Implementation of grain mapping by diffraction contrast tomography on a conventional laboratory tomography setup with various detectors.

Laboratory-based diffraction contrast tomography (LabDCT) is a novel technique used to resolve grain orientations and shapes in three dimensions at the micrometre scale using laboratory X-ray sources, allowing the user to overcome the constraint of limited access to synchrotron facilities. To foster the development of this technique, the implementation of LabDCT is illustrated in detail using a conventional laboratory-based X-ray tomography setup, and it is shown that such implementation is possible with the two most common types of detectors: CCD and flat panel. As a benchmark, LabDCT projections were acquired on an AlCu alloy sample using the two types of detectors at different exposure times. Grain maps were subsequently reconstructed using the open-source grain reconstruction method reported in the authors' previous work. To characterize the detection limit and the spatial resolution for the current implementation, the reconstructed LabDCT grain maps were compared with the map obtained from a synchrotron measurement, which is considered as ground truth. The results show that the final grain maps from measurements by the CCD and flat panel detector are similar and show comparable quality, while the CCD gives a much better contrast-to-noise ratio than the flat panel. The analysis of the grain maps reconstructed from measurements with different exposure times suggests that a grain map of comparable quality could be obtained in less than 1 h total acquisition time without a significant loss of grain reconstruction quality and indicates a clear potential for time-lapse LabDCT experiments. The current implementation is suggested to promote the generic use of the LabDCT technique for grain mapping on conventional tomography setups.

Mission Tara Microplastics: a holistic set of protocols and data resources for the field investigation of plastic pollution along the land-sea continuum in Europe.

The Tara Microplastics mission was conducted for 7 months to investigate plastic pollution along nine major rivers in Europe-Thames, Elbe, Rhine, Seine, Loire, Garonne, Ebro, Rhone, and Tiber. An extensive suite of sampling protocols was applied at four to five sites on each river along a salinity gradient from the sea and the outer estuary to downstream and upstream of the first heavily populated city. Biophysicochemical parameters including salinity, temperature, irradiance, particulate matter, large and small microplastics (MPs) concentration and composition, prokaryote and microeukaryote richness, and diversity on MPs and in the surrounding waters were routinely measured onboard the French research vessel Tara or from a semi-rigid boat in shallow waters. In addition, macroplastic and microplastic concentrations and composition were determined on river banks and beaches. Finally, cages containing either pristine pieces of plastics in the form of films or granules, and others containing mussels were immersed at each sampling site, 1 month prior to sampling in order to study the metabolic activity of the plastisphere by meta-OMICS and to run toxicity tests and pollutants analyses. Here, we fully described the holistic set of protocols designed for the Mission Tara Microplastics and promoted standard procedures to achieve its ambitious goals: (1) compare traits of plastic pollution among European rivers, (2) provide a baseline of the state of plastic pollution in the Anthropocene, (3) predict their evolution in the frame of the current European initiatives, (4) shed light on the toxicological effects of plastic on aquatic life, (5) model the transport of microplastics from land towards the sea, and (6) investigate the potential impact of pathogen or invasive species rafting on drifting plastics from the land to the sea through riverine systems.

In situ synchrotron X-ray multimodal experiment to study polycrystal plasticity.

The microstructure of polycrystals is known to govern the performance of structural materials. This drives the need for mechanical characterization methods capable of probing large representative volumes at the grain and sub-grain scales. In this paper, the use of in situ diffraction contrast tomography (DCT) along with far-field 3D X-ray diffraction (ff-3DXRD) at the Psiché beamline of Soleil is presented and applied to study crystal plasticity in commercially pure titanium. A tensile stress rig was modified to comply with the DCT acquisition geometry and used for in situ testing. DCT and ff-3DXRD measurements were carried out during a tensile test of a tomographic Ti specimen up to 1.1% strain. The evolution of the microstructure was analyzed in a central region of interest comprising about 2000 grains. Using the 6DTV algorithm, DCT reconstructions were successfully obtained and allowed the characterization of the evolution of lattice rotation in the entire microstructure. The results are backed up by comparisons with EBSD and DCT maps acquired at ESRF-ID11 that allowed the validation of the orientation field measurements in the bulk. Difficulties at the grain boundaries are highlighted and discussed in line with increasing plastic strain during the tensile test. Finally, a new outlook is provided on the potential of ff-3DXRD to enrich the present dataset with access to average lattice elastic strain data per grain, on the possibility of performing crystal plasticity simulations from DCT reconstructions, and ultimately on comparisons between experiments and simulations at the scale of the grain.

