Effect of Oxidation on Vivianite Dissolution Rates and Mechanism.

The interest in the mineral vivianite (Fe3(PO4)2·8H2O) as a more sustainable P resource has grown significantly in recent years owing to its efficient recovery from wastewater and its potential use as a P fertilizer. Vivianite is metastable in oxic environments and readily oxidizes. As dissolution and oxidation occur concurrently, the impact of oxidation on the dissolution rate and mechanism is not fully understood. In this study, we disentangled the oxidation and dissolution of vivianite to develop a quantitative and mechanistic understanding of dissolution rates and mechanisms under oxic conditions. Controlled batch and flow-through experiments with pristine and preoxidized vivianite were conducted to systematically investigate the effect of oxidation on vivianite dissolution at various pH-values and temperatures. Using X-ray absorption spectroscopy and scanning transmission X-ray microscopy techniques, we demonstrated that oxidation of vivianite generated a core-shell structure with a passivating oxidized amorphous Fe(III)-PO4 surface layer and a pristine vivianite core, leading to diffusion-controlled oxidation kinetics. Initial (<1 h) dissolution rates and concomitant P and Fe release (∼48 h) decreased strongly with increasing degree of oxidation (0-≤ 100%). Both increasing temperature (5-75 °C) and pH (5-9) accelerated oxidation, and, consequently, slowed down dissolution kinetics.

Microplastic polymer properties as deterministic factors driving terrestrial plastisphere microbiome assembly and succession in the field.

Environmental microplastic (MP) is ubiquitous in aquatic and terrestrial ecosystems providing artificial habitats for microbes. Mechanisms of MP colonization, MP polymer impacts, and effects on soil microbiomes are largely unknown in terrestrial systems. Therefore, we experimentally tested the hypothesis that MP polymer type is an important deterministic factor affecting MP community assembly by incubating common MP polymer types in situ in landfill soil for 14 months. 16S rRNA gene amplicon sequencing indicated that MP polymers have specific impacts on plastisphere microbiomes, which are subsets of the soil microbiome. Chloroflexota, Gammaproteobacteria, certain Nitrososphaerota, and Nanoarchaeota explained differences among MP polymers and time points. Plastisphere microbial community composition derived from different MP diverged over time and was enriched in potential pathogens. PICRUSt predictions of pathway abundances and quantitative PCR of functional marker genes indicated that MP polymers exerted an ambivalent effect on genetic potentials of biogeochemical cycles. Overall, the data indicate that (i) polymer type as deterministic factor rather than stochastic factors drives plastisphere community assembly, (ii) MP impacts greenhouse gas metabolism, xenobiotic degradation and pathogen distribution, and (iii) MP serves as an ideal model system for studying fundamental questions in microbial ecology such as community assembly mechanisms in terrestrial environments.

Vapor-Phase Loading of an Ionic Liquid into a Zeolitic Imidazolate Framework.

Composites formed by a metal-organic framework (MOF) and an ionic liquid (IL) are potentially interesting materials for applications ranging from gas separation to electrochemical devices. Consequently, there is a need for robust and low-cost preparation procedures that are compatible with the desired applications. We herein report a solvent-free, one-step, and vapor-based ship-in-bottle synthesis of the IL@MOF composite 1-butyl-3-methylimidazolium bromide@ZIF-8 in powder and thin film forms. In this approach, volatile IL precursors evaporate and subsequently adsorb and react within the MOF cages to form the IL.

Chemical Vapor Deposition of Ionic Liquids for the Fabrication of Ionogel Films and Patterns.

Film deposition and high-resolution patterning of ionic liquids (ILs) remain a challenge, despite a broad range of applications that would benefit from this type of processing. Here, we demonstrate for the first time the chemical vapor deposition (CVD) of ILs. The IL-CVD method is based on the formation of a non-volatile IL through the reaction of two vaporized precursors. Ionogel micropatterns can be easily obtained via the combination of IL-CVD and standard photolithography, and the resulting microdrop arrays can be used as microreactors. The IL-CVD approach will facilitate leveraging the properties of ILs in a range of applications and microfabricated devices.

