Rhizobiome diversity of field-collected hyperaccumulating Noccaea sp.

Hyperaccumulating plants are able to (hyper)accumulate high concentrations of metal(loid)s in their above-ground tissues without any signs of toxicity. Studies on the root-associated microbiome have been previously conducted in relation to hyperaccumulators, yet much remains unknown about the interactions between hyperaccumulating hosts and their microbiomes, as well as the dynamics within these microbial communities. Here, we assess the impact of the plant host on shaping microbial communities of three naturally occurring populations of Noccaea species in Slovenia: Noccaea praecox and co-occurring N. caerulescens from the non-metalliferous site and N. praecox from the metalliferous site. We investigated the effect of metal enrichment on microbial communities and explored the interactions within microbial groups and their environment. The abundance of bacterial phyla was more homogeneous than fungal classes across all three Noccaea populations and across the three root-associated compartments (roots, rhizosphere, and bulk soil). While most fungal and bacterial Operational Taxonomic Units (OTUs) were found at both sites, the metalliferous site comprised more unique OTUs in the root and rhizosphere compartments than the non-metalliferous site. In contrast to fungi, bacteria exhibited differentially significant abundance between the metalliferous and non-metalliferous sites as well as statistically significant correlations with most of the soil parameters. Results revealed N. caerulescens had the highest number of negative correlations between the bacterial phyla, whereas the population from the metalliferous site had the fewest. This decrease was accompanied by a big perturbation in the bacterial community at the metalliferous site, indicating increased selection between the bacterial taxa and the formation of potentially less stable rhizobiomes. These findings provide fundamentals for future research on the dynamics between hyperaccumulators and their associated microbiome.

Exploring the Benefits of Ablation Grid Adaptation in 2D/3D Laser Ablation Inductively Coupled Plasma Mass Spectrometry Mapping through Geometrical Modeling.

This study aims to investigate the potential benefits of adapting the ablating grid in two-dimensional (2D) and three-dimensional (3D) laser ablation inductively coupled plasma mass spectrometry in a single pulse mapping mode. The goals include enhancing the accuracy of surface sampling of element distributions, improving the control of depth-related sampling, smoothing the post-ablation surface for layer-by-layer sampling, and increasing the image quality. To emulate the capabilities of currently unavailable laser ablation stages, a computational approach using geometrical modeling was employed to compound square or round experimentally obtained 3D crater profiles on variable orthogonal or hexagonal ablation grids. These grids were optimized by minimizing surface roughness as a function of average ablation depth, followed by simulating the post-ablation surface and related image quality. An online application (https://laicpms-apps.ki.si/webapps/home/) is available for users to virtually experiment with contracting/expanding orthogonal and hexagonal ablation grids for generic 3D super-Gaussian laser crater profiles, allowing for exploration of the resulting post-ablation surface layer roughness and depth.

Semiquantitative Analysis for High-Speed Mapping Applications of Biological Samples Using LA-ICP-TOFMS.

Laser ablation (LA) in combination with inductively coupled plasma time-of-flight mass spectrometry (ICP-TOFMS) enables monitoring of elements from the entire mass range for every pixel, regardless of the isotopes of interest for a certain application. This provides nontargeted multi-element (bio-)imaging capabilities and the unique possibility to screen for elements that were initially not expected in the sample. Quantification of a large range of elements is limited as the preparation of highly multiplexed calibration standards for bioimaging applications by LA-ICP-(TOF)MS is challenging. In this study, we have developed a workflow for semiquantitative analysis by LA-ICP-TOFMS based on multi-element gelatin micro-droplet standards. The presented approach is intended for the mapping of biological samples due to the requirement of matrix-matched standards for accurate quantification in LA-ICPMS, a prerequisite that is given by the use of gelatin-based standards. A library of response factors was constructed based on 72 elements for the semiquantitative calculations. The presented method was evaluated in two stages: (i) on gelatin samples with known elemental concentrations and (ii) on real-world samples that included prime examples of bioimaging (mouse spleen and tumor tissue). The developed semiquantification approach was based on 10 elements as calibration standards and provided the determination of 136 nuclides of 63 elements, with errors below 25%, and for half of the nuclides, below 10%. A web application for quantification and semiquantification of LA-ICP(-TOF)MS data was developed, and a detailed description is presented to easily allow others to use the presented method.

