NanoSIMS Analysis Research Articles

Automated identification of soil functional components based on NanoSIMS data

NanoSIMS technique allows to investigate the micro-spatial organization in complex structures in multiple scientific fields such as material science, cosmochemistry, and biogeochemistry. In soil biogeochemistry applications, NanoSIMS-based approaches aim to disentangle the interactions of organic matter (OM) and mineral phases in the heterogeneous soil microstructure. Investigating the spatial arrangement of distinct organic and mineral functional components is necessary to understand how these components interact and contribute to biogeochemical processes in soil systems. Identifying soil functional components within NanoSIMS measurements necessitates advanced and efficient data processing tools capable of accessibility and automation. We have developed a pre-processing tool to streamline NanoSIMS data preparation and handling. The tool is provided as an open-source software toolbox (NanoT). In addition, a two-step unsupervised segmentation method was developed to identify soil functional components based on NanoSIMS analyses. To illustrate the segmentation method, here we describe its application to two exemplary NanoSIMS measurements. This allows to distinguish mineral- and OM-dominated regions, as well as different mineral phases. To improve the detection of iron oxides and aluminosilicates, the 56Fe16O− channel was separately processed. The presented NanoSIMS-based processing workflow helps to disentangle functional components within a biogeochemically-diverse microstructure in soils and further warrants applications to a wide range of complex environmental samples.

Uptake of dissolved inorganic nitrogen and N2 fixation by Crocosphaera watsonii under climate change scenarios

The response of N2 fixation to projected future conditions in the ocean cannot be reliably predicted to date. We conducted a minicosm experiment with pre-acclimated cultures of the globally significant diazotroph Crocosphaera watsonii strain WH8501 (“Crocosphaera”). PH and temperature were altered simultaneously to match the RCP scenarios 4.5 and 6 and investigate a more realistic future scenario compared to studies that focus on changes of a single stressor only. The cell abundance and nitrogen metabolism of Crocosphaera was monitored over 5 days. Our results imply that Crocosphaera is able to simultaneously perform N2 fixation and assimilate dissolved inorganic nitrogen (DIN, i.e., nitrate and ammonium) under all the conditions tested and implies a competition with non-diazotrophic phytoplankton for DIN, which should be further investigated. Using NanoSIMS analysis of single cells, our results point towards a preference for DIN assimilation over N2 fixation under more acidic and warmer conditions. Overall, our results show that while the combined alteration of pH and temperature had a negative effect on the diazotroph’s growth and N2 fixation, Crocosphaera is likely to cope well with conditions in the future ocean. The high intra-population variability in nitrogen assimilation pathways may give this species the flexibility to quickly react to environmental changes.

Magnetron Sputtering as a Microstructural Screening Tool for Laser Additive Manufacturing: Study on Ni Superalloys

In this work, magnetron sputtering coupled with a heat treatment is demonstrated as a route to obtain surrogate microstructures comparable to those achieved by laser‐based additive manufacturing (AM) for Ni superalloys. Furthermore, this technique is shown to be a novel and efficient way of screening elemental additions with high compositional resolution for AM, without the need for designing and characterizing custom‐atomized powders. Herein, Inconel 718 films are sputtered from both arc‐melted and AM targets to capture any compositional changes and to develop a comprehensive methodology. Films are characterized via electron microscopy techniques to establish similarities between sputtered plus heat‐treated films and bulk AM Inconel 718 microstructures reported in literature. Since Inconel 718 is susceptible to high‐temperature S embrittlement, films were then co‐sputtered with small amounts of Zr or Hf, which are found to facilitate sulfur segregation via nano secondary ion mass spectrometry analysis. Overall, this work highlights how magnetron sputtering plus heat treatment can be leveraged to rapidly screen novel AM microstructures, thereby accelerating the development and deployment of AM materials.

