Cluster analysis of soft X-ray spectromicroscopy data

Location, speciation, and quantification of carbon in silica phytoliths using synchrotron scanning transmission X-ray microspectroscopy

Phytoliths of biogenic silica play a vital role in the silicon biogeochemical cycle and occlude a fraction of organic carbon. The location, chemical speciation, and quantification of this carbon within phytoliths have remained elusive due to limited direct experimental evidence. In this work, phytoliths (bilobate morphotype) from the sugarcane stalk epidermis are sectioned with a focused ion beam to produce lamellas (≈10 × 10 μm2 size, <500 nm thickness) and probed by synchrotron scanning transmission X-ray microspectroscopy (≈100-200 nm pixel size; energies near the silicon and carbon K-absorption edges). Analysis of the spectral image stacks reveals the complementarity of the silica and carbon spatial distributions, with carbon found at the borders of the lamellas, in islands within the silica, and dispersed in extended regions that can be described as a mixed silica-carbonaceous matrix. Carbon spectra are assigned mainly to lignin-like compounds as well as to proteins. Carbon contents of 3-14 wt.% are estimated from the spectral maps of four distinct phytolith lamellas. The results provide unprecedented spatial and chemical information on the carbon in phytoliths obtained without interference from wet-chemical digestion.

Undersampling raster scans in spectromicroscopy for a reduced dose and faster measurements

Combinations of spectroscopic analysis and microscopic techniques are used across many disciplines of scientific research, including material science, chemistry and biology. X-ray spectromicroscopy, in particular, is a powerful tool used for studying chemical state distributions at the micro and nano scales. With the beam fixed, a specimen is typically rastered through the probe with continuous motion and a range of multimodal data is collected at fixed time intervals. The application of this technique is limited in some areas due to: long scanning times to collect the data, either because of the area/volume under study or the compositional properties of the specimen; and material degradation due to the dose absorbed during the measurement. In this work, we propose a novel approach for reducing the dose and scanning times by undersampling the raster data. This is achieved by skipping rows within scans and reconstructing the x-ray spectromicroscopic measurements using low-rank matrix completion. The new method is robust and allows for 5 to 6-fold reduction in sampling. Experimental results obtained on real data are illustrated.

Multivariate hyperspectral data analytics across length scales to probe compositional, phase, and strain heterogeneities in electrode materials

The origins of performance degradation in batteries can be traced to atomistic phenomena, accumulated at mesoscale dimensions, and compounded up to the level of electrode architectures. Hyperspectral X-ray spectromicroscopy techniques allow for the mapping of compositional variations, and phase separation across length scales with high spatial and energy resolution. We demonstrate the design of workflows combining singular value decomposition, principal-component analysis, k-means clustering, and linear combination fitting, in conjunction with a curated spectral database, to develop high-accuracy quantitative compositional maps of the effective depth of discharge across individual positive electrode particles and ensembles of particles. Using curated reference spectra, accurate and quantitative mapping of inter- and intraparticle compositional heterogeneities, phase separation, and stress gradients is achieved for a canonical phase-transforming positive electrode material, α-V₂O₅. Phase maps from single-particle measurements are used to reconstruct directional stress profiles showcasing the distinctive insights accessible from a standards-informed application of high-dimensional chemical imaging.

Surface chemical heterogeneous distribution in over-lithiated Li1+xCoO2 electrodes

In commercial Li-ion batteries, the internal short circuits or over-lithiation often cause structural transformation in electrodes and may lead to safety risks. Herein, we investigate the over-discharged mechanism of LiCoO₂/graphite pouch cells, especially spatially resolving the morphological, surface phase, and local electronic structure of LiCoO₂ electrode. With synchrotron-based X-ray techniques and Raman mapping, together with spectroscopy simulations, we demonstrate that over-lithiation reaction is a surface effect, accompanied by Co reduction and surface structure transformation to Li₂CoO₂/Co₃O₄/CoO/Li₂O-like phases. This surface chemical distribution variation is relevant to the depth and exposed crystalline planes of LiCoO₂ particles, and the distribution of binder/conductive additives. Theoretical calculations confirm that Li₂CoO₂-phase has lower electronic/ionic conductivity than LiCoO₂-phase, further revealing the critical effect of distribution of conductive additives on the surface chemical heterogeneity evolution. Our findings on such surface phenomena are non-trivial and highlight the capability of synchrotron-based X-ray techniques for studying the spatial chemical phase heterogeneity.

Over-lithiation often causes structural transformation in electrodes and may lead to safety issues in Li-ion batteries. Here, authors investigate the over-discharged mechanism of LiCoO2/graphite pouch cells, and spatially resolve the morphological, surface phase, and local electronic structure of LiCoO2 electrode.

Nanoscale chemical mapping of exometabolites at fungal-mineral interfaces

Mineral-associated organic matter is an integral part of soil carbon pool. Biological processes contribute to the formation of such organo-mineral complexes when soil microbes, and in particular soil fungi, deposit a suite of extracellular metabolic compounds and their necromass on the mineral surfaces. While studied in bulk, micro- to nanoscale fungal-mineral interactions remain elusive. Of particular interest are the mutual effects at the interface between the fungal exometabolites and proximal mineral particles. In this work, we have grown saprotrophic and symbiotic fungi in contact with two soil minerals with contrasting properties: quartz and goethite, on top of X-ray transparent silicon nitride membrane windows and analyzed fungal hyphae by synchrotron-based scanning transmission X-ray microscopy in combination with near edge X-ray fine structure spectroscopy at C(K) and Fe(L) absorption edges. In the resultant chemical maps, we were able to visualize and differentiate organic compounds constituting the fungal cells, their extracellular metabolites, and the exometabolites adsorbing on the minerals. We found that the composition of the exometabolites differed between the fungal functional guilds, particularly, in their sugar to protein ratio and potassium concentration. In samples with quartz and goethite, we observed adsorption of the exometabolic compounds on the mineral surfaces with variations in their chemical composition around the particles. Although we did not observe clear alteration in the exometabolite chemistry upon mineral encounters, we show that fungal-mineral interaction result in reduction of Fe(III) in goethite. This process has been demonstrated for bulk systems, but, to our knowledge, this is the first observation on a single hypha scale offering insight into its underlying biological mechanisms. This demonstrates the link between processes initiated at the single-cell level to macroscale phenomena. Thus, spatially resolved chemical characterization of the microbial-mineral interfaces is crucial for an increased understanding of overall carbon cycling in soil.

