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X-ray microtomography (microCT) is becoming a valuable noninvasive tool for advancing our understanding of plant–water relations. Laboratory-based microCT systems are becoming more affordable and provide better access than synchrotron facilities. However, some systems come at the cost of comparably lower signal quality and spatial resolution than synchrotron facilities. In this study, we evaluated laboratory-based X-ray microCT imaging as a tool to nondestructively analyse hydraulic vulnerability to drought-induced embolism in a woody plant species. We analysed the vulnerability to drought-induced embolism of benchtop-dehydrated Eucalyptus camaldulensis plants using microCT and hydraulic flow measurements on the same sample material, allowing us to directly compare the two methods. Additionally, we developed a quantitative procedure to improve microCT image analysis at limited resolution and accurately measure vessel lumens. Hydraulic measurements matched closely with microCT imaging of the current-year growth ring, with similar hydraulic conductivity and loss of conductivity due to xylem embolism. Optimized thresholding of vessel lumens during image analysis, based on a physiologically meaningful parameter (theoretical conductivity), allowed us to overcome common potential constraints of some lab-based systems. Our results indicate that estimates of vulnerability to embolism provided by microCT visualization agree well with those obtained from hydraulic measurements on the same sample material.

Virtual histology is increasingly utilized to reconstruct the cell mechanisms underlying dental morphology for fragile fossils when physical thin sections are not permitted. Yet, the comparability of data derived from virtual and physical thin sections is rarely tested. Here, the results from archaeological human deciduous incisor physical sections are compared with virtual ones obtained by phase‐contrast synchrotron radiation computed microtomography (SRµCT) of intact specimens using a multi‐scale approach. Moreover, virtual prenatal daily enamel secretion rates are compared with those calculated from physical thin sections of the same tooth class from the same archaeological skeletal series. Results showed overall good visibility of the enamel microstructures in the virtual sections which are comparable to that of physical ones. The highest spatial resolution SRµCT setting (effective pixel size = 0.9 µm) produced daily secretion rates that matched those calculated from physical sections. Rates obtained using the lowest spatial resolution setup (effective pixel size = 2.0 µm) were higher than those obtained from physical sections. The results demonstrate that virtual histology can be applied to the investigated samples to obtain reliable and quantitative measurements of prenatal daily enamel secretion rates. The implementation of synchrotron radiation X‐ray microtomography for non‐destructive visualization of the dental prenatal enamel microstructure of intact archaeological human deciduous teeth is presented and compared with the physical thin‐sectioning of the same archaeological dental series. Prenatal daily enamel secretion rates, i.e. the distance between two adjacent daily enamel microstructures, have been measured with the two approaches. Results show a good agreement between physical and virtual histology.

The ANATOMIX beamline at Synchrotron SOLEIL, operational since 2018, is dedicated to hard X-ray full-field tomography techniques. Operating in a range of photon energies from approximately 5 to 50 keV, it offers both parallel-beam projection microtomography, in absorption and phase contrast, and nanotomography using a zone-plate transmission X-ray microscope. With these methods, the beamline covers a range of spatial resolution from 20 nm to 20 µm, expressed in terms of useful pixel size. The variable beam size of up to 40 mm allows users to image large objects. Here we describe the microtomography instrumentation of the beamline.

[This corrects the article DOI: 10.1371/journal.pone.0158544.].

The formation of emboli in xylem conduits can dramatically reduce hydraulic capacity and represents one of the principal mechanisms of drought‐induced mortality in woody plants. However, our understanding of embolism formation and repair is constrained by a lack of tools to directly and nondestructively measure these processes at high spatial resolution. Using synchrotron‐based microcomputed tomography (microCT), we examined embolism in the xylem of coast redwood (Sequoia sempervirens) saplings that were subjected to cycles of drought and rewatering. Embolism formation was observed occurring by three different mechanisms: as tracheids embolizing in wide tangential bands; as isolated tracheids in seemingly random events; and as functional groups connected to photosynthetic organs. Upon rewatering, stem water potential recovered to predrought stress levels within 24 h; however, no evidence of embolism repair was observed even after a further 2 wk under well‐watered conditions. The results indicate that intertracheid air seeding is the primary mechanism by which embolism spreads in the xylem of S. sempervirens, but also show that a small number of tracheids initially become gas‐filled via another mechanism. The inability of S. sempervirens saplings to reverse drought‐induced embolism is likely to have important ecological impacts on this species.

