Dynamic nitrogen fixation in an aerobic endophyte of Populus.

Biological nitrogen fixation by microbial diazotrophs can contribute significantly to nitrogen availability in non-nodulating plant species. In this study of molecular mechanisms and gene expression relating to biological nitrogen fixation, the aerobic nitrogen-fixing endophyte Burkholderia vietnamiensis, strain WPB, isolated from Populus trichocarpa served as a model for endophyte-poplar interactions. Nitrogen-fixing activity was observed to be dynamic on nitrogen-free medium with a subset of colonies growing to form robust, raised globular like structures. Secondary ion mass spectrometry (NanoSIMS) confirmed that N-fixation was uneven within the population. A fluorescent transcriptional reporter (GFP) revealed that the nitrogenase subunit nifH is not uniformly expressed across genetically identical colonies of WPB and that only ~11% of the population was actively expressing the nifH gene. Higher nifH gene expression was observed in clustered cells through monitoring individual bacterial cells using single-molecule fluorescence in situ hybridization. Through 15N2 enrichment, we identified key nitrogenous metabolites and proteins synthesized by WPB and employed targeted metabolomics in active and inactive populations. We cocultivated WPB Pnif-GFP with poplar within a RhizoChip, a synthetic soil habitat, which enabled direct imaging of microbial nifH expression within root epidermal cells. We observed that nifH expression is localized to the root elongation zone where the strain forms a unique physical interaction with the root cells. This work employed comprehensive experimentation to identify novel mechanisms regulating both biological nitrogen fixation and beneficial plant-endophyte interactions.

Direct visualization of radiation-induced transformations at alkali halide-air interfaces.

Radiation driven reactions at mineral/air interfaces are important to the chemistry of the atmosphere, but experimental constraints (e.g. simultaneous irradiation, in situ observation, and environmental control) leave process understanding incomplete. Using a custom atomic force microscope equipped with an integrated X-ray source, transformation of potassium bromide surfaces to potassium nitrate by air radiolysis species was followed directly in situ at the nanoscale. Radiolysis initiates dynamic step edge dissolution, surface composition evolution, and ultimately nucleation and heteroepitaxial growth of potassium nitrate crystallites mediated by surface diffusion at rates controlled by adsorbed water. In contrast to in situ electron microscopy and synchrotron-based imaging techniques where high radiation doses are intrinsic, our approach illustrates the value of decoupling irradiation and the basis of observation.

Isotopic Heterogeneity Imaged in a Uranium Fuel Pellet with Extreme Ultraviolet Laser Ablation and Ionization Time-of-Flight Mass Spectrometry.

We use extreme ultraviolet laser ablation and ionization time-of-flight mass spectrometry (EUV TOF) to map uranium isotopic heterogeneity at the nanoscale (≤100 nm). Using low-enriched uranium fuel pellets that were made by blending two isotopically distinct feedstocks, we show that EUV TOF can map the 235U/238U content in 100 nm-sized pixels. The two-dimensional (2D) isotope maps reveal U ratio variations in sub-microscale to ≥1 µm areas of the pellet that had not been fully exposed by microscale or bulk mass spectrometry analyses. Compared to the ratio distribution measured in a homogeneous U reference material, the ratios in the enriched pellet follow a ∼3× wider distribution. These results indicate U heterogeneity in the fuel pellet from incomplete blending of the different source materials. EUV TOF results agree well with those obtained on the same enriched pellets by nanoscale secondary ionization mass spectrometry (NanoSIMS), which reveals a comparable U isotope ratio distribution at the same spatial scale. EUV TOF's ability to assess and map isotopic heterogeneity at the nanoscale makes it a promising tool in fields such as nuclear forensics, geochemistry, and biology that could benefit from uncovering sub-microscale sources of chemical modifications.

Calcareous organic matter coatings sequester siderophores in alkaline soils.