Anabolic and Catabolic Microbial Activity in Hydrocarbon-rich Sediments of Guaymas Basin

Guaymas Basin, located in the Gulf of California, Mexico, is a young marginal ocean basin with high sedimentation rates of >1 mm/year, active seafloor spreading, and steep geothermal gradients in its sediment. It hosts a unique microbial subseafloor biosphere as these conditions lead to thermal cracking of sedimentary organic matter and the production of bioavailable organic carbon compounds and hydrocarbons already at shallow depths. The abundance and diversity of potential microbial substrates raise the question of which substrates are being used for catabolic and anabolic microbial metabolism. We thus analyzed the microbial uptake of hydrocarbons and inorganic nitrogen using nanoscale secondary ion mass spectrometry (NanoSIMS) analysis after incubation with stable-isotope labeled substrates. Incubations were carried out with samples from two International Ocean Discovery Program (IODP) Exp. 385 drill sites. Site U1545 is characterized by undisturbed sedimentary strata and a temperature gradient of 225°C/km, whereas Site U1546 has experienced a sill intrusion at greater depth, below the cored interval. The intrusion led to temporary heating of the sediment, but a temperature gradient of 221°C/km indicates thermal equilibration with the surrounding sediment since sill emplacement. Incubations were carried out with 13C-benzene + 2H-hexadecane + 15NH4Cl or 13C-methane + 15NH4Cl at in-situ temperature (4-62°C) and pressure (25 MPa) for 42 days. Additionally, sulfate reduction rates (SRR) were measured by incubating the samples with four aliphatic hydrocarbons + four aromatic hydrocarbons or methane and radioisotope-labeled 35SO42- for 10 days, also at in-situ temperature and pressure. The NanoSIMS analyses reveal that a few samples showed detectable microbial assimilation of hydrocarbons. Nitrogen was significantly assimilated in some samples incubated with methane. The assimilation mostly occurred in samples from near the seafloor (2 and 44 meter below seafloor (mbsf)). Our results indicate that anaerobic microorganisms in Guaymas Basin take up measurable amounts of hydrocarbons and inorganic nitrogen even in the relatively short incubation time of 42 days. The results of the SRR measurements indicate that a mixture of hydrocarbons and methane increases the SRR in samples from near the seafloor (2 mbsf) and around the sulfate-methane transition zone (44 and 55 mbsf) but not in samples from greater depths. Our results show that anaerobic microorganisms in Guaymas Basin can use hydrocarbons for anabolic and catabolic metabolism in this extreme environment. Given the high abundance of various carbon compounds, nitrogen appears to be a limiting factor for cellular growth.

Trophic interactions shape the spatial organization of medium-chain carboxylic acid producing granular biofilm communities.

Granular biofilms producing medium-chain carboxylic acids (MCCA) from carbohydrate-rich industrial feedstocks harbor highly streamlined communities converting sugars to MCCA either directly or via lactic acid as intermediate. We investigated the spatial organization and growth activity patterns of MCCA producing granular biofilms grown on an industrial side stream to test (i) whether key functional guilds (lactic acid producing Olsenella and MCCA producing Oscillospiraceae) stratified in the biofilm based on substrate usage, and (ii) whether spatial patterns of growth activity shaped the unique, lenticular morphology of these biofilms. First, three novel isolates (one Olsenella and two Oscillospiraceae species) representing over half of the granular biofilm community were obtained and used to develop FISH probes, revealing that key functional guilds were not stratified. Instead, the outer 150-500 µm of the granular biofilm consisted of a well-mixed community of Olsenella and Oscillospiraceae, while deeper layers were made up of other bacteria with lower activities. Second, nanoSIMS analysis of 15N incorporation in biofilms grown in normal and lactic acid amended conditions suggested Oscillospiraceae switched from sugars to lactic acid as substrate. This suggests competitive-cooperative interactions may govern the spatial organization of these biofilms, and suggests that optimizing biofilm size may be a suitable process engineering strategy. Third, growth activities were similar in the polar and equatorial biofilm peripheries, leaving the mechanism behind the lenticular biofilm morphology unexplained. Physical processes (e.g., shear hydrodynamics, biofilm life cycles) may have contributed to lenticular biofilm development. Together, this study develops an ecological framework of MCCA-producing granular biofilms that informs bioprocess development.