Quantification anomalies in single pulse LA-ICP-MS analysis associated with laser fluence and beam size.

Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) has undergone major improvements in recent years which have led to reduction of the analysis time, higher spatial resolution, and better sensitivity. However, quantification and accurate analysis remain one of the bottlenecks in LA-ICP-MS analysis and so far satisfactory calibration solutions are restricted to well-documented matrices and suitable internal standards. Additional uncertainties associated with laser fluence and beam size via various ablation cells and interfaces make quantification even more challenging. This work is focused on the influence of fluence, beam size and aerosol transport on quantification in single pulse LA-ICP-MS analysis via approaches based on pulse intensity, LA spot volumes, noise characteristics, etc. for different elements (As, Gd, La, Ni, Te and Zn), concentrations (between 10 and 1000 µg g-1), and matrices (gelatin standards and NIST SRM 612). The findings indicate that selection of the appropriate laser fluence, just above the ablation threshold, and beam size, depending on the interface of LA and ICP-MS, are critical for reliable quantification and should be properly adjusted to avoid excessive Poisson and Flicker noise, achieve maximum sensitivity, and prevent the formation of double peaks in single pulses.

Multiple copies of the oxytetracycline gene cluster in selected Streptomyces rimosus strains can provide significantly increased titers.

BACKGROUND: Natural products are a valuable source of biologically active compounds that have applications in medicine and agriculture. One disadvantage with natural products is the slow, time-consuming strain improvement regimes that are necessary to ensure sufficient quantities of target compounds for commercial production. Although great efforts have been invested in strain selection methods, many of these technologies have not been improved in decades, which might pose a serious threat to the economic and industrial viability of such important bioprocesses. RESULTS: In recent years, introduction of extra copies of an entire biosynthetic pathway that encodes a target product in a single microbial host has become a technically feasible approach. However, this often results in minor to moderate increases in target titers. Strain stability and process reproducibility are the other critical factors in the industrial setting. Industrial Streptomyces rimosus strains for production of oxytetracycline are one of the most economically efficient strains ever developed, and thus these represent a very good industrial case. To evaluate the applicability of amplification of an entire gene cluster in a single host strain, we developed and evaluated various gene tools to introduce multiple copies of the entire oxytetracycline gene cluster into three different Streptomyces rimosus strains: wild-type, and medium and high oxytetracycline-producing strains. We evaluated the production levels of these engineered S. rimosus strains with extra copies of the oxytetracycline gene cluster and their stability, and the oxytetracycline gene cluster expression profiles; we also identified the chromosomal integration sites. CONCLUSIONS: This study shows that stable and reproducible increases in target secondary metabolite titers can be achieved in wild-type and in high oxytetracycline-producing strains, which always reflects the metabolic background of each independent S. rimosus strain. Although this approach is technically very demanding and requires systematic effort, when combined with modern strain selection methods, it might constitute a very valuable approach in industrial process development.

Nanoparticle Analysis in Biomaterials Using Laser Ablation-Single Particle-Inductively Coupled Plasma Mass Spectrometry.

In the past decade, the development of single particle-inductively coupled plasma mass spectrometry (SP-ICPMS) has revolutionized the field of nanometallomics. Besides differentiation between dissolved and particulate metal signals, SP-ICPMS can quantify the nanoparticle (NP) number concentration and size. Because SP-ICPMS is limited to characterization of NPs in solution, we show how solid sampling by laser ablation (LA) adds spatial-resolution characteristics for localized NP analysis in biomaterials. Using custom-made gelatin standards doped with dissolved gold and commercial or synthesized gold nanoparticles, LA-SP-ICPMS conditions such as laser fluence, beam size, and dwell time were optimized for NP analysis to minimize NP degradation, peak overlap, and interferences from dissolved gold. A data-processing algorithm to retrieve the NP number concentration and size was developed for this purpose. As a proof-of-concept, a sunflower-root-sample cross-section, originating from a sunflower plant exposed to gold NPs, was successfully imaged using the optimized LA-SP-ICPMS conditions for localized NP characterization.