Although most studies of organic matter (OM) stabilization in soils have focused on adsorption to aluminosilicate and iron-oxide minerals due to their strong interactions with organic nucleophiles, stabilization within alkaline soils has been empirically correlated with exchangeable Ca. Yet the extent of competing processes within natural soils remains unclear because of inadequate characterization of soil mineralogy and OM distribution within the soil in relation to minerals, particularly in C poor alkaline soils. In this study, we employed bulk and surface-sensitive spectroscopic methods including X-ray diffraction, 57Fe-Mössbauer, and X-ray photoemission spectroscopy (XPS), and transmission electron microscopy (TEM) methods to investigate the minerology and soil organic C and N distribution on individual fine particles within an alkaline soil. Microscopy and XPS analyses demonstrated preferential sorption of Ca-containing OM onto surfaces of Fe-oxides and calcite. This result was unexpected given that the bulk combined amounts of quartz and Fe-containing feldspars of the soil constitute ~90% of total minerals and the surface atomic composition was largely Fe and Al (>10% combined) compared to Ca (4.2%). Soil sorption experiments were conducted with two siderophores, pyoverdine and enterobactin, to evaluate the adsorption of organic molecules with functional groups that strongly and preferentially bind Fe. A greater fraction of pyoverdine was adsorbed compared to enterobactin, which is smaller, less polar, and has a lower aqueous solubility. Using NanoSIMS to map the distribution of isotopically-labeled siderophores, we observed correlations with Ca and Fe, along with strong isotopic dilution with native C, indicating associations with OM coatings rather than with bare mineral surfaces. We propose a mechanism of adsorption by which organics aggregate within alkaline soils via cation bridging, favoring the stabilization of larger molecules with a greater number of nucleophilic functional groups.

Focused ion beam for improved spatially-resolved mass spectrometry and analysis of radioactive materials for uranium isotopic analysis.

The ability to acquire high-quality spatially-resolved mass spectrometry data is sought in many fields of study, but it often comes with high cost of instrumentation and a high level of expertise required. In addition, techniques highly regarded for isotopic analysis applications such as thermal ionization mass spectrometry (TIMS) do not have the ability to acquire spatially-resolved data. Another drawback is that for radioactive materials, which are often of interest for isotopic analysis in geochemistry and nuclear forensics applications, high-end instruments often have restrictions on radioactivity and non-dispersibility requirements. We have applied the use of a traditional microanalysis tool, the focused ion beam/scanning electron microscope (FIB/SEM), for preparation of radioactive materials either for direct analysis by spatially-resolved instruments such as secondary ion mass spectrometry (SIMS) and laser ablation inductively-coupled mass spectrometry (LA-ICP-MS), or similarly to provide some level of spatial resolution to techniques that do not inherently have that ability such as TIMS or quadrupole inductively coupled plasma mass spectrometry (Q-ICP-MS). We applied this preparation technique to various uranium compounds, which was especially useful for reducing sample sizes and ensuring non-dispersibility to allow for entry into non-radiological or ultra-trace facilities. Our results show how this site-specific preparation can provide spatial context for nominally bulk techniques such as TIMS and Q-ICP-MS. In addition, the analysis of samples extracted from a uranium dioxide fuel pellet via all methods, but especially NanoSIMS and LA-ICP-MS, showed enrichment heterogeneities that are important for nuclear forensics and are of interest for fuel performance.

Forfeiting the priority effect: turnover defines biofilm community succession.

Microbial community succession is a fundamental process that affects underlying functions of almost all ecosystems; yet the roles and fates of the most abundant colonizers are often poorly understood. Does early abundance spur long term persistence? How do deterministic and stochastic processes influence the ecological contribution of colonizers? We performed a succession experiment within a hypersaline ecosystem to investigate how different processes contributed to the turnover of founder species. Bacterial and eukaryotic colonizers were identified during primary succession and tracked through a defined, 79-day biofilm maturation period using 16S and 18S rRNA gene sequencing in combination with high resolution imaging that utilized stable isotope tracers to evaluate successional patterns of primary producers and nitrogen fixers. The majority of the founder species did not maintain high abundance throughout succession. Species replacement (versus loss) was the dominant process shaping community succession. We also asked if different ecological processes acted on bacteria versus Eukaryotes during succession and found deterministic and stochastic forces corresponded more with microeukaryote and bacterial colonization, respectively. Our results show that taxa and functions belonging to different kingdoms, which share habitat in the tight spatial confines of a biofilm, were influenced by different ecological processes and time scales of succession.