The Hard X-ray Nanoprobe beamline at Diamond Light Source

The Hard X-ray Nanoprobe beamline, I14, at Diamond Light Source is a new facility for nanoscale microscopy. The beamline was designed with an emphasis on multi-modal analysis, providing elemental mapping, speciation mapping by XANES, structural phase mapping using nano-XRD and imaging through differential phase contrast and ptychography. The 185 m-long beamline operates over a 5 keV to 23 keV energy range providing a ≤50 nm beam size for routine user experiments and a flexible scanning system allowing fast acquisition. The beamline achieves robust and stable operation by imaging the source in the vertical direction and implementing horizontally deflecting primary optics and an overfilled secondary source in the horizontal direction. This paper describes the design considerations, optical layout, aspects of the hardware engineering and scanning system in operation as well as some examples illustrating the beamline performance.

Iterative X-ray spectroscopic ptychography

Spectroscopic ptychography is a powerful technique to determine the chemical composition of a sample with high spatial resolution. This paper presents a novel algorithm to iteratively solve the spectroscopic blind ptychography problem.

Spectroscopic ptychography is a powerful technique to determine the chemical composition of a sample with high spatial resolution. In spectro-ptychography, a sample is rastered through a focused X-ray beam with varying photon energy so that a series of phaseless diffraction data are recorded. Each chemical component in the material under investigation has a characteristic absorption and phase contrast as a function of photon energy. Using a dictionary formed by the set of contrast functions of each energy for each chemical component, it is possible to obtain the chemical composition of the material from high-resolution multi-spectral images. This paper presents SPA (spectroscopic ptychography with alternating direction method of multipliers), a novel algorithm to iteratively solve the spectroscopic blind ptychography problem. First, a nonlinear spectro-ptychography model based on Poisson maximum likelihood is designed, and then the proposed method is constructed on the basis of fast iterative splitting operators. SPA can be used to retrieve spectral contrast when considering either a known or an incomplete (partially known) dictionary of reference spectra. By coupling the redundancy across different spectral measurements, the proposed algorithm can achieve higher reconstruction quality when compared with standard state-of-the-art two-step methods. It is demonstrated how SPA can recover accurate chemical maps from Poisson-noised measurements, and its enhanced robustness when reconstructing reduced-redundancy ptychography data using large scanning step sizes is shown.

Robust framework and software implementation for fast speciation mapping

One of the greatest benefits of synchrotron radiation is the ability to perform chemical speciation analysis through X-ray absorption spectroscopies (XAS). XAS imaging of large sample areas can be performed with either full-field or raster-scanning modalities. A common practice to reduce acquisition time while decreasing dose and/or increasing spatial resolution is to compare X-ray fluorescence images collected at a few diagnostic energies. Several authors have used different multivariate data processing strategies to establish speciation maps. In this manuscript, the theoretical aspects and assumptions that are often made in the analysis of these datasets are focused on. A robust framework is developed to perform speciation mapping in large bulk samples at high spatial resolution by comparison with known references. Two fully operational software implementations are provided: a user-friendly implementation within the MicroAnalysis Toolkit software, and a dedicated script developed under the R environment. The procedure is exemplified through the study of a cross section of a typical fossil specimen. The algorithm provides accurate speciation and concentration mapping while decreasing the data collection time by typically two or three orders of magnitude compared with the collection of whole spectra at each pixel. Whereas acquisition of spectral datacubes on large areas leads to very high irradiation times and doses, which can considerably lengthen experiments and generate significant alteration of radiation-sensitive materials, this sparse excitation energy procedure brings the total irradiation dose greatly below radiation damage thresholds identified in previous studies. This approach is particularly adapted to the chemical study of heterogeneous radiation-sensitive samples encountered in environmental, material, and life sciences.

Complexation by Organic Matter Controls Uranium Mobility in Anoxic Sediments

Uranium contamination threatens the availability of safe and clean drinking water globally. This toxic element occurs both naturally and as a result of mining and ore-processing in alluvial sediments, where it accumulates as tetravalent U [U(IV)], a form once considered largely immobile. Changing hydrologic and geochemical conditions cause U to be released into groundwater. Knowledge of the chemical form(s) of U(IV) is essential to understand the release mechanism, yet the relevant U(IV) species are poorly characterized. There is growing belief that natural organic matter (OM) binds U(IV) and mediates its fate in the subsurface. In this work, we combined nanoscale imaging (nano secondary ion mass spectrometry and scanning transmission X-ray microscopy) with a density-based fractionation approach to physically and microscopically isolate organic and mineral matter from alluvial sediments contaminated with uranium. We identified two populations of U (dominantly +IV) in anoxic sediments. Uranium was retained on OM and adsorbed to particulate organic carbon, comprising both microbial and plant material. Surprisingly, U was also adsorbed to clay minerals and OM-coated clay minerals. The dominance of OM-associated U provides a framework to understand U mobility in the shallow subsurface, and, in particular, emphasizes roles for desorption and colloid formation in its mobilization.

Integumentary structure and composition in an exceptionally well-preserved hadrosaur (Dinosauria: Ornithischia)

Preserved labile tissues (e.g., skin, muscle) in the fossil record of terrestrial vertebrates are increasingly becoming recognized as an important source of biological and taphonomic information. Here, we combine a variety of synchrotron radiation techniques with scanning electron and optical microscopy to elucidate the structure of 72 million-year-old squamous (scaly) skin from a hadrosaurid dinosaur from the Late Cretaceous of Alberta, Canada. Scanning electron and optical microscopy independently reveal that the three-dimensionally preserved scales are associated with a band of carbon-rich layers up to a total thickness of ∼75 microns, which is topographically and morphologically congruent with the stratum corneum in modern reptiles. Compositionally, this band deviates from that of the surrounding sedimentary matrix; Fourier-transform infrared spectroscopy and soft X-ray spectromicroscopy analyses indicate that carbon appears predominantly as carbonyl in the skin. The regions corresponding to the integumentary layers are distinctively enriched in iron compared to the sedimentary matrix and appear with kaolinite-rich laminae. These hosting carbonyl-rich layers are apparently composed of subcircular bodies resembling preserved cell structures. Each of these structures is encapsulated by calcite/vaterite, with iron predominantly concentrated at its center. The presence of iron, calcite/vaterite and kaolinite may, independently or collectively, have played important roles in the preservation of the layered structures.

