Contrast-enhanced repacked soil cores as a proxy for soil organic matter spatial arrangement

Soil Research ◽  
2019 ◽  
Vol 57 (6) ◽  
pp. 535
Author(s):  
Ilaria Piccoli ◽  
Nicola Dal Ferro ◽  
Patrice J. Delmas ◽  
Andrea Squartini ◽  
Francesco Morari
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Contrast Agents ◽  
Mineral Soil ◽  
Morphological Characteristics ◽  
Linear Attenuation Coefficient ◽  
Morphological Operations ◽  
Soil Cores ◽  
Soil Matrix ◽  
X Ray

Soil organic matter (SOM) plays a key role in soil structure formation, although the bidirectional relationship between SOM and the soil pore network is complex and needs further investigation. Despite great advances provided by X-ray computed microtomography (µCT), it has only been used in a few studies to investigate the organic matter 3D-arrangement within the soil matrix. Results are based on the X-ray linear attenuation coefficient (α), and mixtures of organic and mineral soil fractions could imply overlapping of information that makes any segmentation procedure difficult. The aim of this study was to visualise, segment, and quantify the particulate organic matter fraction (POM) within the soil matrix through X-ray µCT in combination with contrast agents (phosphomolybdic acid and silver nitrate). Two series of repacked soil cores, ‘dry’ and ‘wet’, were scanned through X-ray µCT at a 7-µm resolution. Different segmentation approaches were tested to separate POM from other soil phases: manual, global, and local thresholding methods. Reported algorithms were also compared with a supervised grey value-based (GV) approach followed by morphological operations. Results showed contrast agents increased α of POM, simplifying its identification and the following segmentation on dry cores. The POM was discriminated from the mineral fraction and its content correctly estimated. This was particularly accurate when applying manual thresholding or GV approach with respect to indicator kriging, suggesting that operator-based ability to set threshold level is still the best solution for accurate POM segmentation. Beyond single-phase accounting, different thresholding algorithms and morphological operations also affected POM morphological characteristics. In particular, the simpler was an object shape, the easier was its segmentation. Improvements are thus required to increase the efficiency of automated thresholding algorithms. Moreover, wet cores were exposed to washing-out phenomena that compromised any digital image processing and further POM quantification, implying that more effort should be made to find other suitable staining agents.

Carbon mineralisation and pore size classes in undisturbed soil cores

Soil Research ◽  
2013 ◽  
Vol 51 (1) ◽  
pp. 14 ◽  
Author(s):  
Liesbeth Bouckaert ◽  
Steven Sleutel ◽  
Denis Van Loo ◽  
Loes Brabant ◽  
Veerle Cnudde ◽  
...  
Keyword(s):  
Organic Matter ◽  
Pore Network ◽  
Order Kinetic ◽  
Soil Cores ◽  
Undisturbed Soil ◽  
Soil Matrix ◽  
X Ray ◽  
C Mineralisation ◽  
The Impact ◽  
Undisturbed Soil Cores

Soil pore network effects on organic matter turnover have, until now, been studied indirectly because of lack of data on the 3D structure of the pore network. Application of X-ray computed tomography (X-ray CT) to quantify the distribution of pore neck size and related pore sizes from undisturbed soil cores, with simultaneous assessment of carbon (C) mineralisation, could establish a relationship between soil organic matter (SOM) decomposition and soil pore volumes. Eighteen miniature soil cores (diameter 1.2 cm, height 1.2 cm) covering a range of bulk densities were incubated at 20°C for 35 days. Respiration was modelled with a parallel first- and zero-order kinetic model. The cores were scanned at 9.44 µm resolution using an X-ray CT scanner developed in-house. Correlation analysis between the slow pool C mineralisation rate, ks, and pore volume per pore neck class yielded significant (P < 0.05) positive correlations: r = 0.572, 0.598, and 0.516 for the 150–250, 250–350, and >350 µm pore neck classes, respectively. Because larger pores are most probably mainly air-filled, a positive relation with ks was ascribed to enhanced aeration of smaller pores surrounding large pores. The weak and insignificant relationship between the smallest pore neck class (<9.44 µm) and ks could be explained by obstructed microbial activity and mobility or diffusion of exo-enzymes and hydrolysis products as a result of limited oxygen availability. This study supports the hypothesis that the impact of soil structure on microbial processes occurs primarily via its determination of soil water distribution, which is possibly the main driver for the location of C mineralisation in the soil matrix.