Effect of oxygen fugacity on the storage of water in wadsleyite and olivine in H and H–C fluids and implications for melting atop the transition zone

Abstract. This study aims to experimentally constrain the water storage capacities of olivine and wadsleyite at a depth near 410 km (12–14 GPa) under water-saturated conditions, as a function of temperature, oxygen fugacity, and the presence of carbon (molar H / C of 2). Experiments have been conducted in the multi-anvil press, with sealed double capsules to preserve fluids, at 1200 to 1400 ∘C and three different oxygen fugacities fixed at the rhenium–rhenium oxide buffer (RRO), nickel–nickel oxide buffer (NNO), and iron-wüstite (IW) for oxidizing, intermediate, and reducing conditions, respectively. The water contents of minerals were measured by Raman spectroscopy that allows a very small beam size to be used and were cross-checked on a few samples with NanoSIMS analyses. We observe an effect, although slight, of fO2 on the water storage capacity of both wadsleyite and olivine and also on their solidus temperatures. At 1200 ∘C, the storage capacity of the nominally anhydrous minerals (NAMS) increases with increasing oxygen fugacity (from the IW to the RRO buffer) from 1 wt % to 1.5 wt % H2O in wadsleyite and from 0.1 wt % to 0.2 wt % in olivine, owing to the increase in H2O / H2 speciation in the fluid, whereas at 1400 ∘C the storage capacity decreases from 1 wt % to 0.75 wt % H2O in wadsleyite and down to 0.03 wt % for olivine. At high temperature, the water storage capacity is lowered due to melting, and the more oxidized the conditions are the more the solidus is depressed. Still, at 1400 ∘C and IW, wadsleyite can store substantial amounts of water: 0.8 wt % to 1 wt % H2O. The effect of carbon is to decrease water storage capacity in both wadsleyite and olivine by an average factor 2 at 1300–1400 ∘C. The trends in water storage as a function of fO2 and C presence are confirmed by NanoSIMS measurements. The solidus at IW without C is located between 1300 and 1400 ∘C in the wadsleyite stability field and drops to temperatures below 1300 ∘C in the olivine stability field. With the addition of C, the solidus is found between 1200 and 1300 ∘C in both olivine and wadsleyite stability fields.

Gold-FISH enables targeted NanoSIMS analysis of plant-associated bacteria.

Bacteria colonize plant roots and engage in reciprocal interactions with their hosts. However, the contribution of individual taxa or groups of bacteria to plant nutrition and fitness is not well characterized due to a lack of insitu evidence of bacterial activity. To address this knowledge gap, we developed an analytical approach that combines the identification and localization of individual bacteria on root surfaces via gold-based insitu hybridization with correlative NanoSIMS imaging of incorporated stable isotopes, indicative of metabolic activity. We incubated Kosakonia strain DS-1-associated, gnotobiotically grown rice plants with 15 N-N2 gas to detect insitu N2 fixation activity. Bacterial cells along the rhizoplane showedheterogeneous patterns of 15 N enrichment, ranging from the natural isotope abundance levels up to 12.07 at% 15 N (average and median of 3.36 and 2.85 at% 15 N, respectively, n = 697 cells). The presented correlative optical and chemical imaging analysis is applicable to a broad range of studies investigating plant-microbe interactions. For example, it enables verification of the insitu metabolic activity of host-associated commercialized strains or plant growth-promoting bacteria, thereby disentangling their role in plant nutrition. Such data facilitate the design of plant-microbe combinations for improvement of crop management.

Carbon sequestration in paddy soils: Contribution and mechanisms of mineral-associated SOC formation

In this work, comparative study of paddy and upland soils were carried out to unravel mechanisms of enhanced soil organic carbon (SOC) sequestration in paddy soils using fractionation methods, 13C NMR and Nano-SIMS analysis, as well as organic layer thickness calculations (Core-Shell model). The results showed that although there is a strong increase in particulate SOC in paddy soils compared to that in the upland soils, the increase in mineral-associated SOC is more important, explaining 60–75% of SOC increase in the paddy soils. In the wet and dry alternate cycles of paddy soil, iron (hydr)oxides adsorb relatively small and soluble organic molecules (fulvic acid-like), promote catalytic oxidation and polymerization, thus accelerating formation of larger organic molecules. Upon reductive iron dissolution, these molecules are released and incorporated into existing less soluble organic compounds (humic acid or humin-like), which are coagulated and associated with clay minerals, becoming part of the mineral-associated SOC. The functioning of this “iron wheel” process stimulates accumulation of relatively young SOC into mineral-associated organic carbon pool, and reduces the difference in chemical structure between oxides-bound and clay-bound SOC. Further, the faster turnover of oxides and soil aggregates in paddy soil also facilities interaction between SOC and minerals. The formation of mineral-associated SOC may delay degradation of organic matter during both wet and dry period in the paddy field, therefore enhancing carbon sequestration in paddy soils.