Sub-micron level investigation reveals the inaccessibility of stabilized carbon in soil microaggregates

Direct evidence-based approaches are vital to evaluating newly proposed theories on the persistence of soil organic carbon and establishing the contributions of abiotic and biotic controls. Our primary goal was to directly identify the mechanisms of organic carbon stabilization in native-state, free soil microaggregates without disrupting the aggregate microstructure using scanning transmission x-ray microscopy coupled with near edge x-ray absorption fine structure spectroscopy (STXM-NEXAFS). The influence of soil management practices on microaggregate associated-carbon was also assessed. Free, stable soil microaggregates were collected from a tropical agro-ecosystem in Cruz Alta, Brazil. The long-term experimental plots (>25 years) comparing two tillage systems: no-till and till with a complex crop rotation. Based on simultaneously collected multi-elemental associations and speciation, STXM-NEXAFS successfully provided submicron level information on organo-mineral associations. Simple organic carbon sources were found preserved within microaggregates; some still possessing original morphology, suggesting that their stabilization was not entirely governed by the substrate chemistry. Bulk analysis showed higher and younger organic carbon in microaggregates from no-till systems than tilled systems. These results provide direct submicron level evidence that the surrounding environment is involved in stabilizing organic carbon, thus favoring newly proposed concepts on the persistence of soil organic carbon.

Development of small particle speciation for nuclear forensics by soft X-ray scanning transmission spectromicroscopy

Synchrotron radiation spectromicroscopy provides a combination of submicron spatial resolution and chemical sensitivity that is well-suited to analysis of heterogeneous nuclear materials. The chemical and physical characteristics determined by scanning transmission X-ray microscopy (STXM) are complementary to information obtained from standard radiochemical analysis methods. In addition, microscopic quantities of radioactive material can be characterized rapidly by STXM with minimal sample handling and intrusion, especially in the case of particulate materials. The STXM can accommodate a diverse range of samples including wet materials, complex mixtures, and small quantities of material contained in a larger matrix. In these cases, the inventory of species present in a sample is likely to carry information on its process history; STXM has the demonstrated capability to identify contaminants and sample matrices. Operating in the soft X-ray regime provides particular sensitivity to the chemical state of specimens containing low-Z materials, via the K-edges of light elements. Here, recent developments in forensics-themed spectromicroscopy, sample preparation, and data acquisition methods at the Molecular Environmental Science Beamline 11.0.2 of the Advanced Light Source are described. Results from several initial studies are presented, demonstrating the capability to identify the distribution of the species present in heterogeneous uranium-bearing materials. Future opportunities for STXM forensic studies and potential methodology development are discussed.

Preservation of organic matter in marine sediments by inner-sphere interactions with reactive iron

Interactions between organic matter and mineral matrices are critical to the preservation of soil and sediment organic matter. In addition to clay minerals, Fe(III) oxides particles have recently been shown to be responsible for the protection and burial of a large fraction of sedimentary organic carbon (OC). Through a combination of synchrotron X-ray techniques and high-resolution images of intact sediment particles, we assessed the mechanism of interaction between OC and iron, as well as the composition of organic matter co-localized with ferric iron. We present scanning transmission x-ray microscopy images at the Fe L₃ and C K₁ edges showing that the organic matter co-localized with Fe(III) consists primarily of C=C, C=O and C-OH functional groups. Coupling the co-localization results to iron K-edge X-ray absorption spectroscopy fitting results allowed to quantify the relative contribution of OC-complexed Fe to the total sediment iron and reactive iron pools, showing that 25–62% of total reactive iron is directly associated to OC through inner-sphere complexation in coastal sediments, as much as four times more than in low OC deep sea sediments. Direct inner-sphere complexation between OC and iron oxides (Fe-O-C) is responsible for transferring a large quantity of reduced OC to the sedimentary sink, which could otherwise be oxidized back to CO₂.

Uranium(IV) adsorption by natural organic matter in anoxic sediments

Uranium is an important carbon-free fuel source and environmental contaminant that accumulates in the tetravalent state, U(IV), in anoxic sediments, such as ore deposits, marine basins, and contaminated aquifers. However, little is known about the speciation of U(IV) in low-temperature geochemical environments, inhibiting the development of a conceptual model of U behavior. Until recently, U(IV) was assumed to exist predominantly as the sparingly soluble mineral uraninite (UO_2+x) in anoxic sediments; however, studies now show that this is not often the case. Yet a model of U(IV) speciation in the absence of mineral formation under field-relevant conditions has not yet been developed. Uranium(IV) speciation controls its reactivity, particularly its susceptibility to oxidative mobilization, impacting its distribution and toxicity. Here we show adsorption to organic carbon and organic carbon-coated clays dominate U(IV) speciation in an organic-rich natural substrate under field-relevant conditions. Whereas previous research assumed that U(IV) speciation is dictated by the mode of reduction (i.e., whether reduction is mediated by microbes or by inorganic reductants), our results demonstrate that mineral formation can be diminished in favor of adsorption, regardless of reduction pathway. Projections of U transport and bioavailability, and thus its threat to human and ecosystem health, must consider U(IV) adsorption to organic matter within the sediment environment.