Reconstruction algorithms for grain mapping by laboratory X-ray diffraction contrast tomography.

X-ray-based non-destructive 3D grain mapping techniques are well established at synchrotron facilities. To facilitate everyday access to grain mapping instruments, laboratory diffraction contrast tomography (LabDCT), using a laboratory-based conical polychromatic X-ray beam, has been developed and commercialized. Yet the currently available LabDCT grain reconstruction methods are either ill-suited for handling a large number of grains or require a commercial licence bound to a specific instrument. To promote the availability of LabDCT, grain reconstruction methods have been developed with multiple reconstruction algorithms based on both forward and back calculations. The different algorithms are presented in detail and their efficient implementation using parallel computing is described. The performance of different reconstruction methods is assessed on synthetic data. The code to implement all the described algorithms has been made publicly accessible with the intention of fostering the development of grain mapping techniques on widely available laboratory instruments.

Response to Comment on "The missing ocean plastic sink: Gone with the rivers".

Mai et al. are mistaken in their assertions that we incorrectly calculated the residence time for floating microplastic stock at the ocean surface, and that most of our results are not novel. Their claim that our field-measured data and methods were not rigorous is wrong, as shown by a more careful consideration of what was done.

Reconstructing dual-phase nanometer scale grains within a pearlitic steel tip in 3D through 4D-scanning precession electron diffraction tomography and automated crystal orientation mapping.

The properties of polycrystalline materials are related to their microstructures and hence a complete description, including size, shape, and orientation of the grains, is necessary to understand the behavior of materials. Here, we use Scanning Precession Electron Diffraction (SPED) in the Transmission Electron Microscope (TEM) combined with a tilt series to reconstruct individual grains in 3D within a polycrystalline dual-phase cold wire-drawn pearlitic steel sample. Nanoscale ferrite grains and intragranular cementite particles were indexed using an Automated Crystallographic Orientation Mapping (ACOM) tool for each tilt dataset. The grain orientations were tracked through the tilt datasets and projections of the individual grains were reconstructed from the diffraction data using an orientation-specific Virtual Dark Field (VDF) approach for tomographic reconstruction. The algorithms used to process and reconstruct such datasets are presented. These algorithms represent an extension to the ACOM approach that may be straightforwardly applied to other multi-phase polycrystalline materials to enable 3D spatial and orientation reconstructions.

The missing ocean plastic sink: Gone with the rivers.

Plastic floating at the ocean surface, estimated at tens to hundreds of thousands of metric tons, represents only a small fraction of the estimated several million metric tons annually discharged by rivers. Such an imbalance promoted the search for a missing plastic sink that could explain the rapid removal of river-sourced plastics from the ocean surface. On the basis of an in-depth statistical reanalysis of updated data on microplastics-a size fraction for which both ocean and river sampling rely on equal techniques-we demonstrate that current river flux assessments are overestimated by two to three orders of magnitude. Accordingly, the average residence time of microplastics at the ocean surface rises from a few days to several years, strongly reducing the theoretical need for a missing sink.

Release LTP_12_2020, featuring a new ARB alignment and improved 16S rRNA tree for prokaryotic type strains.

