Search

The microstructure of permafrost ground contains clues to its formation and hence its preconditioning to future change. We applied X-ray computed microtomography (CT) to obtain high-resolution data (Δx=50 µm) of the composition of a 164 cm long permafrost core drilled in a Yedoma upland in north-eastern Siberia. The CT analysis allowed the microstructures to be directly mapped and volumetric contents of excess ice, gas inclusions, and two distinct sediment types to be quantified. Using laboratory measurements of coarsely resolved core samples, we statistically estimated the composition of the sediment types and used it to indirectly quantify volumetric contents of pore ice, organic matter, and mineral material along the core. We conclude that CT is a promising method for obtaining physical properties of permafrost cores which opens novel research potentials.

Soil structure in terms of the spatial arrangement of pores and solids is highly relevant for most physical and biochemical processes in soil. While this was known for a long time, a scientific approach to quantify soil structural characteristics was also missing for a long time. This was due to its buried nature but also due to the three-dimensional complexity. During the last two decades, tools to acquire full 3D images of undisturbed soil became more and more available and a number of powerful software tools were developed to reduce the complexity to a set of meaningful numbers. However, the standardization of soil structure analysis for a better comparability of the results is not well developed and the accessibility of required computing facilities and software is still limited. At this stage, we introduce an open-access Soil Structure Library (https://structurelib.ufz.de/, last access: 22 July 2022) which offers well-defined soil structure analyses for X-ray CT (computed tomography) data sets uploaded by interested scientists. At the same time, the aim of this library is to serve as an open data source for real pore structures as developed in a wide spectrum of different soil types under different site conditions all over the globe, by making accessible the uploaded binarized 3D images. By combining pore structure metrics with essential soil information requested during upload (e.g., bulk density, texture, organic carbon content), this Soil Structure Library can be harnessed towards data mining and development of soil-structure-based pedotransfer functions. In this paper, we describe the architecture of the Soil Structure Library and the provided metrics. This is complemented by an example of how the database can be used to address new research questions.

Land use is known to exert a dominant impact on a range of essential soil functions like water retention, carbon sequestration, organic matter cycling and plant growth. At the same time, land use management is known to have a strong influence on soil structure, e.g., through bioturbation, tillage and compaction. However, it is often unclear whether the differences in soil structure are the actual cause of the differences in soil functions or if they only co-occur. This impact of land use (conventional and organic farming, intensive and extensive meadow, extensive pasture) on the relationship between soil structure and short-term carbon mineralization was investigated at the Global Change Exploratory Facility, in Bad Lauchstädt, Germany. Intact topsoil cores (upper 10 cm, n=75) were sampled from all land use types at the early growing season. Soil structure and microbial activity were measured using X-ray-computed tomography and respirometry, respectively. Differences in microstructural properties between land uses were small in comparison to the variation within land uses. The most striking difference between land uses was larger macropore diameters in grassland soils due to the presence of large biopores that are periodically destroyed in croplands. Grasslands had larger amounts of particulate organic matter (POM), including root biomass, and also greater microbial activity than croplands, both in terms of basal respiration and rate of carbon mineralization during growth. Basal respiration among soil cores varied by more than 1 order of magnitude (0.08–1.42 µg CO2-C h−1 g−1 soil) and was best explained by POM mass (R2=0.53, p<0.001). Predictive power was only slightly improved by considering all bulk, microstructure and microbial properties jointly. The predictive power of image-derived microstructural properties was low, because aeration did not limit carbon mineralization and was sustained by pores smaller than the image resolution limit (<30 µm). The frequently postulated dependency of basal respiration on soil moisture was not evident even though some cores were apparently water limited, as it was likely disguised by the co-limitation of POM mass. This finding was interpreted in regards to the microbial hotspots which form on decomposing plant residues and which are decoupled from water limitation in bulk soil. The rate of glucose mineralization during growth was explained well by substrate-induced respiration (R2=0.84) prior to growth, which in turn correlated with total microbial biomass, basal respiration and POM mass, and was not affected by pore metrics. These findings stress that soil structure had little relevance in predicting carbon mineralization in well-aerated soil, as mineralization appeared to by predominantly driven by the decomposition of plant residues in intact soil. Land use therefore affects carbon mineralization in well-aerated soil mainly in the amount and quality of labile carbon.

The ploughing of soils in autumn drastically loosens the soil structure and, at the same time, reduces its stability against external stresses. A fragmentation of these artificially produced soil clods during wintertime is often observed in areas with air temperatures fluctuating around the freezing point. From the pore perspective, it is still unclear (i) under which conditions frost action has a measurable effect on soil structure, (ii) what the impact on soil hydraulic properties is, and (iii) how many freeze–thaw cycles (FTCs) are necessary to induce soil structure changes. The aim of this study was to analyse the cumulative effects of multiple FTC on soil structure and soil hydraulic properties for two different textures and two different initial structures. A silt clay with a substantial amount of swelling clay minerals and a silty loam with fewer swell/shrink dynamics were either kept intact in undisturbed soil cores taken from the topsoil from a grassland or repacked with soil clods taken from a ploughed field nearby. FTCs were simulated under controlled conditions and changes in pore structure ≥ 48 µm were regularly recorded using X-ray µCT. After 19 FTCs, the impact on hydraulic properties were measured, and the resolution of structural characteristics were enhanced towards narrow macropores with subsamples scanned at 10 µm. The impact of FTC on soil structure was dependent on the initial structure, soil texture, and the number of FTCs. Frost action induced a consolidation of repacked soil clods, resulting in a systematic reduction in pore sizes and macropore connectivity. In contrast, the macropore systems of the undisturbed soils were only slightly affected. Independent of the initial structure, a fragmentation of soil clods and macro-aggregates larger than 0.8 to 1.2 mm increased the connectivity of pores smaller than 0.5 to 0.8 mm. The fragmentation increased the unsaturated hydraulic conductivity of all treatments by a factor of 3 in by a factor of 3 in a matrix potential range of −100 to −350 hPa, while water retention was only slightly affected for the silt clay soil. Already 2 to 5 FTCs enforced a well-connected pore system of narrow macropores in all treatments, but it was steadily improved by further FTCs. The implications of fewer FTCs during milder winters caused by global warming are twofold. In ploughed soils, the beneficial seedbed consolidation will be less intense. In grassland soils, which have reached a soil structure in dynamic equilibrium that has experienced many FTCs in the making, there is still a beneficial increase in water supply through increasing unsaturated hydraulic conductivity by continued FTCs that might also be less efficient in the future.