Nanobubbles at Hydrophilic Particle-Water Interfaces

The puzzling persistence of nanobubbles breaks Laplace's law for bubbles, which is of great interest for promising applications in surface processing, H₂ and CO₂ storage, water treatment, and drug delivery. So far, nanobubbles have mostly been reported on hydrophobic planar substrates with atomic flatness. It remains a challenge to quantify nanobubbles on rough and irregular surfaces because of the lack of a characterization technique that can detect both the nanobubble morphology and chemical composition inside individual nanobubble-like objects. Here, by using synchrotron-based scanning transmission soft X-ray microscopy (STXM) with nanometer resolution, we discern nanoscopic gas bubbles of >25 nm with direct in situ proof of O₂ inside the nanobubbles at a hydrophilic particle-water interface under ambient conditions. We find a stable cloud of O₂ nanobubbles at the diatomite particle-water interface hours after oxygen aeration and temperature variation. The in situ technique may be useful for many surface nanobubble-related studies such as material preparation and property manipulation, phase equilibrium, nucleation kinetics, and relationships with chemical composition within the confined nanoscale space. The oxygen nanobubble clouds may be important in modifying particle-water interfaces and offering breakthrough technologies for oxygen delivery in sediment and/or deep water environments.

Assessing adsorption of polycyclic aromatic hydrocarbons on Rhizopus oryzae cell wall components with water-methanol cosolvent model

The contribution of different fungal cell wall components in adsorption of polycyclic aromatic hydrocarbons (PAHs) is still unclear. We isolated Rhizopus oryzae cell walls components with sequential extraction, characterized functional groups with NEXAFS spectra, and determined partition coefficients of PAHs on cell walls and cell wall components with cosolvent model. Spectra of NEXAFS indicated that isolated cell walls components were featured with peaks at ~532.7 and ~534.5eV energy. The lipid cosolvent partition coefficients were approximately one order of magnitude higher than the corresponding carbohydrate cosolvent partition coefficients. The partition coefficients for four tested carbohydrates varied at approximate 0.5 logarithmic units. Partition coefficients between biosorbents and water calculated based cosolvent models ranged from 0.8 to 4.2. The present study proved the importance of fungal cell wall components in adsorption of PAHs, and consequently the role of fungi in PAHs bioremediation.

Non-negative matrix analysis in x-ray spectromicroscopy: choosing regularizers

In x-ray spectromicroscopy, a set of images can be acquired across an absorption edge to reveal chemical speciation. We previously described the use of non-negative matrix approximation methods for improved classification and analysis of these types of data. We present here an approach to find appropriate values of regularization parameters for this optimization approach.

Deciphering the Complex Chemistry of Deep-Ocean Particles Using Complementary Synchrotron X-ray Microscope and Microprobe Instruments

The reactivity and mobility of natural particles in aquatic systems have wide ranging implications for the functioning of Earth surface systems. Particles in the ocean are biologically and chemically reactive, mobile, and complex in composition. The chemical composition of marine particles is thought to be central to understanding processes that convert globally relevant elements, such as C and Fe, among forms with varying bioavailability and mobility in the ocean. The analytical tools needed to measure the complex chemistry of natural particles are the subject of this Account. We describe how a suite of complementary synchrotron radiation instruments with nano- and micrometer focusing, and X-ray absorption spectroscopy (XAS) and X-ray diffraction (XRD) capabilities are changing our understanding of deep-ocean chemistry and life. Submarine venting along mid-ocean ridges creates hydrothermal plumes where dynamic particle-forming reactions occur as vent fluids mix with deep-ocean waters. Whether plumes are net sources or sinks of elements in ocean budgets depends in large part on particle formation, reactivity, and transport properties. Hydrothermal plume particles have been shown to host microbial communities and exhibit complex size distributions, aggregation behavior, and composition. X-ray microscope and microprobe instruments can address particle size and aggregation, but their true strength is in measuring chemical composition. Plume particles comprise a stunning array of inorganic and organic phases, from single-crystal sulfides to poorly ordered nanophases and polymeric organic matrices to microbial cells. X-ray microscopes and X-ray microprobes with elemental imaging, XAS, and XRD capabilities are ideal for investigating these complex materials because they can (1) measure the chemistry of organic and inorganic constituents in complex matrices, usually within the same particle or aggregate, (2) provide strong signal-to-noise data with exceedingly small amounts of material, (3) simplify the chemical complexity of particles or sets of particles with a focused-beam, providing spatial resolution over 6 orders of magnitude (nanometer to millimeter), (4) provide elemental specificity for elements in the soft-, tender-, and hard-X-ray energies, (5) switch rapidly among elements of interest, and (6) function in the presence of water and gases. Synchrotron derived data sets are discussed in the context of important advances in deep-ocean technology, sample handling and preservation, molecular microbiology, and coupled physical-chemical-biological modeling. Particle chemistry, size, and morphology are all important in determining whether particles are reactive with dissolved constituents, provide substrates for microbial respiration and growth, and are delivered to marine sediments or dispersed by deep-ocean currents.

Chemical imaging of single catalyst particles with scanning μ-XANES-CT and μ-XRF-CT

The physicochemical state of a catalyst is a key factor in determining both activity and selectivity; however these materials are often not structurally or compositionally homogeneous. Here we report on the 3-dimensional imaging of an industrial catalyst, Mo-promoted colloidal Pt supported on carbon. The distribution of both the active Pt species and Mo promoter have been mapped over a single particle of catalyst using microfocus X-ray fluorescence computed tomography. X-ray absorption near edge spectroscopy (XANES) and extended X-ray absorption fine structure revealed a mixed local coordination environment, including the presence of both metallic Pt clusters and Pt chloride species, but also no direct interaction between the catalyst and Mo promoter. We also report on the benefits of scanning μ-XANES computed tomography for chemical imaging, allowing for 2- and 3-dimensional mapping of the local electronic and geometric environment, in this instance for both the Pt catalyst and Mo promoter throughout the catalyst particle.

