Nonlinear Effects Induced by Interactions among Functional Groups of Bacteria and Fungi Regulate the Priming Effect in Malagasy Soils.

The priming effect (PE) occurs when fresh organic matter (FOM) supplied to soil alters the rate of decomposition of older soil organic matter (SOM). The PE can be generated by different mechanisms driven by interactions between microorganisms with different live strategies and decomposition abilities. Among those, stoichiometric decomposition results from FOM decomposition, which induces the decomposition of SOM by the release of exoenzymes by FOM-decomposers. Nutrient mining results from the co-metabolism of energy-rich FOM with nutrient-rich SOM by SOM-decomposers. While existing statistical approaches enable measurement of the effect of community composition (linear effect) on the PE, the effect of interactions among co-occurring populations (non-linear effect) is more difficult to grasp. We compare a non-linear, clustering approach with a strictly linear approach to separately and comprehensively capture all linear and non-linear effects induced by soil microbial populations on the PE and to identify the species involved. We used an already published data set, acquired from two climatic transects of Madagascar Highlands, in which the high-throughput sequencing of soil samples was applied parallel to the analysis of the potential capacity of microbial communities to generate PE following a 13C-labeled wheat straw input. The linear and clustering approaches highlight two different aspects of the effects of microbial biodiversity on SOM decomposition. The comparison of the results enabled identification of bacterial and fungal families, and combinations of families, inducing either a linear, a non-linear, or no effect on PE after incubation. Bacterial families mainly favoured a PE proportional to their relative abundances in soil (linear effect). Inversely, fungal families induced strong non-linear effects resulting from interactions among them and with bacteria. Our findings suggest that bacteria support stoichiometric decomposition in the first days of incubation, while fungi support mainly the nutrient mining of soil's organic matter several weeks after the beginning of incubation. Used together, the clustering and linear approaches therefore enable the estimation of the relative importance of linear effects related to microbial relative abundances, and non-linear effects related to interactions among microbial populations on soil properties. Both approaches also enable the identification of key microbial families that mainly regulate soil properties.

Multiscale Analysis of Metal Oxide Nanoparticles in Tissue: Insights into Biodistribution and Biotransformation.

Metal oxide nanoparticles have emerged as exceptionally potent biomedical sensors and actuators due to their unique physicochemical features. Despite fascinating achievements, the current limited understanding of the molecular interplay between nanoparticles and the surrounding tissue remains a major obstacle in the rationalized development of nanomedicines, which is reflected in their poor clinical approval rate. This work reports on the nanoscopic characterization of inorganic nanoparticles in tissue by the example of complex metal oxide nanoparticle hybrids consisting of crystalline cerium oxide and the biodegradable ceramic bioglass. A validated analytical method based on semiquantitative X-ray fluorescence and inductively coupled plasma spectrometry is used to assess nanoparticle biodistribution following intravenous and topical application. Then, a correlative multiscale analytical cascade based on a combination of microscopy and spectroscopy techniques shows that the topically applied hybrid nanoparticles remain at the initial site and are preferentially taken up into macrophages, form apatite on their surface, and lead to increased accumulation of lipids in their surroundings. Taken together, this work displays how modern analytical techniques can be harnessed to gain unprecedented insights into the biodistribution and biotransformation of complex inorganic nanoparticles. Such nanoscopic characterization is imperative for the rationalized engineering of safe and efficacious nanoparticle-based systems.

Tuning graphene transistors through ad hoc electrostatics induced by a nanometer-thick molecular underlayer.

We report on the modulation of the electrical properties of graphene-based transistors that mirror the properties of a few nanometers thick layer made of dipolar molecules sandwiched in between the 2D material and the SiO2 dielectric substrate. The chemical composition of the films of quinonemonoimine zwitterion molecules adsorbed onto SiO2 has been explored by means of X-ray photoemission and mass spectroscopy. Graphene-based devices are then fabricated by transferring the 2D material onto the molecular film, followed by the deposition of top source-drain electrodes. The degree of supramolecular order in disordered films of dipolar molecules was found to be partially improved as a result of the electric field at low temperatures, as revealed by the emergence of hysteresis in the transfer curves of the transistors. The use of molecules from the same family, which are suitably designed to interact with the dielectric surface, results in the disappearance of the hysteresis. DFT calculations confirm that the dressing of the molecules by an external electric field exhibits multiple minimal energy landscapes that explain the thermally stabilized capacitive coupling observed. This study demonstrates that the design and exploitation of ad hoc molecules as an interlayer between a dielectric substrate and graphene represents a powerful tool for tuning the electrical properties of the 2D material. Conversely, graphene can be used as an indicator of the stability of molecular layers, by providing insight into the energetics of ordering of dipolar molecules under the effect of electrical gating.