Experimental Insights into the Growth of Single Truncated Anatase Bipyramids.

Fluorine has been recognized to selectively stabilize anatase titanium dioxide (TiO2 ) crystal facets; however, resolving its physical location at the nanometer scale remains empirically elusive. Here, we provide direct experimental evidence to reveal the spatial distribution of fluorine on single truncated anatase bipyramids (TABs) using nanoscale secondary ion mass spectrometry (NanoSIMS). Fluorine was found to preferentially adsorb on the (001) facet compared to the (101) facet of TABs. Moreover, NanoSIMS depth profiling exhibited a significantly different fluorine distribution between these two facets in the near-surface region, illustrating the essential role of lattice-doped fluorine in the anisotropic crystal growth of TABs.

Phenazine-1-carboxylic acid and soil moisture influence biofilm development and turnover of rhizobacterial biomass on wheat root surfaces.

Phenazine-1-carboxylic acid (PCA) is produced by rhizobacteria in dryland but not in irrigated wheat fields of the Pacific Northwest, USA. PCA promotes biofilm development in bacterial cultures and bacterial colonization of wheat rhizospheres. However, its impact upon biofilm development has not been demonstrated in the rhizosphere, where biofilms influence terrestrial carbon and nitrogen cycles with ramifications for crop and soil health. Furthermore, the relationships between soil moisture and the rates of PCA biosynthesis and degradation have not been established. In this study, expression of PCA biosynthesis genes was upregulated relative to background transcription, and persistence of PCA was slightly decreased in dryland relative to irrigated wheat rhizospheres. Biofilms in dryland rhizospheres inoculated with the PCA-producing (PCA+ ) strain Pseudomonas synxantha 2-79RN10 were more robust than those in rhizospheres inoculated with an isogenic PCA-deficient (PCA- ) mutant strain. This trend was reversed in irrigated rhizospheres. In dryland PCA+ rhizospheres, the turnover of 15 N-labelled rhizobacterial biomass was slower than in the PCA- and irrigated PCA+ treatments, and incorporation of bacterial 15 N into root cell walls was observed in multiple treatments. These results indicate that PCA promotes biofilm development in dryland rhizospheres, and likely influences crop nutrition and soil health in dryland wheat fields.

NanoSIMS for biological applications: Current practices and analyses.

Secondary ion mass spectrometry (SIMS) has become an increasingly utilized tool in biologically relevant studies. Of these, high lateral resolution methodologies using the NanoSIMS 50/50L have been especially powerful within many biological fields over the past decade. Here, the authors provide a review of this technology, sample preparation and analysis considerations, examples of recent biological studies, data analyses, and current outlooks. Specifically, the authors offer an overview of SIMS and development of the NanoSIMS. The authors describe the major experimental factors that should be considered prior to NanoSIMS analysis and then provide information on best practices for data analysis and image generation, which includes an in-depth discussion of appropriate colormaps. Additionally, the authors provide an open-source method for data representation that allows simultaneous visualization of secondary electron and ion information within a single image. Finally, the authors present a perspective on the future of this technology and where they think it will have the greatest impact in near future.

Link between light-triggered Mg-banding and chamber formation in the planktic foraminifera Neogloboquadrina dutertrei.

