A symbiotic physical niche in Drosophila melanogaster regulates stable association of a multi-species gut microbiota.

The gut is continuously invaded by diverse bacteria from the diet and the environment, yet microbiome composition is relatively stable over time for host species ranging from mammals to insects, suggesting host-specific factors may selectively maintain key species of bacteria. To investigate host specificity, we used gnotobiotic Drosophila, microbial pulse-chase protocols, and microscopy to investigate the stability of different strains of bacteria in the fly gut. We show that a host-constructed physical niche in the foregut selectively binds bacteria with strain-level specificity, stabilizing their colonization. Primary colonizers saturate the niche and exclude secondary colonizers of the same strain, but initial colonization by Lactobacillus species physically remodels the niche through production of a glycan-rich secretion to favor secondary colonization by unrelated commensals in the Acetobacter genus. Our results provide a mechanistic framework for understanding the establishment and stability of a multi-species intestinal microbiome.

A novel endocast technique providing a 3D quantitative analysis of the gastrovascular system in Rhizostoma pulmo: An unexpected through-gut in cnidaria.

The investigation of jellyfish gastrovascular systems mainly focused on stain injections and dissections, negatively affected by thickness and opacity of the mesoglea. Therefore, descriptions are incomplete and data about tridimensional structures are scarce. In this work, morphological and functional anatomy of the gastrovascular system of Rhizostoma pulmo (Macri 1778) was investigated in detail with innovative techniques: resin endocasts and 3D X-ray computed microtomography. The gastrovascular system consists of a series of branching canals ending with numerous openings within the frilled margins of the oral arms. Canals presented a peculiar double hemi-canal structure with a medial adhesion area which separates centrifugal and centripetal flows. The inward flow involves only the "mouth" openings on the internal wing of the oral arm and relative hemi-canals, while the outward flow involves only the two outermost wings' hemi-canals and relative "anal" openings on the external oral arm. The openings differentiation recalls the functional characteristics of a through-gut apparatus. We cannot define the gastrovascular system in Rhizostoma pulmo as a traditional through-gut, rather an example of adaptive convergence, that partially invalidates the paradigm of a single oral opening with both the uptake and excrete function.

PyPore3D: An Open Source Software Tool for Imaging Data Processing and Analysis of Porous and Multiphase Media.

In this work, we propose the software library PyPore3D, an open source solution for data processing of large 3D/4D tomographic data sets. PyPore3D is based on the Pore3D core library, developed thanks to the collaboration between Elettra Sincrotrone (Trieste) and the University of Trieste (Italy). The Pore3D core library is built with a distinction between the User Interface and the backend filtering, segmentation, morphological processing, skeletonisation and analysis functions. The current Pore3D version relies on the closed source IDL framework to call the backend functions and enables simple scripting procedures for streamlined data processing. PyPore3D addresses this limitation by proposing a full open source solution which provides Python wrappers to the the Pore3D C library functions. The PyPore3D library allows the users to fully use the Pore3D Core Library as an open source solution under Python and Jupyter Notebooks PyPore3D is both getting rid of all the intrinsic limitations of licensed platforms (e.g., closed source and export restrictions) and adding, when needed, the flexibility of being able to integrate scientific libraries available for Python (SciPy, TensorFlow, etc.).

The hard x-ray nanotomography microscope at the advanced light source.

Beamline 11.3.1 at the Advanced Light Source is a tender/hard (6-17 keV) x-ray bend magnet beamline recently re-purposed with a new full-field, nanoscale transmission x-ray microscope. The microscope is designed to image composite and porous materials possessing a submicrometer structure and compositional heterogeneity that determine materials' performance and geologic behavior. The theoretical and achieved resolutions are 55 and <100 nm, respectively. The microscope is used in tandem with a <25 nm eccentricity rotation stage for high-resolution volume imaging using nanoscale computed tomography. The system also features a novel bipolar illumination condenser for the illumination of an ∼100 µm spot of interest on the sample, followed by a phase-type zone plate magnifying objective of ∼52 µm field of view and a phase detection ring. The zone plate serves as the system objective and magnifies the sample with projection onto an indirect x-ray detection system, consisting of a polished single crystal CsI(Tl) scintillator and a range of high-quality Plan Fluorite visible light objectives. The objectives project the final visible light image onto a water-cooled CMOS 2048 × 2048-pixel2 detector. Here, we will discuss the salient features of this instrument and describe early results from imaging the internal three-dimensional microstructure and nanostructure of target materials, including fiber-reinforced composites and geomaterials.