Direct in vivo imaging of ferrous iron dyshomeostasis in ageing Caenorhabditis elegans

Iron is essential for eukaryotic biochemistry. Systematic trafficking and storage is required to maintain supply of iron while preventing it from catalysing unwanted reactions, particularly the generation of oxidising reactive species. Iron dyshomeostasis has been implicated in major age-associated diseases including cancers, neurodegeneration and heart disease. Here, we employ population-level X-ray fluorescence imaging and native-metalloproteomic analysis to determine that altered iron coordination and distribution is a pathological imperative of ageing in the nematode, Caenorhabditis elegans. Our approach provides a method to simultaneously study iron metabolism across different scales of biological organisation, from populations to cells. Here we report how and where iron homeostasis is lost during C. elegans ageing, and its relationship to the age-related elevation of damaging reactive oxygen species. We find that wild types utilise ferritin to sustain longevity, buffering against exogenous iron and showing rapid ageing if ferritin is ablated. After reproduction, escape of iron from safe-storage in ferritin raised cellular Fe2+ load in the ageing C. elegans, and increased generation of reactive species. These findings support the hypothesis that iron-mediated processes drive senescence. We propose that loss of iron homeostasis may be a fundamental and inescapable consequence of ageing that could represent a critical target for therapeutic strategies to improve health outcomes in ageing.

Correlative electron and X-ray microscopy: probing chemistry and bonding with high spatial resolution

Two powerful and complementary techniques for chemical characterisation of nanoscale systems are electron energy-loss spectroscopy in the scanning transmission electron microscope, and X-ray absorption spectroscopy in the scanning transmission X-ray microscope. A correlative approach to spectro-microscopy may not only bridge the gaps in spatial and spectral resolution which exist between the two instruments, but also offer unique opportunities for nanoscale characterisation. This review will discuss the similarities of the two spectroscopy techniques and the state of the art for each microscope. Case studies have been selected to illustrate the benefits and limitations of correlative electron and X-ray microscopy techniques. In situ techniques and radiation damage are also discussed.

Validating the scalability of soft X-ray spectromicroscopy for quantitative soil ecology and biogeochemistry research

Synchrotron-based soft-X-ray scanning transmission X-ray microscopy (STXM) has the potential to provide nanoscale resolution of the associations among biological and geological materials. However, standard methods for how samples should be prepared, measured, and analyzed to allow the results from these nanoscale imaging and spectroscopic tools to be scaled to field scale biogeochemical results are not well established. We utilized a simple sample preparation technique that allows one to assess detailed mineral, metal, and microbe spectroscopic information at the nano- and microscale in soil colloids. We then evaluated three common approaches to collect and process nano- and micronscale information by STXM and the correspondence of these approaches to millimeter scale soil measurements. Finally, we assessed the reproducibility and spatial autocorrelation of nano- and micronscale protein, Fe(II) and Fe(III) densities in a soil sample. We demonstrate that linear combination fitting of entire spectra provides slightly different Fe(II) mineral densities compared to image resonance difference mapping but that difference mapping results are highly reproducible between among sample replicates. Further, STXM results scale to the mm scale in complex systems with an approximate geospatial range of 3 μm in these samples.

Investigation of soil legacy phosphorus transformation in long-term agricultural fields using sequential fractionation, P K-edge XANES and solution P NMR spectroscopy

Understanding legacy phosphorus (P) build-up and draw-down from long-term fertilization is essential for effective P management. Using replicated plots from Saskatchewan, Canada, with P fertilization from 1967 to 1995 followed by either P fertilization or P cessation (1995-2010), soil P was characterized in surface and subsurface layers using sequential fractionation, P K-edge X-ray absorption near-edge structure (XANES) and solution (31)P nuclear magnetic resonance (P NMR) spectroscopy. Legacy P from a 28-year build-up was sufficient for 15 years of wheat cultivation, resulting in no significant differences in crop yield in 2010. In surface soils, soil test (Olsen) P decreased significantly in unfertilized plots compared with 1995, which was reflected in declining aluminum (hydr)oxide-associated inorganic P by fractionation and XANES. Furthermore, XANES analysis revealed a decrease of calcium-associated P in 2010-unfertilized soils at both depths and an increase of Fe (hydr)oxides-associated P in the 2010-fertilized and -unfertilized surface soils relative to the 1995 soils. Increased total organic P and orthophosphate diesters by P NMR and accumulated inositol hexaphosphate by XANES were observed in surface soils with P fertilization cessation. In subsurface soils, few legacy P transformations were detected. These results provide important information about legacy P to improve agricultural sustainability while mitigating water quality deterioration.

Direct and up-close views of plant cell walls show a leading role for lignin-modifying enzymes on ensuing xylanases

BACKGROUND

A key barrier that limits the full potential of biological processes to create new, sustainable materials and fuels from plant fibre is limited enzyme accessibility to polysaccharides and lignin that characterize lignocellulose networks. Moreover, the heterogeneity of lignocellulosic substrates means that different enzyme combinations might be required for efficient transformation of different plant resources. Analytical techniques with high chemical sensitivity and spatial resolution that permit direct characterization of solid samples could help overcome these challenges by allowing direct visualization of enzyme action within plant fibre, thereby identify barriers to enzyme action.

RESULTS

In the current study, the high spatial resolution (about 30 nm) of scanning transmission X-ray microscopy (STXM), and the detection sensitivity (ppm) of time-of-flight secondary ion mass spectrometry (ToF-SIMS), were harnessed for the first time to investigate the progression of laccase, cellulase and xylanase activities through wood samples, and to evaluate complementary action between lignin-modifying and polysaccharide-degrading enzymes. In particular, complementary insights from the STXM and ToF-SIMS analyses revealed the key role of laccase in promoting xylanase activity throughout and between plant cell walls.

CONCLUSIONS

The spatial resolution of STXM clearly revealed time-dependent progression and spatial distribution of laccase and xylanase activities, whereas ToF-SIMS analyses confirmed that laccase promoted protein penetration into fibre samples, leading to an overall increase in polysaccharide degradation. Spectromicroscopic visualizations of plant cell wall chemistry allowed simultaneous tracking of changes to lignin and polysaccharide contents, which provides new possibilities for investigating the complementary roles of lignin-modifying and carbohydrate-active enzymes.

