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Application of a Canny edge filter to refine pore detection in the sample. A: Original grayscale values. B: Pore segmentation without the Canny edge detection. C: Canny edge detection applied to find the edges of pore elements (Young, 2014); notice how the canny edges do not always connect with the features from B and add internal complexity to the pore phase. D: Morphological closing applied to reconnect the pore features to their edges (Matlab tool imclose).
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Subsurface structures and especially the interactions between pores, roots and other organic matter elements have a strong impact on ecosystem functioning. Yet despite recent progress in the application of X-ray Computed Microtomography (µCT) to soil structure in agricultural science, applications to the more complex and heterogeneous substrates fo...
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... to their original size. but a characteristic tubular shape, thin cracks in the sediment can have an intermediate grayscale value due to the partial volume effect, but a visible jagged edge. To capture these remaining pore elements, we used a canny edge detection that detects both strong edges and weak edges connected to strong edges (Canny, 1986) (Fig. ...
Citations
... Recent advancements in X-ray microtomography enable the noninvasive imaging of roots developing in soil medium and the sequential monitoring of root growth. Quantifying the amount of contact between roots and soil components remains an important challenge to define interactions of roots with soil structure and the heterogeneous distribution of many nutrients, microtomography is facilitating such studies (Gregory et al. 2009;Chirol et al. 2021). Historically, RSA has been detected in the field by manually measuring the roots and excavating the soil surrounding the root system or removing the plant from the field before separating the roots from the soil strata. ...
Roots are important organs associated with water and nutrient uptake from soil to all the plant parts. Besides plant metabolite storage organ, it also provides anchorage and mechanical support. The root "hidden half" plays a decisive role in root system architecture trait to affect grain yield and abiotic stress tolerance. Genetic study of root trait harbored due to the complex nature of root and unavailability of the rhizosphere. Identification of root system architecture provides a basic understanding of plant fitness, crop performance and grain yield. With increasing interest in root phenotyping, breeders overcome these barriers through the development of advanced phenotyping platforms based on field, laboratories and greenhouses such as soil coring, hydroponics, GLO-roots, rhizotron and mini-rhizotron. The advanced 2-D, 3-D and 4-D root imaging techniques such as magnetic resonance technique, RGB imaging, infrared thermal imaging and X-ray computed tomography are complex , but it gives the most desirable and accurate results to understand the root system architecture. This review focused on root architecture studies methods for root phenotyping using advanced recent techniques.
... Shallow subsidence was previously linked to the volume of coarse pore spaces in mineral mangrove soils in Moreton Bay (Xiong et al. 2019b). Compaction from overburden has also been identified in mangroves in southern Australia (Rogers and Saintilan 2021) and marshlands in Essex, UK (Chirol et al. 2021). Coarse pore soil volumes may be higher in mangroves dominated by A. marina compared to R. stylosa due to their belowground root structure that may lead to higher subsidence in A. marina dominated mangroves, although this remains to be assessed. ...
Coastal wetlands surrounding urban environments provide many important ecosystem services including protection from coastal erosion, soil carbon sequestration and habitat for marine and terrestrial fauna. Their persistence with sea-level rise depends upon their capacity to increase their soil surface elevation at a rate comparable to the rate of sea-level rise. Both sediment and organic matter from plant growth contribute to gains in soil surface elevation, but the importance of these components varies among sites and with variation in climate over long time scales, for which monitoring is seldom available. Here, we analysed variation in surface elevation, surface accretion and mangrove tree growth over 15 years in Moreton Bay, Queensland, Australia, a period that spans variation in the El Niño/La Niña (ENSO) cycle, which strongly influences rainfall and sea level in the region. Piecewise structural equation models were used to assess the effects of biotic (tree growth, plant cover and bioturbation by invertebrates) and environmental factors on annual surface elevation increments throughout this period. Our model for mangroves identified that surface accretion and tree growth were both positively influenced by rainfall, but surface elevation was not, and thus, higher levels of compaction of the soil profile in high rainfall/high sea level years were inferred. In contrast, our saltmarsh model found that rainfall positively influenced surface accretion and elevation gains. Declines in surface elevation in the mangroves were influenced by the species composition of the mangrove, with higher levels of elevation loss occurring in mangrove forests dominated by Avicennia marina compared to those with a higher proportion of Rhizophora stylosa . Decadal-scale variation in ENSO affected mangrove tree growth, but surface elevation trends were more strongly influenced by variation in environmental conditions than by tree growth, although effects of biotic factors (mangrove species composition and bioturbation) on surface elevation trends were observed. Further research into tipping points with extreme ENSO events (either La Niña with high rainfall and high sea level or El Niño with low rainfall and low sea levels) will help clarify the future of mangrove and saltmarsh distribution within Moreton Bay.