The new release of the All-Species Living Tree Project (LTP) represents an important step forward in the reconstruction of 16S rRNA gene phylogenies, since we not only provide an updated set of type strain sequences until December 2020, but also a series of improvements that increase the quality of the database. An improved universal alignment has been introduced that is implemented in the ARB format. In addition, all low-quality sequences present in the previous releases have been substituted by new entries with higher quality, many of them as a result of whole genome sequencing. Altogether, the improvements in the dataset and 16S rRNA sequence alignment allowed us to reconstruct robust phylogenies. The trees made available through this current LTP release feature the best topologies currently achievable. The given nomenclature and taxonomic hierarchy reflect all the changes available up to December 2020. The aim is to regularly update the validly published nomenclatural classification changes and new taxa proposals. The new release can be found at the following URL: https://imedea.uib-csic.es/mmg/ltp/.

Cyclic Deformation Induced Residual Stress Evolution and 3D Short Fatigue Crack Growth Investigated by Advanced Synchrotron Tomography Techniques.

Diffraction and phase contrast tomography techniques were successfully applied to an austenitic-ferritic duplex stainless steel representing exemplarily a metallic material containing two phases with different crystal structures. The reconstructed volumes of both phases were discretized by finite elements. A crystal plasticity finite-element analysis was executed in order to simulate the development of the experimentally determined first and second order residual stresses, which built up due to the manufacturing process of the material. Cyclic deformation simulations showed the single-grain-resolved evolution of initial residual stresses in both phases and were found to be in good agreement with the experimental results. Solely in ferritic grains, residual stresses built up due to cyclic deformation, which promoted crack nucleation in this phase. Furthermore, phase contrast tomography was applied in order to analyze the mechanisms of fatigue crack nucleation and short fatigue crack propagation three-dimensionally and nondestructively. The results clearly showed the significance of microstructural barriers for short fatigue crack growth at the surface, as well as into the material. The investigation presented aims for a better understanding of the three-dimensional mechanisms governing short fatigue crack propagation and, in particular, the effect of residual stresses on these mechanisms. The final goal was to generate tailored microstructures for improved fatigue resistance and enhanced fatigue life.

Quantifying microscale drivers for fatigue failure via coupled synchrotron X-ray characterization and simulations.

During cyclic loading, localization of intragranular deformation due to crystallographic slip acts as a precursor for crack initiation, often at coherent twin boundaries. A suite of high-resolution synchrotron X-ray characterizations, coupled with a crystal plasticity simulation, was conducted on a polycrystalline nickel-based superalloy microstructure near a parent-twin boundary in order to understand the deformation localization behavior of this critical, 3D microstructural configuration. Dark-field X-ray microscopy was spatially linked to high energy X-ray diffraction microscopy and X-ray diffraction contrast tomography in order to quantify, with cutting-edge resolution, an intragranular misorientation and high elastic strain gradients near a twin boundary. These observations quantify the extreme sub-grain scale stress gradients present in polycrystalline microstructures, which often lead to fatigue failure.

Microplastic fluxes in a large and a small Mediterranean river catchments: The Têt and the Rhône, Northwestern Mediterranean Sea.

This paper aims at quantifying current riverine fluxes of microplastics (MPs) in two Mediterranean river catchments, a large one and a small one, namely the Rhône and the Têt, which are discharging to the Gulf of Lion in the Northwestern Mediterranean Sea. MP fluxes change markedly through time and space in both river systems. However, no clear relationships between MP concentrations and hydroclimatic conditions have been observed. In the Rhône River a non-linear dilution pattern of MPs in total suspended matter (TSM) during flood conditions could be observed. Although dilution is important, samples during floods exert a strong control on average MP fluxes. Compared to the Rhône River, average MP concentrations in the Têt River were throughout greater and more variable in shape and polymer composition. However, as the study year was exceptionally dry, the average specific MP flux, 76 g km-2 y-1, is only slightly larger than the non-flooding value of the Rhône River. We further monitored MP concentrations in shoreline sediments at the mouth of the Têt River to test whether these sediments can represent MP transport in the river. Besides fibers, which probably are easily washed out and transported offshore, MP concentrations and compositions are in agreement with MP loads upstream the river. We also examined the potential role of atmospheric deposition as a source of MP to the Têt River. The average atmospheric MP deposition of 6 kg km-2 y-1 exceeds by far the river average specific MP flux. Moreover, all MPs in atmospheric deposits were fibers, which in terms of mass are of minor importance in the bulk river fluxes. Atmospheric MP deposits may either have been overestimated and/or may be removed from surface waters by efficient removal processes (such as waste water treatment plants).

