Three-dimensional soil organic matter distribution, accessibility and microbial respiration in macroaggregates using osmium staining and synchrotron X-ray computed tomography

Abstract. The spatial distribution and accessibility of organic matter (OM) to soil microbes in aggregates – determined by the fine-scale, 3-D distribution of OM, pores and mineral phases – may be an important control on the magnitude of soil heterotrophic respiration (SHR). Attempts to model SHR on fine scales requires data on the transition probabilities between adjacent pore space and soil OM, a measure of microbial accessibility to the latter. We used a combination of osmium staining and synchrotron X-ray computed tomography (CT) to determine the 3-D (voxel) distribution of these three phases (scale 6.6 µm) throughout nine aggregates taken from a single soil core (range of organic carbon (OC) concentrations: 4.2–7.7 %). Prior to the synchrotron analyses we had measured the magnitude of SHR for each aggregate over 24 h under controlled conditions (moisture content and temperature). We test the hypothesis that larger magnitudes of SHR will be observed in aggregates with (i) shorter length scales of OM variation (more aerobic microsites) and (ii) larger transition probabilities between OM and pore voxels. After scaling to their OC concentrations, there was a 6-fold variation in the magnitude of SHR for the nine aggregates. The distribution of pore diameters and tortuosity index values for pore branches was similar for each of the nine aggregates. The Pearson correlation between aggregate surface area (normalized by aggregate volume) and normalized headspace C gas concentration was both positive and reasonably large (r  =  0.44), suggesting that the former may be a factor that influences SHR. The overall transition probabilities between OM and pore voxels were between 0.07 and 0.17, smaller than those used in previous simulation studies. We computed the length scales over which OM, pore and mineral phases vary within each aggregate using 3-D indicator variograms. The median range of models fitted to variograms of OM varied between 38 and 175 µm and was generally larger than the other two phases within each aggregate, but in general variogram models had ranges <  250 µm. There was no evidence to support the hypotheses concerning scales of variation in OM and magnitude of SHR; the linear correlation was 0.01. There was weak evidence to suggest a statistical relationship between voxel-based OM–pore transition probabilities and the magnitudes of aggregate SHR (r  =  0.12). We discuss how our analyses could be extended and suggest improvements to the approach we used.

Download Full-text

Three dimensional soil organic matter distribution, accessibility and microbial respiration in macro-aggregates using osmium staining and synchrotron X-ray CT

10.5194/soil-2016-32 ◽

2016 ◽

Cited By ~ 1

Author(s):

Barry G Rawlins ◽

Joanna Wragg ◽

Christina Rheinhard ◽

Robert C Atwood ◽

Alasdair Houston ◽

...

Keyword(s):

Organic Matter ◽

Transition Probabilities ◽

Solid Phase ◽

Pore Space ◽

Three Dimensional ◽

Soil Core ◽

Length Scales ◽

X Ray ◽

Mineral Phases ◽

Indicator Variograms

Abstract. The spatial distribution and accessibility of organic matter (OM) to soil microbes in aggregates – determined by the fine-scale, 3-D distribution of organic matter, pores and mineral phases – may be an important control on the magnitude of soil heterotrophic respiration (SHR). Attempts to model SHR at fine scales requires data on the transition probabilities between adjacent pore space and soil OM, a measure of microbial accessibility to the latter. We used a combination of osmium staining and synchrotron X-ray CT to determine the 3-D (voxel) distribution of these three phases (scale 6.6 μm) throughout nine aggregates taken from a single soil core (range of organic carbon (OC) concentrations 4.2–7.7 %). Prior to the synchrotron analyses we had measured the magnitude of SHR for each aggregate over 24 hours under controlled conditions (moisture content and temperature). We test the hypothesis that larger magnitudes of SHR will be observed in aggregates with shorter length scales of OM variation (i.e. more frequent, and possibly more finely disseminated, OM and a larger number of aerobic microsites). After scaling to their OC concentrations, there was a six-fold variation in the magnitude of SHR for the nine aggregates. The distribution of pore volumes, pore shape and volume normalised surface area were similar for each of the nine aggregates. The overall transition probabilities between OM and pore voxels were between 0.02 and 0.03, significantly smaller than those used in previous simulation studies. We computed the length scales over which OM, pore and mineral phases vary within each aggregate using indicator variograms. The median range of models fitted to variograms of OM varied between 178 and 487 μm. The linear correlation between these median length scales of OM variation and the magnitudes of SHR for each aggregate was −0.42, providing some evidence to support our hypothesis. We require a larger number of observations to make a statistical inference. There was no evidence to suggest a statistical relationship between OM:pore transition probabilities and the magnitudes of aggregate SHR. The solid-phase volume proportions (45–63 %) of OM we report for our aggregates were surprisingly large by comparison to those assumed in previous modelling approaches. We suggest this requires further assessment using accurate measurements of OM bulk density in a range of soil types.

