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ABSTRACT We report the complete genome sequence of Variovorax sp. EBFNA2, a fava bean nodule endophyte. The strain appears to be a new species, and its genome provides insight into its interactions with host plants and potential to promote plant growth and crop yield.
Oxygen-terminated diamond has a wide breadth of applications, which include stabilizing near-surface color centers, semiconductor devices, and biological sensors. Despite the vast literature on characterizing functionalization groups on diamond, the chemical composition of the shallowest portion of the surface (<1 nm) is challenging to probe with conventional techniques like XPS and FTIR. In this work, we demonstrate the use of angleresolved XPS to probe the first ten nanometers of both oxygen and hydrogen terminated (100) single-crystalline diamond grown via chemical vapor deposition (CVD). With the use of consistent peakfitting methods, the peak identities and relative peak binding energies were identified for sp 2 carbon, ether, hydroxyl, carbonyl, and C−H groups for both of these diamond surface terminations. For the oxygen-terminated sample, we also quantified the thickness of the sp 2 carbon layer situated on top of the bulk sp 3 diamond bonded carbon to be 0.3 ± 0.1 nm, based on the analysis of the Auger electron spectra and D-parameter calculations. These results indicate that the majority of the oxygen is bonded to the sp 2 carbon layer on the diamond, and not directly to the sp 3 diamond bonded carbon.
We report the emergence of adsorption-induced magnetism from heterohelicene molecules on a nonmagnetic Cu(100) surface. Spin-polarized low-energy electron microscopy measurements reveal spin-dependent electron reflectivity for enantiopure 7,12,17-trioxa[11]helicene (TO[11]H) monolayers, indicating the formation of a spin-polarized state localized in the topmost copper layer. Control experiments on clean Cu(100) and TO[11]H on highly oriented pyrolytic graphite show no such effect, excluding artifacts and chirality-induced spin selectivity as origins. Spin-polarized density functional theory calculations with hybrid functionals attribute the magnetism to strong chemisorption, which induces hybridization between the molecular HOMO and copper s- and d-states, driving asymmetric spin-polarized charge redistribution at the interface. An extended Newns-Anderson-Grimley model incorporating on-site Coulomb repulsion in Cu d-orbitals reproduces the emergence of interfacial spin polarization above a threshold interaction strength, highlighting the key roles of hybridization parameters and Coulomb correlation. These findings reveal a mechanism for inducing magnetism at molecule-metal interfaces without inherently magnetic components, offering avenues for engineering spin-polarized states in organic-inorganic hybrid systems.
Dynamic nuclear polarization surface enhanced NMR spectroscopy has enabled the determination of high-resolution structures from surface-supported molecules, including singlesite heterogeneous catalysts. Structure determinations have largely mimicked the approaches used in biomolecular NMR spectroscopy, namely, using distance measurements to constrain a conformational search. These early demonstrations made use of purpose-built software, which has limited the adoption of the technique. Herein, we describe the open-source program INTERFACES (Interpret NMR to Elucidate or Reconstruct the Full Atomistic Configurations of External Surfaces) which automates the analysis of RE(SP)DOR data as well as the structure determination for surface sites. Distances, angles, dihedral angles, complex orientation, and distance from the support can all be sampled to find all structures that agree with the experimental data. A χ 2 metric is used to define the error ranges of the REDOR fits and produce structures with an arbitrary level of confidence. Structural solutions are then provided as both overlays and ORTEP-like probability ellipsoids.
Representing subgrid variabilities of land surface processes and their upscaled effects is crucial for global climate modeling. Here, we implement a Multiple Atmosphere Multiple Land (MAML) framework in the superparamaterized version of E3SM (SP32 E3SM) to explicitly simulate the subgrid variabilities of land states and fluxes at cloud-resolving scale and their interactions with atmosphere. Comparing to the standard SP-E3SM in which all the atmospheric columns of the cloud resolving model embedded within the global atmospheric model grid interact with the same land surface (i.e., Multiple Atmosphere Single Land (MASL)), the impact of MAML on the strength of land-atmosphere coupling is limited, partly because the current implementation mainly facilitates one-way coupling between the cloud-resolving model and the land surface model. Despite such limitation, MAML increases the surface latent heat flux at the expense of sensible heat flux, and increases precipitation in India, Amazon, and Central Africa, reducing the model dry bias compared to the standard SP-E3SM. By employing a normalized gross moist stability (NGMS) diagnostic framework, we find that the increase in precipitation minus evaporation (PE) is primarily driven by the change in large-scale moisture convergence, particularly by the increase of water vapor in the lower atmosphere, while the local effect of total surface energy flux plays a minor role in the P-E change. More specifically, MAML changes the surface energy partitioning (evaporative fraction), increases the atmosphere water vapor, and further increases P-E by decreasing the NGMS. Finally, future development in the MAML framework is discussed.