Electrochemistry as a Tool for Studies of Complex Reaction Mechanisms: The Case of the Atmospheric Aqueous-Phase Aging of Catechols.

The ultimate goal in the understanding of complex chemical processes is a complete description of the underlying reaction mechanism. In the present study and for this purpose, a novel experimental platform is introduced that builds upon electrochemistry capable of generating reactive intermediate species at the electrode surface. The atmospherically relevant nitration of catechols is taken as a case example. First, we confirm the recently proposed nitration mechanism, advancing the understanding of atmospheric brown carbon formation in the dark. We are able to selectively quantify aromatic isomers, which is beyond the limits of conventional electroanalysis. Second, we identify a new pathway of nitrocatechol hydroxylation, which proceeds simply by oxidation and the addition of water. This pathway can be environmentally significant in the dark aqueous-phase formation of secondary organic aerosols. Third, the developed methodology is capable of selectively detecting a wide range of nitroaromatics; a possible application in environmental monitoring is proposed.

A Double-Passivation Water-Based Galvanic Displacement Method for Reproducible Gram-Scale Production of High-Performance Platinum-Alloy Electrocatalysts.

Preparation of large quantities of high-performance supported Pt-alloy electrocatalysts is crucial for the faster development and implementation of low-temperature proton exchange membrane fuel cells (PEMFCs). One of the prospective nanofabrication synthesis methods is based on the galvanic displacement (GD) reaction. A facile, highly reproducible, gram scale, water-based double passivation GD method is now presented for the synthesis of carbon-supported Pt-M nanoparticles (M=Cu, Ni, Co). It offers great flexibility over the catalyst design, such as the choice of the sacrificial metal (M), variation of the chemical composition of alloy, variation of total metal loading (Pt+M) on carbon support, or even variation of the carbon support itself. The obtained Pt-alloy catalysts are several times more active compared to a Pt reference and exhibits better stability during accelerated degradation tests performed at 60 °C.

Perceptual Image Quality Metrics Concept in Continuous Scanning 2D Laser Ablation-Inductively Coupled Plasma Mass Spectrometry Bioimaging.

This work focuses on the structural similarity (SSIM) index as a tool for optimization of the perceived visual image quality obtainable by continuous scanning 2D LA-ICPMS bioimaging, but also other mass spec imaging techniques may benefit from this approach. This index quantifies the differences between a distorted image and a reference image based on parameters associated with luminance, contrast, and noise. Since reference images are not normally available, a protocol was developed to virtually apply distortion-related information introduced by the LA-ICPMS imaging system to a reference image of one's choice. Distortion-related information in the form of blur and noise was experimentally retrieved from line scans across a laser milled knife edge on custom-prepared gelatin standards (mimicking proteinaceous biomatrixes). Distorted images were generated via computational procedures developed earlier, warranting objective image quality assessment via the SSIM indices. We illustrate the potential of this approach for image quality optimization for a suite of LA-ICPMS imaging conditions.

Imaging Artifacts in Continuous Scanning 2D LA-ICPMS Imaging Due to Nonsynchronization Issues.

Pulsed laser ablation (LA) devices in laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS) imaging have become very advanced, delivering laser pulses with high temporal accuracy and stable energy density. However, unintentional imaging artifacts may be generated in 2D element maps when the LA repetition rate and the data acquisition parameters of ICPMS instruments with a sequential mass spectrometer (i.e., quadrupole filter or sector-field mass spectrometer) are desynchronized. This may potentially lead to interference patterns, visible as ripples in elemental images, and thus, compromised image quality. This paper describes the background of aliasing in continuous scanning mode through simulation experiments and ways to modulate the effect. The existence of this image degradation source is demonstrated experimentally via real-life imaging of a homogeneous glass standard.

Nighttime Aqueous-Phase Formation of Nitrocatechols in the Atmospheric Condensed Phase.

