydraulic non-equilibrium. ► Insights into how structural connectivity affects hydraulic non-equilibrium. ► Shortcomings of an upscaled Richards model extended by hydraulic non-equilibrium. Water infiltration into heterogeneous, structured soil leads to hydraulic non-equilibrium across the infiltration front. That is, the water content and pressure head are not in equilibrium according to some static water retention curve. The water content increases more rapidly in more conductive regions followed by a slow relaxation towards an equilibrium state behind the front. An extreme case is preferential infiltration into macropores. Since flow paths adapt to the structural heterogeneity of the porous medium, there is a direct link between structure and non-equilibrium. The aim of our study is to develop an upscaled description of water dynamics which conserves the macroscopic effects of non-equilibrium and which can be directly linked to structural properties of the material. A critical question is how to define averaged state variables at the larger scale. We propose a novel approach based on flux-weighted averaging of pressure head, and compare its performance to alternative methods for averaging. Further, we suggest some meaningful indicators of hydraulic non-equilibrium that can be related to morphological characteristics of infiltration fronts in quantitative terms. These methods provide a sound basis to assess the impact of structural connectivity on hydraulic non-equilibrium. We demonstrate our approach using numerical case studies for infiltration into two-dimensional heterogeneous media using three different structure models with distinct differences in connectivity. Our results indicate that an increased isotropic, short-range connectivity reduces non-equilibrium, whereas anisotropic structures that are elongated in the direction of flow enforce it. We observe a good agreement between front morphology and effective hydraulic non-equilibrium. A detailed comparison of averaged state variables with results from an upscaled model that includes hydraulic non-equilibrium outlines potential improvements in the description of non-equilibrium dynamics including preferential flow in simplified, upscaled models based on Richards equation.
    Keywords: Transient Flow ; Upscaling ; Pressure Head Averaging ; Hydraulic Non-Equilibrium ; Preferential Flow ; Connectivity ; Engineering
    ISSN: 0309-1708
    E-ISSN: 1872-9657
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  • 7
    Language: English
    In: Journal of Plant Nutrition and Soil Science, 06/2011, Vol.174(3), pp.395-403
    ISSN: Journal of Plant Nutrition and Soil Science
    E-ISSN: 14368730
    E-ISSN: 15222624
    Source: Wiley (via CrossRef)
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  • 8
    Language: English
    In: Nature, 22 February 2018, Vol.554(7693), pp.423
    Keywords: Soil ; Plant Roots -- Chemistry
    ISSN: 00280836
    E-ISSN: 1476-4687
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  • 9
    Language: English
    In: Vadose Zone Journal, 2011, Vol.10(3), p.1082
    Description: Predicting solute transport through structured soil based on observable structural properties of the material has not been accomplished to date. We evaluated a new approach to predicting breakthrough curves (BTCs) of dissolved chemicals in intact structured soil columns based on attributes of the pore structure at hierarchical spatial scales. The methodology centers on x-ray computed microtomography of a hierarchic suite of undisturbed soil samples (diameters 1, 4.6, 7.5, and 16 cm) to identify the network of pores 〉10 mu m in diameter. The pore structure was quantified in terms of pore size distribution, interface area density, and connectivity. The pore size distribution and pore connectivity were used to set up an equivalent pore network model (PNM) for predicting the BTCs of Br (super -) and Brilliant Blue FCF (BB) at unsaturated, steady-state flux. For a structured silt loam soil column, the predictions of Br (super -) tracer breakthrough were within the variation observed in the column experiments. A similarly good prediction was obtained for Br (super -) breakthrough in a sandy soil column. The BB breakthrough observed in the silt loam was dominated by a large variation in sorption (retardation factors between R = 2.9 and 24.2). The BB sorption distribution coefficient, k (sub d) , was measured in batch tests. Using the average k (sub d) in the PNM resulted in an overestimated retardation (R = 28). By contrast, breakthrough of BB in the sandy soil (experimental R = 3.3) could be roughly predicted using the batch test k (sub d) (PNM simulation R = 5.3). The prediction improved when applying a sorption correction function accounting for the deviation between measured interface area density distribution and its realization in the network model (R = 4.1). Overall, the results support the hypothesis that solute transport can be estimated based on a limited number of characteristics describing pore structure: the pore size distribution, pore topology, and pore-solid interfacial density.
