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At least 127 records · Page 7

Quantifying Dynamic Water Storage in Unsaturated Bedrock with Borehole Nuclear Magnetic Resonance

Quantifying the volume of water that is stored in the subsurface is critical to studies of water availability to ecosystems, slope stability, and water-rock interactions. In a variety of settings, water is stored in fractured and weathered bedrock as rock moisture. However, few techniques are available to measure rock moisture in unsaturated rock, making direct estimates of water storage dynamics difficult to obtain. Here, we use borehole nuclear magnetic resonance (NMR) at two sites in seasonally dry California to quantify dynamic rock moisture storage. Additionally, we show strong agreement between NMR estimates of dynamic storage and estimates derived from neutron logging and mass balance techniques. The depths of dynamic storage are up to 9 m and likely reflect the depth extent of root water uptake. To our knowledge, these data are the first to quantify the volume and depths of dynamic water storage in the bedrock vadose zone via NMR.

58 GEOSCIENCES↗

Interactions with microbial consortia have variable effects in organic carbon and production of exometabolites among genotypes of Populus trichocarpa

Abstract Poplar is a short‐rotation woody crop frequently studied for its significance as a sustainable bioenergy source. The successful establishment of a poplar plantation partially depends on its rhizosphere—a dynamic zone governed by complex interactions between plant roots and a plethora of commensal, mutualistic, symbiotic, or pathogenic microbes that shape plant fitness. In an exploratory endeavor, we investigated the effects of a consortium consisting of ectomycorrhizal fungi and a beneficial Pseudomonas sp. strain GM41 on plant growth (including height, stem girth, leaf, and root growth) and as well as growth rate over time, across four Populus trichocarpa genotypes. Additionally, we compared the level of total organic carbon and plant exometabolite profiles across different poplar genotypes in the presence of the microbial consortium. These data revealed no significant difference in plant growth parameters between the treatments and the control across four different poplar genotypes at 7 weeks post‐inoculation. However, total organic carbon and exometabolite profiles were significantly different between the genotypes and the treatments. These findings suggest that this microbial consortium has the potential to trigger early signaling responses in poplar, influencing its metabolism in ways crucial for later developmental processes and stress tolerance.

59 BASIC BIOLOGICAL SCIENCES↗

Molecular Dynamics Simulation of Atomic Interactions in the Vancomycin Binding Site

Vancomycin is a glycopeptide antibiotic produced by Amycolaptopsis orientalis used to treat serious infections by Grampositive pathogens including methicillin-resistant Staphylococcus aureus. Vancomycin inhibits cell wall biosynthesis by targeting lipid II, which is the membrane-bound peptidoglycan precursor. The heptapeptide aglycon structure of vancomycin binds to the D-Ala-D-Ala of the pentapeptide stem structure in lipid II. The third residue of vancomycin aglycon is asparagine, which is not directly involved in the dipeptide binding. Nonetheless, asparagine plays a crucial role in substrate recognition, as the vancomycin analogue with asparagine substituted by aspartic acid (V D ) shows a reduction in antibacterial activities. To characterize the function of asparagine, binding of vancomycin and its aspartic-acid-substituted analogue V D to L-Lys-D-Ala-D-Ala and L-Lys-D-Ala-D-Lac was investigated using molecular dynamic simulations. Binding interactions were analyzed using root-mean-square deviation (RMSD), two-dimensional (2D) contour plots, hydrogen bond analysis, and free energy calculations of the complexes. The analysis shows that the aspartate substitution introduced a negative charge to the binding cleft of V D , which altered the aglycon conformation that minimized the repulsive lone pair interaction in the binding of a depsipeptide. Our findings provide new insight for the development of novel glycopeptide antibiotics against the emerging vancomycin-resistant pathogens by chemical modification at the third residue in vancomycin to improve its binding affinity to the D-Ala-D-Lac-terminated peptidoglycan in lipid II found in vancomycin-resistant enterococci and vancomycinresistant S. aureus.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Specialized Plant Growth Chamber Designs to Study Complex Rhizosphere Interactions