Influence of soil organic matter on sulfate retention in two Podzols in Quebec, Canada

1999 ◽  
Vol 79 (1) ◽  
pp. 103-109 ◽  
Author(s):  
F. Courchesne ◽  
J.-F. Laberge ◽  
A. Dufresne
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Ammonium Oxalate ◽  
X Ray Diffraction ◽  
Weighted Mean ◽  
Fine Silt ◽  
Mineral Horizon ◽  
Organic C ◽  
X Ray

The role of soil organic matter (OM) on SO4 retention was investigated by comparing OM content, SO4 retention, and the distribution of Fe, Al and Si compounds in OM-poor (Grands-Jardins, PGJ) and OM-rich (Hermine, HER) Podzols from Québec, Canada. At both sites, four pedons were sampled by horizon; soil pH in H2O, organic C, phosphate-extractable SO4 and, sodium pyrophosphate, acid ammonium oxalate and dithionite-citrate-bicarbonate (DCB) extractable Fe, Al and Si were measured for each mineral horizon. The mineralogy of the clay (<2 µm) and fine silt (2–20 µm) fractions of selected horizons was determined by X-ray diffraction (XRD) and infrared spectroscopy (IR). Weighted mean organic C and pyrophosphate extractable Fe and Al contents were significantly higher in the HER than in the PGJ sola, while the PGJ soils were richer in amorphous inorganic Al. No trends were observed for inorganic Fe compounds. Chemical dissolution and IR allowed the identification of short-range ordered aluminosilicates, probably allophane, in the OM-poor and slightly acidic to neutral PGJ soils. These materials were absent from the OM-rich and acidic HER soils. Phosphate extractions showed that the weighted mean native SO4 content was five times higher in the PGJ than in the HER soil. Finally, native SO4 was strongly related to inorganic Fe, Al and Si (associated with allophane) at PGJ but only to inorganic Fe at HER. These results indicate that OM indirectly affects SO4 sorption through the influence organic substances exerts on the nature and distribution of pedogenic Fe, Al and Si compounds, such as allophane, in Podzolic profiles. Key words: Organic matter, sulfate, imogolite, allophane, silica, Podzol

scholarly journals Biomass of Coarse Woody Debris Following Fire and Clearcutting in Lodgepole Pine Forests

1997 ◽  
Vol 21 ◽  
pp. 33-35
Author(s):  
Dennis Knight ◽  
Daniel Tinker
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Coarse Woody Debris ◽  
Significant Contribution ◽  
Woody Debris ◽  
Mineral Soil ◽  
Primary Source ◽  
Timber Harvesting ◽  
Micro Organisms

In forest ecosystems, the decomposition of coarse woody debris, woody roots, twigs, leaves and micro-organisms is a primary source of mineral soil organic matter. Primary productivity, the accumulation of nutrients, and other important ecosystem processes are largely dependent on the mineral soil organic matter that has developed during hundreds or thousands of years. Large quantities of coarse woody debris are typically produced following natural disturbances such as fires, pest/pathogen outbreaks, and windstorms, and make a significant contribution to the formation of soil organic matter (SOM). In contrast, timber harvesting often removes much of the coarse woody debris (CWD), which could result in a decrease in the quantity and a change in the quality of mineral soil organic matter.

EFFECT OF SOIL ORGANIC MATTER OXIDATION ON THE COLLAPSE OF VERMICULITE

1985 ◽  
Vol 65 (3) ◽  
pp. 593-597 ◽  
Author(s):  
N. M. MILES ◽  
M. SCHNITZER ◽  
C. R. DE KIMPE
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Key Words ◽  
Mixed Layer ◽  
Ir Spectrum ◽  
X Ray Diffraction ◽  
X Ray ◽  
Organic Matter Oxidation ◽  
Ir Spectrophotometry ◽  
Complete Collapse

Oxidation of organic matter with H2O2 produced substantial amounts of NH3 which was then fixed by vermiculite, causing partial or complete collapse and converting the mineral to a mica-like product. The collapse of the mineral was indicated by shifts in the 001 spacing from 1.476 to 1.030 nm and the appearance of a well-defined band at 1430 cm−1 in the IR spectrum, indicative of the presence of NH4+ in the interlayer positions of the clay. Our data suggest that: (a) the transformation of vermiculite to mica during H2O2 oxidation may result in underestimation of the vermiculite content of soils by XRD, and (b) the wide occurrence of mixed-layer minerals in soils may in part have resulted from the fixation of NH3 liberated from the microbial mineralization of organically bound N. Key words: Ammonia, X-ray diffraction, IR spectrophotometry, mixed-layer minerals, H2O2 pretreatment

Obvious and less obvious processes of aggregate formation in soil

2021 ◽  
Author(s):  
Hans-Jörg Vogel ◽  
Mar­ia Balseiro-Romero ◽  
Philippe C. Baveye ◽  
Alexandra Kravchenko ◽  
Wilfred Otten ◽  
...  
Keyword(s):  
Organic Matter ◽  
Soil Structure ◽  
Solid Phase ◽  
Pore Space ◽  
Imaging Techniques ◽  
Mineral Soil ◽  
Aggregate Formation ◽  
Conceptual Approach ◽  
Soil Matrix ◽  
Biophysical Processes

