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.

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.

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.

Suitability of lectin binding studies for the characterization of redox-active microbial environmental biofilms

Aquatic environmental microbial biofilms grow in a broad range of redox environments from oxic to methanogenic, and they often also establish internal redox gradients. In technical applications, biofilms are also subjected to controlled redox conditions. Studies on biofilms often make use of fluorescence microscopic imaging techniques together with lectin binding analysis to gain insights into structure, composition, and functions of the biofilms. Here we studied the direct influence of redox potentials on fluorescence lectin binding analyses (FLBA) for two commonly used lectin-fluorophore conjugates. An effect of the electrical potential on signal intensity was observed and found to be statistically significant. The signal intensity changes however, remained within the range of a few percent total. A significant drop in intensity was only observed for extremely oxidizing potentials, typically not found under environmental conditions. Our results showed that the fluorophore itself and not the lectin binding to the respective glycoconjugate causes fluorescence changes. The two tested lectin-fluorophores are shown to be suitable for studying the distribution and composition of EPS in environmental biofilms or technical applications and under varying redox conditions.

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.

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.

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.

Effect of different oxide and hybrid precursors on MOF-CVD of ZIF-8 films

Chemical vapor deposition of metal-organic frameworks (MOF-CVD) will facilitate the integration of porous and crystalline coatings in electronic devices. In the two-step MOF-CVD process, a precursor layer is first deposited and subsequently converted to a MOF through exposure to linker vapor. We herein report the impact of different metal oxide and metalcone layers as precursors for zeolitic imidazolate framework ZIF-8 films.

Complexation by cysteine and iron mineral adsorption limit cadmium mobility during metabolic activity of Geobacter sulfurreducens

Cadmium (Cd) adversely affects human health by entering the food chain via anthropogenic activity. In order to mitigate risk, a better understanding of the biogeochemical mechanisms limiting Cd mobility in the environment is needed. While Cd is not redox-active, Cd speciation varies (i.e., aqueous, complexed, adsorbed), and influences mobility. Here, the cycling of Cd in relation to initial speciation during the growth of Geobacter sulfurreducens was studied. Either fumarate or ferrihydrite (Fh) was provided as an electron acceptor and Cd was present as: (1) an aqueous cation, (2) an aqueous complex with cysteine, which is often present in metal stressed soil environments, or (3) adsorbed to Fh. During microbial Fe(iii) reduction, the removal of Cd was substantial (∼80% removal), despite extensive Fe(ii) production (ratio Fe(ii)total : Fetotal = 0.8). When fumarate was the electron acceptor, there was higher removal from solution when Cd was complexed with cysteine (97-100% removal) compared to aqueous Cd (34-50%) removal. Confocal laser scanning microscopy (CLSM) demonstrated the formation of exopolymeric substances (EPS) in all conditions and that Cd was correlated with EPS in the absence of Fe minerals (r = 0.51-0.56). Most notable is that aqueous Cd was more strongly correlated with Geobacter cells (r = 0.72) compared to Cd-cysteine complexes (r = 0.51). This work demonstrates that Cd interactions with cell surfaces and EPS, and Cd solubility during metabolic activity are dependent upon initial speciation. These processes may be especially important in soil environments where sulfur is limited and Fe and organic carbon are abundant.

Aggregation-dependent electron transfer via redox-active biochar particles stimulate microbial ferrihydrite reduction