Occurrence and precipitation mechanism of silver in pyrite from chimney fragments in the Edmond hydrothermal field, Central Indian Ridge

The enrichment of precious elements including Au and Ag in submarine hydrothermal sulfide deposits attracts more and more attention. Previous studies indicate that Au and Ag combine distinctly different ligands under the physico-chemical conditions of submarine hydrothermal systems, therefore, the factors controlling their precipitation may be different. In general, silver mineralization has been much less studied than gold mineralization in submarine hydrothermal sulfide deposits. The Ag mineralization process and precipitation mechanism of submarine hydrothermal sulfide deposits formed at Mid-ocean Ridges are still poorly constrained. In this study, we studied the occurrence and precipitation mechanism of Ag in sulfide deposits of Edmond hydrothermal field, located on the intermediate-spreading Central Indian Ridge (CIR).Three ore-forming stages were identified in chimney fragments collected in the Edmond hydrothermal field. The corresponding minerals are (stage I) anhydrite + barite + colloidal/porous pyrite (Py1) + fine-grained sphalerite; (stage II) marcasite; (stage III) euhedral pyrite (Py2) + coarse-grained sphalerite + chalcopyrite + isocubanite. Py1, characterized by colloidal, porous, and micro-sized anhedral morphology, was usually overgrown by marcasite, which is, in turn, surrounded by euhedral-subhedral Py2, usually coexisting with coarse-grained sphalerite, chalcopyrite, and isocubanite. Compared to marcasite and Py2, only Py1 contains abundant native silver nanoparticles. LA-ICP-MS analyses suggest that Py1 contains higher Pb, Cu, Ag, Mn, Tl, Mo, Au, and lower Co as compared to Py2. In-situ LA-ICP-MS and nanoSIMS analyses indicate that Py1 with higher Ag contents (101–586 ppm) has larger variation in sulfur isotopic compositions (0.8 to 6.6‰) than those of Py2 with lower Ag contents (0.22–15.5 ppm; δ34S values: 2.1 to 4.8‰ for Fe-rich samples and 0 to 2.8‰ for Zn-rich samples).Texture, mineral assemblage, pyrite trace element and sulfur isotopic compositions indicate a progressive decrease on the degree of fluid-seawater mixing as the temperature gradually increases during the growth of the chimneys in Edmond hydrothermal field. Phase diagram analysis indicates that the increase in pH and in particular cooling, due to the mixing of the hot hydrothermal fluid with cold seawater, can significantly decrease the solubility of Ag and be the effective mechanisms of silver precipitation. Our results suggest that mixing of hydrothermal fluid with seawater is the main Ag precipitation mechanism for submarine hydrothermal sulfide deposits formed at Mid-ocean Ridges.

NanoSIMS analysis of water content in bridgmanite at the micron scale: An experimental approach to probe water in Earth's deep mantle.

Water, in trace amounts, can greatly alter chemical and physical properties of mantle minerals and exert primary control on Earth's dynamics. Quantifying how water is retained and distributed in Earth's deep interior is essential to our understanding of Earth's origin and evolution. While directly sampling Earth's deep interior remains challenging, the experimental technique using laser-heated diamond anvil cell (LH-DAC) is likely the only method available to synthesize and recover analog specimens throughout Earth's lower mantle conditions. The recovered samples, however, are typically of micron sizes and require high spatial resolution to analyze their water abundance. Here we use nano-scale secondary ion mass spectrometry (NanoSIMS) to characterize water content in bridgmanite, the most abundant mineral in Earth's lower mantle. We have established two working standards of natural orthopyroxene that are likely suitable for calibrating water concentration in bridgmanite, i.e., A119(H2O) = 99 ± 13μg/g (1SD) and A158(H2O) = 293 ± 23μg/g (1SD). We find that matrix effect among orthopyroxene, olivine, and glass is less than 10%, while that between orthopyroxene and clinopyroxene can be up to 20%. Using our calibration, a bridgmanite synthesized by LH-DAC at 33 ± 1GPa and 3,690 ± 120K is measured to contain 1,099 ± 14μg/g water, with partition coefficient of water between bridgmanite and silicate melt ∼0.025, providing the first measurement at such condition. Applying the unique analytical capability of NanoSIMS to minute samples recovered from LH-DAC opens a new window to probe water and other volatiles in Earth's deep mantle.