... In the two decades since, remarkable progress has been achieved in the quantitative description of the geometry of the pore space and the architecture of soils (e.g., Pierret et al., 2002;Vogel et al., 2010Vogel et al., , 2021Beckers et al., 2014;Smet et al., 2018;Chirol et al., 2021;Baveye et al., 2022), the heterogeneous microscale distribution of inorganic or organic chemical species (e.g., Schumacher et al., 2005;Solomon et al., 2005;Kinyangi et al., 2006;Jacobson et al., 2007;Strawn and Baker, 2008;Mueller et al., 2012;Spohn et al., 2013;Pedersen et al., 2015;Yamaguchi et al., 2021;Kravchenko et al., 2022), the microscale spatial distribution of microorganisms (Nunan et al., 2002(Nunan et al., , 2003Otten et al., 2004;Eickhorst and Tippkötter, 2008;Young et al., 2008;Schmidt et al., 2012;Fraser et al., 2016;Juyal et al., 2018Juyal et al., , 2019Juyal et al., , 2021, as well as that of plant roots and the dynamics of the associated rhizosphere (e.g., Roose et al., 2016;Zarebanadkouki et al., 2018;Schnepf et al., 2022). In recent years, efforts have been made to perform these different complementary measurements on the same soil samples (Hapca et al., 2015;Schlüter et al., 2019;Bandara et al., 2021;Kravchenko et al., 2022), as well as on 2-dimensional micromodels simulating the architecture of soils (e.g., Deng et al., 2015;Soufan et al., 2018;Aleklett et al., 2018;Pucetaite et al., 2021). ...
Over the last few years, several researchers working on the development of “biogeochemical” or “ecosystem-scale” models of soil carbon dynamics have reported struggling with a number of difficult challenges. At the same time, work in this area has focused exclusively on microbial activity described at a macro-ecological level, and has entirely bypassed the abundant literature produced in the last two decades on the study of soil processes at the microscale. Juxtaposition of these different observations suggests that a radical shift of perspective is in order. In this general context, the present article carries out an in-depth analysis of several of the key limitations of current ecosystem-scale models and recommends a number of steps to shift the perspective to one that is argued to have a better chance of success in the relatively short time we have to address several pressing soil-related environmental problems. These steps, in particular, require the development of large-spatial-scale models of soil carbon dynamics to be far more interdisciplinary than it has been till now, and to adopt a “bottom-up” approach, building on what the research at the microscale reveals about soil processes. Nevertheless, because it may assist in upscaling efforts, it is argued that some room should be preserved for work to continue on the search for empirical models applicable at large spatial scales.
... Soil science studies have used microCT scanning to image intact soil blocks to characterise and quantify solid soil components, physical properties (e.g. porosity and structure) and soil biota without losing 3D contextual information (Cássaro et al., 2017;Chirol et al., 2021;Helliwell et al., 2014;Katuwal et al., 2015;Taina et al., 2008;Voltolini et al., 2017). Traditional soil analysis methods such as 2D thin-section micromorphology can provide higher resolution coverage and additional information (eg. ...