Microbial Fe(III) reduction plays an important role for biogeochemical carbon and iron cycling in sediments and soils. Biochar is used as a soil amendment to increase fertility and lower N₂O/CO₂ emissions. It is redox-active and can stimulate microbial Fe(III) mineral reduction. It is currently unknown, however, how the aggregation of cells and Fe(III) minerals with biochar particles influence microbial Fe(III) reduction. Therefore, we determined rates and extent of ferrihydrite (Fh) reduction in S. oneidensis MR-1 cell suspensions with different particles sizes of wood-derived Swiss biochar and KonTiki biochar at different biochar/Fh ratios. We found that at small biochar particle size and high biochar/Fh ratios, the biochar, MR-1 cells and Fh closely aggregated, therefore addition of biochar stimulated electron transfer and microbial Fh reduction. In contrast, large biochar particles and low biochar/Fh ratios inhibited the electron transfer and Fe(III) reduction due to the lack of effective aggregation. These results suggest that for stimulating Fh reduction, a certain biochar particle size and biochar/Fh ratio is necessary leading to a close aggregation of all phases. This aggregation favors electron transfer from cells to Fh via redox cycling of the electron donating and accepting functional groups of biochar and via direct electron transfer through conductive biochar carbon matrices. These findings improve our understanding of electron transfer between microorganisms and Fe(III) minerals via redox-active biochar and help to evaluate the impact of biochar on electron transfer processes in the environment.

Instrumentation for in situ flow electrochemical Scanning Transmission X-ray Microscopy (STXM)

We report the design and performance of a 3-electrode device for real time in situ scanning transmission X-ray microscopy studies of electrochemical processes under both static (sealed, non-flow) conditions and with a continuous flow of electrolytes. The device was made using a combination of silicon microfabrication and 3D printing technologies. The performance is illustrated by results of a study of copper deposition and stripping at a gold working electrode. X-ray absorption spectromicroscopy at the Cu 2p edge was used to follow the evolution as a function of potential and time of the spatial distributions of Cu(0) and Cu(i) species electro-deposited from an aqueous solution of copper sulphate. The results are interpreted in terms of competing mechanisms for the reduction of Cu(ii).

Organic coating on biochar explains its nutrient retention and stimulation of soil fertility

Amending soil with biochar (pyrolized biomass) is suggested as a globally applicable approach to address climate change and soil degradation by carbon sequestration, reducing soil-borne greenhouse-gas emissions and increasing soil nutrient retention. Biochar was shown to promote plant growth, especially when combined with nutrient-rich organic matter, e.g., co-composted biochar. Plant growth promotion was explained by slow release of nutrients, although a mechanistic understanding of nutrient storage in biochar is missing. Here we identify a complex, nutrient-rich organic coating on co-composted biochar that covers the outer and inner (pore) surfaces of biochar particles using high-resolution spectro(micro)scopy and mass spectrometry. Fast field cycling nuclear magnetic resonance, electrochemical analysis and gas adsorption demonstrated that this coating adds hydrophilicity, redox-active moieties, and additional mesoporosity, which strengthens biochar-water interactions and thus enhances nutrient retention. This implies that the functioning of biochar in soil is determined by the formation of an organic coating, rather than biochar surface oxidation, as previously suggested.

Biochar promotes plant growth via a slow release of nutrients; however, a mechanistic understanding of nutrient storage in biochar is lacking. Here, using high-resolution spectromicroscopy and mass spectrometry, the authors identify an organic coating on co-composted particles that enhances nutrient retention.

Preparation of Propargyl Amines in a ZnCl2–Dimethylurea Deep-Eutectic Solvent

The coupling of an aldehyde, an amine, and an alkyne to yield propargyl amines was performed in a deep-eutectic solvent composed of zinc chloride and dimethylurea. The deep-eutectic solvent acts simultaneously as catalyst and solvent giving access to a variety of propargyl amines, which were isolated in moderate to very good yields.

