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At least 163 records · Page 9

Root Microbiome Modulates Plant Growth Promotion Induced by Low Doses of Glyphosate

Since the introduction of glyphosate-resistant crops, glyphosate has become the most common and widely used herbicide around the world. Due to its intensive use and ability to bind to soil particles, it can be found at low concentrations in the environment. The effect of these remnants of glyphosate in plants has not been broadly studied; however, glyphosate 1,000 to 100,000 times less concentrated than the recommended field dose promoted growth in several species in laboratory and greenhouse experiments. However, this effect is rarely observed in agricultural fields, where complex communities of microbes have a central role in the way plants respond to external cues. Our study reveals how root-associated bacteria modulate the responses of Arabidopsis to low doses of glyphosate, shifting between growth promotion and growth inhibition.

59 BASIC BIOLOGICAL SCIENCES↗

Changes in environmental and engineered conditions alter the plasma membrane lipidome of fractured shale bacteria

ABSTRACT Microorganisms that persist in fractured shale reservoirs cause several problems including secreting foul gases and forming biofilms. Current biocontrol measures often fail due to limited knowledge of their in situ activities. The plasma membrane protects the cell, mediates many of its critical functions, and responds to intracellular cues and ecological perturbations through physicochemical modifications. As such, it provides valuable insight into the physiological adaptation of microorganisms in disturbed environmental systems. Here, we (i) demonstrate how changes in salinity and hydraulic retention time (HRT) influence the plasma membrane intact polar lipid (IPL) chemistry of model bacterium, Halanaerobium congolense WG10, and mixed microbial consortia enriched from shale-produced fluids and (ii) elucidate adjustments in membrane IPL chemistry during biofilm growth relative to planktonic cells. We incubated H. congolense WG10 in chemostats under three salinities (7%, 13%, and 20% NaCl), operated under three HRTs (19.2, 24, and 48 h), and in drip flow biofilm reactors under the same salinity gradients. Also, mixed microbial consortia in produced fluids were enriched in triplicate chemostat vessels under three HRTs (19.2, 24, and 72 h) and biofilm reactors. Lipids were analyzed by ultra high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Our results show that phosphatidylglycerols, cardiolipins, and phosphatidylethanolamines were predominantly enriched in planktonic H. congolense WG10 cells grown at hypersalinity (20%) compared to optimum (13%). In addition, several zwitterionic phosphatidylcholines and phosphatidylethanolamines were higher in abundance during biofilm growth. These observations suggest that microbial adaptation and biofilm formation in fractured shale are enabled by strategic plasma membrane IPL chemistry adjustments. IMPORTANCE Microorganisms inadvertently introduced into the shale reservoir during fracturing face multiple stressors including brine-level salinities and starvation. However, some anaerobic halotolerant bacteria adapt and persist for long periods of time. They produce hydrogen sulfide, which sours the reservoir and corrodes engineering infrastructure. In addition, they form biofilms on rock matrices, which decrease shale permeability and clog fracture networks. These reduce well productivity and increase extraction costs. Under stress, microbes remodel their plasma membrane to optimize its roles in protection and mediating cellular processes such as signaling, transport, and energy metabolism. Hence, by observing changes in the membrane lipidome of model shale bacteria, Halanaerobium congolense WG10, and mixed consortia enriched from produced fluids under varying subsurface conditions and growth modes, we provide insight that advances our knowledge of the fractured shale biosystem. We also offer data-driven recommendations for improving biocontrol efficacy and the efficiency of energy recovery from unconventional formations.

03 NATURAL GAS↗

Super-swelling behavior of stacked lipid bilayer systems

Bilayer systems comprising lipid mixtures are the most well-studied model of biological membranes. While the plasma membrane of the cell is a single bilayer, many intra- and extra-cellular biomembranes comprise stacks of bilayers. Most bilayer stacks in nature are periodic, maintaining a precise water layer separation between bilayers. That equilibrium water separation is governed by multiple inter-bilayer forces and is highly responsive. Biomembranes re-configure inter-bilayer spacing in response to temperature, composition, or mass transport cues. In synthetic bilayer systems for applications in cosmetics or topical treatments, control of the hydration level is a critical design handle. Herein we investigate a binary lipid system that leverages key inter-bilayer forces leading to unprecedented levels of aqueous swelling while maintaining a coherent multilamellar form. We found that combining cationic lipids with bicontinuous cubic phase-forming lipids (lipids with positive Gaussian modulus), results in the stabilization of multilamellar phases against repulsive steric forces that typically lead to bilayer delamination at high degrees of swelling. Using ultra-small-angle X-ray scattering alongside confocal laser scanning microscopy, we characterized various super-swelled states of 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) and glycerol monooleate (GMO) lipids, as well as other analogous systems, at varied concentration and molar ratios. Through these experiments we established swelling profiles of various binary lipid systems that were near-linear with decreasing lipid volume fraction, showing maximum swelling with periodicity well above 200 nanometers.