Yellow-colored methylnitrocatechols (MNC) contribute to the total organic aerosol mass and significantly alter absorption properties of the atmosphere. To date, their formation mechanisms are still not understood. In this work, the intriguing role of HNO2 (catalytic and oxidative) in the dark transformation of 3-methylcatechol (3MC) under atmospherically relevant aqueous-phase conditions is emphasized. Three possible pathways of dark 3-methyl-5-nitrocatechol and 3-methyl-4-nitrocatechol formation, markedly dependent on reaction conditions, were considered. In the dominant pathway, HNO2 is directly involved in the transformation of 3MC via consecutive oxidation and conjugated addition reactions (nonradical reaction mechanism). The two-step nitration dominates at a pH around the p Ka of HNO2, which is typical for atmospheric aerosols, and is moderately dependent on temperature. Under very acidic conditions, the other two nitration pathways, oxidative aromatic nitration (electrophilic) and recombination of radical species, gain in importance. The predicted atmospheric lifetime of 3MC according to the dominant mechanism at these conditions (2.4 days at pH 4.5 and 25 °C) is more than 3-times shorter than that via the other two competitive pathways. Our results highlight the significance of a catechol oxidation-conjugated addition reaction in a nighttime secondary nitroaromatic chromophore formation in the atmosphere, especially in polluted environments with high NO x concentrations and relatively acidic particles (pH around 3).

Electrochemical Dissolution of Iridium and Iridium Oxide Particles in Acidic Media: Transmission Electron Microscopy, Electrochemical Flow Cell Coupled to Inductively Coupled Plasma Mass Spectrometry, and X-ray Absorption Spectroscopy Study.

Iridium-based particles, regarded as the most promising proton exchange membrane electrolyzer electrocatalysts, were investigated by transmission electron microscopy and by coupling of an electrochemical flow cell (EFC) with online inductively coupled plasma mass spectrometry. Additionally, studies using a thin-film rotating disc electrode, identical location transmission and scanning electron microscopy, as well as X-ray absorption spectroscopy have been performed. Extremely sensitive online time-and potential-resolved electrochemical dissolution profiles revealed that Ir particles dissolve well below oxygen evolution reaction (OER) potentials, presumably induced by Ir surface oxidation and reduction processes, also referred to as transient dissolution. Overall, thermally prepared rutile-type IrO2 particles are substantially more stable and less active in comparison to as-prepared metallic and electrochemically pretreated (E-Ir) analogues. Interestingly, under OER-relevant conditions, E-Ir particles exhibit superior stability and activity owing to the altered corrosion mechanism, where the formation of unstable Ir(>IV) species is hindered. Due to the enhanced and lasting OER performance, electrochemically pre-oxidized E-Ir particles may be considered as the electrocatalyst of choice for an improved low-temperature electrochemical hydrogen production device, namely a proton exchange membrane electrolyzer.

Gelatin gels as multi-element calibration standards in LA-ICP-MS bioimaging: fabrication of homogeneous standards and microhomogeneity testing.

Highly homogeneous multi-element gelatin calibration standards were fabricated for quantitative LA-ICP-MS bioimaging. Heterogeneity issues caused by the so-called "coffee-stain" and/or "Marangoni" effects were found to be element-dependent but could be circumvented by careful selection of drying/setting conditions. A micro-homogeneity test was developed for certification of the standards.

Importance of non-intrinsic platinum dissolution in Pt/C composite fuel cell catalysts.

The dissolution of different platinum-based nanoparticles deposited on a commercial high-surface area carbon (HSAC) support in thin catalyst films is investigated using a highly sensitive electrochemical flow cell (EFC) coupled to an inductively coupled plasma mass spectrometer (ICP-MS). The previously reported particle-size-dependent dissolution of Pt is confirmed on selected industrial samples with a mean Pt particle size ranging from 1 to 4.8 nm. This trend is significantly altered when a catalyst is diluted by the addition of HSAC. This indicates that the intrinsic dissolution properties are masked by local oversaturation phenomena, the so-called confinement effect. Furthermore, by replacing the standard HSAC support with a support having an order of magnitude higher specific surface area (a micro- and mesoporous nitrogen-doped high surface area carbon, HSANDC), Pt dissolution is reduced even further. This is due to the so-called non-intrinsic confinement and entrapment effects of the (large amount of) micropores and small mesopores doped with N atoms. The observed more effective Pt re-deposition is presumably induced by local Pt oversaturation and the presence of nitrogen nucleation sites. Overall, our study demonstrates the high importance and beneficial effects of porosity, loading and N doping of the carbon support on the Pt stability in the catalyst layer.