Conditions affecting biofilm formation differ among bacterial species and this presents a challenge to studying biofilms in the lab. This work leverages functionalized silanes to control surface chemistry in the study of early biofilm propagation, quantified with a semi-automated image processing algorithm. These methods support the study of Pantoea sp. YR343, a gram-negative bacterium isolated from the poplar rhizosphere. We found that Pantoea sp. YR343 does not readily attach to hydrophilic surfaces but will form biofilms with a “honeycomb” morphology on hydrophobic surfaces. Our image processing algorithm described here quantified the evolution of the honeycomb morphology over time, and found the propagation to display a logarithmic behavior. This methodology was repeated with a flagella-deficient fliR mutant of Pantoea sp. YR343 which resulted in reduced surface attachment. Quantifiable differences between Pantoea WT and ΔfliR biofilm morphologies were captured by the image processing algorithm, further demonstrating the insight gained from these methods.
A novel employment of single particle-inductively coupled plasma-mass spectrometry (SP-ICP-MS) was developed, where a microextraction (ME) probe is used to sample nanoparticles from a surface and analyze them in a single analytical step. The effects of several parameters on the performance of ME-SP-ICP-MS were investigated, including the flow rate, choice of carrier solution, particle size, and the design of the microextraction probe head itself. The optimized ME-SP-ICP-MS technique was used to compare the extraction efficiency (EE, defined as the ratio of particles measured to particles deposited on the surface) of the commercial probe head to a newly designed SP polyether ether ketone (PEEK) probe head. The SP PEEK probe head was found to have increased EE compared to the commercial probe head (8.5 ± 3% vs 3.9 ± 3%, respectively). Increasing the carrier solution flow rate was found to decrease the total analysis time at the cost of decreasing EE. Extraction efficiencies for ME-SP-ICP-MS were typically 4–10%, which is similar to transport efficiencies (1–10%) for conventional SP-ICP-MS. Lastly, ME-SP-ICP-MS was employed for the analysis of nano- and microparticles. The sizes of gold nanoparticles, 30 ± 3 and 51 ± 1.9 nm (certified sizes), and iron-based microparticles, 1000 ± 50 nm (certified size), were accurately determined to be 32.2 ± 2.5, 50.8 ± 3.4, and 1030 ± 57 nm, respectively, by ME-SP-ICP-MS. Further, this work demonstrates the potential of ME-SP-ICP-MS for the direct analysis of particles on common collection surfaces (GSR tabs, carbon planchettes, etc.) while retaining spatial information on particle distribution across the surface.
The profound stability of bacterial spores makes them a promising platform for biotechnological applications like biocatalysis, bioremediation, drug delivery, etc. However, though the Bacillus subtilis spore is composed of >40 types of proteins, only ∼12 have been explored as fusion carriers for protein display. Here, we assessed the suitability of 33 spore proteins (SPs) as enzyme display carriers by direct allele tagging at native genomic loci. Of the 33 SPs investigated, 26 formed functional fusions with β-glucuronidase (GUS)─a ∼272 kDa homotetramer. This almost triples the number of SPs assessed for enzyme display and doubles the number of functional fusions documented in the literature. We quantitatively assessed 1) SP promoter activation dynamics, 2) GUS activity on spores, 3) surface availability, and 4) protection from thermal and proteolytic degradation. Multicopy expression and pairwise coexpression of the most promising SP-GUS fusions highlighted the complexity of spore structure/assembly and the difficulty in predicting compatibility between different SP fusions. We also assessed the suitability of engineered spores to degrade PET (polyethylene terephthalate) films and found that surface-exposed SPs were most effective. Beyond the broad survey, a key outcome of our work was the identification of SscA (small spore coat assembly protein A) as an effective spore display carrier. SscA supported enzyme activity at least 4-fold higher than any other SP, including the well-established anchor, CotY. We attribute this to its promoter, which demonstrated early and sustained activation relative to other SPs and its small size (∼3 kDa), which likely minimally interferes with enzyme folding, oligomerization, and activity. Labeling and genetic studies, its hydrophobic nature, and low surface availability suggest that SscA assembles within the inner spore coat, which makes it stabilizing and suitable for many biocatalytic applications. Overall, this work serves as a knowledge base to advance the biotechnological utility of B. subtilis spores.