The rhizosphere is a dynamic ecosystem shaped by complex interactions between plant roots, soil, microbial communities and other micro- and macro-fauna. Although studied for decades, critical gaps exist in the study of plant roots, the rhizosphere microbiome and the soil system surrounding roots, partly due to the challenges associated with measuring and parsing these spatiotemporal interactions in complex heterogeneous systems such as soil. To overcome the challenges associated with in situ study of rhizosphere interactions, specialized plant growth chamber systems have been developed that mimic the natural growth environment. This review discusses the currently available lab-based systems ranging from widely known rhizotrons to other emerging devices designed to allow continuous monitoring and non-destructive sampling of the rhizosphere ecosystems in real-time throughout the developmental stages of a plant. We categorize them based on the major rhizosphere processes it addresses and identify their unique challenges as well as advantages. We find that while some design elements are shared among different systems (e.g., size exclusion membranes), most of the systems are bespoke and speaks to the intricacies and specialization involved in unraveling the details of rhizosphere processes. We also discuss what we describe as the next generation of growth chamber employing the latest technology as well as the current barriers they face. We conclude with a perspective on the current knowledge gaps in the rhizosphere which can be filled by innovative chamber designs.

59 BASIC BIOLOGICAL SCIENCES↗

Neutron Radiography and Computed Tomography of Biological Systems at the Oak Ridge National Laboratory's High Flux Isotope Reactor

Neutrons have historically been used for a broad range of biological applications employing techniques such as small-angle neutron scattering, neutron spin echo, diffraction, and inelastic scattering. Unlike neutron scattering techniques that obtain information in reciprocal space, attenuation-based neutron imaging measures a signal in real space that is resolved on the order of tens of micrometers. The principle of neutron imaging follows the Beer-Lambert law and is based on the measurement of the bulk neutron attenuation through a sample. Greater attenuation is exhibited by some light elements (most notably, hydrogen), which are major components of biological samples. Contrast agents such as deuterium, gadolinium, or lithium compounds can be used to enhance contrast in a similar fashion as it is done in medical imaging, including techniques such as optical imaging, magnetic resonance imaging, X-ray, and positron emission tomography. For biological systems, neutron radiography and computed tomography have increasingly been used to investigate the complexity of the underground plant root network, its interaction with soils, and the dynamics of water flux in situ. Moreover, efforts to understand contrast details in animal samples, such as soft tissues and bones, have been explored. This manuscript focuses on the advances in neutron bioimaging such as sample preparation, instrumentation, data acquisition strategy, and data analysis using the High Flux Isotope Reactor CG-1D neutron imaging beamline. The aforementioned capabilities will be illustrated using a selection of examples in plant physiology (herbaceous plant/root/soil system) and biomedical applications (rat femur and mouse lung).

Bilheux, Hassina↗

Real-Time High-Accuracy Digital Wireless Time, Frequency, and Phase Calibration for Coherent Distributed Antenna Arrays

his work presents a fully-digital high-accuracy real-time calibration procedure for frequency and time alignment of open-loop wirelessly coordinated coherent distributed antenna array (CDA) modems, enabling radio frequency (RF) phase coherence of spatially separated commercial off-the-shelf (COTS) software-defined radios (SDRs) without cables or external references such as the global navigation satellite system (GNSS). Building on previous work using high-accuracy spectrally-sparse time of arrival (ToA) waveforms and a multistep ToA refinement process, a high-accuracy two-way time transfer (TWTT)-based time–frequency coordination approach is demonstrated. Due to the two-way nature of the high-accuracy TWTT approach, the time and frequency estimates are Doppler and multipath tolerant, so long as the channel is reciprocal over the synchronization epoch. This technique is experimentally verified using COTS SDRs in a lab environment in static and dynamic scenarios and with significant multipath scatterers. Time, frequency, and phase stability were evaluated by beamforming over coaxial cables to an oscilloscope which achieved time and phase precisions of ~60– 70 ps , with median coherent gains above 99% using optimized coordination parameters, and a beamforming frequency root-mean-square error (RMSE) of 3.73 ppb in a dynamic scenario. Finally, experiments were conducted to compare the performance of this technique with previous works using an analog continuous-wave two-tone (CWTT) frequency reference technique in both static and dynamic settings.