Determination of triacylglycerol regioisomers using differential mobility spectrometry.

RATIONALE: Triacylglycerols (TG) contain three fatty acyls attached to the glycerol backbone in stereochemically numbered positions sn-1, 2 and 3. Isobaric TG with exchanged fatty acyl chains in positions sn-1/3 vs. sn-2 are referred to as regioisomers and the determination of their regioisomeric ratios is important for nutrition purposes. METHODS: Differential mobility spectrometry (DMS) coupled to electrospray ionization mass spectrometry (ESI-MS) is applied for the separation of simple unsaturated TG regioisomers extracted from porcine adipose tissue using their silver-ion molecular adducts. RESULTS: Four pairs of TG regioisomers containing combinations of unsaturated and saturated fatty acyl chains are successfully separated using DMS with 1-butanol or 1-propanol as the chemical modifier. Various experimental parameters are carefully optimized, such as the separation and compensation voltages applied to DMS electrodes, the type and flow rate of chemical modifier and the dwell time of analyte ions in the DMS cell. The optimized DMS approach is used for the characterization of TG regioisomers in less than one minute, compared to tens of minutes typical for silver-ion or reversed-phase high-performance liquid chromatography/mass spectrometry approaches. CONCLUSIONS: The application of this method for the characterization of TG regioisomers in porcine adipose tissue shows the method suitability for analyses of other animal fats.

Quantum Chemical Calculations Resolved Identification of Methylnitrocatechols in Atmospheric Aerosols.

Methylnitrocatechols (MNCs) are secondary organic aerosol (SOA) tracers and major contributors to atmospheric brown carbon; however, their formation and aging processes in atmospheric waters are unknown. To investigate the importance of aqueous-phase electrophilic substitution of 3-methylcatechol with nitronium ion (NO2(+)), we performed quantum calculations of their favorable pathways. The calculations predicted the formation of 3-methyl-5-nitrocatechol (3M5NC), 3-methyl-4-nitrocatechol (3M4NC), and a negligible amount of 3-methyl-6-nitrocatechol (3M6NC). MNCs in atmospheric PM2 samples were further inspected by LC/(-)ESI-MS/MS using commercial as well as de novo synthesized authentic standards. We detected 3M5NC and, for the first time, 3M4NC. In contrast to previous reports, 3M6NC was not observed. Agreement between calculated and observed 3M5NC/3M4NC ratios cannot unambiguously confirm the electrophilic mechanism as the exclusive formation pathway of MNCs in aerosol water. However, the examined nitration by NO2(+) is supported by (1) the absence of 3M6NC in the ambient aerosols analyzed and (2) the constant 3M5NC/3M4NC ratio in field aerosol samples, which indicates their common formation pathway. The magnitude of error one could make by incorrectly identifying 3M4NC as 3M6NC in ambient aerosols was also assessed, suggesting the importance of evaluating the literature regarding MNCs with special care.

Rapid identification of atypical tetracyclines using tandem mass spectrometric fragmentation patterns.

