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.

The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks.

SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA genes. This article describes the improvements the SILVA taxonomy has undergone in the last 3 years. Specifically we are focusing on the curation process, the various resources used for curation and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies. Our comparisons not only revealed a reasonable overlap between the taxa names, but also points to significant differences in both names and numbers of taxa between the three resources.

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.

From source to sink: part 1-characterization and Lagrangian tracking of riverine microplastics in the Mediterranean Basin.

The Mediterranean Sea is one of the most critically polluted areas due to its semi-enclosed structure and its highly anthropized shoreline. Rivers are significant vectors for pollutant transfers from the continental to the marine environment. In this context, a 3D Lagrangian simulation of the dispersion of riverine microplastics (MPs) was performed, which included the application of a recently developed model that reassessed the MP fluxes discharged by rivers. MP physical properties from river samples were further investigated to approximate vertical displacement in modeled ocean currents. The use of a high-resolution circulation model, integrating Stokes drift, turbulent diffusion, and MP sinking and rising velocities, enabled us to establish stock balances. Our simulation suggested that 65% of river inputs may be made of floating MPs drifting in the surface layer and 35% of dense MPs sinking to deeper layers. The Eastern Mediterranean tends to accumulate floating MPs, primarily originating from the Western Mediterranean Basin, where major river sources are concentrated. After 2 years of simulation, modeled stranding sequestered 90% of the MP inputs, indicating relatively short average residence times from a few days to months at most for particles at sea. Although spatial distribution patterns stabilized after this period and a steady state may have been approached, the surface concentrations we modeled generally remained below field observations. This suggested either an underestimation of sources (rivers and unaccounted sources), by a factor of 6 at most, or an overestimation of MP withdrawal through stranding, to be reduced from 90 to around 60% or less if unaccounted sinks were considered.

Small microplastics have much higher mass concentrations than large microplastics at the surface of nine major European rivers.

Understanding the fates and impacts of microplastics requires information on their sizes, polymer types, concentrations, and spatial and temporal distributions. Here, we focused on large (LMPs, 500 µm to 5 mm) and small (SMPs, 25 to 500 µm) microplastics sampled with the exact same protocol in nine of the major European rivers during the seven months of the Tara Microplastic Expedition. Attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) and pyrolysis coupled with gas chromatography and mass spectrometry (Py-GC-MS) analyses were used to determine the microplastics contents by number and mass. The median LMP concentration was 6.7 particles m-3, which was lower than those in other regions of the world (America and Asia). The SMP mass concentration was much higher to the LMP concentrations, with SMP/LMP ratios up to 1000 in some rivers. We did not observe a systematic positive effect of urban areas for the two size classes or polymers; this could be explained by the fact that the transport of microplastic is highly heterogeneous in rivers. We believe that this study has important implications for predictive models of plastics distribution and fate in aquatic environments.

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.

Acidobacteria in freshwater ponds at Doñana National Park, Spain.

The Acidobacteria show a widespread distribution in natural ecosystems. In this study, we analyzed the presence of Acidobacteria in freshwater ponds at Doñana National Park (southwestern Spain). Nucleic acid sequence analysis, quantitative, real-time RT-PCR, and fluorescence in situ hybridization (FISH) were carried out. Acidobacteria in these aquatic environments were investigated using their 16S and 23S rDNA sequences and acidobacterial specific primer pairs through phylogenetic approaches. The presence of up to five subdivisions of Acidobacteria was detected during this study. The analyzed ponds exhibited distinctive patterns of acidobacterial clades. In order to detect their role in ecosystem functions, metabolically active Acidobacteria were detected based upon rRNA analyses. Quantitative, real-time RT-PCR showed a low percentage of metabolically active Acidobacteria at suboxic zones within the water column covered by surface Fe-rich films. Oxygen-saturated areas showed around 4% of total bacterial RNA belonging to Acidobacteria both in the water column and the sediment surface. The morphology of the most abundant Acidobacteria was revealed by FISH as cocci generally in pairs or chains. Enrichment cultures were also obtained and indicated a putative metabolism based on aerobic and heterotrophic characteristics likely taking advantage of the abundant organic matter present at the investigated sites. These results represent a significant contribution toward understanding the distribution and ecological role of the phylum Acidobacteria in natural ecosystems, specifically at Doñana National Park freshwater ponds.

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.

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.

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.

Description of Undibacterium oligocarboniphilum sp. nov., isolated from purified water, and Undibacterium pigrum strain CCUG 49012 as the type strain of Undibacterium parvum sp. nov., and emended descriptions of the genus Undibacterium and the species Undibacterium pigrum.