The formation of technologically valuable nanocarbon structures under extreme conditions, such as those produced during high-explosive detonations, remains poorly understood but holds significant potential for the development of controlled synthesis pathways. While detonation shockwaves provide the high-pressure, high-temperature environment required for nanodiamond formation, subsequent cooling and decompression dictate whether the diamond phase is preserved or transformed into other nanocarbon structures. Here, in this study, we employ GPU-accelerated reactive molecular dynamics (ReaxFF) simulations to investigate the graphitization and structural remodeling of detonation nanodiamond under nonlinear quench and pressure-release trajectories. We further investigate how the initial nanodiamond morphology; cuboctahedral, octahedral, or hexagonal prism influences the resulting transformation products. Evolution of nanostructure, allotrope (via simulated x-ray diffraction), carbon hybridization, and ring statistics are tracked during a two-stage quench from 5000 K to 60 GPa. Rapid cooling combined with slow decompression optimizes cubic diamond retention, whereas slow cooling with rapid pressure release promotes surface-to-core graphitization, producing concentric sp 2 -hybridized layers and hollowed inner shells. Octahedral nanodiamonds evolve into carbon nano-onions, initially forming bucky diamonds that progressively transform into fully sp 2 -hybridized structures, while hexagonal prisms preferentially form parallel-stacked graphite layers resembling carbon dots. Transient hexagonal diamond (lonsdaleite) emerges as an interfacial phase, suggesting potential reversibility in the shock-induced graphite-to-diamond transformation pathway transformation route. To extend predictive capabilities, we trained machine learning (ML) regressors on over 10 5 node-hours of molecular dynamics (MD) trajectories. A multilayer perceptron (MLP) model reliably predicts the number of graphitized layers from temperature–pressure trajectories with a coefficient of determination (R 2 ) exceeding 0.90. This high predictive fidelity enables efficient, high-throughput mapping of the synthesis parameter space for optimized graphitization outcomes. Collectively, morphological control combined with optimized quench–decompression conditions promote the selective synthesis of nanocarbon allotropes. This work establishes a data-driven framework for the rational, a priori design of carbon nanomaterials for applications in energy storage, sensing, and biomedicine.
Holey graphene (HG), formed by introducing nanoscale perforations into graphene sheets, combines the structural advantages of continuous sp 2 conjugation with the beneficial effects of high surface area and enhanced chemical reactivity associated with nanoscopic holes. Conventional HG fabrication methods often rely on harsh oxidative treatments that compromise graphene's intrinsic electronic properties by disrupting its sp 2 conjugation. A new approach is introduced to fabricate HG directly from single-layer graphene (SLG), using two-dimensional covalent organic frameworks (COFs) as a template followed by controlled oxygen plasma etching. This method preserves the integrity of the SLG's sp 2 network while producing well-defined holes with an average diameter of 2.7 nm. These hole edges act as reactive sites that facilitate the confined, autoreductive growth of palladium nanoparticles (PdNPs) without external reducing agents. The confined hole geometry prevents NP agglomeration and ensures a uniform size distribution. The resulting Pd@HG hybrid exhibits exceptional chemiresistive hydrogen sensing characteristics, including ultrahigh sensitivity, low detection limits, rapid response and recovery, and long-term stability under both dry and humid conditions. Mechanistic investigations reveal a two-step sensing process involving surface redox interactions and hydrogen absorption into the PdNP lattices. This strategy presents a scalable platform for integrating metal NPs within conductive carbon frameworks for advanced sensing applications.
Biofilms are complex microbial communities critical in medical, industrial, and environmental contexts. Understanding their assembly, structure, genetic regulation, interspecies interactions, and environmental responses is key to developing effective control and mitigation strategies. While atomic force microscopy (AFM) offers critically important high-resolution insights on structural and functional properties at the cellular and even sub-cellular level, its limited scan range and labor-intensive nature restricts the ability to link these smaller scale features to the functional macroscale organization of the films. We begin to address this limitation by introducing an automated large area AFM approach capable of capturing high-resolution images over millimeter-scale areas, aided by machine learning for seamless image stitching, cell detection, and classification. Large area AFM is shown to provide a very detailed view of spatial heterogeneity and cellular morphology during the early stages of biofilm formation which were previously obscured. Using this approach, we examined the organization of Pantoea sp. YR343 on PFOTS-treated glass surfaces. Our findings reveal a preferred cellular orientation among surface-attached cells, forming a distinctive honeycomb pattern. Detailed mapping of flagella interactions suggests that flagellar coordination plays a role in biofilm assembly beyond initial attachment. Additionally, we use large-area AFM to characterize surface modifications on silicon substrates, observing a significant reduction in bacterial density. This highlights the potential of this method for studying surface modifications to better understand and control bacterial adhesion and biofilm formation.