Nano-scale spatial assessment of calcium distribution in coccolithophores using synchrotron-based nano-CT and STXM-NEXAFS

Calcified coccolithophores generate calcium carbonate scales around their cell surface. In light of predicted climate change and the global carbon cycle, the biomineralization ability of coccoliths has received growing interest. However, the underlying biomineralization mechanism is not yet well understood; the lack of non-invasive characterizing tools to obtain molecular level information involving biogenic processes and biomineral components remain significant challenges. In the present study, synchrotron-based Nano-computed Tomography (Nano-CT) and Scanning Transmission X-ray Microscopy-Near-edge X-ray Absorption Fine Structure Spectromicroscopy (STXM-NEXAFS) techniques were employed to identify Ca spatial distribution and investigate the compositional chemistry and distinctive features of the association between biomacromolecules and mineral components of calcite present in coccoliths. The Nano-CT results show that the coccolith scale vesicle is similar as a continuous single channel. The mature coccoliths were intracellularly distributed and immediately ejected and located at the exterior surface to form a coccoshpere. The NEXAFS spectromicroscopy results of the Ca L edge clearly demonstrate the existence of two levels of gradients spatially, indicating two distinctive forms of Ca in coccoliths: a crystalline-poor layer surrounded by a relatively crystalline-rich layer. The results show that Sr is absorbed by the coccoliths and that Sr/Ca substitution is rather homogeneous within the coccoliths. Our findings indicate that synchrotron-based STXM-NEXAFS and Nano-CT are excellent tools for the study of biominerals and provide information to clarify biomineralization mechanism.

ScatterJ: An ImageJ plugin for the evaluation of analytical microscopy datasets

We present ScatterJ, an ImageJ plugin that allows for extracting qualitative as well as quantitative information from analytical microscopy datasets. A large variety of analytical microscopy methods are used to obtain spatially resolved chemical information. The resulting datasets are often large and complex, and can contain information that is not obvious or directly accessible. ScatterJ extends and complements existing methods to extract information on correlation and colocalization from pairs of species-specific or element-specific maps. We demonstrate the possibilities to extract information using example datasets from biogeochemical studies, although the plugin is not restricted to this type of research. The information that we could extract from our existing data helped to further our understanding of biogeochemical processes such as mineral formation or heavy metal sorption. ScatterJ can be used for a variety of different two-dimensional (2D) and three-dimensional (3D) datasets such as energy-dispersive X-ray spectroscopy maps, 3D confocal laser scanning microscopy maps, and 2D scanning transmission X-ray microscopy maps.

Non-negative matrix analysis for effective feature extraction in X-ray spectromicroscopy

X-Ray absorption spectromicroscopy provides rich information on the chemical organization of materials down to the nanoscale. However, interpretation of this information in studies of "natural" materials such as biological or environmental science specimens can be complicated by the complex mixtures of spectroscopically complicated materials present. We describe here the shortcomings that sometimes arise in previously-employed approaches such as cluster analysis, and we present a new approach based on non-negative matrix approximation (NNMA) analysis with both sparseness and cluster-similarity regularizations. In a preliminary study of the large-scale biochemical organization of human spermatozoa, NNMA analysis delivers results that nicely show the major features of spermatozoa with no physically erroneous negative weightings or thicknesses in the calculated image.

MANTiS: a program for the analysis of X-ray spectromicroscopy data

Spectromicroscopy combines spectral data with microscopy, where typical datasets consist of a stack of images taken across a range of energies over a microscopic region of the sample. Manual analysis of these complex datasets can be time-consuming, and can miss the important traits in the data. With this in mind we have developed MANTiS, an open-source tool developed in Python for spectromicroscopy data analysis. The backbone of the package involves principal component analysis and cluster analysis, classifying pixels according to spectral similarity. Our goal is to provide a data analysis tool which is comprehensive, yet intuitive and easy to use. MANTiS is designed to lead the user through the analysis using story boards that describe each step in detail so that both experienced users and beginners are able to analyze their own data independently. These capabilities are illustrated through analysis of hard X-ray imaging of iron in Roman ceramics, and soft X-ray imaging of a malaria-infected red blood cell.

Soft X-ray spectromicroscopy for speciation, quantitation and nano-eco-toxicology of nanomaterials

There is a critical need for methods that provide simultaneous detection, identification, quantitation and visualization of nanomaterials at their interface with biological and environmental systems. The approach should allow speciation as well as elemental analysis. Using the intrinsic X-ray absorption properties, soft X-ray scanning transmission X-ray spectromicroscopy (STXM) allows characterization and imaging of a broad range of nanomaterials, including metals, oxides and organic materials, and at the same time is able to provide detailed mapping of biological components. Thus, STXM offers considerable potential for application to research on nanomaterials in biology and the environment. The potential and limitations of STXM in this context are discussed using a range of examples, focusing on the interaction of nanomaterials with microbial cells, biofilms and extracellular polymers. The studies outlined include speciation and mapping of metal-containing nanomaterials (Ti, Ni, Cu) and carbon-based nanomaterials (multiwalled carbon nanotubes, C60 fullerene). The benefits of X-ray fluorescence detection in soft X-ray STXM are illustrated with a study of low levels of Ni in a natural river biofilm.

Unsupervised cell identification on multidimensional X-ray fluorescence datasets

A novel approach to locate, identify and refine positions and whole areas of cell structures based on elemental contents measured by X-ray fluorescence microscopy is introduced. It is shown that, by initializing with only a handful of prototypical cell regions, this approach can obtain consistent identification of whole cells, even when cells are overlapping, without training by explicit annotation. It is robust both to different measurements on the same sample and to different initializations. This effort provides a versatile framework to identify targeted cellular structures from datasets too complex for manual analysis, like most X-ray fluorescence microscopy data. Possible future extensions are also discussed.

Dynamic imaging using ptychography

We demonstrate through experiment an example of "mixed state" reconstruction using x-ray ptychography. We demonstrate successful imaging of a vibrating sample that has dynamics that are of one order magnitude faster than the measurement times. We show how increased vibrational amplitude leads to an increased population of illumination modes, a characteristic of partial coherence. Implications of a vibrating sample are explored, with its possible use in manipulating coherent wave field mode shapes and coherence properties.