Iron Isotope Fractionation during Fe(II) Oxidation Mediated by the Oxygen-Producing Marine Cyanobacterium Synechococcus PCC 7002

In this study, we couple iron isotope analysis to microscopic and mineralogical investigation of iron speciation during circumneutral Fe(II) oxidation and Fe(III) precipitation with photosynthetically produced oxygen. In the presence of the cyanobacterium Synechococcus PCC 7002, aqueous Fe(II) (Fe(II)_aq) is oxidized and precipitated as amorphous Fe(III) oxyhydroxide minerals (iron precipitates, Fe_ppt), with distinct isotopic fractionation (ε⁵⁶Fe) values determined from fitting the δ⁵⁶Fe(II)_aq (1.79‰ and 2.15‰) and the δ⁵⁶Fe_ppt (2.44‰ and 2.98‰) data trends from two replicate experiments. Additional Fe(II) and Fe(III) phases were detected using microscopy and chemical extractions and likely represent Fe(II) and Fe(III) sorbed to minerals and cells. The iron desorbed with sodium acetate (Fe_NaAc) yielded heavier δ⁵⁶Fe compositions than Fe(II)_aq. Modeling of the fractionation during Fe(III) sorption to cells and Fe(II) sorption to Fe_ppt, combined with equilibration of sorbed iron and with Fe(II)_aq using published fractionation factors, is consistent with our resulting δ⁵⁶Fe_NaAc. The δ⁵⁶Fe_ppt data trend is inconsistent with complete equilibrium exchange with Fe(II)_aq. Because of this and our detection of microbially excreted organics (e.g., exopolysaccharides) coating Fe_ppt in our microscopic analysis, we suggest that electron and atom exchange is partially suppressed in this system by biologically produced organics. These results indicate that cyanobacteria influence the fate and composition of iron in sunlit environments via their role in Fe(II) oxidation through O₂ production, the capacity of their cell surfaces to sorb iron, and the interaction of secreted organics with Fe(III) minerals.

Solvent-free coupling of aryl halides with pyrroles applying visible-light photocatalysis

A novel reactor for solvent-free, visible-light-driven photocatalytic transformations was developed.

Application and characterization of electroactive membranes based on carbon nanotubes and zerovalent iron nanoparticles

Carbon nanotube (CNT) membranes were produced from multi-walled CNTs by a filtration technique and used for the removal of the betablocker metoprolol by adsorptive and reactive processes. The reactivity of CNT membranes was enhanced by nanoparticulate zero-valent iron (NZVI) which was deposited on the CNT membranes by pulsed voltammetry applying defined number of pulses (Fe-CNT (100) and Fe-CNT (400) membranes). Surface analysis with SEM showed iron nanoparticle sizes between 19 and 425 nm. Pore size distribution for the different membranes was determined by capillary flow porometry (Galwick fluid). Pore size distribution for all membranes was similar (40 nm), which resulted in a water permeability typical for microfiltration membranes. Metoprolol was removed by the CNT membrane only by sorption, whereas the Fe-CNT membrane revealed also metoprolol degradation due to Fenton type reactions. Further application of electrochemical potentials on both the CNT and the Fe-CNT membranes improved the removal efficiencies to 74% for CNT membranes at 1 V and to 97% for Fe-CNT (400) membranes at 1 V. Seven transformation products have been identified for metoprolol by high-resolution mass spectrometry when electrochemical degradation was performed with CNT and Fe-CNT membranes. Additionally, two of the identified transformation products (TPs) were also observed for Fe-CNT membranes without the application of electrochemical potential. However, only 10% of the degraded metoprolol could be explained by the formation of TPs.

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.

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.

A novel approach to study the structure-property relationships and applications in living systems of modular Cu(2+) fluorescent probes

A series of Cu²⁺ probe which contains 9 probes have been synthesized and established. All the probes were synthesized using Rhodamine B as the fluorophore, conjugated to various differently substituted cinnamyl aldehyde with C=N Schiff base structural motif as their core moiety. The structure-property relationships of these probes have been investigated. The change of optical properties, caused by different electronic effect and steric effect of the recognition group, has been analyzed systematically. DFT calculation simulation of the Ring-Close and Ring-Open form of all the probes have been employed to illuminate, summarize and confirm these correlations between optical properties and molecular structures. In addition, biological experiment demonstrated that all the probes have a high potential for both sensitive and selective detection, mapping of adsorbed Cu²⁺ both in vivo and environmental microbial systems. This approach provides a significant strategy for studying structure-property relationships and guiding the synthesis of probes with various optical properties.