Drought-induced xylem embolism is a serious threat to plant survival under future climate scenarios. Hence, accurate quantification of species-specific vulnerability to xylem embolism is a key to predict the impact of climate change on vegetation. Low-cost hydraulic measurements of embolism rate have been suggested to be prone to artefacts, thus requiring validation by direct visualization of the functional status of xylem conduits using nondestructive imaging techniques, such as X-ray microtomography (microCT). We measured the percentage loss of conductance (PLC) of excised stems of Laurus nobilis (laurel) dehydrated to different xylem pressures, and compared results with direct observation of gas-filled vs water-filled conduits at a synchrotron-based microCT facility using a phase contrast imaging modality. Theoretical PLC calculated on the basis of microCT observations in stems of laurel dehydrated to different xylem pressures overall were in agreement with hydraulic measurements, revealing that this species suffers a 50% loss of xylem hydraulic conductance at xylem pressures averaging −3.5 MPa. Our data support the validity of estimates of xylem vulnerability to embolism based on classical hydraulic techniques. We discuss possible causes of discrepancies between data gathered in this study and those of recent independent reports on laurel hydraulics.

There is growing interest in using advanced imaging techniques to describe the complex pore-space of natural rocks at resolutions that allow for quantitative assessment of the flow and transport behaviors in these complex media. Here, we focus on representations of the complex pore-space obtained from X-ray microtomography and the subsequent use of such ‘pore-scale’ representations to characterize the overall porosity and permeability of the rock sample. Specifically, we analyze the impact of sub-resolution porosity on the macroscopic (Darcy scale) flow properties of the rock. The pore structure of a rock sample is obtained using high-resolution X-ray microtomography ( 3 . 16 3 μ m 3 / voxel ) . Image analysis of the Berea sandstone sample indicates that about 2 % of the connected porosity lies below the resolution of the instrument. We employ a Darcy–Brinkman approach, in which a Darcy model is used for the sub-resolution porosity, and the Stokes equation is used to describe the flow in the fully resolved pore-space. We compare the Darcy–Brinkman numerical simulations with core flooding experiments, and we show that proper interpretation of the sub-resolution porosity can be essential in characterizing the overall permeability of natural porous media.

The ForMAX beamline at the MAX IV Laboratory provides multiscale and multimodal structural characterization of hierarchical materials in the nanometre to millimetre range by combining small‐ and wide‐angle X‐ray scattering with full‐field microtomography. The modular design of the beamline is optimized for easy switching between different experimental modalities. The beamline has a special focus on the development of novel fibrous materials from forest resources, but it is also well suited for studies within, for example, food science and biomedical research. ForMAX is a new beamline at the MAX IV Laboratory, providing multiscale and multimodal structural characterization by combining small‐ and wide‐angle X‐ray scattering with full‐field tomographic imaging.

Delineation of microbial habitats within the soil matrix and characterization of their environments and metabolic processes are crucial to understand soil functioning, yet their experimental identification remains persistently limited. We combined single- and triple-energy X-ray computed microtomography with pore specific allocation of 13 C labeled glucose and subsequent stable isotope probing to demonstrate how long-term disparities in vegetation history modify spatial distribution patterns of soil pore and particulate organic matter drivers of microbial habitats, and to probe bacterial communities populating such habitats. Here we show striking differences between large (30-150 µm Ø) and small (4-10 µm Ø) soil pores in (i) microbial diversity, composition, and life-strategies, (ii) responses to added substrate, (iii) metabolic pathways, and (iv) the processing and fate of labile C. We propose a microbial habitat classification concept based on biogeochemical mechanisms and localization of soil processes and also suggests interventions to mitigate the environmental consequences of agricultural management. The work proposes the concept of distinct micro-habitats within an intact soil matrix and describes composition and metabolic pathways of their bacterial inhabitants, as a first step towards a generalizable C processing-focused classification of soil micro-environmental conditions.

Synchrotron X‐ray microtomography (XMT) was used to measure total air‐water interfacial areas (Aaw) as a function of water saturation (Sw) for several soils that comprise a range of physical and geochemical properties. Measurements were also conducted for glass beads and quartz sands for comparison. Apparent near‐linear Aaw‐Sw relationships are observed for the three sands and the three sandy soils. In contrast, the measured interfacial areas for two soils that contain greater proportions of silt and clay are strongly nonlinear functions of water saturation. The greater degree of nonlinearity observed for these two soils is due to their much greater particle‐size distributions (i.e., uniformity coefficients) and their concomitant greater range in pore sizes. Interfacial areas determined with the thermodynamic method were used to benchmark the XMT measurements. XMT‐measured interfacial areas compare well to the thermodynamic‐determined values for the sands and sandy soils. In contrast, the XMT‐measured interfacial areas for the two soils with larger particle‐size distributions are not fully congruent with the thermodynamic‐determined values. Both of these soils have large fractions of pore space comprising nominal pore diameters smaller than the resolution of the XMT imaging. These results suggest that air‐water interfacial area may not always be fully characterized by standard XMT for soils with large particle‐size distributions. Plain Language Summary High‐resolution pore‐scale imaging is conducted for several sands and soils to examine the relationship between the magnitude of air‐water interfacial area and water saturation as well as to evaluate the effectiveness of the imaging method. Key Points X‐ray microtomography (XMT) measurements of air‐water interfacial area are reported for soils The relationship between air‐water interfacial area and water saturation is nonlinear Benchmarking results indicate that XMT may not measure all interfacial area for soils with higher silt and clay contents