Retention of dissolved organic matter during podzolisation: Testing processes in laboratory experiments and at the submicron scale

Immobilisation of organic matter in illuvial subsoil horizons is a characteristic result of Podzol formation and development. We tested dissolved organic matter (DOM) immobilisation by mineral mixtures as models of initial illuvial horizons and conducted laboratory experiments by irrigating mineral mixtures with a DOM solution and analysing the eluate solutions. The mineral mixtures consisted of quartz with accessory H+-saturated illite, or Ca2+-saturated illite, or quartz with ferrihydrite. Furthermore, we studied the transport of colloidal proto-imogolite in the ferrihydrite-containing mixture and analysed the spatial distribution of elements by nanoscale secondary ion mass spectrometry (NanoSIMS). Retention of DOM in the presence of Ca2+-saturated illite did not exceed that in the presence of H+-saturated illite, as the promoting effect of the divalent cation was counterbalanced by the initially higher pH. The mineral mixture containing ferrihydrite retained most DOM. In all experiments, aromatic and oxidised DOM moieties were preferentially adsorbed. Colloidal proto-imogolite co-precipitated with DOM and reduced the pore space of the mineral mixture, which increased the residence time and DOM adsorption on ferrihydrite. NanoSIMS analyses showed proto-imogolite deposited on ferrihydrite, with ferrihydrite as the more important DOM adsorbent in ferrihydrite-proto-imogolite assemblages. Furthermore, NanoSIMS revealed less N in adsorbed DOM closer to the mineral surface. Thus, we differentiated between processes of DOM retention in simulated early podzolisation, detecting preferentially adsorbed species and compositional differences within adsorbed DOM layers.

NanoSIMS as an analytical tool for measuring oxygen and hydrogen isotopes in clay minerals from palaeosols: Analytical procedure and preliminary results

Oxygen and hydrogen isotope composition of neoformed clay minerals is commonly used as a palaeoclimatic proxy. Usually, sediments and rocks (including palaeosols) contain not only neoformed clay minerals, but also detrital and/or diagenetic ones. Together with the usually small size (micro- or nanometric) of the clay minerals in these materials, this can generate difficulties during isotopic analyses by conventional spectrometry. To avoid this problem, we used nanoscale secondary ion mass spectrometry (NanoSIMS) to analyse neoformed clay minerals included in palaeosol levels in early Barremian continental profiles located in NE Spain. The bottom levels of the profiles are rich in kaolinite, whereas the top levels contain smectite (beidellite-type). The isotopic compositions of pure powder standards of kaolinite and beidellite were measured in bulk by conventional mass spectrometry to obtain reference values for calibrating the instrumental mass fractionation. Two common preparation techniques for geological samples were tested (thin sections and thick polished sections), revealing that thin sections are more suitable for NanoSIMS analysis due to their lower resin content. The high spatial resolution of the instrument allowed the elemental mapping of the samples, permitting the localization of the minerals of interest and the measurement of isotopic ratios at selected points (1 x 1 μm2) within the samples. The preliminary isotopic results allowed to distinguish a decrease in the average 18O/16O and D/H ratios from the kaolinite in the bottom levels to the smectite in the top levels, reflecting a change in the climatic conditions. The average δ18O and δD values obtained for kaolinite (δ18OSMOW=18±15‰; δDSMOW=-82±36‰ and δ18OSMOW=14±4‰; δDSMOW=-97±37‰) and smectite (δ18OSMOW=13±14‰; δDSMOW=-167±87‰ and δ18OSMOW=11±6‰; δDSMOW=-180±40‰;), respectively, are consistent with the crystallization of the clays in weathering conditions. Despite the uncertainties of these preliminary isotopic measures, the results obtained allowed to estimate an average temperature for kaolinite formation of 21-22°C, and of 16-17°C for smectite. Given suitable calibration using pure isotopic standards and adequate sample preparation, NanoSIMS can thus have a great applicability in palaeoclimatic studies involving the oxygen and hydrogen isotopic composition of nanometre-sized clay minerals from palaeosols samples.