    Keywords: Soils ; Bad Lauchstadt Germany ; Boundary Conditions ; Breakthrough Curves ; Bromine ; Central Europe ; Central Germany ; Chemical Dispersion ; Chernozems ; Computed Tomography ; Convection ; Density ; Dye Tracers ; Equations ; Europe ; Experimental Studies ; Fuhrberg Germany ; Germany ; Halogens ; Image Analysis ; Laboratory Studies ; Lower Saxony Germany ; Microtomography ; Minckowski Functions ; Morphology ; Networks ; Podzols ; Porosity ; Quantitative Analysis ; Saxony-Anhalt Germany ; Simulation ; Soils ; Solute Transport ; Spectra ; Tomography ; Topology ; Transport ; X-Ray Spectra;
    ISSN: Vadose Zone Journal
    E-ISSN: 1539-1663
    Source: CrossRef
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  • 10
    Language: English
    In: Vadose Zone Journal, 2013, Vol.12(4), p.0
    Description: The hydraulic behavior of soil is determined by its hydraulic properties and their variability in space. In agricultural soils, this heterogeneity may stem from tillage or may have natural origin. The root distribution of plants will adapt to some extent to this soil heterogeneity. However, the combined impact of soil heterogeneity and root water uptake (RWU) on long-term soil water budgets has not received much attention. Numerical experiments helped identify how soil heterogeneity affects plant transpiration, soil evaporation, and groundwater recharge. Two-dimensional virtual soils with hierarchical heterogeneity, both natural and tillage induced, served as a basis for modeling soil water dynamics for a 10-yr climate record from two weather stations in Germany that vastly differ in annual precipitation. The complex interactions between soil and vegetation were explored by (i) comparing different RWU strategies (depth-, structure-, and time-dependent root profiles), (ii) land use types (perennial grass and annual winter crops), (iii) a combination of textures (silt above sand and sand above loam), and (iv) RWU with or without a compensation mechanism. The simulations were repeated with one-dimensional, effective representations of these virtual soils. In the framework of hydropedology, this study shed some light on the interaction between plants and pedological features and its impact on the macroscopic soil water budget. We demonstrated that land use has a major impact on the annual water balance through the partitioning of evapotranspiration into bare soil evaporation and plant transpiration. Compensational RWU becomes important for the annual water balance when the root zone comprises contrasting materials with respect to water holding capacity. Soil heterogeneity has in fact a minor impact on long-term soil water budgets. As a consequence, the relative contribution of plant transpiration, soil evaporation, and groundwater recharge to the total soil water loss was well reproduced by simulations in one-dimensional effective soil profiles. This advocates the application of one-dimensional soil-atmosphere-vegetation transfer (SVAT) models at larger scales. These findings only hold for assumptions made in our numerical simulations including flat area without lateral flow and no macropore flow.
    Keywords: Environmental Geology ; Soils ; Atmosphere ; Boundary Conditions ; Central Europe ; Eastern Germany ; Europe ; Field Studies ; Germany ; Grain Size ; Heterogeneity ; Hydrodynamics ; Hydrology ; Hydropedology ; Julicher Borde Germany ; Land Use ; Magdeburg Germany ; Mapping ; North Rhine-Westphalia Germany ; Numerical Models ; One-Dimensional Models ; Rhizosphere ; Saxony-Anhalt Germany ; Scale Factor ; Size Distribution ; Soil-Atmosphere-Vegetation Transfer ; Soils ; Topography ; Two-Dimensional Models ; Unsaturated Zone ; Vegetation ; Water Balance ; Western Germany;
    ISSN: Vadose Zone Journal
    E-ISSN: 1539-1663
    Source: CrossRef
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