Clock synchronization↗

Belowground allocation and dynamics of recently fixed plant carbon in a California annual grassland

Plant roots and the organisms that surround them are a primary source for stabilized soil organic carbon (SOC). While grassland soils have a large capacity to store organic carbon (C), few field-based studies have quantified the amount of plant-fixed C that moves into soil and persists belowground over multiple years. Yet this characteristic of the soil C cycle is critical to C storage, soil water holding capacity, nutrient provisions, and the management of soil health. Here, we tracked the fate of plant-fixed C following a five-day 13 CO 2 labeling of a Northern California annual grassland, measuring C pools starting at the end of the labeling period, at three days, four weeks, six months, one year, and two years. Soil organic carbon was fractionated using a density-based approach to separate the free-light fraction (FLF), occluded-light fraction (OLF), and heavy fraction (HF). Using isotope ratio mass spectrometry, we measured 13 C enrichment and total C content for plant shoots, roots, soil, soil dissolved organic carbon (DOC), and the FLF, OLF, and HF. The chemical nature of C in the HF was further analyzed by solid state 13 C nuclear magnetic resonance (NMR) spectroscopy.

13C-NMR↗

Magnetic dynamics with Weyl fermions

Transport of charge and valley (axial) degrees of freedom coupled to order-parameter dynamics in magnetic Weyl semimetals is studied in the framework of nonequilibrium thermodynamics. In addition to the established valley-related transport anomalies that are rooted in band-structure topology, we construct dissipative couplings between the three dynamic constituents of the system driven out of equilibrium by electromagnetic perturbations. We show how the valley degree of freedom mediates an effective coupling between the charge and magnetic sectors of the system, through a combination of the chiral anomaly, on the electric side, and the Onsager-paired valley torque and pumping, on the magnetic side. This work complements previous studies of magnetic Weyl semimetals by a more systematic analysis of collective dissipation. We discuss several concrete examples of the valley-mediated current-driven magnetic instabilities and charge pumping, and extend the theory to the antiferromagnetic case.

36 MATERIALS SCIENCE↗

Deep root activity overprints weathering of petrogenic organic carbon in shale

The oxidation of organic carbon in sedimentary bedrock (petrogenic OC, OC petro ) is increasingly recognized as a potential source of CO 2 to the atmosphere. Recent studies provide evidence for the mobilization and oxidation of OC petro in sedimentary bedrock during rock weathering. However, the mechanisms and rates remain uncertain, particularly where overlying soils and vegetation drive contemporaneous oxidation of recently fixed organic carbon. Here, in this study, we quantify OC petro weathering across a 16 m shale depth profile in a steep, rapidly eroding forested hillslope in the Northern California Coast Ranges. We report solid and gas phase radiocarbon and stable isotope analyses of samples extracted from specialized in-situ samplers, and a supporting laboratory incubation experiment of the shale regolith. OC petro is removed from the weathered bedrock at a rate of approximately 0.12 gC/m 3 yr, which is orders of magnitude lower than the rate of OC petro oxidation we achieved in the laboratory with crushed samples (557.1 gC/m 3 yr). This disparity occurs despite high O 2(g) content across the depth profile, indicating that physical accessibility of OC petro can regulate oxidative weathering. There is no direct radiocarbon evidence of OC petro oxidation in CO 2(g) across the upper 13 m of the weathering profile during both wet and dry seasons. Instead, vadose zone CO 2(g) production at the site is dominated by respiration of recently fixed carbon associated with deep rooting. OC petro is clearly mobilized across the vadose zone during weathering in this rapidly eroding, oxygen-rich, biologically dynamic hillslope, but at rates far below what can be measured given the contribution of root-derived CO 2(g) .

58 GEOSCIENCES↗

Priming mechanisms providing plants and microbes access to mineral-associated organic matter