The potential applications of microCT scanning in the field of archaeobotany are only just beginning to be explored. The imaging technique can extract new archaeobotanical information from existing archaeobotanical collections as well as create new archaeobotanical assemblages within ancient ceramics and other artefact types. The technique could aid in answering archaeobotanical questions about the early histories of some of the world’s most important food crops from geographical regions with amongst the poorest rates of archaeobotanical preservation and where ancient plant exploitation remains poorly understood. This paper reviews current uses of microCT imaging in the investigation of archaeobotanical questions, as well as in cognate fields of geosciences, geoarchaeology, botany and palaeobotany. The technique has to date been used in a small number of novel methodological studies to extract internal anatomical morphologies and three-dimensional quantitative data from a range of food crops, which includes sexually-propagated cereals and legumes, and asexually-propagated underground storage organs (USOs). The large three-dimensional, digital datasets produced by microCT scanning have been shown to aid in taxonomic identification of archaeobotanical specimens, as well as robustly assess domestication status. In the future, as scanning technology, computer processing power and data storage capacities continue to improve, the possible applications of microCT scanning to archaeobotanical studies will only increase with the development of machine and deep learning networks enabling the automation of analyses of large archaeobotanical assemblages.
... Although their method was able to isolate the roots of different plants, the explanation for multi-root competition has yet to be broken through. Chirol et al. (2021) developed a hybrid segmentation method to visualize and quantify the spatial analysis of wetland roots and enhanced tubular structures with a "Frangi" filter to distinguish living roots from necrotic tissue, but the segmentation method has yet to gain widespread acceptance. The root segmentation algorithm "Rootine" (Gao et al., 2019b) and the subsequent version "Rootine V.2" was developed with higher detection accuracy, but segmentation of root-stubble-soil complexes is still a big challenge. ...
Computed tomography (CT) in combination with advanced image processing can be used to non-invasively and non-destructively visualize complex interiors of living and non-living media in 2 and 3-dimensional space. In addition to medical applications, CT has also been widely used in soil and plant science for visual and quantitative descriptions of physical, chemical, and biological properties and processes. The technique has been used successfully on numerous applications. However, with a rapidly evolving CT technologies and expanding applications, a renewed review is desirable. Only a few attempts have been made to collate and review examples of CT applications involving the integrated field of soil and plant research in recent years. Therefore, the objectives of this work were to: (1) briefly introduce the basic principles of CT and image processing; (2) identify the research status and hot spots of CT using bibliometric analysis based on Web of Science literature over the past three decades; (3) provide an overall review of CT applications in soil science for measuring soil properties (e.g., porous soil structure, soil components, soil biology, heat transfer, water flow, and solute transport); and (4) give an overview of applications of CT in plant science to detect morphological structures, plant material properties, and root-soil interaction. Moreover, the limitations of CT and image processing are discussed and future perspectives are given.
... Medicinal computed tomography image analysis facilitates studying the 3D root morphology of vegetation in undisturbed tidal marsh soils (Davey et al., 2011;Blum and Davey, 2013;Hanson et al., 2016;Wigand et al., 2016). CT-scanning enables the distinction of air-spaces, organic structures and mineral particulates by means of a standardized X-ray response (Hounsfield units HU;Hounsfield, 1980), which allows the 3D root-system structures (root-tissue and root-aerenchyma) to be reconstructed in-silico using segmentation and skeleton analysis methods (Gao et al., 2019;Chirol et al., 2021). ...