Extending the Range of Controlling Protein Adsorption via Subsurface Architecture.

Recently, it has been shown that water, confined in a plasma polymer subsurface chemical gradient, nanometers below the surface, significantly reduced the amount of adsorbed protein bovine serum albumin (BSA). Relating to this effect, we proposed the hypothesis that oriented water molecules within the subsurface gradient generate a long-range dipolar field, which interacts with dipolar proteins such as BSA near the surface region. This study extends the above used in situ multistep plasma deposition process to introduce plasma oxidation modifications of the subsurface architecture with the aim to further control the effect on protein adsorption. Neutron reflectivity measurements reveal that the oxidation time increases the amount of matrix-confined water. There is, however, an optimal oxidation time to obtain minimal protein adsorption, which suggests that a minimal distance between confined water molecules plays an important role. Altogether we can extend the range of controlling the adsorbed protein mass by the introduction of this additional plasma oxidation step.

The fate of bromine after temperature-induced dehydrogenation of on-surface synthesized bisheptahelicene.

The on-surface synthesis of bisheptahelicene by Ullmann coupling of 9-bromoheptahelicene on Au(111) and its temperature-induced dehydrogenation is studied using temperature-programmed reaction spectroscopy and time-of-flight secondary ion mass spectrometry. Specific dehydrogenation products of bisheptahelicene after loss of 6, 8 and 10 hydrogen atoms are identified, corresponding to molecules having undergone Diels-Alder transformations and intramolecular C-C coupling reactions. By combining with atomic hydrogen produced by dehydrogenation, the Ullmann coupling side-product bromine desorbs as HBr. H2 desorption emerges only after all Br has desorbed. Such characteristic behavior is explained by a kinetic model which explicitly considers the coverage of transient atomic H on the surface. Heating experiments performed with saturated layers of different Br-containing molecules reveal that the onset of HBr desorption depends strictly on the dehydrogenation step and therefore on the structure of the molecules.

Hair Analysis: Contamination versus Incorporation from the Circulatory System-Investigations on Single Hair Samples Using Time-of-Flight Secondary Ion Mass Spectrometry and Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry.

Contamination is a highly controversial issue in hair analysis. Therefore, hair testing protocols typically include wash steps to remove contamination. However, recent studies claim that washing could also lead to permanent incorporation of contaminants into hair, thus questioning the validity of hair testing at all. In the present study, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) with longitudinal sectioning of single hairs and different decontamination protocols was used to reveal differences between the incorporation of a substance into hair from external sources and an incorporation via bloodstream. Single hairs were longitudinally sectioned using a custom-made sample holder. Data were acquired with MALDI-MS by rastering each hair individually. Single hair samples from drug users, blank hairs, and zolpidem- and zolpidem-D6-soaked hairs were investigated. Different published washing protocols were tested, and an in-house washing protocol was developed. For images with higher spatial resolution, time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used. Longitudinal sectioning of hairs dramatically increased sensitivity; even single-dose administrations of zolpidem in single hairs could thus be detected using MALDI-MS. Zolpidem from external sources could be detected in large quantities in superficial hair structures. Zolpidem from consumer hairs, proposed to be strongly bound to inner hair structures, could not be completely removed even by the strongest tested decontamination protocol, whereas zolpidem-soaked hairs could be cleared almost completely with the developed in-house wash protocol. The applied methods allowed a first insight into the connection of decontamination protocols and wash-in phenomena in hair analysis. Further studies with other drugs are necessary to assess the general validity of these findings.

Direct Measurement of Ion Redistribution and Resulting Modification of Chemical Equilibria in Polymer Thin Film Light-Emitting Electrochemical Cells.

The redistribution of ions in light-emitting electrochemical cells (LECs) plays a key role in their functionality. The direct quantitative mapping of ion density distributions in operating realistic sandwich-type devices, however, has not been experimentally achieved. Here we operate high-performing [Super Yellow/trimethylolpropane ethoxylate/lithium trifluoromethanesulfonate (Li+CF3SO3-)] LEC devices inside a time-of-flight secondary ion mass spectrometer and cool the devices after different operation times to liquid nitrogen temperatures before depth profiling is performed. The results reveal the dependence of the elemental and molecular distributions across the device layer on operation conditions. We find that the ion displacements lead to a substantial shift of the local chemical equilibria governing the free ion concentration.

