Revealing pore connectivity across scales and resolutions with X‐ray CT
TL;DR: The scale dependence of connectivity metrics needs to be accounted for in this article, where the authors investigated the changes in pore connectivity with changing sample size, covering a range of analysed pore diameters of more than three orders of magnitude.
Abstract: Connectivity is one of the most important parameters to quantify pore structure and link it to soil functions. One of the great challenges in quantifying connectivity with X‐ray microtomography (X‐ray μCT) is that high resolution, as required for small pores, can only be achieved in small samples in which the connectivity of larger pores can no longer be quantified in a meaningful way. The objective of this study was to investigate the changes in pore connectivity with changing sample size, covering a range of analysed pore diameters of more than three orders of magnitude. With this approach, we wanted to address whether pore types formed by different processes in an agricultural chronosequence leave characteristic traces in certain connectivity metrics. The Euler number, χ, and the connection probability of two random points within the pore system, that is, the Γ‐indicator, were determined as a function of minimum pore diameter. The results show that characteristic signatures of certain pore types overlap with scale artifacts in the connectivity functions. The Γ‐indicator, gives highly biased information in small samples. Therefore, we developed a new method for a joint‐Γ‐curve that merges information from three samples sizes. However, χ does not require such a scale fusion. It can be used to define characteristic size ranges for pore types and is very sensitive to the occurrence of bottle necks. Our findings suggest a joint evaluation of both connectivity metrics to disentangle different pore types with χ and to identify the contribution of different pore types to the overall pore connectivity with Γ. This evaluation on the chronosequence showed that biopores mainly connect pores of diameters between 0.5 and 0.1 mm. This was not coupled with an increase in pore volume. In contrast, tillage led to a shift of pores of diameter >0.05 mm towards pores of diameter >0.20 mm and thus increased connectivity of pores >0.20 mm. This work underlines the importance of accounting for the scale dependence of connectivity measures and provides a methodological approach for doing so. HIGHLIGHTS: Scale dependence of connectivity metrics needs to be accounted for. Connectivity metrics can be used to disentangle different pore types across scales. Roots mainly connect the pore system between 0.1 and 0.5 mm. A joint Γ‐connectivity function can be constructed that is free of scale artifacts.
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154 citations
TL;DR: In this article, focused ion beam plus scanning electron microscopy (FIB-SEM) imaging technique was used for the characterization of pore size distributions and observed pore inscribed radii ranging from 2.5 µm to 1 µm.
31 citations
TL;DR: In this paper , the relationship between organic carbon (SOC) in arable topsoil is examined and shown to have beneficial effects on soil physical properties that are important for soil fertility.
Abstract: Soil organic carbon (SOC) in arable topsoil is known to have beneficial effects on soil physical properties that are important for soil fertility. The effects of SOC content on soil aggregate stability have been well documented; however, few studies have investigated its relationship with the soil pore structure, which has a strong influence on water dynamics and biogeochemical cycling. In the present study, we examined the relationships between SOC and clay contents and pore size distributions (PSDs) across an arable field with large spatial variations in topsoil SOC and clay contents by combining X‐ray tomography and measurements of soil water retention. Additionally, we investigated the relationships between fractionated SOC, reactive Fe and Al oxide contents and soil pore structure. We found that porosities in the 0.2–720 μm diameter class were positively correlated with SOC content. A unit increase of SOC content was associated with a relatively large increase in porosity in the 0.2–5 and 480–720 μm diameter classes, which indicates that enhanced SOC content would increase plant available water content and unsaturated hydraulic conductivity. On the other hand, macroporosities (1200–3120 μm diameter classes) and bioporosity were positively correlated with clay content but not with SOC content. Due to strong correlations between soil texture, carbon‐to‐nitrogen ratios and reactive iron contents, we could not separate the relative importance of these soil properties for PSDs. Reactive aluminium and particulate organic carbon contents were poorer predictors for PSDs compared with clay and SOC contents. This study provides new insights on the relations between SOC and soil pore structure in an arable soil and may lead to improved estimations of the effects of enhanced SOC sequestration on soil water dynamics and soil water supply to crops.