The relationship between seawater temperature and the average Mg/Ca ratios in planktic foraminifera is well established, providing an essential tool for reconstructing past ocean temperatures. However, many species display alternating high and low Mg-bands within their shell walls that cannot be explained by temperature alone. Recent experiments demonstrate that intrashell Mg variability in Orbulina universa, which forms a spherical terminal shell, is paced by the diurnal light/dark cycle. Whether Mg-heterogeneity is also diurnally paced in species with more complex shell morphologies is unknown. Here we show that high Mg/Ca-calcite forms at night in cultured specimens of the multi-chambered species Neogloboquadrina dutertrei. Our results demonstrate that N. dutertrei adds a significant amount of calcite, and nearly all Mg-bands, after the final chamber forms. These results have implications for interpreting patterns of calcification in N. dutertrei and suggest that diurnal Mg-banding is an intrinsic component of biomineralization in planktic foraminifera.

Diet-Microbiome Interactions in Health Are Controlled by Intestinal Nitrogen Source Constraints.

Diet influences health and patterns of disease in populations. How different diets do this and why outcomes of diets vary between individuals are complex and involve interaction with the gut microbiome. A major challenge for predicting health outcomes of the host-microbiome dynamic is reconciling the effects of different aspects of diet (food composition or intake rate) on the system. Here we show that microbial community assembly is fundamentally shaped by a dichotomy in bacterial strategies to access nitrogen in the gut environment. Consequently, the pattern of dietary protein intake constrains the host-microbiome dynamic in ways that are common to a very broad range of diet manipulation strategies. These insights offer a mechanism for the impact of high protein intake on metabolic health and form the basis for a general theory of the impact of different diet strategies on host-microbiome outcomes.

Exploring the transfer of recent plant photosynthates to soil microbes: mycorrhizal pathway vs direct root exudation.

Plants rapidly release photoassimilated carbon (C) to the soil via direct root exudation and associated mycorrhizal fungi, with both pathways promoting plant nutrient availability. This study aimed to explore these pathways from the root's vascular bundle to soil microbial communities. Using nanoscale secondary ion mass spectrometry (NanoSIMS) imaging and (13) C-phospho- and neutral lipid fatty acids, we traced in-situ flows of recently photoassimilated C of (13) CO2 -exposed wheat (Triticum aestivum) through arbuscular mycorrhiza (AM) into root- and hyphae-associated soil microbial communities. Intraradical hyphae of AM fungi were significantly (13) C-enriched compared to other root-cortex areas after 8 h of labelling. Immature fine root areas close to the root tip, where AM features were absent, showed signs of passive C loss and co-location of photoassimilates with nitrogen taken up from the soil solution. A significant and exclusively fresh proportion of (13) C-photosynthates was delivered through the AM pathway and was utilised by different microbial groups compared to C directly released by roots. Our results indicate that a major release of recent photosynthates into soil leave plant roots via AM intraradical hyphae already upstream of passive root exudations. AM fungi may act as a rapid hub for translocating fresh plant C to soil microbes.

Visualization of metabolic properties of bacterial cells using nanoscale secondary ion mass spectrometry (NanoSIMS).

NanoSIMS combines high-resolution imaging and mass spectrometry with simultaneous collection of up to seven different masses, providing an invaluable technique for determining the isotopic and elemental composition in microscopic target samples. It has been used in varying fields, from studying the elemental composition of mineral samples to tracking cell uptake of isotope-labelled substrates. In combination with in situ hybridization techniques, NanoSIMS offers a powerful method of linking metabolic capacity to phylogenetic identity in cell samples. Here, we describe methods and considerations for microbial sample preparation, visualization, and analysis using NanoSIMS.

Nanoscale analysis of pyritized microfossils reveals differential heterotrophic consumption in the ~1.9-Ga Gunflint chert.