&lt;p&gt;Soil structure, lately referred to as the ''architecture'' is a key to explain and understand all soil functions. The development of sophisticated imaging techniques over the last decades has led to significant progress in the description of this architecture and in particular of the geometry of the hierarchically-branched pore space in which transport of water, gases, solutes and particles occurs and where myriads of organisms live. Moreover, there are sophisticated tools available today to also visualize the spatial structure of the solid phase including mineral grains and organic matter. Hence, we do have access to virtually all components of soil architecture.&lt;/p&gt;&lt;p&gt;Unfortunately, it has so far proven very challenging to study the dynamics of soil architecture over time, which is of critical importance for soil as habitat and the turnover of organic matter. Several largely conflicting theories have been proposed to account for this dynamics, especially the formation of aggregates. We review these theories, and we propose a conceptual approach to reconcile them based on a consistent interpretation of experimental observations and by integrating known physical and biogeochemical processes. A key conclusion is that rather than concentrating on aggregate formation in the sense of how particles and organic matter reorganize to form aggregates as distinct functional units we should focus on biophysical processes that produce a porous, heterogeneous organo-mineral soil matrix that breaks into fragments of different size and stability when exposed to mechanical stress.&amp;#160; The unified vision we propose for soil architecture and the mechanisms that determine its temporal evolution, should pave the way towards a better understanding of soil processes and functions.&lt;/p&gt;

scholarly journals The Use of Radiocarbon to Measure the Effects of Earthworms On Soil Development

Radiocarbon ◽  
1980 ◽  
Vol 22 (3) ◽  
pp. 892-896 ◽  
Author(s):  
J D Stout ◽  
K M Goh
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Soil Profile ◽  
Mineral Soil ◽  
Soil Development ◽  
Plant Debris ◽  
Grassland Soils ◽  
Fresh Plant

Δ14C and δ13C values for organic matter in forest and grassland soils, in the presence or absence of earthworms, indicate that it should be possible to quantify the effects of earthworms on soil organic matter by this means. Without earthworms, both in forest and grassland soils, plant debris tends to accumulate on the surface of the mineral soil and little organic matter is incorporated into or is translocated down the soil profile. Where earthworms are present, there is much more marked incorporation of fresh plant debris in the mineral soil. This is shown especially by the pulse of ‘bomb’ carbon and also by the δ13C values.

scholarly journals Radiocarbon Dating of Soil Organic Matter Fractions in Andosols in Northern Ecuador

Radiocarbon ◽  
2006 ◽  
Vol 48 (3) ◽  
pp. 337-353 ◽  
Author(s):  
Femke H Tonneijck ◽  
Johannes van der Plicht ◽  
Boris Jansen ◽  
Jacobus M Verstraten ◽  
Henry Hooghiemstra
Keyword(s):  
Organic Matter ◽  
Humic Acid ◽  
Soil Organic Matter ◽  
Forest Floor ◽  
Radiocarbon Dating ◽  
Mineral Soil ◽  
Soil Samples ◽  
Acid Extraction ◽  
Independent Evidence ◽  
Organic Horizons

Volcanic ash soils (Andosols) may offer great opportunities for paleoecological studies, as suggested by their characteristic accumulation of organic matter (OM). However, understanding of the chronostratigraphy of soil organic matter (SOM) is required. Therefore, radiocarbon dating of SOM is necessary, but unfortunately not straightforward. Dating of fractions of SOM obtained by alkali-acid extraction is promising, but which fraction (humic acid or humin) renders the most accurate 14C dates is still subject to debate. To determine which fraction should be used for 14C dating of Andosols and to evaluate if the chronostratigraphy of SOM is suitable for paleoecological research, we measured 14C ages of both fractions and related calibrated ages to soil depth for Andosols in northern Ecuador. We compared the time frames covered by the Andosols with those of peat sequences nearby to provide independent evidence. Humic acid (HA) was significantly older than humin, except for the mineral soil samples just beneath a forest floor (organic horizons), where the opposite was true. In peat sections, 14C ages of HA and humin were equally accurate. In the soils, calibrated ages increased significantly with increasing depth. Age inversions and homogenization were not observed at the applied sampling distances. We conclude that in Andosols lacking a thick organic horizon, dating of HA renders the most accurate results, since humin was contaminated by roots. On the other hand, in mineral soil samples just beneath a forest floor, humin ages were more accurate because HA was then contaminated by younger HA illuviated from the organic horizons. Overall, the chronostratigraphy of SOM in the studied Andosols appears to be suitable for paleoecological research.