Incipient Bulk Polycrystal Plasticity Observed by Synchrotron In-Situ Topotomography.

In this paper, we present a comprehensive 4D study of the early stage of plastic deformation in a polycrystalline binary AlLi alloy. The entire microstructure is mapped with X-ray diffraction contrast tomography, and a set of bulk grains is further studied via X-ray topotomography during mechanical loading. The observed contrast is analyzed with respect to the slip system activation, and the evolution of the orientation spread is measured as a function of applied strain. The experimental observations are augmented by the mechanical response predicted by crystal plasticity finite element simulations to analyze the onset of plasticity in detail. Simulation results show a general agreement of the individual slip system activation during loading and that comparison with experiments at the length scale of the grains may be used to fine tune the constitutive model parameters.

25 years of serving the community with ribosomal RNA gene reference databases and tools.

SILVA (lat. forest) is a comprehensive web resource, providing services around up to date, high-quality datasets of aligned ribosomal RNA gene (rDNA) sequences from the Bacteria, Archaea, and Eukaryota domains. SILVA dates back to the year 1991 when Dr. Wolfgang Ludwig from the Technical University Munich started the integrated software workbench ARB (lat. tree) to support high-quality phylogenetic inference and taxonomy based on the SSU and LSU rDNA marker genes. At that time, the ARB project maintained both, the sequence reference datasets and the software package for data analysis. In 2005, with the massive increase of DNA sequence data, the maintenance of the software system ARB and the corresponding rRNA databases SILVA was split between Munich and the Microbial Genomics and Bioinformatics Research Group in Bremen. ARB has been continuously developed to include new features and improve the usability of the workbench. Thousands of users worldwide appreciate the seamless integration of common analysis tools under a central graphical user interface, in combination with its versatility. The first SILVA release was deployed in February 2007 based on the EMBL-EBI/ENA release 89. Since then, full SILVA releases offering the database content in various flavours are published at least annually, complemented by intermediate web-releases where only the SILVA web dataset is updated. SILVA is the only rDNA database project worldwide where special emphasis is given to the consistent naming of clades of uncultivated (environmental) sequences, where no validly described cultivated representatives are available. Also exclusive for SILVA is the maintenance of both comprehensive aligned 16S/18S rDNA and 23S/28S rDNA sequence datasets. Furthermore, the SILVA alignments and trees were designed to include Eukaryota, another unique feature among rDNA databases. With the termination of the European Ribosomal RNA Database Project in 2007, the SILVA database has become the authoritative rDNA database project for Europe. The application spectrum of ARB and SILVA ranges from biodiversity analysis, medical diagnostics, to biotechnology and quality control for academia and industry.

Multicontamination phenomena occur more often than expected in Mediterranean coastal watercourses: Study case of the Têt River (France).