18 citations
TL;DR: In this paper, the authors discuss how preferential flow can serve as a framework of reference for the spatially and temporally heterogeneous biogeochemical cycling of soil carbon, and highlight the importance of combining current knowledge of pore-scale carbon dynamics with an appreciation of connected networks of hydraulically active pores/paths within the soil profile.
Abstract: Water is a crucial factor controlling the fate and processing of soil organics. Water commonly flows through the vadose zone via preferential flow pathways, resulting in nonuniform and rapid infiltration. Hence, a large portion of the soil matrix is bypassed. Preferential flow paths, often associated with well-connected macropore networks (>300 μm O), offer a unique balance between water availability, nutrient delivery, and re-oxygenation upon drainage. The heightened concentrations of moisture, nutrients, and oxygen make these locations optimal for high rates of microbial activity. Flow paths often display temporal stability. This stability results in repeated wetting and biogeochemical reactivation through time creating a lasting impact on micro-environmental conditions relevant to microbial functioning and carbon cycling in soil. Despite decades of research on preferential flow, there is still a need to link flow paths and the resultant heterogeneous moisture distributions to soil function. In this review, we discuss how preferential flow can serve as a framework of reference for the spatially and temporally heterogeneous biogeochemical cycling of soil carbon. We highlight the importance of combining current knowledge of pore-scale carbon dynamics with an appreciation of connected networks of hydraulically active pores/paths within the soil profile. Such combination opens new possibilities for upscaling pore-scale processes with the inclusion of resource heterogeneity at the macroscale. Working within this hydraulically connected framework can provide insight for the mechanistic representation of hot moments, which are temporally isolated large pulses of CO2 after rewetting or thawing events. We conclude with suggestions on knowledge gaps and stress the critical need of linking soil physics with biology to mechanistically understand soil functions.
17 citations
TL;DR: In this paper, the authors investigated how substrate hydraulic properties respond to the presence of arbuscular mycorrhizal fungi (AMF) in root-containing and root-free substrate zones in a Medicago truncatula-Rhizophagus irregularis model system.
Abstract: We investigated how substrate hydraulic properties respond to the presence of arbuscular mycorrhizal fungi (AMF) in root-containing and root-free substrate zones in a Medicago truncatula-Rhizophagus irregularis model system. Before planting, two compartments constructed from standard soil sampling cores (250 cm3) were implanted into non-mycorrhizal and mycorrhizal pots containing a sand-zeolite-soil mix. One compartment allowed root penetration (1 mm mesh cover) and the other only hyphal ingrowth (42 μm mesh cover). After eight weeks of growth under maintenance of moist conditions, the cores were subjected to water retention measurements. Additionally, we measured water retention of bare substrates before and after drying events to check for successful maintenance of moist conditions in pots. Drying of bare substrates decreased water retention, but planting at least sustained it. The parameters of water retention models responded linearly to root morphological traits across mycorrhizal and non-mycorrhizal substrates. Hyphae-only colonization comparatively affected the course of water retention in ways that suggest increased pore space heterogeneity while maintaining water storage capacity of substrates. Hence, water contents corresponded to different substrate matric potentials in non-mycorrhizal and mycorrhizal pots. We conclude that changes to water retention in AMF colonized substrates can contribute to a widely observed phenomenon, i.e. that mycorrhizal plants differ in their moisture stress response from non-mycorrhizal plants.
14 citations
Cites background from "Revealing pore connectivity across ..."
...These root-induced processes alter the size, the geometry and the wetting properties of the pore space around roots and, thus, affect soil hydraulic properties (Bodner et al. 2014; Kroener et al. 2018; Lucas et al. 2020; Read et al. 2003; Scholl et al. 2014)....
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...The growth and activity of root systems will lead to the formation of a highly connected biopore system and will determine the extent of clogging when roots grow into existing pores (Bodner et al. 2014; Głąb et al. 2013; Lucas et al. 2020; Wiersum 1957)....
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References
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TL;DR: Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis that facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system.
Abstract: Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.
