Localization of soil organic matter in soil aggregates using synchrotron-based X-ray microtomography

Peth, Stephan; Chenu, Claire; Leblond, Nelly; Mordhorst, Anneka; Garnier, Patricia; Nunan, Naoise; Pot, Valérie; Ogurreck, Malte; Beckmann, Felix

doi:10.1016/j.soilbio.2014.07.024

Cited by 87 publications

(96 citation statements)

References 18 publications

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“…In their study, Peth et al (2014) used air-dried soil aggregates, whilst we chose to freeze-dry the aggregates in our experiment to maximize absorption of osmium onto organic carbon bonds. It would be useful to compare the results of both approaches to determine whether the drying process has significant implications for the extent of Os absorption throughout an aggregate.…”

Section: Discussionmentioning

confidence: 99%

“…The filter inserts were then reweighed so that the dry mass of each aggregate could be calculated. The aggregates (each inside a filter insert and centrifuge vial) were placed inside a fume cupboard so that osmium tetroxide (OsO 4 ) could be used to stain the OM in each of the soil aggregates (Peth et al, 2014). A set of strict health and safety procedures were adopted due to the hazardous nature of OsO 4 , but we do not describe these in detail here.…”

Section: Aggregate Samples Preparation and Respiration Measurementsmentioning

confidence: 99%

“…The first procedure was to subtract the absorption values from the 73.2 keV energy level (below the Os absorption edge) from the images created from the 74.4 keV energy level (above the Os absorption edge; see Peth et al, 2014). This was undertaken using a script written in R (R Core Team, 2013), and we subsequently refer to the resulting data and files as "diffedge" (difference at the absorption edge).…”

Section: Synchrotron X-ray Ct Data Processingmentioning

confidence: 99%

“…In a recent study, Hapca et al (2015) used a combination of Xray computed tomography (CT) and scanning electron microscope images to map soil chemical composition, including soil carbon, at a resolution of 15.8 µm in a small block of soil (side length of 1 cm). An alternative approach was recently demonstrated by Peth et al (2014), where differences in X-ray absorption above and below the osmium (Os) edge -using synchrotron beamline X-ray CT -were used to discriminate between OM and mineral phases in aggregates of around 2-3 mm diameter, at a resolution of 9.77 µm.…”

Section: Introductionmentioning

confidence: 99%

“…In this paper we report the results of applying and extending the Os-staining and synchrotron X-ray CT method developed by Peth et al (2014). Specifically we establish the 3-D distribution of mineral, SOM and pore space throughout nine macroaggregates from a single soil core at fine (6.6 µm) length scales.…”

Section: Introductionmentioning

confidence: 99%

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

Rawlins

Wragg

Reinhard

et al. 2016

SOIL

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Abstract. The spatial distribution and accessibility of organic matter (OM) to soil microbes in aggregatesdetermined 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.

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Section: Discussionmentioning

confidence: 99%

Section: Aggregate Samples Preparation and Respiration Measurementsmentioning

confidence: 99%

Section: Synchrotron X-ray Ct Data Processingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Rawlins

Wragg

Reinhard

et al. 2016

SOIL

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Hydration and diffusion processes shape microbial community organization and function in model soil aggregates

Ebrahimi

2015

Water Resources Research

103

131

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The constantly changing soil hydration status affects gas and nutrient diffusion through soil pores and thus the functioning of soil microbial communities. The conditions within soil aggregates are of particular interest due to limitations to oxygen diffusion into their core, and the presence of organic carbon often acting as binding agent. We developed a model for microbial life in simulated soil aggregates comprising of 3-D angular pore network model (APNM) that mimics soil hydraulic and transport properties. Within these APNM, we introduced individual motile (flagellated) microbial cells with different physiological traits that grow, disperse, and respond to local nutrients and oxygen concentrations. The model quantifies the dynamics and spatial extent of anoxic regions that vary with hydration conditions, and their role in shaping microbial community size and activity and the spatial (self) segregation of anaerobes and aerobes. Internal carbon source and opposing diffusion directions of oxygen and carbon within an aggregate were essential to emergence of stable coexistence of aerobic and anaerobic communities (anaerobes become extinct when carbon sources are external). The model illustrates a range of hydration conditions that promote or suppress denitrification or decomposition of organic matter and thus affect soil GHG emissions. Model predictions of CO 2 and N 2 O production rates were in good agreement with limited experimental data. These limited tests support the dynamic modeling approach whereby microbial community size, composition, and spatial arrangement emerge from internal interactions within soil aggregates. The upscaling of the results to a population of aggregates of different sizes embedded in a soil profile is underway.

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Multiscale Investigation on Biofilm Distribution and Its Impact on Macroscopic Biogeochemical Reaction Rates

Yan

Liu

et al. 2017

Water Resources Research

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Biofilms are critical locations for biogeochemical reactions in the subsurface environment. The occurrence and distribution of biofilms at microscale as well as their impacts on macroscopic biogeochemical reaction rates are still poorly understood. This paper investigated the formation and distributions of biofilms in heterogeneous sediments using multiscale models and evaluated the effects of biofilm heterogeneity on local and macroscopic biogeochemical reaction rates. Sediment pore structures derived from X‐ray computed tomography were used to simulate the microscale flow dynamics and biofilm distribution in the sediment column. The response of biofilm formation and distribution to the variations in hydraulic and chemical properties was first examined. One representative biofilm distribution was then utilized to evaluate its effects on macroscopic reaction rates using nitrate reduction as an example. The results revealed that microorganisms primarily grew on the surfaces of grains and aggregates near preferential flow paths where both electron donor and acceptor were readily accessible, leading to the heterogeneous distribution of biofilms in the sediments. The heterogeneous biofilm distribution decreased the macroscopic rate of biogeochemical reactions as compared with those in homogeneous cases. Operationally considering the heterogeneous biofilm distribution in macroscopic reactive transport models such as using dual porosity domain concept can significantly improve the prediction of biogeochemical reaction rates. Overall, this study provided important insights into the biofilm formation and distribution in soils and sediments as well as their impacts on the macroscopic manifestation of reaction rates.

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Localization of soil organic matter in soil aggregates using synchrotron-based X-ray microtomography

Cited by 87 publications

References 18 publications

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

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

Hydration and diffusion processes shape microbial community organization and function in model soil aggregates

Multiscale Investigation on Biofilm Distribution and Its Impact on Macroscopic Biogeochemical Reaction Rates

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