Two- and Three-dimensional Mid-Infrared Chemical Imaging.

This article describes the state-of-the-art in 2D and 3D tomographic mid-IR imaging and its current and potential applications in the imaging of material and biological systems with a focus on cells and tissues. 2D FTIR microscopy is first presented in terms of the basic experimental configurations of the technique, optics, data and image acquisition. This first section provides a basis for the ensuing discussion on 3D FTIR spectro-microtomography. In the second part, examples of 2D and 3D chemical imaging are given with a focus on the use of molecular chemical probes and probe-free applications, respectively.

Novel Fluorescein-Based Fluorescent Probe for Detecting H2S and Its Real Applications in Blood Plasma and Biological Imaging.

A broad-spectrum fluorescent probe, which can be applied to monitoring H2S in various biological systems, has been rationally designed and synthesized. This specific probe was applied to localize the endogenous H2S in living Raw264.7 macrophage cells, HepG2 cells, and H9C2 cells. At the same time, the probe has successfully visualized CBS- and CSE-induced endogenous H2S production and monitored CBS and CSE activity in H9C2 cells. This probe could serve as a powerful molecular imaging tool to further explore the physiological function and the molecular mechanisms of endogenous H2S in living animal systems.

Submicron-Scale Heterogeneities in Nickel Sorption of Various Cell-Mineral Aggregates Formed by Fe(II)-Oxidizing Bacteria.

Fe(II)-oxidizing bacteria form biogenic cell-mineral aggregates (CMAs) composed of microbial cells, extracellular organic compounds, and ferric iron minerals. CMAs are capable of immobilizing large quantities of heavy metals, such as nickel, via sorption processes. CMAs play an important role for the fate of heavy metals in the environment, particularly in systems characterized by elevated concentrations of dissolved metals, such as mine drainage or contaminated sediments. We applied scanning transmission (soft) X-ray microscopy (STXM) spectrotomography for detailed 3D chemical mapping of nickel sorbed to CMAs on the submicron scale. We analyzed different CMAs produced by phototrophic or nitrate-reducing microbial Fe(II) oxidation and, in addition, a twisted stalk structure obtained from an environmental biofilm. Nickel showed a heterogeneous distribution and was found to be preferentially sorbed to biogenically precipitated iron minerals such as Fe(III)-(oxyhydr)oxides and, to a minor extent, associated with organic compounds. Some distinct nickel accumulations were identified on the surfaces of CMAs. Additional information obtained from scatter plots and angular distance maps, showing variations in the nickel-iron and nickel-organic carbon ratios, also revealed a general correlation between nickel and iron. Although a high correlation between nickel and iron was observed in 2D maps, 3D maps revealed this to be partly due to projection artifacts. In summary, by combining different approaches for data analysis, we unambiguously showed the heterogeneous sorption behavior of nickel to CMAs.

Solvent-free, visible-light photocatalytic alcohol oxidations applying an organic photocatalyst.

A method for the solvent-free photocatalytic conversion of solid and liquid substrates was developed, using a novel rod mill apparatus. In this setup, thin liquid films are realized which is crucial for an effective photocatalytic conversion due to the low penetration depth of light in heterogeneous systems. Several benzylic alcohols were oxidized with riboflavin tetraacetate as photocatalyst under blue light irradiation of the reaction mixture. The corresponding carbonyl compounds were obtained in moderate to good yields.

Three-dimensional mid-infrared tomographic imaging of endogenous and exogenous molecules in a single intact cell with subcellular resolution.

Microscopy in the mid-infrared spectral range provides detailed chemical information on a sample at moderate spatial resolution and is being used increasingly in the characterization of biological entities as challenging as single cells. However, a conventional cellular 2D imaging measurement is limited in its ability to associate specific compositional information to subcellular structures because of the interference from the complex topography of the sample. Herein we provide a method and protocols that overcome this challenge in which tilt-series infrared tomography is used with a standard benchtop infrared microscope. This approach gives access to the quantitative 3D distribution of molecular components based on the intrinsic contrast provided by the sample. We demonstrate the method by quantifying the distribution of an exogenous metal carbonyl complex throughout the cell and by reporting changes in its coordination sphere in different locations in the cell.