scholarly journals Characterization of porous microaggregates and soil organic matter sequestered in allophanic paleosols on Holocene tephras using synchrotron-based X-ray microscopy and spectroscopy

2021 ◽  
Author(s):  
Doreen Yu-Tuan Huang ◽  
David J. Lowe ◽  
G. Jock Churchman ◽  
Louis A. Schipper ◽  
Alan Cooper ◽  
...  
Keyword(s):  
Organic Matter ◽  
Fine Structure ◽  
Soil Organic Matter ◽  
Porous Structure ◽  
Functional Groups ◽  
Science Studies ◽  
Organic Chemical ◽  
X Ray ◽  
Nexafs Spectroscopy ◽  
Allophanic Soil

Abstract Allophanic tephra-derived soils can sequester sizable quantities of soil organic matter (SOM). However, no studies have visualized the fine internal porous structure of allophanic soil microaggregates, nor studied the carbon structure preserved in such soils or paleosols. We used synchrotron radiation-based transmission X-ray microscopy (TXM) to perform 3D-tomography of the internal porous structure of allophanic soil microaggregates, and carbon near-edge X-ray absorption fine-structure (C NEXAFS) spectroscopy to characterize SOM in ≤12,000-yr-old tephra-derived allophanic paleosols. The TXM tomography showed a vast network of internal, tortuous nano-pores within an allophanic microaggregate comprising nanoaggregates. SOM in the allophanic paleosols at four sites was dominated by carboxylic/carbonyl functional groups with subordinate quinonic, aromatic, and aliphatic groups. All samples exhibited similar compositions despite differences between the sites. That the SOM does not comprise specific types of functional groups through time implies that the functional groups are relict. The SOM originated at the land/soil surface: ongoing tephra deposition (intermittently or abruptly) then caused the land-surface to rise so that the once-surface horizons were buried more deeply and hence became increasingly isolated from inputs by the surficial/modern organic cycle. The presence of quinonic carbon, from biological processes but vulnerable to oxygen and light, indicates the exceptional protection of SOM and bio-signals in allophanic paleosols, attributable both to the porous allophane aggregates that occlude the relict SOM from degradation, and to rapid burial by successive tephra-fallout, as well as strong Al-organic chemical bonding. TXM and C NEXAFS spectroscopy unravel the fine structure of soils and SOM and are of great potential for soil science studies.

scholarly journals Characterizing porous microaggregates and soil organic matter sequestered in allophanic paleosols on Holocene tephras using synchrotron-based X-ray microscopy and spectroscopy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Doreen Yu-Tuan Huang ◽  
David J. Lowe ◽  
G. Jock Churchman ◽  
Louis A. Schipper ◽  
Alan Cooper ◽  
...  
Keyword(s):  
Organic Matter ◽  
Fine Structure ◽  
Soil Organic Matter ◽  
Porous Structure ◽  
Functional Groups ◽  
Science Studies ◽  
Organic Chemical ◽  
X Ray ◽  
Nexafs Spectroscopy ◽  
Allophanic Soil

AbstractAllophanic tephra-derived soils can sequester sizable quantities of soil organic matter (SOM). However, no studies have visualized the fine internal porous structure of allophanic soil microaggregates, nor studied the carbon structure preserved in such soils or paleosols. We used synchrotron radiation-based transmission X-ray microscopy (TXM) to perform 3D-tomography of the internal porous structure of dominantly allophanic soil microaggregates, and carbon near-edge X-ray absorption fine-structure (C NEXAFS) spectroscopy to characterize SOM in ≤ 12,000-year-old tephra-derived allophane-rich (with minor ferrihydrite) paleosols. The TXM tomography showed a vast network of internal, tortuous nano-pores within an allophanic microaggregate comprising nanoaggregates. SOM in the allophanic paleosols at four sites was dominated by carboxylic/carbonyl functional groups with subordinate quinonic, aromatic, and aliphatic groups. All samples exhibited similar compositions despite differences between the sites. That the SOM does not comprise specific types of functional groups through time implies that the functional groups are relict. The SOM originated at the land/soil surface: ongoing tephra deposition (intermittently or abruptly) then caused the land-surface to rise so that the once-surface horizons were buried more deeply and hence became increasingly isolated from inputs by the surficial/modern organic cycle. The presence of quinonic carbon, from biological processes but vulnerable to oxygen and light, indicates the exceptional protection of SOM and bio-signals in allophanic paleosols, attributable both to the porous allophane (with ferrihydrite) aggregates that occlude the relict SOM from degradation, and to rapid burial by successive tephra-fallout, as well as strong Al-organic chemical bonding. TXM and C NEXAFS spectroscopy help to unravel the fine structure of soils and SOM and are of great potential for soil science studies.

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