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.

Applying X-ray CT to measure macropore diameters in undisturbed soil cores

Geoderma ◽  
1992 ◽  
Vol 53 (3-4) ◽  
pp. 329-340 ◽  
Author(s):  
R.L. Peyton ◽  
B.A. Haeffner ◽  
S.H. Anderson ◽  
C.J. Gantzer
Keyword(s):  
Soil Cores ◽  
Undisturbed Soil ◽  
X Ray ◽  
Undisturbed Soil Cores

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.

Isoproturon movement and dissipation in undisturbed soil cores from a grassed buffer strip

Agronomie ◽  
2000 ◽  
Vol 20 (3) ◽  
pp. 297-307 ◽  
Author(s):  
Pierre Benoit ◽  
Enrique Barriuso ◽  
Philippe Vidon ◽  
Benoit Réal
Keyword(s):  
Soil Cores ◽  
Undisturbed Soil ◽  
Buffer Strip ◽  
Undisturbed Soil Cores

The impact of porosity on organic matter cycling in a two-dimensional porous medium 

2021 ◽  
Author(s):  
Hanbang Zou ◽  
Pelle Ohlsson ◽  
Edith Hammer
Keyword(s):  
Porous Medium ◽  
Organic Matter ◽  
Carbon Sequestration ◽  
Soil Carbon ◽  
Pore Network ◽  
Pore Scale ◽  
Decomposition Of Organic Matter ◽  
Organic Matter Cycling ◽  
The Impact

&lt;p&gt;Carbon sequestration has been a popular research topic in recent years as the rapid elevation of carbon emission has significantly impacted our climate. Apart from carbon capture and storage in e.g. oil reservoirs, soil carbon sequestration offers a long term and safe solution for the environment and human beings. The net soil carbon budget is determined by the balance between terrestrial ecosystem sink and sources of respiration to atmospheric carbon dioxide. Carbon can be long term stored as organic matters in the soil whereas it can be released from the decomposition of organic matter. The complex pore networks in the soil are believed to be able to &quot;protect&quot; microbial-derived organic matter from decomposition. Therefore, it is important to understand how soil structure impacts organic matter cycling at the pore scale. However, there are limited experimental studies on understanding the mechanism of physical stabilization of organic matter. Hence, my project plan is to create a heterogeneous microfluidic porous microenvironment to mimic the complex soil pore network which allows us to investigate the ability of organisms to access spaces starting from an initial ecophysiological precondition to changes of spatial accessibility mediated by interactions with the microbial community.&lt;/p&gt;&lt;p&gt;Microfluidics is a powerful tool that enables studies of fundamental physics, rapid measurements and real-time visualisation in a complex spatial microstructure that can be designed and controlled. Many complex processes can now be visualized enabled by the development of microfluidics and photolithography, such as microbial dynamics in pore-scale soil systems and pore network modification mimicking different soil environments &amp;#8211; earlier considered impossible to achieve experimentally. The microfluidic channel used in this project contains a random distribution of cylindrical pillars of different sizes so as to mimic the variations found in real soil. The randomness in the design creates various spatial availability for microbes (preferential flow paths with dead-end or continuous flow) as an invasion of liquids proceeds into the pore with the lowest capillary entry pressure. In order to study the impact of different porosity in isolation of varying heterogeneity of the porous medium, different pore size chips that use the same randomly generated pore network is created. Those chips have the same location of the pillars, but the relative size of each pillar is scaled. The experiments will be carried out using sterile cultures of fluorescent bacteria, fungi and protists, synthetic communities of combinations of these, or a whole soil community inoculum. We will quantify the consumption of organic matter from the different areas via fluorescent substrates, and the bio-/necromass produced. We hypothesise that lower porosity will reduce the net decomposition of organic matter as the narrower pore throat limits the access, and that net decomposition rate at the main preferential path will be higher than inside branches&lt;/p&gt;

Relationship Between Soil Properties and Nitrogen Mineralization in Undisturbed Soil Cores from California Agroecosystems

2018 ◽  
Vol 50 (1) ◽  
pp. 77-92 ◽  
Author(s):  
Kenneth Miller ◽  
Brenna J. Aegerter ◽  
Nicholas E. Clark ◽  
Michelle Leinfelder-Miles ◽  
Eugene M. Miyao ◽  
...  
Keyword(s):  
Soil Properties ◽  
Nitrogen Mineralization ◽  
Soil Cores ◽  
Undisturbed Soil ◽  
Undisturbed Soil Cores

scholarly journals Soil Infrastructure, Interfaces & Translocation Processes in Inner Space ("Soil-it-is"): towards a road map for the constraints and crossroads of soil architecture and biophysical processes

2009 ◽  
Vol 13 (8) ◽  
pp. 1485-1502 ◽  
Author(s):  
L. W. de Jonge ◽  
P. Moldrup ◽  
P. Schjønning
Keyword(s):  
Organic Matter ◽  
Organic Carbon ◽  
Soil Structure ◽  
Energy Input ◽  
Pore Network ◽  
Health Economy ◽  
Matric Potential ◽  
Soil Matrix ◽  
Micro Scale ◽  
Road Map

Abstract. Soil functions and their impact on health, economy, and the environment are evident at the macro scale but determined at the micro scale, based on interactions between soil micro-architecture and the transport and transformation processes occurring in the soil infrastructure comprising pore and particle networks and at their interfaces. Soil structure formation and its resilience to disturbance are highly dynamic features affected by management (energy input), moisture (matric potential), and solids composition and complexation (organic matter and clay interactions). In this paper we review and put into perspective preliminary results of the newly started research program "Soil-it-is" on functional soil architecture. To identify and quantify biophysical constraints on soil structure changes and resilience, we claim that new approaches are needed to better interpret processes and parameters measured at the bulk soil scale and their links to the seemingly chaotic soil inner space behavior at the micro scale. As a first step, we revisit the soil matrix (solids phase) and pore system (water and air phases), constituting the complementary and interactive networks of soil infrastructure. For a field-pair with contrasting soil management, we suggest new ways of data analysis on measured soil-gas transport parameters at different moisture conditions to evaluate controls of soil matrix and pore network formation. Results imply that some soils form sponge-like pore networks (mostly healthy soils in terms of agricultural and environmental functions), while other soils form pipe-like structures (agriculturally poorly functioning soils), with the difference related to both complexation of organic matter and degradation of soil structure. The recently presented Dexter et al. (2008) threshold (ratio of clay to organic carbon of 10 kg kg−1) is found to be a promising constraint for a soil's ability to maintain or regenerate functional structure. Next, we show the Dexter et al. (2008) threshold may also apply to hydrological and physical-chemical interface phenomena including soil-water repellency and sorption of volatile organic vapors (gas-water-solids interfaces) as well as polycyclic aromatic hydrocarbons (water-solids interfaces). However, data for differently-managed soils imply that energy input, soil-moisture status, and vegetation (quality of eluded organic matter) may be equally important constraints together with the complexation and degradation of organic carbon in deciding functional soil architecture and interface processes. Finally, we envision a road map to soil inner space where we search for the main controls of particle and pore network changes and structure build-up and resilience at each crossroad of biophysical parameters, where, for example, complexation between organic matter and clay, and moisture-induced changes from hydrophilic to hydrophobic surface conditions can play a role. We hypothesize that each crossroad (e.g. between organic carbon/clay ratio and matric potential) may control how soil self-organization will manifest itself at a given time as affected by gradients in energy and moisture from soil use and climate. The road map may serve as inspiration for renewed and multi-disciplinary focus on functional soil architecture.

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