Potential role of nitrite for abiotic Fe(II) oxidation and cell encrustation during nitrate reduction by denitrifying bacteria.

Microorganisms have been observed to oxidize Fe(II) at neutral pH under anoxic and microoxic conditions. While most of the mixotrophic nitrate-reducing Fe(II)-oxidizing bacteria become encrusted with Fe(III)-rich minerals, photoautotrophic and microaerophilic Fe(II) oxidizers avoid cell encrustation. The Fe(II) oxidation mechanisms and the reasons for encrustation remain largely unresolved. Here we used cultivation-based methods and electron microscopy to compare two previously described nitrate-reducing Fe(II) oxidizers ( Acidovorax sp. strain BoFeN1 and Pseudogulbenkiania sp. strain 2002) and two heterotrophic nitrate reducers (Paracoccus denitrificans ATCC 19367 and P. denitrificans Pd 1222). All four strains oxidized ∼8 mM Fe(II) within 5 days in the presence of 5 mM acetate and accumulated nitrite (maximum concentrations of 0.8 to 1.0 mM) in the culture media. Iron(III) minerals, mainly goethite, formed and precipitated extracellularly in close proximity to the cell surface. Interestingly, mineral formation was also observed within the periplasm and cytoplasm; intracellular mineralization is expected to be physiologically disadvantageous, yet acetate consumption continued to be observed even at an advanced stage of Fe(II) oxidation. Extracellular polymeric substances (EPS) were detected by lectin staining with fluorescence microscopy, particularly in the presence of Fe(II), suggesting that EPS production is a response to Fe(II) toxicity or a strategy to decrease encrustation. Based on the data presented here, we propose a nitrite-driven, indirect mechanism of cell encrustation whereby nitrite forms during heterotrophic denitrification and abiotically oxidizes Fe(II). This work adds to the known assemblage of Fe(II)-oxidizing bacteria in nature and complicates our ability to delineate microbial Fe(II) oxidation in ancient microbes preserved as fossils in the geological record.

Synchrotron-based chemical nano-tomography of microbial cell-mineral aggregates in their natural, hydrated state.

Chemical nano-tomography of microbial cells in their natural, hydrated state provides direct evidence of metabolic and chemical processes. Cells of the nitrate-reducing Acidovorax sp. strain BoFeN1 were cultured in the presence of ferrous iron. Bacterial reduction of nitrate causes precipitation of Fe(III)-(oxyhydr)oxides in the periplasm and in direct vicinity of the cells. Nanoliter aliquots of cell-suspension were injected into custom-designed sample holders wherein polyimide membranes collapse around the cells by capillary forces. The immobilized, hydrated cells were analyzed by synchrotron-based scanning transmission X-ray microscopy in combination with angle-scan tomography. This approach provides three-dimensional (3D) maps of the chemical species in the sample by employing their intrinsic near-edge X-ray absorption properties. The cells were scanned through the focus of a monochromatic soft X-ray beam at different, chemically specific X-ray energies to acquire projection images of their corresponding X-ray absorbance. Based on these images, chemical composition maps were then calculated. Acquiring projections at different tilt angles allowed for 3D reconstruction of the chemical composition. Our approach allows for 3D chemical mapping of hydrated samples and thus provides direct evidence for the localization of metabolic and chemical processes in situ.

Nominally identical microplastic models differ greatly in their particle-cell interactions.