Speciation of metal(loid)s in environmental samples by X-ray absorption spectroscopy: a critical review

Element specificity is one of the key factors underlying the widespread use and acceptance of X-ray absorption spectroscopy (XAS) as a research tool in the environmental and geo-sciences. Independent of physical state (solid, liquid, gas), XAS analyses of metal(loid)s in complex environmental matrices over the past two decades have provided important information about speciation at environmentally relevant interfaces (e.g. solid-liquid) as well as in different media: plant tissues, rhizosphere, soils, sediments, ores, mineral process tailings, etc. Limited sample preparation requirements, the concomitant ability to preserve original physical and chemical states, and independence from crystallinity add to the advantages of using XAS in environmental investigations. Interpretations of XAS data are founded on sound physical and statistical models that can be applied to spectra of reference materials and mixed phases, respectively. For spectra collected directly from environmental matrices, abstract factor analysis and linear combination fitting provide the means to ascertain chemical, bonding, and crystalline states, and to extract quantitative information about their distribution within the data set. Through advances in optics, detectors, and data processing, X-ray fluorescence microprobes capable of focusing X-rays to micro- and nano-meter size have become competitive research venues for resolving the complexity of environmental samples at their inherent scale. The application of μ-XANES imaging, a new combinatorial approach of X-ray fluorescence spectrometry and XANES spectroscopy at the micron scale, is one of the latest technological advances allowing for lateral resolution of chemical states over wide areas due to vastly improved data processing and detector technology.

Microscale investigations of the fate of heavy metals associated to iron-bearing particles in a highly polluted stream

As it flows through a dense steelmaking area, the Fensch River does transport iron-rich particles and colloids, displaying high contents in metallic contaminants (Zn, Cr, Pb, Cu, Ni, and As). Chemical analysis using inductively coupled plasma mass spectrometry (ICP-MS) was carried out on three compartments-waters, suspended materials, and sediments-along the river linear. The variations of metallic trace element concentrations along the river were shown to be partially related to external inputs (industrial and domestic wastewaters and urban surfaces leaching). However, some discrepancies of element partitioning were evidenced. Pb, Cu, and Mn tend to concentrate in suspended particulate and in dissolved fraction, while Cr and As follow the trend of Fe and concentrate within sediments of the most downstream station, just before the junction with Moselle waters. Zn appears strongly associated to iron-rich particles, resulting in a decrease of its concentration in waters for the last station. Along the Fensch linear, the variation of metal partitioning between water and particulate phases is accompanied with strong modifications of the nature and mineralogy of iron-rich particles, as evidenced by microanalyses using electron and X-ray beams. The combination of bulk analyses using ICP-MS and microanalyses applied to the three compartments allowed us to propose a three-step process "settling-weathering-resuspension" to explain Zn partitioning.

Combining µXANES and µXRD mapping to analyse the heterogeneity in calcium carbonate granules excreted by the earthworm Lumbricus terrestris

The use of fluorescence full spectral micro-X-ray absorption near-edge structure (µXANES) mapping is becoming more widespread in the hard energy regime. This experimental method using the Ca K-edge combined with micro-X-ray diffraction (µXRD) mapping of the same sample has been enabled on beamline I18 at Diamond Light Source. This combined approach has been used to probe both long- and short-range order in calcium carbonate granules produced by the earthworm Lumbricus terrestris. In granules produced by earthworms cultured in a control artificial soil, calcite and vaterite are observed in the granules. However, granules produced by earthworms cultivated in the same artificial soil amended with 500 p.p.m. Mg also contain an aragonite. The two techniques, µXRD and µXANES, probe different sample volumes but there is good agreement in the phase maps produced.

Microscale speciation of arsenic and iron in ferric-based sorbents subjected to simulated landfill conditions

During treatment for potable use, water utilities generate arsenic-bearing ferric wastes that are subsequently dispatched to landfills. The biogeochemical weathering of these residuals in mature landfills affects the potential mobilization of sorbed arsenic species via desorption from solids subjected to phase transformations driven by abundant organic matter and bacterial activity. Such processes are not simulated with the toxicity characteristic leaching procedure (TCLP) currently used to characterize hazard. To examine the effect of sulfate on As retention in landfill leachate, columns of As(V) loaded amorphous ferric hydroxide were reacted biotically at two leachate sulfate concentrations (0.064 mM and 2.1 mM). After 300 days, ferric sorbents were reductively dissolved. Arsenic released to porewaters was partially coprecipitated in mixed-valent secondary iron phases whose speciation was dependent on sulfate concentration. As and Fe XAS showed that, in the low sulfate column, 75-81% of As(V) was reduced to As(III), and 53-68% of the Fe(III) sorbent was transformed, dominantly to siderite and green rust. In the high sulfate column, Fe(III) solids were reduced principally to FeS(am), whereas As(V) was reduced to a polymeric sulfide with local atomic structure of realgar. Multienergy micro-X-ray fluorescence (ME-μXRF) imaging at Fe and As K-edges showed that As formed surface complexes with ferrihydrite > siderite > green rust in the low sulfate column; while discrete realgar-like phases formed in the high sulfate systems. Results indicate that landfill sulfur chemistry exerts strong control over the potential mobilization of As from ferric sorbent residuals by controlling secondary As and Fe sulfide coprecipitate formation.

Rapid and accurate analysis of an X-ray fluorescence microscopy data set through gaussian mixture-based soft clustering methods

X-ray fluorescence (XRF) microscopy is an important tool for studying trace metals in biology, enabling simultaneous detection of multiple elements of interest and allowing quantification of metals in organelles without the need for subcellular fractionation. Currently, analysis of XRF images is often done using manually defined regions of interest (ROIs). However, since advances in synchrotron instrumentation have enabled the collection of very large data sets encompassing hundreds of cells, manual approaches are becoming increasingly impractical. We describe here the use of soft clustering to identify cell ROIs based on elemental contents, using data collected over a sample of the malaria parasite Plasmodium falciparum as a test case. Soft clustering was able to successfully classify regions in infected erythrocytes as “parasite,” “food vacuole,” “host,” or “background.” In contrast, hard clustering using the k-means algorithm was found to have difficulty in distinguishing cells from background.While initial tests showed convergence on two or three distinct solutions in 60% of the cells studied, subsequent modifications to the clustering routine improved results to yield 100% consistency in image segmentation. Data extracted using soft cluster ROIs were found to be as accurate as data extracted using manually defined ROIs, and analysis time was considerably improved.