Plasma polymer film designs through the eyes of ToF-SIMS.

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is increasingly used for the detailed chemical characterization of complex organic materials. Of particular interest in biointerface materials, it provides the accurate molecular information on their surface, a prerequisite for the understanding of subsequent interaction with biomaterials. Plasma polymer films are promising biointerface materials, as tuning the deposition parameters allows the control over film stability and density of surface functional groups. However, the optimization of these film properties not only requires a detailed characterization of the film chemistry, but also that of the deposition mechanisms. Here, ToF-SIMS is used within its different operation modes to investigate those on several plasma polymer film designs. The detailed information on surface molecular chemistry, interface conformation, vertical and lateral chemical and cross-linking gradients is gathered and linked to the underlying deposition mechanisms. In combination with other techniques, the interpretation and understanding of the final functional property of the films in terms of protein adsorption and site-specific binding is achieved.

Biomaterial surface energy-driven ligand assembly strongly regulates stem cell mechanosensitivity and fate on very soft substrates.

Although mechanisms of cell-material interaction and cellular mechanotransduction are increasingly understood, the mechanical insensitivity of mesenchymal cells to certain soft amorphous biomaterial substrates has remained largely unexplained. We reveal that surface energy-driven supramolecular ligand assembly can regulate mesenchymal stem cell (MSC) sensing of substrate mechanical compliance and subsequent cell fate. Human MSCs were cultured on collagen-coated hydrophobic polydimethylsiloxane (PDMS) and hydrophilic polyethylene-oxide-PDMS (PEO-PDMS) of a range of stiffnesses. Although cell contractility was similarly diminished on soft substrates of both types, cell spreading and osteogenic differentiation occurred only on soft PDMS and not hydrophilic PEO-PDMS (elastic modulus <1 kPa). Substrate surface energy yields distinct ligand topologies with accordingly distinct profiles of recruited transmembrane cell receptors and related focal adhesion signaling. These differences did not differentially regulate Rho-associated kinase activity, but nonetheless regulated both cell spreading and downstream differentiation.

High Microbial Diversity Promotes Soil Ecosystem Functioning.

In soil, the link between microbial diversity and carbon transformations is challenged by the concept of functional redundancy. Here, we hypothesized that functional redundancy may decrease with increasing carbon source recalcitrance and that coupling of diversity with C cycling may change accordingly. We manipulated microbial diversity to examine how diversity decrease affects the decomposition of easily degradable (i.e., allochthonous plant residues) versus recalcitrant (i.e., autochthonous organic matter) C sources. We found that a decrease in microbial diversity (i) affected the decomposition of both autochthonous and allochthonous carbon sources, thereby reducing global CO2 emission by up to 40%, and (ii) shaped the source of CO2 emission toward preferential decomposition of most degradable C sources. Our results also revealed that the significance of the diversity effect increases with nutrient availability. Altogether, these findings show that C cycling in soil may be more vulnerable to microbial diversity changes than expected from previous studies, particularly in ecosystems exposed to nutrient inputs. Thus, concern about the preservation of microbial diversity may be highly relevant in the current global-change context assumed to impact soil biodiversity and the pulse inputs of plant residues and rhizodeposits into the soil.IMPORTANCE With hundreds of thousands of taxa per gram of soil, microbial diversity dominates soil biodiversity. While numerous studies have established that microbial communities respond rapidly to environmental changes, the relationship between microbial diversity and soil functioning remains controversial. Using a well-controlled laboratory approach, we provide empirical evidence that microbial diversity may be of high significance for organic matter decomposition, a major process on which rely many of the ecosystem services provided by the soil ecosystem. These new findings should be taken into account in future studies aimed at understanding and predicting the functional consequences of changes in microbial diversity on soil ecosystem services and carbon storage in soil.

Elucidating the Distribution and Speciation of Boron and Cesium in BCsX Zeolite Catalysts for Styrene Production.