Limited influence of Si on the preservation of Fe mineral-encrusted microbial cells during experimental diagenesis

The reconstruction of the history of microbial life since its emergence on early Earth is impaired by the difficulty to prove the biogenicity of putative microfossils in the rock record. While most of the oldest rocks on Earth have been exposed to different grades of diagenetic alterations, little is known about how the remains of micro-organisms evolve when exposed to pressure (P) and temperature (T) conditions typical of diagenesis. Using spectroscopy and microscopy, we compared morphological, mineralogical, and chemical biosignatures exhibited by Fe mineral-encrusted cells of the bacterium Acidovorax sp. BoFeN1 after long-term incubation under ambient conditions and after experimental diagenesis. We also evaluated the effects of Si on the preservation of microbial cells during the whole process. At ambient conditions, Si affected the morphology but not the identity (goethite) of Fe minerals that formed around cells. Fe-encrusted cells were morphologically well preserved after 1 week at 250 °C-140 MPa and after 16 weeks at 170 °C-120 MPa in the presence or in the absence of Si. Some goethite transformed to hematite and magnetite at 250 °C-140 MPa, but in the presence of Si more goethite was preserved. Proteins-the most abundant cellular components-were preserved over several months at ambient conditions but disappeared after incubations at high temperature and pressure conditions, both in the presence and in the absence of Si. Other organic compounds, such as lipids and extracellular polysaccharides seemed well preserved after exposure to diagenetic conditions. This study provides insights about the composition and potential preservation of microfossils that could have formed in Fe- and Si-rich Precambrian oceans.

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.

Magnetite impregnation effects on the sorbent properties of activated carbons and biochars

This paper discusses the sorbent properties of magnetic activated carbons and biochars produced by wet impregnation with iron oxides. The sorbents had magnetic susceptibilities consistent with theoretical predictions for carbon-magnetite composites. The high BET surface areas of the activated carbons were preserved in the synthesis, and enhanced for one low surface area biochar by dissolving carbonates. Magnetization decreased the point of zero charge. Organic compound sorption correlated strongly with BET surface areas for the pristine and magnetized materials, while metal cation sorption did not show such a correlation. Strong sorption of the hydrophobic organic contaminant phenanthrene to the activated carbon or biochar surfaces was maintained following magnetite impregnation, while phenol sorption was diminished, probably due to enhanced carbon oxidation. Copper, zinc and lead sorption to the activated carbons and biochars was unchanged or slightly enhanced by the magnetization, and iron oxides also contributed to the composite metal sorption capacity. While a magnetic biochar with 219 ± 3.7 m(2)/g surface area nearly reached the very strong organic pollutant binding capacity of the two magnetic activated carbons, a magnetic biochar with 68 ± 2.8 m(2)/g surface area was the best metal sorbent. Magnetic biochars thus hold promise as more sustainable alternatives to coal-derived magnetic activated carbons.

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.

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.

3-D analysis of bacterial cell-(iron)mineral aggregates formed during Fe(II) oxidation by the nitrate-reducing Acidovorax sp. strain BoFeN1 using complementary microscopy tomography approaches