Contaminants found in watercourses are not only the result of anthropogenic activities but also depend on river's seasonal hydrodynamics. This is particularly true in Mediterranean climate regions where long dry periods are interrupted by strong rainfalls. Storm events remobilize particles from soils and sediments and, as a consequence, the load of particulate matter in rivers can be quite considerable, severely affecting water quality. Nevertheless, an absence of fieldwork studies exists concerning the simultaneous dynamics of mixtures of pollutants in river waters, particularly during strong rainfalls and floods. Our study assessed the concentrations of six families of pollutants, including pesticides, at these events, and compared them to those observed at drought sampling periods. We have used as model a typical Mediterranean coastal river from Southeast France, the Têt River, whose hydrodynamics and major elements fluxes have been fairly investigated. As expected, our results show that chemical mixtures due to human activities occur and that they are particularly relevant during storm events. But the results of our study argue that exceptional multicontamination phenomena actually happen more often than expected because they are linked to recurrent sudden intense rainfall events in the Mediterranean. In particular, combined sewer overflows are responsible for this major issue in urbanized areas, whereas runoff and leaching will be the most important sources of pollutant mixtures occurring at flood flow peak. After an overview of the sources responsible for chronic multiple stressors events in regions under a Mediterranean climate regime worldwide, we revisit best management measures to reduce risks from the presence of chemical mixtures in the environment.

Flow cytometric sorting of fecal bacteria after in situ hybridization with polynucleotide probes.

The gut microbiome represents a key contributor to human physiology, metabolism, immune function, and nutrition. Elucidating the composition and genetics of the gut microbiota under various conditions is essential to understand how microbes function individually and as a community. Metagenomic analyses are increasingly used to study intestinal microbiota. However, for certain scientific questions it is sufficient to examine taxon-specific submetagenomes, covering selected bacterial genera in a targeted manner. Here we established a new variant of fluorescence in situ hybridization (FISH) combined with fluorescence-activated cell sorting (FACS), providing access to the genomes of specific taxa belonging to the complex community of the intestinal microbiota. In contrast to standard oligonucleotide probes, the RNA polynucleotide probe used here, which targets domain III of the 23S rRNA gene, extends the resolution power in environmental samples by increasing signal intensity. Furthermore, cells hybridized with the polynucleotide probe are not subjected to harsh pretreatments, and their genetic information remains intact. The protocol described here was tested on genus-specifically labeled cells in various samples, including complex fecal samples from different laboratory mouse types that harbor diverse intestinal microbiota. Specifically, as an example for the protocol described here, RNA polynucleotide probes could be used to label Enterococcus cells for subsequent sorting by flow cytometry. To detect and quantify enterococci in fecal samples prior to enrichment, taxon-specific PCR and qPCR detection systems have been developed. The accessibility of the genomes from taxon-specifically sorted cells for subsequent molecular analyses was demonstrated by amplification of functional genes.

Combining operando synchrotron X-ray tomographic microscopy and scanning X-ray diffraction to study lithium ion batteries.

We present an operando study of a lithium ion battery combining scanning X-ray diffraction (SXRD) and synchrotron radiation X-ray tomographic microscopy (SRXTM) simultaneously for the first time. This combination of techniques facilitates the investigation of dynamic processes in lithium ion batteries containing amorphous and/or weakly attenuating active materials. While amorphous materials pose a challenge for diffraction techniques, weakly attenuating material systems pose a challenge for attenuation-contrast tomography. Furthermore, combining SXRD and SRXTM can be used to correlate processes occurring at the atomic level in the crystal lattices of the active materials with those at the scale of electrode microstructure. To demonstrate the benefits of this approach, we investigate a silicon powder electrode in lithium metal half-cell configuration. Combining SXRD and SRXTM, we are able to (i) quantify the dissolution of the metallic lithium electrode and the expansion of the silicon electrode, (ii) better understand the formation of the Li15Si4 phase, and (iii) non-invasively probe kinetic limitations within the silicon electrode. A simple model based on the 1D diffusion equation allows us to qualitatively understand the observed kinetics and demonstrates why high-capacity electrodes are more prone to inhomogeneous lithiation reactions.

Comparison between diffraction contrast tomography and high-energy diffraction microscopy on a slightly deformed aluminium alloy.