A new mini-triaxial cell for combined high-pressure and high-temperature in situ synchrotron X-ray microtomography experiments up to 400°C and 24†MPa.

A new experimental triaxial cell for in situ synchrotron X-ray micro-computed tomography aimed at imaging small samples of (6 mm × 19 mm) at high temperatures (up to 400°C) and pressures (up to 24 MPa confining) is presented. The system has flow-through capabilities, independent axial and radial pressure control, and has been developed and tested at the 8.3.2. beamline at the Advanced Light Source. The characteristics of this new experimental rig are described, along with the challenges, mainly concerning the combination of X-ray transparency with vessel strength at high temperature, and solutions found during the development stage. An experiment involving oil shale pyrolysis under subsurface conditions, highlighting the importance of a device able to operate in this pressure and temperature range, is also introduced. The availability of this cell enables an unprecedented range of experiments in the Earth Sciences, with a special focus on subsurface geothermal processes.

Supercritical CO2 uptake by nonswelling phyllosilicates.

Interactions between supercritical (sc) CO2 and minerals are important when CO2 is injected into geologic formations for storage and as working fluids for enhanced oil recovery, hydraulic fracturing, and geothermal energy extraction. It has previously been shown that at the elevated pressures and temperatures of the deep subsurface, scCO2 alters smectites (typical swelling phyllosilicates). However, less is known about the effects of scCO2 on nonswelling phyllosilicates (illite and muscovite), despite the fact that the latter are the dominant clay minerals in deep subsurface shales and mudstones. Our studies conducted by using single crystals, combining reaction (incubation with scCO2), visualization [atomic force microscopy (AFM)], and quantifications (AFM, X-ray photoelectron spectroscopy, X-ray diffraction, and off-gassing measurements) revealed unexpectedly high CO2 uptake that far exceeded its macroscopic surface area. Results from different methods collectively suggest that CO2 partially entered the muscovite interlayers, although the pathways remain to be determined. We hypothesize that preferential dissolution at weaker surface defects and frayed edges allows CO2 to enter the interlayers under elevated pressure and temperature, rather than by diffusing solely from edges deeply into interlayers. This unexpected uptake of CO2, can increase CO2 storage capacity by up to ∼30% relative to the capacity associated with residual trapping in a 0.2-porosity sandstone reservoir containing up to 18 mass % of illite/muscovite. This excess CO2 uptake constitutes a previously unrecognized potential trapping mechanism.

The emerging role of 4D synchrotron X-ray micro-tomography for climate and fossil energy studies: five experiments showing the present capabilities at beamline 8.3.2 at the Advanced Light Source.

Continuous improvements at X-ray imaging beamlines at synchrotron light sources have made dynamic synchrotron X-ray micro-computed tomography (SXR-µCT) experiments more routinely available to users, with a rapid increase in demand given its tremendous potential in very diverse areas. In this work a survey of five different four-dimensional SXR-µCT experiments is presented, examining five different parameters linked to the evolution of the investigated system, and tackling problems in different areas in earth sciences. SXR-µCT is used to monitor the microstructural evolution of the investigated sample with the following variables: (i) high temperature, observing in situ oil shale pyrolysis; (ii) low temperature, replicating the generation of permafrost; (iii) high pressure, to study the invasion of supercritical CO2 in deep aquifers; (iv) uniaxial stress, to monitor the closure of a fracture filled with proppant, in shale; (v) reactive flow, to observe the evolution of the hydraulic properties in a porous rock subject to dissolution. For each of these examples, it is shown how dynamic SXR-µCT was able to provide new answers to questions related to climate and energy studies, highlighting the significant opportunities opened recently by the technique.

Wollastonite Carbonation in Water-Bearing Supercritical CO2: Effects of Particle Size.