The 1.88-Ga Gunflint biota is one of the most famous Precambrian microfossil lagerstätten and provides a key record of the biosphere at a time of changing oceanic redox structure and chemistry. Here, we report on pyritized replicas of the iconic autotrophic Gunflintia-Huroniospora microfossil assemblage from the Schreiber Locality, Canada, that help capture a view through multiple trophic levels in a Paleoproterozoic ecosystem. Nanoscale analysis of pyritic Gunflintia (sheaths) and Huroniospora (cysts) reveals differing relic carbon and nitrogen distributions caused by contrasting spectra of decay and pyritization between taxa, reflecting in part their primary organic compositions. In situ sulfur isotope measurements from individual microfossils (δ(34)S(V-CDT) +6.7‰ to +21.5‰) show that pyritization was mediated by sulfate-reducing microbes within sediment pore waters whose sulfate ion concentrations rapidly became depleted, owing to occlusion of pore space by coeval silicification. Three-dimensional nanotomography reveals additional pyritized biomaterial, including hollow, cellular epibionts and extracellular polymeric substances, showing a preference for attachment to Gunflintia over Huroniospora and interpreted as components of a saprophytic heterotrophic, decomposing community. This work also extends the record of remarkable biological preservation in pyrite back to the Paleoproterozoic and provides criteria to assess the authenticity of even older pyritized microstructures that may represent some of the earliest evidence for life on our planet.

Visualising gold inside tumour cells following treatment with an antitumour gold(I) complex.

Gold(I) phosphine complexes, such as [Au(d2pype)(2)]Cl, (1, where d2pype is 1,2-bis(di-2-pyridyl phosphinoethane)), belong to a class of promising chemotherapeutic candidates that have been shown to be selectively toxic to tumourigenic cells, and may act via uptake into tumour cell mitochondria. For a more holistic understanding of their mechanism of action, a deeper knowledge of their subcellular distribution is required, but to date this has been limited by a lack of suitable imaging techniques. In this study the subcellular distribution of gold was visualised in situ in human breast cancer cells treated with 1, using nano-scale secondary ion mass spectrometry. NanoSIMS ion maps of (12)C(14)N(-), (31)P(-), (34)S(-) and (197)Au(-) allowed, for the first time, visualisation of cellular morphology simultaneously with subcellular distribution of gold. Energy filtered transmission electron microscopy (EFTEM) element maps for gold were also obtained, allowing for observation of nuclear and mitochondrial morphology with excellent spatial resolution, and gold element maps comparable to the data obtained with NanoSIMS. Following 2 h treatment with 1, the subcellular distribution of gold was associated with sulfur-rich regions in the nucleus and cytoplasm, supporting the growing evidence for the the mechanism of action of Au(I) compounds based on inhibition of thiol-containing protein families, such as the thioredoxin system. The combination of NanoSIMS and EFTEM has broader applicability for studying the subcellular distribution of other types of metal-based drugs.

Application of nanoscale secondary ion mass spectrometry to plant cell research.

Imaging resource flow in soil-plant systems remains central to understanding plant development and interactions with the environment. Typically, subcellular resolution is required to fully elucidate the compartmentation, behavior, and mode of action of organic compounds and mineral elements within plants. For many situations this has been limited by the poor spatial resolution of imaging techniques and the inability to undertake studies in situ. Here we demonstrate the potential of Nanoscale Secondary Ion Mass Spectrometry (NanoSIMS), which is capable of the quantitative high-resolution spatial imaging of stable isotopes (e.g. (12) C, (13) C, (14) N, (15) N, (16) O, (18) O, (31) P, (34) S) within intact plant-microbial-soil systems. We present examples showing how the approach can be used to investigate competition for (15) N-labeled nitrogen compounds between plant roots and soil microorganisms living in the rhizosphere and the spatial imaging of (31) P in roots. We conclude that NanoSIMS has great potential to elucidate the flow of isotopically-labeled compounds in complex media (e.g. soil) and opens up countless new opportunities for studying plant responses to abiotic stress (e.g. (18) O3, elevated (13) CO2), signal exchange, nutrient flow and plant-microbial interactions.

In situ mapping of nutrient uptake in the rhizosphere using nanoscale secondary ion mass spectrometry.