Nickel bioaccessibility in soils with high geochemical background and anthropogenic contamination

Abnormally high concentrations of metals including nickel (Ni) in soils result from high geochemical background (HB) or anthropogenic contamination (AC). Metal bioaccessibility in AC-soils has been extensively explored, but studies in HB-soils are limited. This study examined the Ni bioaccessibility in basalt and black shale derived HB-soils, with AC-soils and soils without contamination (CT) being used for comparison. Although HB- and AC-soils had similar Ni levels (123 ± 43.0 vs 155 ± 84.7 mg kg−1), their Ni bioaccessibility based on the gastric phase of the Solubility Bioaccessibility Research Consortium (SBRC) in vitro assay was different. Nickel bioaccessibility in HB-soils was 6.42 ± 3.78%, 2-times lower than the CT-soils (12.0 ± 9.71%) and 6-times lower than that in AC-soils (42.6 ± 16.3%). Based on the sequential extraction, a much higher residual Ni fractionation in HB-soils than that in CT- and AC-soils was observed (81.9 ± 9.52% vs 68.6 ± 9.46% and 38.7 ± 16.0%). Further, correlation analysis indicate that the available Ni (exchangeable + carbonate-bound + Fe/Mn hydroxide-bound) was highly correlated with Ni bioaccessibility, which was also related to the organic carbon content in soils. The difference in co-localization between Ni and other elements (Fe, Mn and Ca) from high-resolution NanoSIMS analysis provided additional explanation for Ni bioaccessibility. In short, based on the large difference in Ni bioaccessibility in geochemical background and anthropogenic contaminated soils, it is important to base contamination sources for proper risk assessment of Ni-contaminated soils.

The influence of sediment diagenesis and aluminium on oxygen isotope exchange of diatom frustules

The oxygen isotope composition of diatom frustules, δ18Odiatom, is thought to reflect the isotopic composition of the ambient seawater at the time of biomineralization. However, the δ18Odiatom can be overprinted due to the susceptibility of silanol groups (both external and internal) to isotope exchange. Here, using high-resolution imaging, we investigate what factors may influence this post-mortem isotopic alteration during the initial stages of diagenesis in the sediment. A diatomaceous clay was incubated with 18O-enriched seawater with fresh diatom detritus placed at the sediment–water interface (SWI) and at depth in the sediment. NanoSIMS analysis showed that the fresh diatom detritus as well as fossil frustules became significantly enriched in 18O, and that a relationship between Al-content and 18O-exchange could be observed. To further study the potential role of Al as an inhibitor of oxygen exchange, we measured Al on the surface of fossil frustules and performed additional incubations of diatom detritus in seawater with various concentrations of dissolved Al. The presence of Al-rich material bound to the surface of fossil frustules did not reduce the extent of 18O-enrichment in the underlying silica. However, exposure of diatoms detritus to dissolved Al, which led to a significant increase in frustule Al/Si ratio and a homogenously distributed Al in the frustule valve, significantly lowered the amount of 18O-enrichment. We hypothesize that Al incorporated into the silica structure can slow down 18O exchange while Al present as surface contaminants (clays or other aluminosilicates) has no inhibitory role.

In Vivo Evidence of Single 13C and 15N Isotope-Labeled Methanotrophic Nitrogen-Fixing Bacterial Cells in Rice Roots.