The formation of cell-(iron)mineral aggregates as a consequence of bacterial iron oxidation is an environmentally widespread process with a number of implications for processes such as sorption and coprecipitation of contaminants and nutrients. Whereas the overall appearance of such aggregates is easily accessible using 2-D microscopy techniques, the 3-D and internal structure remain obscure. In this study, we examined the 3-D structure of cell-(iron)mineral aggregates formed during Fe(II) oxidation by the nitrate-reducing Acidovorax sp. strain BoFeN1 using a combination of advanced 3-D microscopy techniques. We obtained 3-D structural and chemical information on different cellular encrustation patterns at high spatial resolution (4-200 nm, depending on the method): more specifically, (1) cells free of iron minerals, (2) periplasm filled with iron minerals, (3) spike- or platelet-shaped iron mineral structures, (4) bulky structures on the cell surface, (5) extracellular iron mineral shell structures, (6) cells with iron mineral filled cytoplasm, and (7) agglomerations of extracellular globular structures. In addition to structural information, chemical nanotomography suggests a dominant role of extracellular polymeric substances (EPS) in controlling the formation of cell-(iron)mineral aggregates. Furthermore, samples in their hydrated state showed cell-(iron)mineral aggregates in pristine conditions free of preparation (i.e., drying/dehydration) artifacts. All these results were obtained using 3-D microscopy techniques such as focused ion beam (FIB)/scanning electron microscopy (SEM) tomography, transmission electron microscopy (TEM) tomography, scanning transmission (soft) X-ray microscopy (STXM) tomography, and confocal laser scanning microscopy (CLSM). It turned out that, due to the various different contrast mechanisms of the individual approaches, and due to the required sample preparation steps, only the combination of these techniques was able to provide a comprehensive understanding of structure and composition of the various Fe-precipitates and their association with bacterial cells and EPS.

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.

Characterization of the physiology and cell-mineral interactions of the marine anoxygenic phototrophic Fe(II) oxidizer Rhodovulum iodosum--implications for Precambrian Fe(II) oxidation

Anoxygenic phototrophic Fe(II)-oxidizing bacteria (photoferrotrophs) are suggested to have contributed to the deposition of banded iron formations (BIFs) from oxygen-poor seawater. However, most studies evaluating the contribution of photoferrotrophs to Precambrian Fe(II) oxidation have used freshwater and not marine strains. Therefore, we investigated the physiology and mineral products of Fe(II) oxidation by the marine photoferrotroph Rhodovulum iodosum. Poorly crystalline Fe(III) minerals formed initially and transformed to more crystalline goethite over time. During Fe(II) oxidation, cell surfaces were largely free of minerals. Instead, the minerals were co-localized with EPS suggesting that EPS plays a critical role in preventing cell encrustation, likely by binding Fe(III) and directing precipitation away from cell surfaces. Fe(II) oxidation rates increased with increasing initial Fe(II) concentration (0.43-4.07 mM) under a light intensity of 12 μmol quanta m(-2) s(-1). Rates also increased as light intensity increased (from 3 to 20 μmol quanta m(-2) s(-1)), while the addition of Si did not significantly change Fe(II) oxidation rates. These results elaborate on how the physical and chemical conditions present in the Precambrian ocean controlled the activity of marine photoferrotrophs and confirm the possibility that such microorganisms could have oxidized Fe(II), generating the primary Fe(III) minerals that were then deposited to some Precambrian BIFs.

3D chemical mapping: application of scanning transmission (soft) X-ray microscopy (STXM) in combination with angle-scan tomography in bio-, geo-, and environmental sciences

The identification of environmental processes and mechanisms often requires information on the organochemical and inorganic composition of specimens at high spatial resolution. X-ray spectroscopy (XAS) performed in the soft X-ray range (100-2,200 eV) provides chemical speciation information for elements that are of high biogeochemical relevance such as carbon, nitrogen, and oxygen but also includes transition metals such as iron, manganese, or nickel. Synchrotron-based scanning transmission X-ray microscopy (STXM) combines XAS with high resolution mapping on the 20-nm scale. This provides two-dimensional (2D) quantitative information about the distribution of chemical species such as organic macromolecules, metals, or mineral phases within environmental samples. Furthermore, the combination of STXM with angle-scan tomography allows for three-dimensional (3D) spectromicroscopic analysis of bio-, geo-, or environmental samples. For the acquisition of STXM tomography data, the sample is rotated around an axis perpendicular to the X-ray beam. Various sample preparation approaches such as stripes cut from TEM grids or the preparation of wet cells allow for preparing environmentally relevant specimens in a dry or in a fully hydrated state for 2D and 3D STXM measurements. In this chapter we give a short overview about the principles of STXM, its application to environmental sciences, different preparation techniques, and the analysis and 3D reconstruction of STXM tomography data.