Inside and Outside: X-ray Absorption Spectroscopy Mapping of Chemical Domains in Graphene Oxide

The oxidative chemistry of graphite has been investigated for over 150 years and has attracted renewed interest given the importance of exfoliated graphene oxide as a precursor to chemically derived graphene. However, the bond connectivities, steric orientations, and spatial distribution of functional groups remain to be unequivocally determined for this highly inhomogeneous nonstoichiometric material. Here, we demonstrate the application of principal component analysis to scanning transmission X-ray microscopy data for the construction of detailed real space chemical maps of graphene oxide. These chemical maps indicate very distinct functionalization motifs at the edges and interiors and, in conjunction with angle-resolved near-edge X-ray absorption fine structure spectroscopy, enable determination of the spatial location and orientations of functional groups. Chemical imaging of graphene oxide provides experimental validation of the modified Lerf-Klinowski structural model. Specifically, we note increased contributions from carboxylic acid moieties at edge sites with epoxide and hydroxyl species dominant within the interior domains.

Mesoscale phase distribution in single particles of LiFePO4 following lithium deintercalation

The chemical phase distribution in hydrothermally grown micrometric single crystals LiFePO4 following partial chemical delithiation was investigated. Full field and scanning X-ray microscopy were combined with X-ray absorption spectroscopy at the Fe K- and O K-edges, respectively, to produce maps with high chemical and spatial resolution. The resulting information was compared to morphological insight into the mechanics of the transformation by scanning transmission electron microscopy. This study revealed the interplay at the mesocale between microstructure and phase distribution during the redox process, as morphological defects were found to kinetically determine the progress of the reaction. Lithium deintercalation was also found to induce severe mechanical damage in the crystals, presumably due to the lattice mismatch between LiFePO4 and FePO4. Our results lead to the conclusion that rational design of intercalation-based electrode materials, such as LiFePO4, with optimized utilization and life requires the tailoring of particles that minimize kinetic barriers and mechanical strain. Coupling TXM-XANES with TEM can provide unique insight into the behavior of electrode materials during operation, at scales spanning from nanoparticles to ensembles and complex architectures.

Nanometer-scale characterization of exceptionally preserved bacterial fossils in Paleocene phosphorites from Ouled Abdoun (Morocco)

Micrometer-sized spherical and rod-shaped forms have been reported in many phosphorites and often interpreted as microbes fossilized by apatite, based on their morphologic resemblance with modern bacteria inferred by scanning electron microscopy (SEM) observations. This interpretation supports models involving bacteria in the formation of phosphorites. Here, we studied a phosphatic coprolite of Paleocene age originating from the Ouled Abdoun phosphate basin (Morocco) down to the nanometer-scale using focused ion beam milling, transmission electron microscopy (TEM), and scanning transmission x-ray microscopy (STXM) coupled with x-ray absorption near-edge structure spectroscopy (XANES). The coprolite, exclusively composed of francolite (a carbonate-fluroapatite), is formed by the accumulation of spherical objects, delimited by a thin envelope, and whose apparent diameters are between 0.5 and 3 μm. The envelope of the spheres is composed of a continuous crown dense to electrons, which measures 20-40 nm in thickness. It is surrounded by two thinner layers that are more porous and transparent to electrons and enriched in organic carbon. The observed spherical objects are very similar with bacteria encrusting in hydroxyapatite as observed in laboratory experiments. We suggest that they are Gram-negative bacteria fossilized by francolite, the precipitation of which started within the periplasm of the cells. We discuss the role of bacteria in the fossilization mechanism and propose that they could have played an active role in the formation of francolite. This study shows that ancient phosphorites can contain fossil biological subcellular structures as fine as a bacterial periplasm. Moreover, we demonstrate that while morphological information provided by SEM analyses is valuable, the use of additional nanoscale analyses is a powerful approach to help inferring the biogenicity of biomorphs found in phosphorites. A more systematic use of this approach could considerably improve our knowledge and understanding of the microfossils present in the geological record.

Micro- and nano-environments of C sequestration in soil: a multi-elemental STXM-NEXAFS assessment of black C and organomineral associations

Black C is an essential component of the terrestrial C pool and its formation is often credited as a CO(2) sink by transferring the fast-cycling C from the atmosphere-biosphere system into slower cycling C in the geosphere. This study is the first multi-element K- (C, N, Ca, Fe, Al and Si) soft-X-ray STXM-NEXAFS investigation conducted at a submicron-scale spatial resolution specifically targeting black C and its interaction with the mineral and non-black C organic matter in the organomineral assemblage. The STXM-NEXAFS micrographs and spectra demonstrated that pyrogenic C was dominated by quinoide, aromatic, phenol, ketone, alcohol, carboxylic and hydroxylated- and ether-linked C species. There was also evidence for the presence of pyridinic, pyridonic, pyrrolic, amine and nitril N functionalities. The non-black C organic matter contained amino acids, amino sugars, nucleic acids and polysaccharides known to exhibit negatively charged carboxylic, phenolic, enolic, thiolate and phosphate functionalities highly reactive towards metal ions and black C. The metal-rich mineral matrix was composed of phyllosilicate clay minerals, Fe and Al hydroxypolycations, oxides, hydroxides and oxyhydroxide that can attract and bind organic biopolymers. STXM-NEXAFS provided evidence for interactive association between pyrogenic C, non-black C organic matter and the mineral oxide and oxyhydroxide communities in the organomineral interface. These intimate associations occurred through a "two-way" direct linkage between black C and the mineral or non-black C organic matter or via a "three-way" indirect association where non-black C organic matter could serve as a molecular cross-linking agent binding black C with the mineral matrix or vice versa where inorganic oxides, hydroxides and polycations could act as a bridge to bind black C with non-black C organic matter. The binding and sequestration of black C in the investigated micro- and nano-C repository environments seem to be the combined action of physical entrapment in seemingly terminal biotic exclusion zone through the action of metal oxides and organic matter induced microaggregation and through molecular-level association ranging from ligand exchange, polyvalent cation bridging to weak hydrophobic interactions including van der Waals and H-bonding.