The grain structure of an Al-0.3 wt%Mn alloy deformed to 1% strain was reconstructed using diffraction contrast tomography (DCT) and high-energy diffraction microscopy (HEDM). 14 equally spaced HEDM layers were acquired and their exact location within the DCT volume was determined using a generic algorithm minimizing a function of the local disorientations between the two data sets. The microstructures were then compared in terms of the mean crystal orientations and shapes of the grains. The comparison shows that DCT can detect subgrain boundaries with disorientations as low as 1° and that HEDM and DCT grain boundaries are on average 4 µm apart from each other. The results are important for studies targeting the determination of grain volume. For the case of a polycrystal with an average grain size of about 100 µm, a relative deviation of about ≤10% was found between the two techniques.

Three-dimensional full-field X-ray orientation microscopy.

A previously introduced mathematical framework for full-field X-ray orientation microscopy is for the first time applied to experimental near-field diffraction data acquired from a polycrystalline sample. Grain by grain tomographic reconstructions using convex optimization and prior knowledge are carried out in a six-dimensional representation of position-orientation space, used for modelling the inverse problem of X-ray orientation imaging. From the 6D reconstruction output we derive 3D orientation maps, which are then assembled into a common sample volume. The obtained 3D orientation map is compared to an EBSD surface map and local misorientations, as well as remaining discrepancies in grain boundary positions are quantified. The new approach replaces the single orientation reconstruction scheme behind X-ray diffraction contrast tomography and extends the applicability of this diffraction imaging technique to material micro-structures exhibiting sub-grains and/or intra-granular orientation spreads of up to a few degrees. As demonstrated on textured sub-regions of the sample, the new framework can be extended to operate on experimental raw data, thereby bypassing the concept of orientation indexation based on diffraction spot peak positions. This new method enables fast, three-dimensional characterization with isotropic spatial resolution, suitable for time-lapse observations of grain microstructures evolving as a function of applied strain or temperature.

Herbinix hemicellulosilytica gen. nov., sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor.

Phenotypic and phylogenetic studies were performed on new isolates of a novel Gram-stain-positive, anaerobic, non-sporulating, rod-shaped bacterium isolated from a thermophilic biogas plant. The novel organisms were able to degrade crystalline cellulose. 16S rRNA gene comparative sequence analysis demonstrated that the isolates formed a hitherto unknown subline within the family Lachnospiraceae. As a representative of the whole group of isolates, strain T3/55T was further characterized. The closest relative of T3/55T among the taxa with validly published names is Mobilitalea sibirica, sharing 93.9% 16S rRNA gene sequence similarity. Strain T3/55T was catalase-negative, indole-negative, and produced acetate, ethanol and propionic acid as major end products from cellulose metabolism. The major cellular fatty acids (>1%) were 16 : 0 dimethyl acetal, 16 : 0 fatty acid methyl ester and 16 : 0 aldehyde. The DNA G+C content was 36.6 mol%. A novel genus and species, Herbinix hemicellulosilytica gen. nov., sp. nov., is proposed based on phylogenetic analysis and physiological properties of the novel isolate. Strain T3/55T ( = DSM 29228T = CECT 8801T), represents the type strain of Herbinix hemicellulosilytica gen. nov., sp. nov.

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences.

Publicly available sequence databases of the small subunit ribosomal RNA gene, also known as 16S rRNA in bacteria and archaea, are growing rapidly, and the number of entries currently exceeds 4 million. However, a unified classification and nomenclature framework for all bacteria and archaea does not yet exist. In this Analysis article, we propose rational taxonomic boundaries for high taxa of bacteria and archaea on the basis of 16S rRNA gene sequence identities and suggest a rationale for the circumscription of uncultured taxa that is compatible with the taxonomy of cultured bacteria and archaea. Our analyses show that only nearly complete 16S rRNA sequences give accurate measures of taxonomic diversity. In addition, our analyses suggest that most of the 16S rRNA sequences of the high taxa will be discovered in environmental surveys by the end of the current decade.