An improved understanding of the nature and distribution of boron and cesium species in BCsX zeolites is a prerequisite to guide future developments in the environmentally attractive, yet challenging, production of styrene through the side-chain alkylation of toluene with methanol. Herein, standard characterization and catalytic tests are complemented by integrated visualization through time-of-flight secondary-ion mass spectrometry and energy-dispersive X-ray spectroscopy and detailed assessment by 133 Cs and 11 B NMR spectroscopy, to correlate the properties and performance during successive ion-exchange and impregnation steps in the preparation of both powders and millimeter-sized granules. The results highlight a significant impact of catalyst scaleup on the effective introduction of boron species, which originates chemical heterogeneity that is linked to selectivity losses. They also illustrate the complexity of elucidating the role of this promotor, which interacts with cesium cations and exhibits different coordination states and chemical environments, depending on the pretreatment.

Soil microbial diversity drives the priming effect along climate gradients: a case study in Madagascar.

The priming effect in soil is proposed to be generated by two distinct mechanisms: 'stoichiometric decomposition' and/or 'nutrient mining' theories. Each mechanism has its own dynamics, involves its own microbial actors, and targets different soil organic matter (SOM) pools. The present study aims to evaluate how climatic parameters drive the intensity of each priming effect generation mechanism via the modification of soil microbial and physicochemical properties. Soils were sampled in the center of Madagascar, along climatic gradients designed to distinguish temperature from rainfall effects. Abiotic and biotic soil descriptors were characterized including bacterial and fungal phylogenetic composition. Potential organic matter mineralization and PE were assessed 7 and 42 days after the beginning of incubation with 13C-enriched wheat straw. Both priming mechanisms were mainly driven by the mean annual temperature but in opposite directions. The priming effect generated by stoichiometric decomposition was fostered under colder climates, because of soil enrichment in less developed organic matter, as well as in fast-growing populations. Conversely, the priming effect generated by nutrient mining was enhanced under warmer climates, probably because of the lack of competition between slow-growing populations mining SOM and fast-growing populations for the energy-rich residue entering the soil. Our study leads to hypotheses about the consequences of climate change on both PE generation mechanisms and associated consequences on soil carbon sequestration.

Fabrication and Microscopic and Spectroscopic Characterization of Planar, Bimetallic, Micro- and Nanopatterned Surfaces.

Micropatterns and nanopatterns of gold embedded in silver and titanium embedded in gold have been prepared by combining either photolithography or electron-beam lithography with a glue-free template-stripping procedure. The obtained patterned surfaces have been topographically characterized using atomic force microscopy and scanning electron microscopy, showing a very low root-mean-square roughness (<0.5 nm), high coplanarity between the two metals (maximum height difference ≈ 2 nm), and topographical continuity at the bimetallic interface. Spectroscopic characterization using X-ray photoelectron spectroscopy (XPS), time-of-flight secondary-ion mass spectrometry (ToF-SIMS), and Auger electron spectroscopy (AES) has shown a sharp chemical contrast between the two metals at the interface for titanium patterns embedded in gold, whereas diffusion of silver into gold was observed for gold patterns embedded in silver. Surface flatness combined with a high chemical contrast makes the obtained surfaces suitable for applications involving functionalization with molecules by orthogonal adsorption chemistries or for instrumental calibration. The latter possibility has been tested by determining the image sharpness and the analyzed area on circular patterns of different sizes for each of the spectroscopic techniques applied for characterization.This is the first study in which the analyzed area has been determined using XPS and AES on a flat surface, and the first example of a method for determining the analyzed area using ToF-SIMS.

Composition and Stability of Plasma Polymer Films Exhibiting Vertical Chemical Gradients.

Controlling the balance between stability and functional group density in grown plasma polymer films is the key to diverse applications such as drug release, tissue-engineered implants, filtration, contact lenses, microfluidics, electrodes, sensors, etc. Highly functional plasma polymer films typically show a limited stability in air or aqueous environments due to mechanisms like molecular reorganization, oxidation, and hydrolysis. Stabilization is achieved by enhancing cross-linking at the cost of the terminal functional groups such as -OH and -COOH, but also -NH2, etc. To overcome such limitations, a structural and chemical gradient was introduced perpendicular to the surface plane; this vertical gradient structure is composed of a highly cross-linked base layer, gradually changing into a more functional nanoscaled surface termination layer. This was achieved using CO2/C2H4 discharges with decreasing power input and increasing gas ratio during plasma polymer deposition. The aging behavior and stability of such oxygen-functional vertical gradient nanostructures were studied in air and in different aqueous environments (acidic pH 4, neutral pH ≈ 6.2, and basic pH 10). Complementary characterization methods were used, including angle-resolved X-ray photoelectron spectroscopy (ARXPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) as well as water contact angle (WCA) measurements. It was found that in air, the vertical gradient films are stabilized over a period of months. The same gradients also appear to be stable in neutral water over a period of at least 1 week. Changes in the oxygen depth profiles have been observed at pH 4 and pH 10 showing structural and chemical aging effects on different time scales. The use of vertical gradient plasma polymer nanofilms thus represents a novel approach providing enhanced stability, thus opening the possibility for new applications.