Plant roots and microorganisms interact and compete for nutrients within the rhizosphere, which is considered one of the most biologically complex systems on Earth. Unraveling the nitrogen (N) cycle is key to understanding and managing nutrient flows in terrestrial ecosystems, yet to date it has proved impossible to analyze and image N transfer in situ within such a complex system at a scale relevant to soil-microbe-plant interactions. Linking the physical heterogeneity of soil to biological processes marks a current frontier in plant and soil sciences. Here we present a new and widely applicable approach that allows imaging of the spatial and temporal dynamics of the stable isotope (15)N assimilated within the rhizosphere. This approach allows visualization and measurement of nutrient resource capture between competing plant cells and microorganisms. For confirmation we show the correlative use of nanoscale secondary ion mass spectrometry, and transmission electron microscopy, to image differential partitioning of (15)NH(4)(+) between plant roots and native soil microbial communities at the submicron scale. It is shown that (15)N compounds can be detected and imaged in situ in individual microorganisms in the soil matrix and intracellularly within the root. Nanoscale secondary ion mass spectrometry has potential to allow the study of assimilatory processes at the submicron level in a wide range of applications involving plants, microorganisms, and animals.

Bayesian-integrated microbial forensics.

In the aftermath of the 2001 anthrax letters, researchers have been exploring ways to predict the production environment of unknown-source microorganisms. Culture medium, presence of agar, culturing temperature, and drying method are just some of the broad spectrum of characteristics an investigator might like to infer. The effects of many of these factors on microorganisms are not well understood, but the complex way in which microbes interact with their environments suggests that numerous analytical techniques measuring different properties will eventually be needed for complete characterization. In this work, we present a Bayesian statistical framework for integrating disparate analytical measurements. We illustrate its application to the problem of characterizing the culture medium of Bacillus spores using three different mass spectral techniques. The results of our study suggest that integrating data in this way significantly improves the accuracy and robustness of the analyses.

Differentiation of spores of Bacillus subtilis grown in different media by elemental characterization using time-of-flight secondary ion mass spectrometry.

We demonstrate the use of time-of-flight secondary ion mass spectrometry (TOF-SIMS) in a forensics application to distinguish Bacillus subtilis spores grown in various media based on the elemental signatures of the spores. Triplicate cultures grown in each of four different media were analyzed to obtain TOF-SIMS signatures comprised of 16 elemental intensities. Analysis of variance was unable to distinguish growth medium types based on 40Ca-normalized signatures of any single normalized element. Principal component analysis proved successful in separating the spores into groups consistent with the media in which they were prepared. Confusion matrices constructed using nearest-neighbor classification of the PCA scores confirmed the predictive utility of TOF-SIMS elemental signatures in identifying sporulation medium. Theoretical calculations based on the number and density of spores in an analysis area indicate an analytical sample size of about 1 ng, making this technique an attractive method for bioforensics applications.

Exploration of inorganic C and N assimilation by soil microbes with time-of-flight secondary ion mass spectrometry.

Stable C and N isotopes have long been used to examine properties of various C and N cycling processes in soils. Unfortunately, relatively large sample sizes are needed for accurate gas phase isotope ratio mass spectrometric analysis. This limitation has prevented researchers from addressing C and N cycling issues on microbially meaningful scales. Here we explored the use of time-of-flight secondary ion mass spectrometry (TOF-SIMS) to detect 13C and 15N assimilation by individual bacterial cells and to quantify N isotope ratios in bacterial samples and individual fungal hyphae. This was accomplished by measuring the relative abundances of mass 26 (12C14N-) and mass 27 (13C14N- and 12C15N-) ions sputtered with a Ga+ probe from cells adhered to an Si contact slide. TOF-SIMS was successfully used to locate and quantify the relative 15N contents of individual hyphae that grew onto Si contact slides in intimate contact with a model organomineral porous matrix composed of kaolin, straw fragments, and freshly deposited manure that was supplemented with 15NO3-. We observed that the 15N content of fungal hyphae grown on the slides was significantly lower in regions where the hyphae were influenced by N-rich manure than in regions influenced by N-deficient straw. This effect occurred over distances of tens to hundreds of microns. Our data illustrate that TOF-SIMS has the potential to locate N-assimilating microorganisms in soil and to quantify the 15N content of cells that have assimilated 15N-labeled mineral N and shows promise as a tool with which to explore the factors controlling microsite heterogeneities in soil.