An Improved Method for the Segmentation of Roots from X-ray Computed Tomography 3D Images: Rootine v.2

Phalempin, Maxime; Lippold, Eva; Vetterlein, Doris; Schlüter, Steffen

doi:10.21203/rs.3.rs-96550/v1

Cited by 3 publications

(11 citation statements)

References 25 publications

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“…Root segmentation of each column scan was performed with the algorithm Rootine v2 (Phalempin et al 2021) Rootine v2 is a free macro for the image processing software ImageJ (Schindelin et al 2012). It combines a series of pre-and postprocessing filters with a shape based detection of cylindrical roots at various scales.…”

Section: Root Segmentationmentioning

confidence: 99%

“…It should be noted that despite major advances in root segmentation in the past years (Phalempin et al 2021;Soltaninejad et al 2020), we still face the trade-off between image resolution and sample size resulting in fine roots being partly missed out. In the present case, this afflicts the differences between sand and loam as the share of fine roots was larger in loam.…”

Section: System Limitations -Relevance For Field Conditionsmentioning

confidence: 99%

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Does the lack of root hairs alter root system architecture of Zea mays?

et al. 2021

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Aims Root hairs are one root trait among many which enables plants to adapt to environmental conditions. How different traits are coordinated and whether some are mutually exclusive is currently poorly understood. Comparing a root hair defective mutant with its corresponding wild-type, we explored if and how the mutant exhibited root growth adaptation strategies and how dependent this was on substrate. Methods Zea mays root hair defective mutant (rth3) and the corresponding wild-type siblings were grown under well-watered conditions on two substrates with contrasting texture and hence nutrient mobility. Root system architecture was investigated over time using repeated X-ray computed tomography. Results There was no plastic adaptation of root system architecture to the lack of root hairs, which resulted in lower uptake of nutrients especially in the substrate with high sorption capacity. The function of the root hairs for anchoring did not result in different root length density profiles between genotypes. Both maize genotypes showed a marked response to substrate. This was well reflected in the spatiotemporal development of rhizosphere volume fraction but especially in the highly significant response of root diameter to substrate, irrespective of genotype. Conclusions The most salient root plasticity trait was root diameter in response to substrate. Coping mechanisms for missing root hairs were limited to a shift in root-shoot ratio in loam. Further experiments are required, to elucidate whether observed differences can be explained by mechanical properties beyond mechanical impedance, root or microbiome ethylene production or differences in diffusion processes within the root or the rhizosphere.

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Section: Root Segmentationmentioning

confidence: 99%

Section: System Limitations -Relevance For Field Conditionsmentioning

confidence: 99%

Does the lack of root hairs alter root system architecture of Zea mays?

et al. 2021

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“…Then, a background removal step was applied via an “absolute difference transform” whose rationale and technical aspects are described by Phalempin et al. (2021). The obtained images served as input for the root segmentation per se.…”

Section: Methodsmentioning

confidence: 99%

“…With the new approach, every image was visually analyzed and the diameter of the roots in the image was measured using the “Measure” tool available in ImageJ. The sigma values of the tubeness filter implemented in ImageJ were then calculated based on the measured root diameters according to the formalizing steps described elsewhere (Phalempin et al., 2021). The results of the tubeness filter were segmented using the “3D Hysteresis Thresholding” (Ollion et al., 2013) available in ImageJ.…”

Section: Methodsmentioning

confidence: 99%

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Soil texture and structure heterogeneity predominantly governs bulk density gradients around roots

Phalempin

Lippold

Vetterlein

et al. 2021

Vadose Zone Journal

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Rhizosphere soil is known to differ from the bulk soil due to numerous physicochemical processes induced by root growth. The spatial extent and magnitude of the influence of roots on the surrounding soil is still debated controversially. To date, most studies focused on a limited number of soil types and plant species and were carried out under homogeneous soil structure conditions (i.e., finely sieved and repacked soil). With the help of X-ray computed tomography (CT), we present the results of an image processing workflow, which enabled to analyze soil structure around roots of maize (Zea mays L.) plants under different degrees of soil structure heterogeneity.We analyzed >400 samples extracted during laboratory and field experiments covering various combinations of texture, bulk density, packing heterogeneity, maize genotype, and soil moisture. We show that soil texture and structure heterogeneity predominantly governs the magnitude of bulk density alteration around roots. In homogeneous soil structure, roots had to create their own pores by pushing away soil particles, which confirms previous findings. Under more heterogeneous conditions, we found that roots predominantly grew in existing pores without inducing compaction. The influence of root hairs, root length density, and plant growth stages had no or little impact on the results. The effect of root diameter was more pronounced in sand than in loam. Fine roots caused sand grains to align along their axis, whereas big roots broke the fragile arrangement of grains. Our findings have implications for water and solute transport dynamics at the root-soil interface, which may affect plant productivity. INTRODUCTIONCharacterizing soil properties at the root-soil interface is key to a better understanding of environmental processes and to the promotion of sustainable agriculture. Indeed, this

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Perspectives from the Fritz‐Scheffer Awardee 2020—The mutual interactions between roots and soil structure and how these affect rhizosphere processes^#

Lucas

2021

J. Plant Nutr. Soil Sci.

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Roots growing into soil interact with soil structure in numerous ways. They can grow into the soil matrix and leave elongated macropores after decomposition, that is, biopores. Conversely, the soil may already have a large and connected macropore system through which the roots can expand, and thus reach deeper soil layers. Both, the formation of new biopores or the reuse and occupation of existing macropore systems are expected to affect major soil processes like water and gas flow through the soil profile, as well as water flow toward the root. Despite the increasing research interest in the limitation of root growth by soil structure, as well as the modification of soil structure by roots, the mutual interactions between the two are largely overlooked. This study highlights new methodological developments which enable describing interactions between roots and soil structure with X‐ray computed microtomography. It further shows how roots affect the pore system and can create a massive biopore system in less than a decade. After this, it is evaluated how the mutual interaction of roots and structure determines the physical properties of the rhizosphere. It is outlined that this has implications for major rhizosphere processes. Thus, it is emphasized, that the role of structure needs to be considered in future experiments with plants, in particular if extrapolation of results from laboratory experiment with sieved, homogenized substrates to field conditions with well‐established soil structure is intended. Lastly, in this study, research gaps are outlined remaining in respect to the dynamics of biopore creation and destruction and their consequences for processes in rhizospheres like carbon storage. These reveal the need for novel research approaches that consider the mutual interactions of root growth and soil structure.

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An Improved Method for the Segmentation of Roots from X-ray Computed Tomography 3D Images: Rootine v.2

Cited by 3 publications

References 25 publications

Does the lack of root hairs alter root system architecture of Zea mays?

Does the lack of root hairs alter root system architecture of Zea mays?

Soil texture and structure heterogeneity predominantly governs bulk density gradients around roots

Perspectives from the Fritz‐Scheffer Awardee 2020—The mutual interactions between roots and soil structure and how these affect rhizosphere processes^#

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An Improved Method for the Segmentation of Roots from X-ray Computed Tomography 3D Images: Rootine v.2

Cited by 3 publications

References 25 publications

Does the lack of root hairs alter root system architecture of Zea mays?

Does the lack of root hairs alter root system architecture of Zea mays?

Soil texture and structure heterogeneity predominantly governs bulk density gradients around roots

Perspectives from the Fritz‐Scheffer Awardee 2020—The mutual interactions between roots and soil structure and how these affect rhizosphere processes#

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Product

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Perspectives from the Fritz‐Scheffer Awardee 2020—The mutual interactions between roots and soil structure and how these affect rhizosphere processes^#