Mineral-associated organic matter (MAOM) is considered a stable reservoir for soil nutrients that influences long-term soil carbon (C) and nitrogen (N) dynamics. However, recent experimental and theoretical evidence shows that root exudates may mobilize MAOM, thereby providing plants and microbes access to a large and N-rich pool. Given the mechanisms underlying MAOM C and N mobilization remain largely untested, we examined direct and indirect pathways by which root exudates destabilize this nutrient pool in laboratory mesocosms. We simulated root exudation with 13 C-labeled oxalic acid to test whether root exudates are directly capable of mobilizing MAOM from mineral surfaces; and with 13 C-labeled glucose to test whether indirect stimulation of microbial and extracellular enzyme activity leads to MAOM decomposition. We also tested the potential for oxalic acid and glucose to mobilize MAOM in an additional subset of sterilized soils to clarify the potential for non-microbial pathways of MAOM destabilization. Over the course of the 12-day MAOM incubation with and without simulated exudates, we measured C cycling (CO 2 respiration rates, 13 C–CO 2 efflux), N cycling (inorganic N pools, gross N mineralization) and related microbial processes (enzyme activities and microbial community composition via phospholipid fatty acid analysis). Both of the simulated root exudates enhanced MAOM-C mineralization, with cumulative respiration increasing 35–89% relative to the water-only control. Likewise, glucose additions enhanced the production of an exo-cellulase and a chitinase by up to 130% and 39%, respectively, while oxalic acid enhanced oxidative enzyme activities up to 91% greater than control rates. We observed a positive association between glucose-induced shifts in enzyme activities, MAOM-C mineralization, and gross ammonification. Oxalic acid additions were associated with initial increases in fungal relative abundance and in sterile soils appeared to stimulate the release of metals and dissolved organic nitrogen into exchangeable pools. Our results indicate that common root exudates, like glucose and oxalic acid, can significantly increase the turnover and potential release of C and N from MAOM through indirect (e.g., enzyme induction) and direct (e.g., mobilization of metal oxides) mechanisms.

54 ENVIRONMENTAL SCIENCES↗

Design of nematic liquid crystals to control microscale dynamics

The dynamics of small particles, both living such as swimming bacteria and inanimate, such as colloidal spheres, has fascinated scientists for centuries. If one could learn how to control and streamline their chaotic motion, that would open technological opportunities in the transformation of stored or environmental energy into systematic motion, with applications in micro-robotics, transport of matter, guided morphogenesis. This review presents an approach to command microscale dynamics by replacing an isotropic medium with a liquid crystal. Orientational order and associated properties, such as elasticity, surface anchoring, and bulk anisotropy, enable new dynamic effects, ranging from the appearance and propagation of particle-like solitary waves to self-locomotion of an active droplet. By using photoalignment, the liquid crystal can be patterned into predesigned structures. In the presence of the electric field, these patterns enable the transport of solid and fluid particles through nonlinear electrokinetics rooted in anisotropy of conductivity and permittivity. Director patterns command the dynamics of swimming bacteria, guiding their trajectories, polarity of swimming, and distribution in space. This guidance is of a higher level of complexity than a simple following of the director by rod-like microorganisms. Namely, the director gradients mediate hydrodynamic interactions of bacteria to produce an active force and collective polar modes of swimming. The patterned director could also be engraved in a liquid crystal elastomer. When an elastomer coating is activated by heat or light, these patterns produce a deterministic surface topography. The director gradients define an activation force that shapes the elastomer in a manner similar to the active stresses triggering flows in active nematics. Finally, the patterned elastomer substrates could be used to define the orientation of cells in living tissues. The liquid-crystal guidance holds a major promise in achieving the goal of commanding microscale active flows.

36 MATERIALS SCIENCE↗

Probing Accuracy-Speedup Tradeoff in Machine Learning Surrogates for Molecular Dynamics Simulations

The performance promise of machine learning surrogates of molecular dynamics simulations of soft materials is significant but generally comes at the cost of acquiring large training datasets to learn the complex relationships between input soft material attributes and output properties. Under the constraint of limited high-performance computing resources, optimizing the size of the training datasets becomes paramount. Using an artificial neural network based surrogate for molecular dynamics simulations of confined electrolytes, we explore the tradeoff between surrogate accuracy and computational gains. Accuracy is assessed by computing the root-mean-square errors between the surrogate predictions and the ground truth results obtained via molecular dynamics simulations. The computational performance is judged by evaluating the speedup which incorporates the training dataset creation time. Improvement in accuracy occurs with a loss of speedup, which scales as the inverse of the training dataset size. Furthermore, the link between surrogate generalizability and the accuracy-speedup tradeoff is assessed by examining the errors incurred in surrogate predictions on unseen, interpolated input variables and developing a net speedup metric to capture the associated gains.