Download Full-text

Soil-Core Breakthrough Measured by X-Ray Computed Tomography

SSSA Special Publications - Tomography of Soil-Water-Root Processes ◽

10.2136/sssaspecpub36.c6 ◽

2015 ◽

pp. 59-71 ◽

Cited By ~ 3

Author(s):

R. Lee Peyton ◽

Stephen H. Anderson ◽

Clark J. Gantzer ◽

John W. Wigger ◽

David J. Heinze ◽

...

Keyword(s):

Computed Tomography ◽

Soil Core ◽

X Ray ◽

X Ray Computed

Download Full-text

Organic Matter Pore Characterization in Lacustrine Shales with Variable Maturity Using Nanometer-Scale Resolution X-ray Computed Tomography

Energy & Fuels ◽

10.1021/acs.energyfuels.6b03313 ◽

2017 ◽

Vol 31 (3) ◽

pp. 2669-2680 ◽

Cited By ~ 13

Author(s):

Fujie Jiang ◽

Jian Chen ◽

Ziyang Xu ◽

Zhifang Wang ◽

Tao Hu ◽

...

Keyword(s):

Computed Tomography ◽

Organic Matter ◽

Nanometer Scale ◽

X Ray ◽

Pore Characterization ◽

X Ray Computed

Download Full-text

Understanding the mechanisms of root-reinforcement in soils: soil shear tests using X-ray computed tomography and digital volume correlation

E3S Web of Conferences ◽

10.1051/e3sconf/20199212009 ◽

2019 ◽

Vol 92 ◽

pp. 12009

Author(s):

Daniel Bull ◽

Ian Sinclair ◽

Fabrice Pierron ◽

Tiina Roose ◽

Joel Smethurst

Keyword(s):

Computed Tomography ◽

Three Dimensions ◽

Digital Volume Correlation ◽

Strain Component ◽

Multiscale Models ◽

Root Reinforcement ◽

Length Scales ◽

X Ray ◽

Shearing Resistance ◽

X Ray Computed

Soil containing plant roots may be expected to exhibit a greater shearing resistance compared with the same ‘unreinforced’ soil, providing enhanced stability and effective erosion control, particularly for earth slopes. To be able to rely on the improved shearing resistance and stiffness of root-reinforced soils, it is important to understand and quantify the effectiveness of root reinforcement. This requires sophisticated multiscale models, building understanding at different length scales, from individual soil-root interaction through to full soil-profile or slope scale. One of the challenges with multiscale models is ensuring that they are representative of real behaviour, and this requires calibration to detailed high-quality experiments. The focus of the work presented was to capture and quantify root-reinforcement behaviour and associated soil and root deformation mechanisms during direct shear at the macroscopic to millimetre length scales. A novel shear box was developed to operate within a large-scale X-ray computed tomography (CT) scanner. Tests were interrupted to be scanned at a series of shear displacements from 0-20 mm to capture the chronology of behaviour in three-dimensions. Digital volume correlation (DVC) was applied to the CT dataset to obtain full-field 3D displacement and strain component information. The study demonstrates feasibility of the technique and presents preliminary DVC results.

Download Full-text

Mineralization of Sialoliths Investigated by Ex Vivo and In Vivo X-ray Computed Tomography

Microscopy and Microanalysis ◽

10.1017/s1431927618016124 ◽

2019 ◽

Vol 25 (1) ◽

pp. 151-163 ◽

Cited By ~ 1

Author(s):

Pedro Nolasco ◽

Paulo V. Coelho ◽

Carla Coelho ◽

David F. Angelo ◽

J. R. Dias ◽

...