ABSTRACTMethane-oxidizing bacteria (methanotrophs) play an ecological role in methane and nitrogen fluxes because they are capable of nitrogen fixation and methane oxidation, as indicated by genomic and cultivation-dependent studies. However, the chemical relationships between methanotrophy and diazotrophy and aerobic and anaerobic reactions, respectively, in methanotrophs remain unclear. No study has demonstrated the cooccurrence of both bioactivities in a single methanotroph bacterium in its natural environment. Here, we demonstrate that both bioactivities in type II methanotrophs occur at the single-cell level in the root tissues of paddy rice (Oryza sativa L. cv. Nipponbare). We first verified that difluoromethane, an inhibitor of methane monooxygenase, affected methane oxidation in rice roots. The results indicated that methane assimilation in the roots mostly occurred due to oxygen-dependent processes. Moreover, the results indicated that methane oxidation-dependent and methane oxidation-independent nitrogen fixation concurrently occurred in bulk root tissues. Subsequently, we performed fluorescence in situ hybridization and NanoSIMS analyses, which revealed that single cells of type II methanotrophs (involving six amplicon sequence variants) in paddy rice roots simultaneously and logarithmically fixed stable isotope gases 15N2 and 13CH4 during incubation periods of 0, 23, and 42 h, providing in vivo functional evidence of nitrogen fixation in methanotrophic cells. Furthermore, 15N enrichment in type II methanotrophs at 42 h varied among cells with an increase in 13C accumulation, suggesting that either the release of fixed nitrogen into root systems or methanotroph metabolic specialization is dependent on different microenvironmental niches in the root.

Root exudate chemistry affects soil carbon mobilization via microbial community reassembly

Plant roots are one of the major mediators that allocate carbon captured from the atmosphere to soils as rhizodeposits, including root exudates. Although rhizodeposition regulates both microbial activity and the biogeochemical cycling of nutrients, the effects of particular exudate species on soil carbon fluxes and key rhizosphere microorganisms remain unclear. By combining high-throughput sequencing, q-PCR, and NanoSIMS analyses, we characterized the bacterial community structure, quantified total bacteria depending on root exudate chemistry, and analyzed the consequences on the mobility of mineral-protected carbon. Using well-controlled incubation experiments, we showed that the three most abundant groups of root exudates (amino acids, carboxylic acids, and sugars) have contrasting effects on the release of dissolved organic carbon (DOC) and bioavailable Fe in an Ultisol through the disruption of organo-mineral associations and the alteration of bacterial communities, thus priming organic matter decomposition in the rhizosphere. High resolution (down to 50 nm) NanoSIMS images of mineral particles indicated that iron and silicon co-localized significantly more organic carbon following amino acid inputs than treatments without exudates or with carboxylic acids. The application of sugar strongly reduced microbial diversity without impacting soil carbon mobilization. Carboxylic acids increased the prevalence of Actinobacteria and facilitated carbon mobilization, whereas amino acid addition increased the abundances of Proteobacteria that prevented DOC release. In summary, root exudate functions are defined by their chemical composition that regulates bacterial community composition and, consequently, the biogeochemical cycling of carbon in the rhizosphere.

Origin of the Shanggong gold deposit, the southern margin of the North China Craton: Constraints from Rb-Sr ages of sericite, and trace elements and sulfur isotope of pyrite

The Shanggong Au deposit is a world-class Au deposit in the southern margin of the North China Craton. Pyrite, as the primary Au carrier in this deposit, is an ideal mineral for dissecting the complex ore-forming process and origin of this deposit. Four types of pyrite were identified by EPMA, SEM, LA-ICP-MS, and NanoSIMS analyses: the coarse-grained cubic, disseminated pyrite (Py1) in the early ore stage (S1) and three types of the fine-grained pentagonal dodecahedron, disseminated pyrite (Py2-1, Py2-2, and Py2-3) with zoning textures in the main ore stage (S2). Py1 is relatively depleted in most metals but enriched in Co and Bi compared with other types of pyrite in S2. On the other hand, both Py2-1 and Py2-3 contain relatively high contents of As, Au, and other metals, whereas Py2-2 contains highest Au, As, Ag, Cu, Sb, Te, Tl, and Pb. Oscillatory zoning in Py2-1 resulted from repeated local fluid phase separation at the near-surface of pyrite crystal due to sharp fluid pressure fluctuation. The Au and As-rich Py2-2 was probably formed under both extrinsic fluctuations in fluid pressure and composition and intrinsic local crystal-fluid interface kinetic effects (e.g., diffusion-limited self-organization, surface electrochemistry-driven adsorption). Crystallization of Py2-1 and Py2-2 has exhausted the metals in the residual fluids, wherein the trace element-poor Py2-3 crystallized and locally replaced Py2-2 through a dissolution-reprecipitation process. Our new data and previous results suggest the ore-forming fluids were likely initial produced by degassing of the concealed pluton, and the metals were sourced from both the crust (e.g., the Taihua complex and Xiong’er Group) and the mantle. The negative δ34S values for pyrite in the S2 stage might result from both the isotopic fractionation between sulfide and sulfate minerals via oxidation of the ore-forming fluid and the input of biogenic sulfur.

