Exploration of soil micromorphology to identify coarse-sized OM assemblages in X-ray CT images of undisturbed cultivated soil cores

N. Elyeznasni, F. Sellami, V. Pot, P. Benoit, L. Vieublé-Gonod, Iain M. Young, S. Peth

Research output: Contribution to journalArticle

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Abstract

We proposed to use micromorphology to help identify coarse-sized organic matter (OM) in X-ray computed tomography (CT) images of fresh undisturbed soil cores. We sampled three soil columns (5-cm diameter, 5-cm height) in the interfurrows that mainly contain macroporosity and straw residues of the ploughed horizon of a silt loamy Albeluvisol. Two of the samples were X-ray scanned at 68 and 88 μm voxel-resolution, and three thin-sections were performed in one of the scanned columns. Retention curve was measured on the third soil column. Micromorphology observations showed macropores from very fine to coarse size and numerous mesopores were heterogeneously distributed in the soil matrix and concentrations of OM of increasing stages of decomposition within and around the macroporosity. CT images easily detected coarse-sized OM concentrations and recovered part of the discontinuous pattern of the coarse-sized OM fragments in the macroporosity. We defined a table of correspondence between the structural features (porosity) and organo-mineral features of size down to about 40 μm and the grey level values of the scanned image. The values of the thresholds were adjusted from the micromorphological observations and the porosities of the 3D segmented images compared well with the measured porosity of the third soil column. The main limitation of the method was in choosing the threshold values separating pores and coarse-sized OM in order to recover the porosity of the zones containing the coarse-sized OM features. The proposed method is a preliminary work that showed to be well suited for undisturbed soil samples containing large pieces of straw residues incompletely mixed with soil matrix but cannot be applied to the identification of fine-sized OM.
Original languageEnglish
Pages (from-to)38-45
Number of pages8
JournalGeoderma
Volume179-180
DOIs
StatePublished - Jun 2012

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organic matter
soil
porosity
computed tomography
micromorphology
soil column
tomography
microstructure
straw
methodology
matrix
soil micromorphology
macropores
silt
soil sampling
minerals
degradation
sampling
Albeluvisols
macropore

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Elyeznasni, N., Sellami, F., Pot, V., Benoit, P., Vieublé-Gonod, L., Young, I. M., & Peth, S. (2012). Exploration of soil micromorphology to identify coarse-sized OM assemblages in X-ray CT images of undisturbed cultivated soil cores. Geoderma, 179-180, 38-45. DOI: 10.1016/j.geoderma.2012.02.023

Elyeznasni, N.; Sellami, F.; Pot, V.; Benoit, P.; Vieublé-Gonod, L.; Young, Iain M.; Peth, S. / Exploration of soil micromorphology to identify coarse-sized OM assemblages in X-ray CT images of undisturbed cultivated soil cores.

In: Geoderma, Vol. 179-180, 06.2012, p. 38-45.

Research output: Contribution to journalArticle

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title = "Exploration of soil micromorphology to identify coarse-sized OM assemblages in X-ray CT images of undisturbed cultivated soil cores",
abstract = "We proposed to use micromorphology to help identify coarse-sized organic matter (OM) in X-ray computed tomography (CT) images of fresh undisturbed soil cores. We sampled three soil columns (5-cm diameter, 5-cm height) in the interfurrows that mainly contain macroporosity and straw residues of the ploughed horizon of a silt loamy Albeluvisol. Two of the samples were X-ray scanned at 68 and 88 μm voxel-resolution, and three thin-sections were performed in one of the scanned columns. Retention curve was measured on the third soil column. Micromorphology observations showed macropores from very fine to coarse size and numerous mesopores were heterogeneously distributed in the soil matrix and concentrations of OM of increasing stages of decomposition within and around the macroporosity. CT images easily detected coarse-sized OM concentrations and recovered part of the discontinuous pattern of the coarse-sized OM fragments in the macroporosity. We defined a table of correspondence between the structural features (porosity) and organo-mineral features of size down to about 40 μm and the grey level values of the scanned image. The values of the thresholds were adjusted from the micromorphological observations and the porosities of the 3D segmented images compared well with the measured porosity of the third soil column. The main limitation of the method was in choosing the threshold values separating pores and coarse-sized OM in order to recover the porosity of the zones containing the coarse-sized OM features. The proposed method is a preliminary work that showed to be well suited for undisturbed soil samples containing large pieces of straw residues incompletely mixed with soil matrix but cannot be applied to the identification of fine-sized OM.",
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Elyeznasni, N, Sellami, F, Pot, V, Benoit, P, Vieublé-Gonod, L, Young, IM & Peth, S 2012, 'Exploration of soil micromorphology to identify coarse-sized OM assemblages in X-ray CT images of undisturbed cultivated soil cores' Geoderma, vol 179-180, pp. 38-45. DOI: 10.1016/j.geoderma.2012.02.023

Exploration of soil micromorphology to identify coarse-sized OM assemblages in X-ray CT images of undisturbed cultivated soil cores. / Elyeznasni, N.; Sellami, F.; Pot, V.; Benoit, P.; Vieublé-Gonod, L.; Young, Iain M.; Peth, S.