A Gram-negative, oxidase- and catalase-positive, flagellated, rod-shaped bacterium, designated strain EM 1(T), was isolated from purified water. 16S rRNA gene sequence analysis indicated that the novel strain belonged to the family Oxalobacteraceae within the class Betaproteobacteria; the closest phylogenetic relative was Undibacterium pigrum DSM 19792(T) (96.7 % gene sequence similarity). The new isolate could be distinguished from the type strain of U. pigrum DSM 19792(T) (=CCUG 49009(T)=CIP 109318(T)) and from strain CCUG 49012(T), which has been described as a second genomovar of this species, on the basis of genotypic data and several phenotypic properties. An S-layer was present in the cell envelope in U. pigrum DSM 19792(T), but was absent in strains EM 1(T) and CCUG 49012(T). Test conditions were established that enabled strain CCUG 49012(T) to be distinguished from U. pigrum DSM 19792(T). As found for U. pigrum, the main fatty acids of strains EM 1(T) and CCUG 49012(T) were summed feature 3 (including unsaturated C(16 : 1)ω7c), straight-chain C(16 : 0) and unsaturated C(18 : 1)ω7c (low percentage in strain CCUG 49012(T)), and C(10 : 0) 3-OH was the sole hydroxylated fatty acid. The polar lipid profile consisted of the predominant lipids phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The polyamine profile was mainly composed of the major compound putrescine and moderate amounts of 2-hydroxyputrescine. In contrast to U. pigrum and strain CCUG 49012(T), where ubiquinone Q8 was reported as the sole quinone component, the quinone system of strain EM 1(T) consisted of ubiquinone Q-8 (64 %) and Q-7 (36 %). The 16S rRNA gene sequence similarity, the polar lipid profile and the absence of C(12)-hydroxylated fatty acids all indicated that strain EM 1(T) was affiliated with the genus Undibacterium. 16S rRNA gene sequence similarity values lower than 97.0 % and several differentiating phenotypic traits demonstrated that strain EM 1(T) represents a novel species for which the name Undibacterium oligocarboniphilum sp. nov. is proposed (type strain EM 1(T)=DSM 21777(T)=CCUG 57265(T)). In addition, based on previously published results and this study, a separate species, Undibacterium parvum sp. nov., is proposed with strain CCUG 49012(T) (=DSM 23061(T)=CIP 109317(T)) as the type strain.

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.

"Candidatus anadelfobacter veles" and "Candidatus cyrtobacter comes," two new rickettsiales species hosted by the protist ciliate Euplotes harpa (Ciliophora, Spirotrichea).

The order Rickettsiales (Alphaproteobacteria) is a well-known group containing obligate endocellular prokaryotes. The order encompasses three families (Rickettsiaceae, Anaplasmataceae, and Holosporaceae) and a fourth, family-level cluster, which includes only one candidate species, "Candidatus Midichloria mitochondrii," as well as several unnamed bacterial symbionts. The broad host range exhibited by the members of the "Candidatus Midichloria" clade suggests their eventual relevance for a better understanding of the evolution of symbiosis and host specificity of Rickettsiales. In this paper, two new bacteria belonging to the "Candidatus Midichloria" clade, hosted by two different strains of the ciliate protist Euplotes harpa, are described on the basis of ultrastructural observations, comparative 16S rRNA gene sequence analysis, and an estimation of the percentage of infection. Ultrastructure of these bacteria shows some unusual features: one has an electron-dense cytoplasm, and the other one lacks a symbiosomal membrane. The latter was up to now considered an exclusive feature of bacteria belonging to the family Rickettsiaceae. 16S rRNA gene phylogenetic analysis unambiguously places the new bacteria in the "Candidatus Midichloria" clade, although their phylogenetic relationships with other members of the clade are not clearly resolved. This is the first report of a ciliate-borne bacterium belonging to the "Candidatus Midichloria" clade. On the basis of the data obtained, the two bacteria are proposed as two new candidate genera and species, "Candidatus Anadelfobacter veles" and "Candidatus Cyrtobacter comes."

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).

Fluorescence in situ hybridization for intracellular localization of nifH mRNA.

Few reports on in situ mRNA detection in bacteria have been published, even though a major aim in environmental microbiology is to link function/activity to the identity of the organisms. This study reports a reliable approach for the in situ detection of nifH mRNA using fluorescence hybridization based on a previously described protocol for pmoA. nifH codes for a dinitrogenase reductase, a key enzyme in dinitrogen fixation. nifH mRNA was hybridized with a digoxigenin-labelled polynucleotide probe. The hybrid was detected with an anti-DIG-antibody labelled with horseradish peroxidase. Subsequently, the signal was amplified by catalyzed reporter deposition (CARD) with fluorochrome-labelled tyramides. Furthermore, the imaged organisms were identified using standard fluorescence in situ hybridization of rRNA. Thus, the approach enabled us specifically to link in situ the information from the dinitrogen fixation activity of an organism to its identity. Unexpectedly, the signals derived from nifH mRNA hybridization showed a distinct uneven pattern within the cells. This indicated that the method used could even give insights about the localization of the detected mRNA within the cell, which is a potential use of mRNA fluorescence in situ hybridization (FISH) that has not been reported up to now for bacterial cells.

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB.

Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction, nucleic acid based detection and quantification of microbial diversity. The ARB software suite with its corresponding rRNA datasets has been accepted by researchers worldwide as a standard tool for large scale rRNA analysis. However, the rapid increase of publicly available rRNA sequence data has recently hampered the maintenance of comprehensive and curated rRNA knowledge databases. A new system, SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains. All sequences are checked for anomalies, carry a rich set of sequence associated contextual information, have multiple taxonomic classifications, and the latest validly described nomenclature. Furthermore, two precompiled sequence datasets compatible with ARB are offered for download on the SILVA website: (i) the reference (Ref) datasets, comprising only high quality, nearly full length sequences suitable for in-depth phylogenetic analysis and probe design and (ii) the comprehensive Parc datasets with all publicly available rRNA sequences longer than 300 nucleotides suitable for biodiversity analyses. The latest publicly available database release 91 (August 2007) hosts 547 521 sequences split into 461 823 small subunit and 85 689 large subunit rRNAs.