43,540 citations
"Revealing pore connectivity across ..." refers methods in this paper
...…into binary images of visible pores and matrix voxels and pore size distribution was computed as described by Lucas et al. (2019) using Fiji/ImageJ (Schindelin et al., 2012) and associated plugins (Legland, ArgandaCarreras, & Andrey, 2016; Ollion, Cochennec, Loll, Escudé, & Boudier, 2013)....
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...Images of all sample sizes were processed and segmented into binary images of visible pores and matrix voxels and pore size distribution was computed as described by Lucas et al. (2019) using Fiji/ImageJ (Schindelin et al., 2012) and associated plugins (Legland, ArgandaCarreras, & Andrey, 2016; Ollion, Cochennec, Loll, Escudé, & Boudier, 2013)....
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TL;DR: In this paper, soil organic carbon (SOC), biota, ionic bridging, clay and carbonates are associated with aggregation by rearrangement, flocculation and cementation.
3,241 citations
"Revealing pore connectivity across ..." refers background in this paper
...Soil properties and processes such as hydraulic conductivity, gas exchange and water retention, as well as erosion, are controlled by the spatial structure of pores and solids (Bronick & Lal, 2005; Rabot, Wiesmeier, Schlüter, & Vogel, 2018)....
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TL;DR: The MorphoLibJ library proposes a large collection of generic tools based on MM to process binary and grey-level 2D and 3D images, integrated into user-friendly plugins.
Abstract: Motivation: Mathematical morphology (MM) provides many powerful operators for processing 2D and 3D images. However, most MM plugins currently implemented for the popular ImageJ/Fiji platform are limited to the processing of 2D images.
Results: The MorphoLibJ library proposes a large collection of generic tools based on MM to process binary and grey-level 2D and 3D images, integrated into user-friendly plugins. We illustrate how MorphoLibJ can facilitate the exploitation of 3D images of plant tissues.
Availability and Implementation: MorphoLibJ is freely available at http://imagej.net/MorphoLibJ
796 citations
TL;DR: TANGO is a coherent framework allowing biologists to perform the complete analysis process of 3D fluorescence images by combining two environments: ImageJ and R, providing an intuitive user interface providing the means to precisely build a segmentation procedure and set-up analyses, without possessing programming skills.
Abstract: Motivation: The cell nucleus is a highly organized cellular organelle that contains the genetic material. The study of nuclear architecture has become an important field of cellular biology. Extracting quantitative data from 3D fluorescence imaging helps understand the functions of different nuclear compartments. However, such approaches are limited by the requirement for processing and analyzing large sets of images.
Results: Here, we describe Tools for Analysis of Nuclear Genome Organization (TANGO), an image analysis tool dedicated to the study of nuclear architecture. TANGO is a coherent framework allowing biologists to perform the complete analysis process of 3D fluorescence images by combining two environments: ImageJ (http://imagej.nih.gov/ij/) for image processing and quantitative analysis and R (http://cran.r-project.org) for statistical processing of measurement results. It includes an intuitive user interface providing the means to precisely build a segmentation procedure and set-up analyses, without possessing programming skills. TANGO is a versatile tool able to process large sets of images, allowing quantitative study of nuclear organization.
Availability: TANGO is composed of two programs: (i) an ImageJ plug-in and (ii) a package (rtango) for R. They are both free and open source, available (http://biophysique.mnhn.fr/tango) for Linux, Microsoft Windows and Macintosh OSX. Distribution is under the GPL v.2 licence.
Contact: rf.ueissuj.vns@reiduob.samoht
Supplementary information: Supplementary data are available at Bioinformatics online.
618 citations
TL;DR: In this paper, the potential of observable soil structural attributes to be used in the assessment of soil functions is evaluated and discussed from a methodological point of view and with respect to their relevance to soil functions.
602 citations
"Revealing pore connectivity across ..." refers background in this paper
...There is typically a fixed factor of 1,000–2,000 between CT image resolution and sample size (Rabot et al., 2018)....
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...Besides porosity and pore size distribution, one of the most important parameters for soil functions is pore connectivity (Rabot et al., 2018)....
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