The efficacy of oxygen (O) surface terminations on diamond is an important factor for the performance and stability for diamond-based quantum sensors and electronics. Given the wide breadth of O-termination techniques, it can be difficult to discern which method would yield the highest and most consistent O coverage. Furthermore, the interpretation of surface characterization techniques is complicated by surface morphology and purity, which if not accounted for will yield inconsistent determination of the oxygen coverage. We present a comprehensive approach to consistently prepare and analyze oxygen termination of surfaces on (100) single-crystalline diamond. We report on x-ray photoelectron spectroscopy (XPS) characterization of diamond surfaces treated with six oxidation methods that include various wet chemical oxidation techniques, photochemical oxidation with UV illumination, and steam oxidation using atomic layer deposition (ALD). Our analysis entails a rigorous XPS peak-fitting procedure for measuring the functionalization of O-terminated diamond. The findings herein have provided molecular-level insights on oxidized surfaces in (100) diamond, including the demonstration of clear correlation between the measured oxygen atomic percentage and the presence of molecular contaminants containing nitrogen, silicon, and sulfur. We also provide a comparison of the sp 2 carbon content with the O1s atomic percentage and discern a correlation with the diamond samples treated with dry oxidation which eventually tapers off at a max O1s atomic percentage value of 7.09 ± 0.40%. Given these results, we conclude that the dry oxidation methods yield some of the highest oxygen amounts, with the ALD water vapor technique proving to be the cleanest technique out of all the oxidation methods explored in this work.
Exchanges of groundwater and surface-water are fundamental to a wide range of water-supply and water-quality management issues but challenging to map beyond the reach scale. Waterborne gradient self-potential (SP) measurements are directly sensitive to water flow through riverbed sediments and can be used to infer exchange locations, direction (gain versus loss), scale, and relative changes, but to date applications to river corridor hydrology are limited. Numerical modeling and field experiments were therefore performed herein, each emphasizing waterborne gradient SP logging for identifying and locating focused vertical groundwater discharge (surface-water gain) and recharge (surface-water loss) in a river. Two and three-dimensional numerical models were constructed to simulate the polarities, appearances, and peak amplitudes of streaming-potential and electric-field anomalies on a riverbed and in the surface-water that were attributable to steady-state vertical fluxes of groundwater through high-permeability conduits in the riverbed. Effects of varied hydraulic length-scale of exchange and surface-water depth were tested through numerical modeling. Modeling results aided in data acquisition and interpretation for three repeated field experiments performed along a 1.5–2.0 km reach of the Quashnet River in Cape Cod, Massachusetts, where focused, meter-scale groundwater discharges occur at discrete locations within otherwise ubiquitous and more diffuse groundwater upwelling conditions. Strong gradient SP anomalies were repeatedly measured in the Quashnet River at previously confirmed locations of focused groundwater discharge, showing the efficacy of waterborne gradient SP logging in identifying and characterizing groundwater/surface water exchange dynamics at multiple river network scales.
Successful deployment of carbon nanomaterials in many applications, such as sensing, energy storage, and catalysis, relies on the selection, synthesis, and tailoring of the surface properties. Predictive analysis of the behavior is difficult without detailed knowledge of the differences between various carbon nanomaterials and their surface functionalization, thus leaving the selection process to traditional trial-and-error work. The present characterization fills this knowledge gap for carbon nanomaterial surface properties with respect to chemical states and functionalization. We present an overview of the chemical trends that can be extracted from soft X-ray absorption spectroscopy (XAS) spectra on an extended set of nonideal carbon nanomaterials as a function of sp 2 bonded carbon and bond ordering. In particular, the surface chemical state, the presence of long-range order in the carbon matrix, and a qualitative estimation of the amount of oxygen and nitrogen and their respective functional group formation on the material surface, together with the detailed material fabrication parameters, are reported. The results expand our understanding of carbon nanomaterial functionalization, which can support material selection in practice, provided that the specifications of the application are known.