The performance of geologic CO2 sequestration (GCS) can be affected by CO2 mineralization and changes in the permeability of geologic formations resulting from interactions between water-bearing supercritical CO2 (scCO2) and silicates in reservoir rocks. However, without an understanding of the size effects, the findings in previous studies using nanometer- or micrometer-size particles cannot be applied to the bulk rock in field sites. In this study, we report the effects of particle sizes on the carbonation of wollastonite (CaSiO3) at 60 °C and 100 bar in water-bearing scCO2. After normalization by the surface area, the thickness of the reacted wollastonite layer on the surfaces was independent of particle sizes. After 20 h, the reaction was not controlled by the kinetics of surface reactions but by the diffusion of water-bearing scCO2 across the product layer on wollastonite surfaces. Among the products of reaction, amorphous silica, rather than calcite, covered the wollastonite surface and acted as a diffusion barrier to water-bearing scCO2. The product layer was not highly porous, with a specific surface area 10 times smaller than that of the altered amorphous silica formed at the wollastonite surface in aqueous solution. These findings can help us evaluate the impacts of mineral carbonation in water-bearing scCO2.

Alteration and Erosion of Rock Matrix Bordering a Carbonate-Rich Shale Fracture.

A novel reactive transport model has been developed to examine the processes that affect fracture evolution in a carbonate-rich shale. An in situ synchrotron X-ray microtomography experiment, flowing CO2 saturated water through a single fracture mini-core of Niobrara Shale provided the experimental observations for the development and testing of the model. The phenomena observed included the development of a porous altered layer, flow channeling, and increasingly limited calcite dissolution. The experimental observations cannot be explained by models that consider only mineral dissolution and development of an altered layer. The difference between the fracture volume change recorded by the microtomography images and what would be expected from mineral dissolution alone suggest that there is erosion of the altered layer as it develops. The numerical model includes this additional mechanism, with the erosion rate based on the thickness of the altered layer, and successfully captures the evolution of the geochemical reactions and morphology of the fracture. The findings imply that the abundance (with a threshold of approximately 35%) and reactivity of the rapidly reacting mineral control the development and erodibility of the altered layer on the fracture surfaces, and therefore fracture opening.

A 2.5D Reactive Transport Model for Fracture Alteration Simulation.

Understanding fracture alteration resulting from geochemical reactions is critical in predicting fluid migration in the subsurface and is relevant to multiple environmental challenges. Here, we present a novel 2.5D continuum reactive transport model that captures and predicts the spatial pattern of fracture aperture change and the development of an altered layer in the near-fracture region. The model considers permeability heterogeneity in the fracture plane and updates fracture apertures and flow fields based on local reactions. It tracks the reaction front of each mineral phase and calculates the thickness of the altered layer. Given this treatment, the model is able to account for the diffusion limitation on reaction rates associated with the altered layer. The model results are in good agreement with an experimental study in which a CO2-acidified brine was injected into a fracture in the Duperow Dolomite, causing dissolution of calcite and dolomite that result in the formation of a preferential flow channel and an altered layer. With an effective diffusion coefficient consistent with the experimentally observed porosity of the altered layer, the model captures the progressive decrease in the dissolution rate of the fast-reacting mineral in the altered layer.

Evaluation of microstructural properties of coffee beans by synchrotron X-ray microtomography: a methodological approach.

UNLABELLED: Synchrotron radiation microtomography was used as a nondestructive imaging technique to investigate the microstructural properties of green and roasted coffee beans. After image acquisition, 2D images have been reconstructed and 3D images of the beans have been then obtained. Qualitative and quantitative analysis of the images allow to fully characterize the morphological and structural features of the coffee beans. Roasting causes meaningful changes in the microstructure of the coffee bean tissue with the development in the entire bean of a porous structure with pores of different shape and size depending on the zone of the bean and cracks occurring mainly in the more external regions and between parenchyma and mucilage. The highly contrasted X-ray images have been analyzed to determine the pore size and its distribution in different regions of the coffee beans by selecting Volume-of-Interest (VoI). The use of phase-contrast hard X-rays imaging techniques represents an interesting tool of investigation of the internal structure, morphology, as well as the quality of whole coffee beans. Moreover, the high potentiality of 3D X-ray imaging and the approach used in this study could be applied in understanding the effects of roasting process conditions on the evolution of microstructural properties of the bean that may affect the stability as well the grinding and brewing performances. PRACTICAL APPLICATION: Synchrotron radiation microtomography is an elegant nondestructive imaging technique to investigate the microstructural properties of porous cellular matrices like the green and roasted coffee beans. The quantitative analysis of the resulting 2D and 3D images allows a more comprehensive and objective characterization of the sample under investigation as a whole or of extracted Volumes-of-Interest in the bean. This imaging technique could have a major role in understanding the effects of roasting process conditions on the microstructural properties of the bean.