Root-aerenchyma in wetland plants facilitate transport of oxygen from aboveground sources (atmosphere and photosynthesis) to belowground roots and rhizomes, where oxygen can leak out and oxygenate the otherwise anoxic soils. In salt marshes, the soil oxygenation capacity varies among different Spartina-taxa, but little is known about structural pattern and connectivity of root-aerenchyma that facilitates this gas transport. Both environmental conditions and ploidy level play a role for the root-system morphology. Root-system morphology of polyploid Spartina-taxa was studied, quantifying root-tissue volume and root-aerenchyma volume of hexaploid Spartina alterniflora, Spartina maritima, and Spartina × townsendii as well as dodecaploid Spartina anglica from different habitats. Computed tomography (CT)-scan image analysis was applied to quantify the volume of roots and aerenchyma, and to determine the root-system structure (ratio of aerenchyma to root-tissue volumes) and aerenchyma connectivity. On average, Spartina-roots accounted for 12% (v/v) and root-aerenchyma accounted for 1% (v/v) of the soil volume in the pioneer marsh. About 90% (v/v) of all roots were associated with aerenchyma. Root-system structures of S. × townsendii and S. anglica differed and showed clear responses to habitat conditions, such as flooding regime and redox potential. The development of large well-connected aerenchyma fragments were specifically shown in S. anglica and to a minor extend in S. maritima. Aerenchyma in S. alterniflora and S. × townsendii consisted only of smaller fragments. Spartina-dominated tidal pioneer marsh soils show high connectivity with the atmosphere via root-aerenchyma. The high ploidy level in S. anglica comes along with high connectivity in root-aerenchyma.
... Traditional root research methods, such as excavation methods, monoliths, etc. [6,7], are limited in their application and development due to their heavy workload, destructive sampling approach and unachievable repeated measurements [8]. With the innovation and development of technology, some in situ non-destructive observation methods have become the hotspots of plant root parameter estimation and distribution modeling research [9], such as minirhizotrons [10], X-ray Computed Tomography (CT) [11], magnetic resonance imaging (MRI) [12], ground-penetrating radar (GPR) method [13][14][15][16], etc. Among them, GPR is a non-intrusive geophysical technology that uses high-frequency electromagnetic waves to locate underground targets [17]. ...
The in situ non-destructive quantitative observation of plant roots is difficult. Traditional detection methods are not only time-consuming and labor-intensive, but also destroy the root environment. Ground penetrating radar (GPR), as a non-destructive detection method, has great potential in the estimation of root parameters. In this paper, we use GprMax software to perform forward modeling of plant roots under different soil dielectric constants, and analyze the situation of plant roots with different dielectric constants and different root diameters under 1.5 GHz frequency antenna detection. Firstly, root systems with increasing diameter under different values of root and soil dielectric constant were scanned. Secondly, from the scanning results, two time points T1 and T2 of radar wave entering and penetrating the root system were defined, and the correlation between root diameter D and time interval ∆T between T1 and T2 was analyzed. Finally, the least square regression model and back propagation (BP) neural network model for root diameter parameter estimation were established, and the estimation effects of the two models were compared and evaluated. The research results show that the root diameter (12–48 mm) is highly correlated with the time interval. Given the dielectric constants of the root and soil, the prediction results of the two models are accurate, but the prediction result of the neural network model is more stable, and the residual between the predicted value and the actual value is mainly concentrated in the [−1.5 mm, 1.5 mm] range, as well as the average of prediction error percentage being 3.62%. When the dielectric constants of the root and soil are unknown, the accuracy of the prediction results of the two models is decreased, but the stability of the neural network model is still superior to the least squares model, and the residual error is mainly concentrated in the range of [−5.3 mm, 5.0 mm], the average of prediction error percentage is 10.19%. This study uses GprMax to simulate root system detection and reveals the theoretical potential of GPR technology for non-destructive estimation of root diameter parameters. It is also pointed out that in the field exploration process, if the dielectric constants of the root and soil in the experimental site are sampled and measured first, the prediction accuracy of the model for root diameter would be effectively improved. This research is based on simulation experiments, so further simulation followed by laboratory and field testing is warranted using non-uniform roots and soil.
