21 Search Results

Soil organic matter (SOM) is a key reservoir for global carbon (C), supporting soil fertility and influencing greenhouse gas emissions. Microbial residues, composed of dead cells and cellular fragments, are major contributors to SOM formation. Yet, mechanisms by which minerals enhance the accumulation of microbial residues remain poorly understood. Here, we used ¹³C-labeled glucose in a year-long incubation to trace microbial residue in sandy and silty soils. Across both soils, approximately 89% of retained microbial ¹³C was recovered in the fine (<53 μm) mineral-associated organic matter (MAOM) pool. Within this pool, the light MAOM fraction, enriched in poorly crystalline Femore » minerals, held 4.3 times more ¹³C than the heavy, phyllosilicate-dominated MAOM fraction, despite accounting for only 17.2% of the total MAOM mass and 12.3% of the total soil mass. Along with ¹³C enrichment, the light MAOM fraction showed greater abundance of N-containing groups, e.g., (amides and amino groups), indicative of microbial-derived compounds like proteins and amino sugars. Fe oxides in light MAOM from both soils were spatially dispersed. Microbial residue accumulation was greater in finer-textured silty soil. These findings demonstrate that mineral composition and texture jointly regulate microbial necromass accrual, highlighting light MAOM as a key pool for enhancing soil C storage.« less

The ability to simultaneously monitor the flux of iron atoms within the solution and solid phases can provide considerable insight into mechanisms of iron oxide mineral transformations. The autocatalytic interaction between hematite and Fe(II)-oxalate has long been of interest for its environmental and industrial relevance. In this study we take advantage of iron isotopic labelling and mass-sensitive imaging at the single particle scale to determine how changes in solution composition correlate with the morphologic evolution of faceted, micrometer-sized hematite platelets. Net dissolution is confirmed through analyses of aqueous iron chemistry, as well as by quantitative atomic force microscopy. Isotopic mappingmore » techniques show that Fe(II) readily adsorbs to (001) and (012) surfaces in the absence of oxalate, but when oxalate is present selective dissolution of the (001) surface prevails and Fe deposition via recrystallization is not observed. Comparison between particle microtopographies following reaction with Fe(II), oxalate, and Fe(II)-oxalate show substantially different behaviors, consistent with distinct mechanisms of interaction with hematite surfaces. The extensive characterization conducted on the coupled solution/solid dynamics in this system provides new insight for distinguishing crystal growth, dissolution, and recrystallization processes.« less

Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single-cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing 8 new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMBmore » consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescence in situ hybridization (FISH) combined with nanoscale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal noncanonical amino acid tagging (BONCAT), we explored their in situ activity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.« less

Abstract Understanding biomineralization relies on imaging chemically heterogeneous organic–inorganic interfaces across a hierarchy of spatial scales. Further, organic minority phases are often responsible for emergent inorganic structures from the atomic arrangement of different polymorphs, to nano- and micrometer crystal dimensions, up to meter size mollusk shells. The desired simultaneous chemical and elemental imaging to identify sparse organic moieties across a large field-of-view with nanometer spatial resolution has not yet been achieved. Here, we combine nanoscale secondary ion mass spectroscopy (NanoSIMS) with spectroscopic IR s -SNOM imaging for simultaneous chemical, molecular, and elemental nanoimaging. At the example of Pinctada margaritifera molluskmore » shells we identify and resolve ~ 50 nm interlamellar protein sheets periodically arranged in regular ~ 600 nm intervals. The striations typically appear ~ 15 µm from the nacre-prism boundary at the interface between disordered neonacre to mature nacre. Using the polymorph distinctive IR-vibrational carbonate resonance, the nacre and prismatic regions are consistently identified as aragonite ( $$$${\overline{\nu }}_{a}=860$$$$ ${\overline{\nu }}_a=860$ cm ⁻¹ ) and calcite ( $$$${\overline{\nu }}_{c}=880$$$$ ${\overline{\nu }}_c=880$ cm ⁻¹ ), respectively. We observe previously unreported morphological features including aragonite subdomains encapsulated in extensions of the prism-covering organic membrane and regions of irregular nacre tablet formation coincident with dispersed organics. We also identify a ~ 200 nm region in the incipient nacre region with less well-defined crystal structure and integrated organics. These results show with the identification of the interlamellar protein layer how correlative nano-IR chemical and NanoSIMS elemental imaging can help distinguish different models proposed for shell growth in particular, and how organic function may relate to inorganic structure in other biomineralized systems in general.« less

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 expressedmore » 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.« less

Fe-rich mobile colloids play vital yet poorly understood roles in the biogeochemical cycling of Fe in groundwater by influencing organic matter (OM) preservation and fluxes of Fe, OM, and other essential (micro-)nutrients. Yet, few studies have provided molecular detail on the structures and compositions of Fe-rich mobile colloids and factors controlling their persistence in natural groundwater. Here, we provide comprehensive new information on the sizes, molecular structures, and compositions of Fe-rich mobile colloids that accounted for up to 72% of aqueous Fe in anoxic groundwater from a redox-active floodplain. The mobile colloids are multi-phase assemblages consisting of Si-coated ferrihydrite nanoparticlesmore » and Fe(II)-OM complexes. Ferrihydrite nanoparticles persisted under both oxic and anoxic/sulfidic conditions, which we attribute to passivation by Si and OM. These findings suggest that mobile Fe-rich colloids generated in floodplains can persist during transport through redox-variable soils and could be discharged to surface waters. These results shed new light on their potential to transport Fe, OM, and nutrients across terrestrial-aquatic interfaces.« less

New insight into the geochemistry of ancient environments can be gained through structural and chemical analyses of nanometer-scale features within minerals. Here, we present recent developments using atom probe tomography (APT) enabling direct visualization of nanoscale fluid inclusions trapped within pyrite (FeS₂) and thereby chemical characterization of remnant seawater. Pyrite framboids (spherical clusters of nanocrystals) were sampled from the Middle Devonian Leicester Pyrite Member (New York). Scanning transmission electron microscopy shows low density regions distributed within the pyrite consistent with nanoscale pores (<4 nm in size). APT 3D visualization and compositional mapping reveals that the nanopores are filled with water.more » The inclusions appear to preserve the elemental signature of the water column in which the framboids formed, specifically seawater components including Na, K, Mg, and Ca. Mg/Ca ratios within the pyrite were generally measured to be within 0.6±0.2 – consistent with calcite-dominated seawater conditions existing in the Middle Devonian. Furthermore, this study demonstrates the potential for a novel approach to reconstruct paleoenvironmental conditions from coupled elemental and structural analyses of nanoscale fluid inclusions.« less

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. Finally, in contrast to in situ electron microscopy and synchrotron-basedmore » imaging techniques where high radiation doses are intrinsic, our approach illustrates the value of decoupling irradiation and the basis of observation.« less

Accurate measurements of ²³⁵U enrichment within metallic nuclear fuels are essential for understanding material performance in a neutron irradiation environment, and the origin of secondary phases (e.g. uranium carbides). In this work, we analyse ²³⁵U enrichment in matrix and carbide phases in low enriched uranium alloyed with 10 wt% Mo via two chemical imaging modalities—nanoscale secondary ion mass spectrometry (NanoSIMS) and atom probe tomography (APT). Additionally, results from NanoSIMS and APT are compared to understand accuracy and utility of both approaches across length scales. NanoSIMS and APT provide consistent results, with no statistically significant difference between nominal enrichment (19.95 ±more » 0.14 at% ²³⁵U) and that measured for metal matrix and carbide inclusions.« less