In: Geoderma, Vol. 179-180, 06.2012, p. 38-45.

Research output: Contribution to journalArticle

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T1 - Exploration of soil micromorphology to identify coarse-sized OM assemblages in X-ray CT images of undisturbed cultivated soil cores

AU - Elyeznasni,N.

AU - Sellami,F.

AU - Pot,V.

AU - Benoit,P.

AU - Vieublé-Gonod,L.

AU - Young,Iain M.

AU - Peth,S.

PY - 2012/6

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N2 - We proposed to use micromorphology to help identify coarse-sized organic matter (OM) in X-ray computed tomography (CT) images of fresh undisturbed soil cores. We sampled three soil columns (5-cm diameter, 5-cm height) in the interfurrows that mainly contain macroporosity and straw residues of the ploughed horizon of a silt loamy Albeluvisol. Two of the samples were X-ray scanned at 68 and 88 μm voxel-resolution, and three thin-sections were performed in one of the scanned columns. Retention curve was measured on the third soil column. Micromorphology observations showed macropores from very fine to coarse size and numerous mesopores were heterogeneously distributed in the soil matrix and concentrations of OM of increasing stages of decomposition within and around the macroporosity. CT images easily detected coarse-sized OM concentrations and recovered part of the discontinuous pattern of the coarse-sized OM fragments in the macroporosity. We defined a table of correspondence between the structural features (porosity) and organo-mineral features of size down to about 40 μm and the grey level values of the scanned image. The values of the thresholds were adjusted from the micromorphological observations and the porosities of the 3D segmented images compared well with the measured porosity of the third soil column. The main limitation of the method was in choosing the threshold values separating pores and coarse-sized OM in order to recover the porosity of the zones containing the coarse-sized OM features. The proposed method is a preliminary work that showed to be well suited for undisturbed soil samples containing large pieces of straw residues incompletely mixed with soil matrix but cannot be applied to the identification of fine-sized OM.

AB - We proposed to use micromorphology to help identify coarse-sized organic matter (OM) in X-ray computed tomography (CT) images of fresh undisturbed soil cores. We sampled three soil columns (5-cm diameter, 5-cm height) in the interfurrows that mainly contain macroporosity and straw residues of the ploughed horizon of a silt loamy Albeluvisol. Two of the samples were X-ray scanned at 68 and 88 μm voxel-resolution, and three thin-sections were performed in one of the scanned columns. Retention curve was measured on the third soil column. Micromorphology observations showed macropores from very fine to coarse size and numerous mesopores were heterogeneously distributed in the soil matrix and concentrations of OM of increasing stages of decomposition within and around the macroporosity. CT images easily detected coarse-sized OM concentrations and recovered part of the discontinuous pattern of the coarse-sized OM fragments in the macroporosity. We defined a table of correspondence between the structural features (porosity) and organo-mineral features of size down to about 40 μm and the grey level values of the scanned image. The values of the thresholds were adjusted from the micromorphological observations and the porosities of the 3D segmented images compared well with the measured porosity of the third soil column. The main limitation of the method was in choosing the threshold values separating pores and coarse-sized OM in order to recover the porosity of the zones containing the coarse-sized OM features. The proposed method is a preliminary work that showed to be well suited for undisturbed soil samples containing large pieces of straw residues incompletely mixed with soil matrix but cannot be applied to the identification of fine-sized OM.

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DO - 10.1016/j.geoderma.2012.02.023

M3 - Article

VL - 179-180

SP - 38

EP - 45

JO - Geoderma

T2 - Geoderma

JF - Geoderma

SN - 0016-7061

ER -

Elyeznasni N, Sellami F, Pot V, Benoit P, Vieublé-Gonod L, Young IM et al. Exploration of soil micromorphology to identify coarse-sized OM assemblages in X-ray CT images of undisturbed cultivated soil cores. Geoderma. 2012 Jun;179-180:38-45. Available from, DOI: 10.1016/j.geoderma.2012.02.023