The Origin of the Catalytic Activity of a Metal Hydride in CO2 Reduction.

Atomic hydrogen on the surface of a metal with high hydrogen solubility is of particular interest for the hydrogenation of carbon dioxide. In a mixture of hydrogen and carbon dioxide, methane was markedly formed on the metal hydride ZrCoHx in the course of the hydrogen desorption and not on the pristine intermetallic. The surface analysis was performed by means of time-of-flight secondary ion mass spectroscopy and near-ambient pressure X-ray photoelectron spectroscopy, for the in situ analysis. The aim was to elucidate the origin of the catalytic activity of the metal hydride. Since at the initial stage the dissociation of impinging hydrogen molecules is hindered by a high activation barrier of the oxidised surface, the atomic hydrogen flux from the metal hydride is crucial for the reduction of carbon dioxide and surface oxides at interfacial sites.

Ultraviolet Plasmonic Chirality from Colloidal Aluminum Nanoparticles Exhibiting Charge-Selective Protein Detection.

Chiral aluminum nanoparticles, dispersed in water, are prepared, which provide strong ultraviolet plasmonic circular dichroism, high-energy superchiral near-fields, and charge-selective protein detection.

Plant Roots Increase Bacterivorous Nematode Dispersion through Nonuniform Glass-bead Media.

Dispersion of bacterivorous nematodes in soil is a crucial ecological process that permits settlement and exploitation of new bacterial-rich patches. Although plant roots, by modifying soil structure, are likely to influence this process, they have so far been neglected. In this study, using an original three-compartment microcosm experimental design and polyvinyl chloride (PVC) bars to mimic plant roots, we tested the ability of roots to improve the dispersion of bacterivorous nematode populations through two wet, nonuniform granular (glass bead) media imitating contrasting soil textures. We showed that artificial roots increased migration time of bacterivorous nematode populations in the small-bead medium, suggesting that plant roots may play an important role in nematode dispersion in fine-textured soils or when soil compaction is high.

Nanostructure characterization by a combined x-ray absorption/scanning force microscopy system.

A combined x-ray transmission and scanning force microscope setup (NanoXAS) recently installed at a dedicated beamline of the Swiss Light Source combines complementary experimental techniques to access chemical and physical sample properties with nanometer scale resolution. While scanning force microscopy probes physical properties such as sample topography, local mechanical properties, adhesion, electric and magnetic properties on lateral scales even down to atomic resolution, scanning transmission x-ray microscopy offers direct access to the local chemical composition, electronic structure and magnetization. Here we present three studies which underline the advantages of complementary access to nanoscale properties in prototype thin film samples.

Endogeic earthworms shape bacterial functional communities and affect organic matter mineralization in a tropical soil.

Priming effect (PE) is defined as a stimulation of the mineralization of soil organic matter (SOM) following a supply of fresh organic matter. This process can have important consequences on the fate of SOM and on the management of residues in agricultural soils, especially in tropical regions where soil fertility is essentially based on the management of organic matter. Earthworms are ecosystem engineers known to affect the dynamics of SOM. Endogeic earthworms ingest large amounts of soil and assimilate a part of organic matter it contains. During gut transit, microorganisms are transported to new substrates and their activity is stimulated by (i) the production of readily assimilable organic matter (mucus) and (ii) the possible presence of fresh organic residues in the ingested soil. The objective of our study was to see (i) whether earthworms impact the PE intensity when a fresh residue is added to a tropical soil and (ii) whether this impact is linked to a stimulation/inhibition of bacterial taxa, and which taxa are affected. A tropical soil from Madagascar was incubated in the laboratory, with a (13)C wheat straw residue, in the presence or absence of a peregrine endogeic tropical earthworm, Pontoscolex corethrurus. Emissions of (12)CO(2) and (13)CO(2) were followed during 16 days. The coupling between DNA-SIP (stable isotope probing) and pyrosequencing showed that stimulation of both the mineralization of wheat residues and the PE can be linked to the stimulation of several groups especially belonging to the Bacteroidetes phylum.