Due to the abundance of microplastics in the environment, research about its possible adverse effects is increasing exponentially. Most studies investigating the effect of microplastics on cells still rely on commercially available polystyrene microspheres. However, the choice of these model microplastic particles can affect the outcome of the studies, as even nominally identical model microplastics may interact differently with cells due to different surface properties such as the surface charge. Here, we show that nominally identical polystyrene microspheres from eight different manufacturers significantly differ in their ζ-potential, which is the electrical potential of a particle in a medium at its slipping plane. The ζ-potential of the polystyrene particles is additionally altered after environmental exposure. We developed a microfluidic microscopy platform to demonstrate that the ζ-potential determines particle-cell adhesion strength. Furthermore, we find that due to this effect, the ζ-potential also strongly determines the internalization of the microplastic particles into cells. Therefore, the ζ-potential can act as a proxy of microplastic-cell interactions and may govern adverse effects reported in various organisms exposed to microplastics.

Interactions between iron and carbon in permafrost thaw ponds.

Thawing permafrost forms "thaw ponds" that accumulate and transport organic carbon (OC), redox-active iron (Fe), and other elements. Although Fe has been shown to act as a control on the microbial degradation of OC in permafrost soils, the role of iron in carbon cycling in thaw ponds remains poorly understood. Here, we investigated Fe-OC interactions in thaw ponds in partially and fully thawed soils ("bog" and "fen" thaw ponds, respectively) in a permafrost peatland complex in Abisko, Sweden, using size separation (large particulate fraction (LPF), small particulate fraction (SPF), and dissolved fraction (DF)), acid extractions, scanning electron microscopy (SEM), Fe K-edge X-ray absorption spectroscopy (XAS), and Fourier Transform Infrared (FTIR) spectroscopy. The bulk total Fe (total suspended Fe) in the bogs ranged from 135 mg/L (mean = 13 mg/L) whereas the fens exhibited higher total Fe (1.5 to 212 mg/L, mean = 30 mg/L). The concentration of bulk total OC (TOC) in the bog thaw ponds ranged from 50 to 352 mg/L (mean = 170 mg/L), higher than the TOC concentration in the fen thaw ponds (8.5 to 268 mg/L, mean = 17 mg/L). The concentration of 1 M HCl-extractable Fe in the bog ponds was slightly lower than that in the fens (93 ± 1.2 and 137 ± 3.5 mg/L Fe, respectively) with Fe predominantly (>75 %) in the DF in both thaw stages. Fe K-edge XAS analysis showed that while Fe(II) was the predominant species in LPF, Fe(III) was more abundant in the DF, indicating that the stage of thawing and particle size may control Fe redox state. Furthermore, Fe(II) and Fe(III) were partially complexed with natural organic matter (NOM, 8 to 80 %) in both thaw ponds. Results of our work suggest that Fe and OC released during permafrost thaw into thaw ponds (re-)associate, potentially protecting OC from microbial decomposition while also stabilizing the redox state of Fe.

Mapping of heavy metal ion sorption to cell-extracellular polymeric substance-mineral aggregates by using metal-selective fluorescent probes and confocal laser scanning microscopy.

Biofilms, organic matter, iron/aluminum oxides, and clay minerals bind toxic heavy metal ions and control their fate and bioavailability in the environment. The spatial relationship of metal ions to biomacromolecules such as extracellular polymeric substances (EPS) in biofilms with microbial cells and biogenic minerals is complex and occurs at the micro- and submicrometer scale. Here, we review the application of highly selective and sensitive metal fluorescent probes for confocal laser scanning microscopy (CLSM) that were originally developed for use in life sciences and propose their suitability as a powerful tool for mapping heavy metals in environmental biofilms and cell-EPS-mineral aggregates (CEMAs). The benefit of using metal fluorescent dyes in combination with CLSM imaging over other techniques such as electron microscopy is that environmental samples can be analyzed in their natural hydrated state, avoiding artifacts such as aggregation from drying that is necessary for analytical electron microscopy. In this minireview, we present data for a group of sensitive fluorescent probes highly specific for Fe(3+), Cu(2+), Zn(2+), and Hg(2+), illustrating the potential of their application in environmental science. We evaluate their application in combination with other fluorescent probes that label constituents of CEMAs such as DNA or polysaccharides and provide selection guidelines for potential combinations of fluorescent probes. Correlation analysis of spatially resolved heavy metal distributions with EPS and biogenic minerals in their natural, hydrated state will further our understanding of the behavior of metals in environmental systems since it allows for identifying bonding sites in complex, heterogeneous systems.