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.

Helium Ion Microscopy (HIM) for the imaging of biological samples at sub-nanometer resolution

Scanning Electron Microscopy (SEM) has long been the standard in imaging the sub-micrometer surface ultrastructure of both hard and soft materials. In the case of biological samples, it has provided great insights into their physical architecture. However, three of the fundamental challenges in the SEM imaging of soft materials are that of limited imaging resolution at high magnification, charging caused by the insulating properties of most biological samples and the loss of subtle surface features by heavy metal coating. These challenges have recently been overcome with the development of the Helium Ion Microscope (HIM), which boasts advances in charge reduction, minimized sample damage, high surface contrast without the need for metal coating, increased depth of field, and 5 angstrom imaging resolution. We demonstrate the advantages of HIM for imaging biological surfaces as well as compare and contrast the effects of sample preparation techniques and their consequences on sub-nanometer ultrastructure.

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.

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.

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.

Advances in the detection of as in environmental samples using low energy X-ray fluorescence in a scanning transmission X-ray microscope: arsenic immobilization by an Fe(II)-oxidizing freshwater bacteria

Speciation and quantitative mapping of elements, organic and inorganic compounds, and mineral phases in environmental samples at high spatial resolution is needed in many areas of geobiochemistry and environmental science. Scanning transmission X-ray microscopes (STXMs) provide a focused beam which can interrogate samples at a fine spatial scale. Quantitative chemical information can be extracted using the transmitted and energy-resolved X-ray fluorescence channels simultaneously. Here we compare the relative merits of transmission and low-energy X-ray fluorescence detection of X-ray absorption for speciation and quantitative analysis of the spatial distribution of arsenic(V) within cell-mineral aggregates formed by Acidovorax sp. strain BoFeN1, an anaerobic nitrate-reducing Fe(II)-oxidizing β-proteobacteria isolated from the sediments of Lake Constance. This species is noted to be highly tolerant to high levels of As(V). Related, As-tolerant Acidovorax-strains have been found in As-contaminated groundwater wells in Bangladesh and Cambodia wherein they might influence the mobility of As by providing sorption sites which might have different properties as compared to chemically formed Fe-minerals. In addition to demonstrating the lower detection limits that are achieved with X-ray fluorescence relative to transmission detection in STXM, this study helps to gain insights into the mechanisms of As immobilization by biogenic Fe-mineral formation and to further the understanding of As-resistance of anaerobic Fe(II)-oxidizing bacteria.

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.

Green rust formation during Fe(II) oxidation by the nitrate-reducing Acidovorax sp. strain BoFeN1

Green rust (GR) as highly reactive iron mineral potentially plays a key role for the fate of (in)organic contaminants, such as chromium or arsenic, and nitroaromatic compounds functioning both as sorbent and reductant. GR forms as corrosion product of steel but is also naturally present in hydromorphic soils and sediments forming as metastable intermediate during microbial Fe(III) reduction. Although already suggested to form during microbial Fe(II) oxidation, clear evidence for GR formation during microbial Fe(II) oxidation was lacking. In the present study, powder XRD, synchrotron-based XAS, Mössbauer spectroscopy, and TEM demonstrated unambiguously the formation of GR as an intermediate product during Fe(II) oxidation by the nitrate-reducing Fe(II)-oxidizer Acidovorax sp. strain BoFeN1. The spatial distribution and Fe redox-state of the precipitates associated with the cells were visualized by STXM. It showed the presence of extracellular Fe(III), which can be explained by Fe(III) export from the cells or extracellular Fe(II) oxidation by an oxidant diffusing from the cells. Moreover, GR can be oxidized by nitrate/nitrite and is known as a catalyst for oxidation of dissolved Fe(II) by nitrite/nitrate and may thus contribute to the production of extracellular Fe(III). As a result, strain BoFeN1 may contribute to Fe(II) oxidation and nitrate reduction both by an direct enzymatic pathway and an indirect GR-mediated process.