Anions↗

Simulating measurable ecosystem carbon and nitrogen dynamics with the mechanistically defined MEMS 2.0 model

Abstract. For decades, predominant soil biogeochemical models have used conceptual soil organic matter (SOM) pools and only simulated them to a shallow depth in soil. Efforts to overcome these limitations have prompted the development of the new generation SOM models, including MEMS 1.0, which represents measurable biophysical SOM fractions, over the entire root zone, and embodies recent understanding of the processes that govern SOM dynamics. Here we present the result of continued development of the MEMS model, version 2.0. MEMS 2.0 is a full ecosystem model with modules simulating plant growth with above- and belowground inputs, soil water and temperature by layer, decomposition of plant inputs and SOM, and mineralization and immobilization of nitrogen (N). The model simulates two commonly measured SOM pools – particulate and mineral-associated organic matter (POM and MAOM, respectively). We present results of calibration and validation of the model with several grassland sites in the US. MEMS 2.0 generally captured the soil carbon (C) stocks (R2 of 0.89 and 0.6 for calibration and validation, respectively) and their distributions between POM and MAOM throughout the entire soil profile. The simulated soil N matches measurements but with lower accuracy (R2 of 0.73 and 0.31 for calibration and validation of total N in SOM, respectively) than for soil C. Simulated soil water and temperature were compared with measurements, and the accuracy is comparable to the other commonly used models. The seasonal variation in gross primary production (GPP; R2 = 0.83), ecosystem respiration (ER; R2 = 0.89), net ecosystem exchange (NEE; R2 = 0.67), and evapotranspiration (ET; R2 = 0.71) was well captured by the model. We will further develop the model to represent forest and agricultural systems and improve it to incorporate new understanding of SOM decomposition.

54 ENVIRONMENTAL SCIENCES↗

Long-time memory effects in a localizable central spin problem

We study the properties of the Nakajima–Zwanzig memory kernel for a qubit immersed in a many-body localized (i.e. disordered and interacting) bath. We argue that the memory kernel decays as a power law in both the localized and ergodic regimes, and show how this can be leveraged to extract t → ∞ populations for the qubit from finite time (Jt ≤ 10 2 ) data in the thermalizing phase. This allows us to quantify how the long-time values of the populations approach the expected thermalized state as the bath approaches the thermodynamic limit. This approach should provide a good complement to state-of-the-art numerical methods, for which the long-time dynamics with large baths are impossible to simulate in this phase. Additionally, our numerics on finite baths reveal the possibility for unbounded exponential growth in the memory kernel, a phenomenon rooted in the appearance of exceptional points in the projected Liouvillian governing the reduced dynamics. In small systems amenable to exact numerics, we find that these pathologies may have some correlation with delocalization.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Root traits reveal safety and efficiency differences in grasses and shrubs exposed to different fire regimes

Plant roots are important components of terrestrial ecosystems, but little is known about how root traits differ between plant species or vary across space in natural ecosystems. In this study, we investigated how root traits vary across grasses and woody shrubs in a tallgrass prairie located in Manhattan, KS, USA. Specifically, were interested in understanding how anatomical traits vary across these different plant groups, across different depths in the soil, and also across multiple areas of tallgrass prairie that are burned at different frequencies. We compared traits that allow roots to use soil water efficiently and those that help roots persist through extended periods of drought. We found that woody roots exhibited traits that allow them to use water efficiently in shallow soils but persist through drought in deeper soil. Here, these traits may allow shrubs to transport water from shallow soils to deeper soil after large rain events and resist extended periods without rain when soils become dry, which may allow woody plants to successfully compete for water in less frequently burned, more diverse plant communities. Grasses had traits that allow them to use water efficiently but also tolerate drought in shallow soils, regardless of fire treatment. This unique trait combination likely gives grasses a competitive advantage over other tallgrass prairie plants across different fire regimes. Together, these results show that anatomical root traits can be used to enhance mechanistic understanding of plant functioning in dynamic ecosystems.