Dissimilatory reduction and transformation of ferrihydrite-humic acid coprecipitates.

Organic matter (OM) is present in most terrestrial environments and is often found coprecipitated with ferrihydrite (Fh). Sorption or coprecipitation of OM with Fe oxides has been proposed to be an important mechanism for long-term C preservation. However, little is known about the impact of coprecipitated OM on reductive dissolution and transformation of Fe(III) (oxyhydr)oxides. Thus, we study the effect of humic acid (HA) coprecipitation on Fh reduction and secondary mineral formation by the dissimilatory Fe(III)-reducing bacterium Shewanella putrefaciens strain CN32. Despite similar crystal structure for all coprecipitates investigated, resembling 2-line Fh, the presence of coprecipitated HA resulted in lower specific surface areas. In terms of reactivity, coprecipitated HA resulted in slower Fh bioreduction rates at low C/Fe ratios (i.e., C/Fe ≤ 0.8), while high C/Fe ratios (i.e., C/Fe ≥ 1.8) enhanced the extent of bioreduction compared to pure Fh. The coprecipitated HA also altered the secondary Fe mineralization pathway by inhibiting goethite formation, reducing the amount of magnetite formation, and increasing the formation of a green rust-like phase. This study indicates that coprecipitated OM may influence the rates, pathway, and mineralogy of biogeochemical Fe cycling and anaerobic Fe respiration within soils.

Fate of Cd during microbial Fe(III) mineral reduction by a novel and Cd-tolerant Geobacter species.

Fe(III) (oxyhydr)oxides affect the mobility of contaminants in the environment by providing reactive surfaces for sorption. This includes the toxic metal cadmium (Cd), which prevails in agricultural soils and is taken up by crops. Fe(III)-reducing bacteria can mobilize such contaminants by Fe(III) mineral dissolution or immobilize them by sorption to or coprecipitation with secondary Fe minerals. To date, not much is known about the fate of Fe(III) mineral-associated Cd during microbial Fe(III) reduction. Here, we describe the isolation of a new Geobacter sp. strain Cd1 from a Cd-contaminated field site, where the strain accounts for 10(4) cells g(-1) dry soil. Strain Cd1 reduces the poorly crystalline Fe(III) oxyhydroxide ferrihydrite in the presence of at least up to 112 mg Cd L(-1). During initial microbial reduction of Cd-loaded ferrihydrite, sorbed Cd was mobilized. However, during continuous microbial Fe(III) reduction, Cd was immobilized by sorption to and/or coprecipitation within newly formed secondary minerals that contained Ca, Fe, and carbonate, implying the formation of an otavite-siderite-calcite (CdCO3-FeCO3-CaCO3) mixed mineral phase. Our data shows that microbially mediated turnover of Fe minerals affects the mobility of Cd in soils, potentially altering the dynamics of Cd uptake into food or phyto-remediating plants.

Organic carbon and reducing conditions lead to cadmium immobilization by secondary Fe mineral formation in a pH-neutral soil.

Cadmium (Cd) is of environmental relevance as it enters soils via Cd-containing phosphate fertilizers and endangers human health when taken up by crops. Cd is known to associate with Fe(III) (oxyhydr)oxides in pH-neutral to slightly acidic soils, though it is not well understood how the interrelation of Fe and Cd changes under Fe(III)-reducing conditions. Therefore, we investigated how the mobility of Cd changes when a Cd-bearing soil is faced with organic carbon input and reducing conditions. Using fatty acid profiles and quantitative PCR, we found that both fermenting and Fe(III)-reducing bacteria were stimulated by organic carbon-rich conditions, leading to significant Fe(III) reduction. The reduction of Fe(III) minerals was accompanied by increasing soil pH, increasing dissolved inorganic carbon, and decreasing Cd mobility. SEM-EDX mapping of soil particles showed that a minor fraction of Cd was transferred to Ca- and S-bearing minerals, probably carbonates and sulfides. Most of the Cd, however, correlated with a secondary iron mineral phase that was formed during microbial Fe(III) mineral reduction and contained mostly Fe, suggesting an iron oxide mineral such as magnetite (Fe3O4). Our data thus provide evidence that secondary Fe(II) and Fe(II)/Fe(III) mixed minerals could be a sink for Cd in soils under reducing conditions, thus decreasing the mobility of Cd in the soil.