RATIONALE: When applying biosynthetic engineering approaches at the early stages of drug discovery, e.g. aiming to develop novel tetracycline analogues, target compounds are generally produced by engineered microorganisms in low yields. Rapid and reliable identification of metabolites with desired structural modification directly from bacterial cultures is therefore of great importance. METHODS: Structural elucidation of atypical tetracyclines was carried out by fragmentation applying electrospray ionisation tandem mass spectrometry (ESI-MS/MS) (triple quadrupole - linear ion trap; Applied Biosystems 4000 QTRAP) and a high-resolution mass spectrometer (Agilent Technologies 6224 TOF). Fragmentation patterns were obtained either with direct injection or by applying separation of target compounds with high-performance liquid chromatography (HPLC) prior to mass spectrometry. In-source and CID fragmentation were compared. Theoretical calculations of target structures using the Gaussian programme suite were carried out with the aim of strengthening experimental structural elucidation. RESULTS: Recombinant strains of Amycolatopsis sulphurea producing atypical tetracyclines chelocardin, modified chelocardin analogues (9-demethylchelocardin and 2-carboxyamido-2-deacetyl-chelocardin (CDCHD), and anhydrotetracycline (ATC) were analysed by collision-induced dissociation (CID) fragmentation with higher collision energies to yield structurally important fragments which were identified. We have demonstrated that ATC is more prone to fragmentation compared to its epimer, which was further supported by comparison of both structures calculated with ab initio calculations. CONCLUSIONS: We have demonstrated that fragmentation patterns of atypical tetracyclines in CID-MS spectra enable rapid structural elucidation of target metabolites produced by cultures of genetically engineered bacteria. This method is of significant importance for early stages of drug development considering that isolation of target metabolites produced at low concentration is challenging. Copyright © 2015 John Wiley & Sons, Ltd.

Construction of a new class of tetracycline lead structures with potent antibacterial activity through biosynthetic engineering.

Antimicrobial resistance and the shortage of novel antibiotics have led to an urgent need for new antibacterial drug leads. Several existing natural product scaffolds (including chelocardins) have not been developed because their suboptimal pharmacological properties could not be addressed at the time. It is demonstrated here that reviving such compounds through the application of biosynthetic engineering can deliver novel drug candidates. Through a rational approach, the carboxamido moiety of tetracyclines (an important structural feature for their bioactivity) was introduced into the chelocardins, which are atypical tetracyclines with an unknown mode of action. A broad-spectrum antibiotic lead was generated with significantly improved activity, including against all Gram-negative pathogens of the ESKAPE panel. Since the lead structure is also amenable to further chemical modification, it is a platform for further development through medicinal chemistry and genetic engineering.

Utilizing ablation volume for calibration in LA-ICP-MS mapping to address variations in ablation rates within and between matrices.

Quantification in 2D LA-ICP-MS mapping generally requires matrix-matched standards to minimize issues related to elemental fractionation. In addition, internal standardization is commonly applied to correct for instrumental drift and fluctuation, whereas also differences in ablated mass can be rectified for samples that cannot be sectioned and subjected to total ablation. However, it is crucial that the internal standard element is homogeneously distributed in the sample and that the laser light absorptivity is uniform over the surface. As in practice these requirements are often not met, this work will focus on correction of ablation rate differences within/between samples and standards by normalizing the element maps using the associated ablation volume per pixel as measured by optical profilometry. Due to the volume correction approach the element concentrations are no longer defined as mass per mass concentrations (in µg g-1) but by mass per volume concentrations (in µg cm-3), which can be interconverted in case matrix densities are known. The findings show that ablation volume-aided calibration yields more accurate element concentrations in 2D LA-ICP-MS maps for a decorative glass with highly varying elemental concentrations (murrina). This research presents a warning that if there are variations in ablation rates between samples and standards within and across matrices, even when their sensitivities are the same, generic LA-ICP-MS calibration protocols may not accurately depict the actual element concentrations.

Non-matrix-matched calibration in bulk multi-element laser ablation - Inductively coupled plasma - Mass spectrometry analysis of diverse materials.

Laser ablation inductively coupled plasma - mass spectrometry (LA-ICP-MS) is a frequently used microanalytical technique in elemental analysis of solid samples. In most instances the use of matrix-matched calibration standards is necessary for the accurate determination of elemental concentrations. However, the main drawback of this approach is the limited availability of certified reference materials. Here, we present a novel conceptual framework in LA-ICP-MS quantification without the use of matrix-matched calibration standards but instead employment of an ablation volume-normalization method (via measurement of post-ablation line scan volumes by optical profilometry) in combination with a matrix-adapted fluence (slightly above the ablation threshold). This method was validated by cross-matrix quantification of reference materials typically investigated by LA-ICP-MS, including geological and biological materials. This allows for more accurate and precise multi-element quantification, and enables quantification of previously unquantifiable elements/materials.