Quantitative high-resolution mapping of phenanthrene sorption to black carbon particles

Sorption of hydrophobic organic contaminants such as polycyclic aromatic hydrocarbons (PAHs) to black carbon (BC) particles has been the focus of numerous studies. Conclusions on sorption mechanisms of PAH on BC were mostly derived from studies of sorption isotherms and sorption kinetics, which are based on batch experiments. However, mechanistic modeling approaches consider processes at the subparticle scale, some including transport within the pore-space or different spatial pore-domains. Direct evidence based on analytical techniques operating at the submicrometer scale for the location of sorption sites and the adsorbed species is lacking. In this work, we identified, quantified, and mapped the sorption of PAHs on different BC particles (activated carbon, charcoal and diesel soot) on a 25-100 nm scale using scanning transmission X-ray microscopy (STXM). In addition, we visualized the pore structure of the particles by transmission electron microscopy (TEM) on the 1-10 nm-scale. The combination of the chemical information from STXM with the physical information from TEM revealed that phenanthrene accumulates in the interconnected pore-system along primary "cracks" in the particles, confirming an adsorption mechanism.

Study of the crystallographic architecture of corals at the nanoscale by scanning transmission X-ray microscopy and transmission electron microscopy

We have investigated the nanotexture and crystallographic orientation of aragonite in a coral skeleton using synchrotron-based scanning transmission X-ray microscopy (STXM) and transmission electron microscopy (TEM). Polarization-dependent STXM imaging at 40-nm spatial resolution was used to obtain an orientation map of the c-axis of aragonite on a focused ion beam milled ultrathin section of a Porites coral. This imaging showed that one of the basic units of coral skeletons, referred to as the center of calcification (COC), consists of a cluster of 100-nm aragonite globules crystallographically aligned over several micrometers with a fan-like distribution and with the properties of single crystals at the mesoscale. The remainder of the skeleton consists of aragonite single-crystal fibers in crystallographic continuity with the nanoglobules comprising the COC. Our observation provides information on the nm-scale processes that led to biomineral formation in this sample. Importantly, the present study illustrates how the methodology described here, which combines HRTEM and polarization-dependent synchrotron-based STXM imaging, offers an interesting new approach for investigating biomineralizing systems at the nm-scale.

Microbial architecture of environmental sulfur processes: a novel syntrophic sulfur-metabolizing consortia

Microbial oxidation of sulfur-rich mining waste materials drives acid mine drainage (AMD) and affects the global sulfur biogeochemical cycle. The generation of AMD is a complex, dynamic process that proceeds via multiple reaction pathways. The role of natural consortia of microbes in AMD generation, however, has received very little attention despite their widespread occurrence in mining environments. Through a combination of geochemical experimentation and modeling, scanning transmission X-ray microscopy, and fluorescent in situ hybridization, we show a novel interdependent metabolic arrangement of two ubiquitous and abundant AMD bacteria: chemoautotrophic sulfur-oxidizing Acidithiobacillus sp. and heterotrophic Acidiphilium sp. Highly reminiscent of anaerobic methane oxidation (AOM) consortia, these bacteria are spatially segregated within a planktonic macrostructure of extracellular polymeric substance in which they syntrophically couple sulfur oxidation and reduction reactions in a mutually beneficial arrangement that regenerates their respective sulfur substrates. As discussed here, the geochemical impacts of microbial metabolism are linked to the consortial organization and development of the pod structure, which affects cell-cell interactions and interactions with the surrounding geochemical microenvironment. If these pods are widespread in mine waters, echoing the now widespread discovery of AOM consortia, then AMD-driven CO(2) atmospheric fluxes from H(2)SO(4) carbonate weathering could be reduced by as much as 26 TgC/yr. This novel sulfur consortial discovery indicates that organized metabolically linked microbial partnerships are likely widespread and more significant in global elemental cycling than previously considered.