Abstract Cyanobacteria are new sources of value-added compounds but also ubiquitous and harmful microfoulers on marine biofouling. In this work, the isolation and identification of two cyanobacterial strains isolated from Cape Verde and Morocco, as well as their biofilm-forming ability on glass and Perspex under controlled hydrodynamic conditions, were performed. Phylogenetic analysis revealed that cyanobacterial strains isolated belong to Leptothoe and Jaaginema genera (Leptothoe sp. LEGE 181153 and Jaaginema sp. LEGE 191154). From quantitative and qualitative data of wet weight, chlorophyll a content and biofilm thickness obtained by optical coherence tomography, no significant differences were found in biofilms developed by the same cyanobacterial strain on different surfaces (glass and Perspex). However, the biofilm-forming potential of Leptothoe sp. LEGE 181153 proved to be higher compared with Jaaginema sp. LEGE 191154, particularly at the maturation stage of biofilm development. Three-dimensional biofilm images obtained from confocal laser scanning microscopy showed different patterns between both cyanobacterial strains and also among the two surfaces. Because standard methodologies to evaluate cyanobacterial biofilm formation, as well as two different optical imaging techniques, were used, this work also highlights the possibility of integrating different techniques to evaluate a complex phenomenon like cyanobacterial biofilm development.
The discovery of linear scaling relations has fundamentally changed the field of heterogeneous catalysis. The scaling relations have been rationalized based on the d-band theory, specifically a separation of sp and d electron contributions to adsorption energies. Within the framework of energy decomposition analysis, a full understanding of such a separation would require one to further break down the adsorption energy into distinct energy components such as electrostatics, polarization, charge transfer, and van der Waals interactions, and to examine the sp and d contributions to each of them. As a step in this direction, we analyzed the interaction energy between CH x (x = 1–4) adsorbates and fcc(100) transition metal surfaces (M = Cu, Ag, Au, Rh, and Pt), with the surfaces represented both as slabs in plane-wave density functional theory (pw-DFT) calculations and as atomic clusters in atomic-orbital basis density functional theory (ao-DFT) calculations. Through an absolutely localized molecular orbital (ALMO) based energy decomposition analysis of the ao-DFT adsorption energy, each of the interaction energy components (electrostatics, polarization, van der Waals, and charge transfer) was found to follow its own scaling relations, with an intricate interplay among these energy components yielding the overall scaling relations for the total adsorption energies. Using the recently introduced ALMO-based polarization and charge-transfer analysis schemes, we further dissected polarization into metal surface and adsorbate contributions, and charge transfer into metal → adsorbate and adsorbate → metal contributions. The contributions from the sp and d electrons of the metal to these terms were further quantified, and the dominant role of the metal d electrons was reaffirmed. These results shed light on how CHx adsorbates interact with metal surfaces and further reveal the physical origin of the scaling relations.
Microbial colonization of plant roots is a highly complex process that requires the coordination and regulation of many gene networks, yet the identities and functions of many of these gene products have yet to be discovered. Pantoea sp. YR343, a gamma-proteobacterium isolated from the rhizosphere of Populus deltoides , forms robust biofilms along the root surfaces of Populus and possesses plant growth-promoting characteristics. In this work, we identified three diguanylate cyclases in the plant-associated microbe Pantoea sp. YR343 that are expressed in the presence of plant roots. One of these diguanylate cyclases, DGC2884, localizes to discrete sites in the cells and its overexpression results in reduced motility and increased EPS production and biofilm formation. We performed a genetic screen by expressing this diguanylate cyclase from an inducible promoter in order to identify candidate gene products that may be involved in root colonization by Pantoea sp. YR343. Further, we demonstrate the importance of other domains in DGC2884 to its activity, which in combination with the genes identified by transposon mutagenesis, may yield insights into the mechanisms of plant association as well as the activity and regulation of homologous enzymes in medically and agriculturally relevant microbes.
This work demonstrates how photoactive compounds can be used to tune the surface chemistry, surface free energy, and the wetting velocity of fluids on Spiropyran functionalized surfaces with different surface microstructures. Evidence of this photowetting effect is based on data showing: (1) the cyclic changes in the static, advancing, and receding contact angles $\theta$ CA for multiple UV$\rightleftarrows$vis photoswitching cycles with both smooth and microstructured surfaces and (2) the changes in the fluid wicking velocity (via UV$\rightleftarrows$vis photoswitching) on different Spiropyran functionalized hemiwicking surfaces. X-ray photoelectron spectroscopy is used to determine the efficiency of photoswitching caused by the quality of the Spiropyran functionalization. Reversible photoisomerization of Spiropyran generates a gradient in surface free energy, resulting in a similar change in contact angle ($\theta$ CA ) in the photoswitchable surfaces. In conclusion, by incorporating these changes into the Owens-Wendt and Van Oss surface energy models, the energy of smooth Au surfaces can also be predicted for both UV and visible light irradiations, where reversible contact angle variations of $\Delta$$\theta$ CA ≈ 5–10° are achieved with both water and water-ethanol mixtures due to the conversion of SP to merocyanine, which corresponds to a total free energy change of ~13% on the photoswitchable surface.