The prediction of nitrous oxide (N2O) and of dinitrogen (N2) emissions formed by biotic denitrification in soil is notoriously difficult due to challenges in capturing co-occurring processes at microscopic scales. N2O production and reduction depend on the spatial extent of anoxic conditions in soil, which in turn are a function of oxygen (O2) supply through diffusion and O2 demand by respiration in the presence of an alternative electron acceptor (e.g. nitrate). This study aimed to explore controlling factors of complete denitrification in terms of N2O and (N2O + N2) fluxes in repacked soils by taking micro-environmental conditions directly into account. This was achieved by measuring microscale oxygen saturation and estimating the anaerobic soil volume fraction (ansvf) based on internal air distribution measured with X-ray computed tomography (X-ray CT). O2 supply and demand were explored systemically in a full factorial design with soil organic matter (SOM; 1.2 % and 4.5 %), aggregate size (2–4 and 4–8 mm), and water saturation (70 %, 83 %, and 95 % water-holding capacity, WHC) as factors. CO2 and N2O emissions were monitored with gas chromatography. The 15N gas flux method was used to estimate the N2O reduction to N2. N gas emissions could only be predicted well when explanatory variables for O2 demand and O2 supply were considered jointly. Combining CO2 emission and ansvf as proxies for O2 demand and supply resulted in 83 % explained variability in (N2O + N2) emissions and together with the denitrification product ratio [N2O / (N2O + N2)] (pr) 81 % in N2O emissions. O2 concentration measured by microsensors was a poor predictor due to the variability in O2 over small distances combined with the small measurement volume of the microsensors. The substitution of predictors by independent, readily available proxies for O2 demand (SOM) and O2 supply (diffusivity) reduced the predictive power considerably (60 % and 66 % for N2O and (N2O+N2) fluxes, respectively). The new approach of using X-ray CT imaging analysis to directly quantify soil structure in terms of ansvf in combination with N2O and (N2O + N2) flux measurements opens up new perspectives to estimate complete denitrification in soil. This will also contribute to improving N2O flux models and can help to develop mitigation strategies for N2O fluxes and improve N use efficiency.

Soil denitrification is the most important terrestrial process returning reactive nitrogen to the atmosphere, but remains poorly understood. In upland soils, denitrification occurs in hotspots of enhanced microbial activity, even under well-aerated conditions, and causes harmful emissions of nitric (NO) and nitrous oxide (N2O). The timing and magnitude of such emissions are difficult to predict due to the delicate balance of oxygen (O2) consumption and diffusion in soil. To study how spatial distribution of hotspots affects O2 exchange and denitrification, we embedded microbial hotspots composed of porous glass beads saturated with growing cultures of either Agrobacterium tumefaciens (a denitrifier lacking N2O reductase) or Paracoccus denitrificans (a “complete” denitrifier) in different architectures (random vs. layered) in sterile sand that was adjusted to different water saturations (30 %, 60 %, 90 %). Gas kinetics (O2, CO2, NO, N2O and N2) were measured at high temporal resolution in batch mode. Air connectivity, air distance and air tortuosity were determined by X-ray tomography after the experiment. The hotspot architecture exerted strong control on microbial growth and timing of denitrification at low and intermediate saturations, because the separation distance between the microbial hotspots governed local oxygen supply. Electron flow diverted to denitrification in anoxic hotspot centers was low (2 %–7 %) but increased markedly (17 %–27 %) at high water saturation. X-ray analysis revealed that the air phase around most of the hotspots remained connected to the headspace even at 90 % saturation, suggesting that the threshold response of denitrification to soil moisture could be ascribed to increasing tortuosity of air-filled pores and the distance from the saturated hotspots to these air-filled pores. Our findings suggest that denitrification and its gaseous product stoichiometry depend not only on the amount of microbial hotspots in aerated soil, but also on their spatial distribution. We demonstrate that combining measurements of microbial activity with quantitative analysis of diffusion lengths using X-ray tomography provides unprecedented insights into physical constraints regulating soil microbial respiration in general and denitrification in particular. This paves the way to using observable soil structural attributes to predict denitrification and to parameterize models. Further experiments with natural soil structure, carbon substrates and microbial communities are required to devise and parametrize denitrification models explicit for microbial hotspots.

Centrifugation provides a fast method to measure soil water retention curves over a wide moisture range. However, deformation of soil structure may occur at high angular velocities in the centrifuge. The objective of this study was to capture these changes in soil structure with X-ray microtomography and to measure local deformations via digital volume correlation. Two samples were investigated that differ in texture and rock content. A detailed analysis of the pore space reveals an interplay between shrinkage due to drying and soil compaction due to compression. Macroporosity increases at moderate angular velocity because of crack formation due to moisture release. At higher angular velocities, corresponding to capillary pressure of ψ