High-Resolution Multi-Isotope Imaging Mass Spectrometry (MIMS) Imaging Applications in Stem Cell Biology.

Multi-isotope imaging mass spectrometry (MIMS) allows the measurement of turnover of molecules within intracellular compartments with a spatial resolution down to 30 nm. We use molecules enriched in stable isotopes administered to animals by diet or injection, or to cells through the culture medium. The stable isotopes used are, in general, 15 N, 13 C, 18 O, and 2 H. For stem cell studies, we essentially use 15 N-thymidine, 13 C-thymidine, and 81 Br from BrdU. This protocol describes the practical use of MIMS with specific reference to applications in stem cell research. This includes choice and administration of stable isotope label(s), sample preparation, best practice for high-resolution imaging, secondary ion mass spectrometry using the Cameca NanoSIMS 50L, and methods for robust statistical analysis of label incorporation in regions of interest (ROI). © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Stable isotope labeling of DNA in cultured cells Basic Protocol 2: Stable isotope labeling of DNA in animals Basic Protocol 3: Preparation of Si chips, the general sample support for NanoSIMS analysis Basic Protocol 4: Stable isotope analysis of DNA replication in single nuclei in a population of cells with NanoSIMS Basic Protocol 5: Data reduction and processing.

NanoSIMS analysis of hydrogen and deuterium in metallic alloys: Artefacts and best practice

Hydrogen embrittlement can cause catastrophic failure of high strength alloys, yet determining localised hydrogen in the microstructure is analytically challenging. NanoSIMS is one of the few techniques that can map hydrogen and deuterium in metal samples at microstructurally relevant length scales. Therefore it is essential to understand the artefacts and determine the optimum methodology for its reliable detection. An experimental methodology/protocol for NanoSIMS analysis of deuterium (as a proxy for hydrogen) has been established uncovering unreported artefacts and a new approach is presented to minimise these artefacts in mapping hydrogen and deuterium in alloys. This method was used to map deuterium distributions in electrochemically charged austenitic stainless steel and precipitation hardened nickel-based alloys. Residual deuterium contamination was detected in the analysis chamber as a result of deuterium outgassing from the samples, and the impact of this deuterium contamination was assessed by a series of NanoSIMS experiments. A new analysis protocol was developed that involves mapping deuterium in the passive oxide layer thus mitigating beam damage effects that may prevent the detection of localised deuterium signals when the surface is highly deuterated.

Porosity and organic matter distribution in jarositic phyto tubules of sulfuric soils assessed by combined µCT and NanoSIMS analysis

Acid sulfate soils contain hypersulfidic material, e.g. pyrite (FeS2). Under oxidizing conditions, it transforms to sulfuric material (pH < 4), which is accompanied with the formation of jarosite [KFe3(SO4)2(OH)6] along root channels (designated as jarositic phyto tubules). The encapsulation of root residues with jarosite can lead to reduced spatial availability of organic carbon which is necessary as substrate for microbes. This can limit microbial activity which might be crucial for prospective remediation success. We investigated jarositic phyto tubules by combining X-ray computed microtomography (µCT) and nanoscale secondary ion mass spectrometry (NanoSIMS), to elucidate the porosity and organic matter distribution at the spatial scale most relevant for microbial processes.We demonstrated that the jarosite can be differentiated into zones with either high or low jarosite concentrations at distances of < 0.5 mm and 0.5–1.9 mm from the relict root channel, respectively. The results showed a closer association between jarosite and organic matter in the zone with high jarosite concentration. However, the pore space in immediate vicinity of the root is almost completely filled by jarosite and the organic matter is completely encapsulated. We conclude that the overall poor accessibility of organic matter will strongly retard remediation processes of sulfuric soils after re-submergence.