Keyword(s):

Electron Microscopy ◽

Computed Tomography ◽

Organic Matter ◽

Ex Vivo ◽

Correct Selection ◽

Quantitative Relation ◽

Helical Computed Tomography ◽

X Ray ◽

X Ray Computed

AbstractThe fraction of organic matter present affects the fragmentation behavior of sialoliths; thus, pretherapeutic information on the degree of mineralization is relevant for a correct selection of lithotripsy procedures. This work proposes a methodology for in vivo characterization of salivary calculi in the pretherapeutic context. Sialoliths were characterized in detail by X-ray computed microtomography (μCT) in combination with atomic emission spectroscopy, Fourier transform infrared spectroscopy, X-ray diffraction, scanning electron microscopy, and transmission electron microscopy. Correlative analysis of the same specimens was performed by in vivo and ex vivo helical computed tomography (HCT) and ex vivo μCT. The mineral matter in the sialoliths consisted essentially of apatite (89 vol%) and whitlockite (11 vol%) with average density of 1.8 g/cm3. In hydrated conditions, the mineral mass prevailed with 53 ± 13 wt%, whereas the organic matter, with a density of 1.2 g/cm3, occupied 65 ± 10% of the sialoliths’ volume. A quantitative relation between sialoliths mineral density and X-ray attenuation is proposed for both HCT and μCT.

Download Full-text

Petrophysical characterization of coquinas from Morro do Chaves Formation (Sergipe-Alagoas Basin) by x-ray computed tomography

Geologia USP Série Científica ◽

10.11606/issn.2316-9095.v18-124101 ◽

2018 ◽

Vol 18 (3) ◽

pp. 3-13

Author(s):

Aline Maria Poças Belila ◽

Michelle Chaves Kuroda ◽

João Paulo Da Ponte Souza ◽

Alexandre Campane Vidal ◽

Osvair Vidal Trevisan

Keyword(s):

Computed Tomography ◽

Pore Space ◽

Three Dimensional ◽

Petroleum Reservoirs ◽

Self Organizing Maps ◽

X Ray ◽

The Neural Network ◽

Rock Structure ◽

X Ray Computed

Carbonate rocks constitute a large number of petroleum reservoirs worldwide. Notwithstanding, the characterization of these rocks is still a challenge due to their high complexity and pore space variability, indicating the importance of further studies to reduce uncertainty in reservoir interpretation and characterization. This work was performed for coquina samples from Morro do Chaves Formation (Sergipe-Alagoas Basin), analogous to important Brazilian reservoirs. Computed tomography (CT) was used for three-dimensional characterization of rock structure. The neural network named Self-Organizing Maps (SOM) was used for CT images segmentation. According to our tests, CT demonstrated to be a consistent tool for quantitative and qualitative analysis of heterogeneous pore space, by the evaluation of porosity, connectivity and the representative elementary volume.

Download Full-text

X-ray computed tomography as a method of reconstruction of 3d-characteristics of disseminated sulfides and spinel in plagiodunites from the Yoko-Dovyren intrusion

Петрология ◽

10.31857/s0869-5903274401-419 ◽

2019 ◽

Vol 27 (4) ◽

pp. 401-419

Author(s):

D. V. Korost ◽

A. A. Ariskin ◽

I. V. Pshenitsyn ◽

A. N. Khomyak

Keyword(s):

Computed Tomography ◽

Morphological Characteristics ◽

3D Models ◽

Statistical Characteristics ◽

Ultramafic Rocks ◽

Reliable Technique ◽

X Ray ◽

Mineral Phases ◽

Low Concentrations ◽

X Ray Computed

The paper describes a methodology of applying X-ray computed tomography (CT) in studying textural–morphological characteristics of sulfide-bearing ultramafic rocks from the Yoko-Dovyren layered massif in the northern Baikal area, Buryatia, Russia. The dunites are used to illustrate the applicability of a reliable technique for distinguishing between grains of sulfides and spinel. The technique enables obtaining statistical characteristics of the 3D distribution and size of the mineral phases. The method of 3D reconstructions is demonstrated to be applicable at very low concentrations of sulfides: no than 0.1–0.2 vol %. Differences between 3D models are determined for sulfide segregations of different size, in some instances with features of their orientation suggesting the direction of percolation and accumulation of the sulfide liquids. These data are consistent with the morphology of the largest sulfide segregations, whose concave parts adjoin the surface of the cumulus olivine and simultaneously grow into grains of the poikilitic plagioclase. Detailed information of these features is useful to identify fingerprints of infiltration and concentration of protosulfide liquids in highly crystallized cumulate systems.

Download Full-text