Silicon and calcium controls on iron and aluminum mobility in Arctic soils.

Arctic permafrost soils store large amounts of organic carbon and nutrients. With deepening of the perennial thawing upper active layer due to rising temperatures in the Arctic, not only the mobility of organic matter (OM), but also those of elements like silicon (Si) or calcium (Ca) may increase. It is known that major elements like Si and Ca can affect mineralization rates of OM, consequently influencing the carbon cycle. But only little is known about the interactions of Si and Ca with inorganic nutrients like iron (Fe) or potentially toxic elements like aluminum (Al) in Artic soils. In this study, we analyzed the effect of Si and Ca fertilization in laboratory incubation experiments with soil samples from several Arctic regions. Our results show a significant increase in Fe and Al mobility (Mehlich-3 extractable) after increasing Si. Using high resolution X-ray microscopy (STXM/NEXAFS), we show that Si promotes Fe(II) phases and by this increases Fe mobility. Al mobility was increased for acidic and neutral pH soils but decreased for alkaline soils after increasing Si. Furthermore, we show a decreased Al mobility after increasing Ca, independent on the original pH values and the OM content of the soils. These results demonstrate the importance of interactions between Si and Ca on one hand and Fe and Al mobility on the other hand for Arctic soils.

Linking environmental processes to the in situ functioning of microorganisms by high-resolution secondary ion mass spectrometry (NanoSIMS) and scanning transmission X-ray microscopy (STXM).

Environmental microbiology research increasingly focuses on the single microbial cell as the defining entity that drives environmental processes. The interactions of individual microbial cells with each other, the environment and with higher organisms shape microbial communities and control the functioning of whole ecosystems. A single-cell view of microorganisms in their natural environment requires analytical tools that measure both cell function and chemical speciation at the submicrometre scale. Here we review the technical capabilities and limitations of high-resolution secondary ion mass spectrometry (NanoSIMS) and scanning transmission (soft) X-ray microscopy (STXM) and give examples of their applications. Whereas NanoSIMS can be combined with isotope-labelling, thereby localizing the distribution of cellular activities (e.g. carbon/nitrogen fixation/turnover), STXM provides information on the location and chemical speciation of metabolites and products of redox reactions. We propose the combined use of both techniques and discuss the technical challenges of their joint application. Both techniques have the potential to enhance our understanding of cellular mechanisms and activities that contribute to microbially mediated processes, such as the biogeochemical cycling of elements, the transformation of contaminants and the precipitation of mineral phases.

Three-dimensional structure and defects in colloidal photonic crystals revealed by tomographic scanning transmission X-ray microscopy.

Self-assembled colloidal crystals have attracted major attention because of their potential as low-cost three-dimensional (3D) photonic crystals. Although a high degree of perfection is crucial for the properties of these materials, little is known about their exact structure and internal defects. In this study, we use tomographic scanning transmission X-ray microscopy (STXM) to access the internal structure of self-assembled colloidal photonic crystals with high spatial resolution in three dimensions for the first time. The positions of individual particles of 236 nm in diameter are identified in three dimensions, and the local crystal structure is revealed. Through image analysis, structural defects, such as vacancies and stacking faults, are identified. Tomographic STXM is shown to be an attractive and complementary imaging tool for photonic materials and other strongly absorbing or scattering materials that cannot be characterized by either transmission or scanning electron microscopy or optical nanoscopy.