54 ENVIRONMENTAL SCIENCES↗

Linked nitrogen and carbon dynamics reveal distinct pools and patterns in a deep, weathered bedrock rhizosphere

Nitrogen is one of the most limiting nutrients to forest productivity worldwide. Recently, it has been established that diverse ecosystems source a substantial fraction of their water from weathered bedrock, leading to questions about whether root-driven nitrogen cycling extends into weathered bedrock as well. In this study, we specifically examined nitrogen dynamics using specialized instrumentation distributed across a 16 m weathered bedrock vadose zone (WBVZ) underlying an old growth forest in northern California where the rhizosphere—composed of plant roots and their associated microbiome—extends meters into rock. We documented total dissolved nitrogen (TDN), dissolved organic carbon (DOC), inorganic nitrogen (ammonium and nitrate), and CO 2 and O 2 gases every 1.5 m to 16 m depth for 2 y. We found that TDN concentrations increased with depth, were an order of magnitude greater at 15 m than in the upper 30 cm, and that the majority of TDN throughout the weathered bedrock vadose zone was organic. We also found that TDN concentrations are influenced by depth, season, and interannual precipitation patterns. Carbon isotope composition of the DOC suggests that dissolved organic matter in the WBVZ is primarily derived from plant sources, and not the nitrogen-rich bedrock. We conclude that nitrogen dynamics in the WBVZ may be driven, in part, by an active rhizosphere, meters below the base of soil, and we argue that weathered bedrock horizons may play a key role in C-N cycling in ecosystems with deep-rooted plants.

Science & Technology - Other Topics↗

Contribution of decomposing plant roots to N 2 O emissions by water absorption

The “sponge effect”, or water absorption by incorporated plant leaf residues, was recently identified as one of the mechanisms that drives activity in microbial hotspots. We explored the presence of the sponge effect in plant root residues, and its role in root decomposition and associated N 2 O and CO 2 emissions. Young soybean (Glycine max) plants were grown in microcosms with two soil materials dominated by (i) large (>30 μm Ø) and (ii) small (<10 μm Ø) pores. After termination, the microcosms with the decomposing roots were incubated at 50% and 75% water-filled pore space (WFPS) soil moisture levels. Root decomposition, water absorption by the decomposing roots, and water redistribution were quantified using X-ray computed micro-tomography (μCT), including dual-energy scanning. The results demonstrated occurrence of the sponge effect in young, in-situ grown soybean roots and sharp gradients in the distribution of the added liquid within ~150 µm distance from the decomposing roots. At 50% WFPS the large pore soil emitted 185% more N 2 O than the small pore soil; and, during the first 5 days of incubation, more N 2 O than the large pore soil at 75% WFPS. This finding indicates that the decomposing roots acted as hotspots of N 2 O production, potentially due to sponge effect and associated anoxic conditions. This study suggests that the interactions between pore characteristics and soil moisture can play a significant role in defining the contribution of detritusphere, specifically, decomposing young roots, to soil biogeochemical processes, including microbial activity and denitrification dynamics.

54 ENVIRONMENTAL SCIENCES↗

Molecular Origin of Nanoscale Anion Ordering of LiTFSI Electrolytes Revealed through SAXS/WAXS and Molecular Dynamics Simulations

Recent developments in “water-in-salt” electrolytes have precipitated a renewed effort to study imide-based electrolytes. While previous small-/wide-angle X-ray scattering (SAXS/WAXS) studies have attributed the emergence of a low-Q peak in the SAXS profile of aqueous LiTFSI electrolytes to nanometer-scale anion clustering, a molecular-level understanding of the root of these clusters remains unclear. Here, in this study, we combined molecular dynamics simulations and SAXS/WAXS to study the solvation structures of LiTFSI in acetonitrile, methanol, and water. We concluded that hydrogen bonding in water and MeOH stabilizes anion clusters, while nonpolar methyl groups on methanol and acetonitrile interrupt the nanoscale ordering of TFSI anions. This causes LiTFSI in water and MeOH electrolytes to exhibit two low-Q SAXS profile peaks while LiTFSI in acetonitrile exhibits only a single peak below Q = 1 Å –1 . These findings shed light on the underlying molecular origins of nanoscale anion clusters, which may help in the design of the next generation of electrolyte chemistries.

Trojanowski, Lucas [Univ. of Michigan, Ann Arbor, ↗