Au cours des dernières années, plusieurs chercheurs travaillant au développement de modèles « biogéochimiques » ou « à l'échelle de l'écosystème » de la dynamique du carbone dans les sols ont rapporté être confrontés avec un certain nombre de défis difficiles. Parallèlement, les travaux dans ce domaine se sont concentrés exclusivement sur l'activité microbienne décrite au niveau macro-écologique et ont complètement ignoré l'abondante littérature produite au cours des deux dernières décennies sur l'étude des processus du sol à l'échelle microscopique. Juxtaposition de ces différentes observations suggère qu'un changement radical de perspective s'impose. Dans ce contexte général, le présent article procède à une analyse approfondie de plusieurs des principales limites des modèles actuels à l'échelle de l'écosystème et recommande un certain nombre d'étapes pour déplacer l'attention vers une perspective qui est censée avoir de meilleures chances de succès dans le laps de temps relativement court dont nous disposons, nous devons résoudre plusieurs problèmes environnementaux urgents liés aux sols. Ces étapes nécessitent en particulier que le développement de modèles à grande échelle de la dynamique du carbone dans les sols soit beaucoup plus interdisciplinaire qu'il ne l'a été jusqu'à présent, et qu'il adopte une approche « ascendante », en s'appuyant sur ce que la recherche à l'échelle microscopique révèle sur les processus du sol. Néanmoins, parce que cela peut contribuer à intensifier les efforts, il faudrait préserver un peu d'espace à la marge pour poursuivre les travaux sur la recherche de modèles empiriques applicables à de grandes échelles spatiales. 1. Contexte Au cours des quatre dernières décennies, un nombre considérable de recherches ont été consacrées au développement et à l'utilisation de modèles informatiques « biogéochimiques » ou « à l'échelle de l'écosystème » de la dynamique du carbone dans le sol. Parmi d'autres applications pratiques, ils ont largement servi à prédire la séquestration à long terme du carbone du sol résultant de diverses activités agricoles ou des pratiques de géo-ingénierie destinées à atténuer le changement climatique (voir, par exemple, Riggers et al., 2021; Berthelin et al., 2022; Bruni et al., 2022; Baveye et al., 2023). Initialement, ces modèles supposaient que la matière organique pourrait être répartie en pools distincts avec des temps de résidence distincts, et que sa cinétique de minéralisation pourrait être décrite par de simples réactions de premier ordre, sans tenir compte explicitement de la présence ou activité des micro-organismes. Ces a Ceci est la traduction en français de l'article de 2023 intitulé " Ecosystem-scale modelling of soil carbon dynamics: Time for a radical shift of perspective? ", Soil Biology and Biochemistry 184, 109112.
Understanding the relationship between root systems, soil macropore networks, and soil hydraulic properties is important to better assess ecosystem health. In this study, treatments were performed in forested wetland soils with different vegetation densities, i.e., large (LWa) and small communities (LWb) of reed (Phragmites australis (Cav.) Trin. ex Steud.). At each plot, three undisturbed PVC cylinders (10 cm in diameter and 50 cm in height) were obtained, and X-ray microtomography (μCT) scanning was used to determine the root and macropore architectures. Results showed that the values of total root length and total root volume at LWa were significantly larger than those at LWb (p < 0.05). Imaged macroporosity, macropore volume, macropore length density, macropore node density, macropore branch density, mean macropore surface area, mean macropore diameter, and mean macropore volume at LWa were significantly larger than those at LWb (p < 0.05), whereas mean macropore length, mean macropore branch length, and mean macropore tortuosity at LWb were larger than those at LWa. Total root length and total root volume were positively correlated with soil saturated hydraulic conductivity. Imaged macroporosity, macropore volume, macropore length density, macropore node density, macropore branch density, mean macropore surface area, mean macropore diameter, and mean macropore volume were positively correlated with soil saturated hydraulic conductivity, whereas mean macropore length, mean macropore branch length, and mean macropore tortuosity were negatively correlated with soil saturated hydraulic conductivity. In conclusion, root systems and soil macropore networks constitute a complex synthesis inside soil environments, and together affect soil hydrological responses.