42 ENGINEERING↗

Structure Perception in 3D Point Clouds

Understanding human perception is critical to the design of effective visualizations. The relative benefits of using 2D versus 3D techniques for data visualization is a complex decision space, with varying levels of uncertainty and disagreement in both the literature and in practice. This study aims to add easily reproducible, empirical evidence on the role of depth cues in perceiving structures or patterns in 3D point clouds. We describe a method to synthesize a 3D point cloud that contains a 3D structure, where 2D projections of the data strongly resemble a Gaussian distribution. We performed a within-subjects structure identification study with 128 participants that compared scatterplot matrices (canonical 2D projections) and 3D scatterplots under three types of motion: rotation, xy-translation, and z-translation. We found that users could consistently identify three separate hidden structures under rotation, while those structures remained hidden in the scatterplot matrices and under translation. This work contributes a set of 3D point clouds that provide definitive examples of 3D patterns perceptible in 3D scatterplots under rotation but imperceptible in 2D scatterplots.

data analysis↗

Decision Making Under Uncertainty Human Subjects Data - Fire Evacuation Task

This dataset contains de-identified data from human subjects experiments, along with the images and code that were used to run the experiments (as a crowdsourced online study). In this study, participants were shown the probability of a house being in the burn zone of a wildfire. They were asked if they would stay in the house or evacuate in that scenario. The probability information was presented in different ways, including text and maps. The studies tested the impact of different visual cues on the participants' patterns of decisions.

Matzen, Laura E. [Sandia National Laboratories (SN↗

ShadeLab/PAPER_Howe_2023_switchgrass_MetaT

The raw data (metagenomes and metatranscriptomes) for this study are available in the Joint Genomes Institute Genome Portal (https://genome.jgi.doe.gov/portal/ Project ID 503249) with projects designated by year and product type. The MAG genomes analyzed in this paper are available on NCBI, as bioproject PRJNA800073. Plants and microorganisms form beneficial associations. Understanding plant-microbe interactions will inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on field-grown switchgrass and miscanthus and to quantify their activities for switchgrass over two growing seasons. We integrate metagenome and metatranscriptome sequencing from 192 leaf samples collected over representative time points in crop phenology. We curated 40 medium- and high-quality metagenome-assembled-genomes (MAGs) and focused analysis on seasonal transcript recruitment to them. Classes represented by these focal MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) were active and had increases in transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase in the late season. The majority of MAGs had activated stress-associated pathways, including trehalose metabolism, indole acetic acid degradation, betaine biosynthesis, and reactive oxygen species degradation, suggesting direct engagement with the host environment. We also detected seasonally activated biosynthetic pathways for terpenes (carotenoids and isoprenoids) and for various non-ribosomal peptide pathways that were poorly annotated. Overall, this study overcame laboratory and bioinformatic challenges associated with field-based leaf metatranscriptome analysis to inform both general and likely specialized activities of these phyllosphere populations. These activities collectively support that leaf-associated bacterial populations are seasonally dynamic, responsive to host cues, and interactively engage in feedback with the plant. This analysis represented quality filtering of metagenomes and metatranscriptomes (data-preparation folder), metagenome assemblies (metagenome-assembly folder) and metagenome-assembled genome binning, curation, refinement, annotation (mag-evaluation folder). Abundances of sequencing libraries were calculated based on reads mapped (mapping folder). Additionallly, analysis of our annotated results are also included (analysis folder).

Howe, Adina↗

Modeling immunity in microphysiological systems

There is a need for better predictive models of the human immune system to evaluate safety and efficacy of immunomodulatory drugs and biologics for successful product development and regulatory approvals. Current in vitro models, which are often tested in two-dimensional (2D) tissue culture polystyrene, and preclinical animal models fail to fully recapitulate the function and physiology of the human immune system. Microphysiological systems (MPSs) that can model key microenvironment cues of the human immune system, as well as of specific organs and tissues, may be able to recapitulate specific features of the in vivo inflammatory response. This minireview provides an overview of MPS for modeling lymphatic tissues, immunity at tissue interfaces, inflammatory diseases, and the inflammatory tumor microenvironment in vitro and ex vivo. Broadly, these systems have utility in modeling how certain immunotherapies function in vivo, how dysfunctional immune responses can propagate diseases, and how our immune system can combat pathogens.

Research & Experimental Medicine↗

Data for “Fast-decaying plant litter enhances soil carbon in temperate forests, but not through microbial physiological traits”

This data package contains data and code used in the paper “Fast-decaying plant litter enhances soil carbon in temperate forests, but not through microbial physiological traits”. This paper details results from two studies: 1) a laboratory leaf litter incubation experiment (lab experiment) and 2) a multi-site observational field study (field study). Both studies were designed to test the relationships among litter quality, microbial physiological traits, and mineral-associated soil carbon (C). In the lab experiment, we incubated 16 temperate tree litters of differing chemical quality with isotopically distinct soil, measuring microbial physiological traits and the flow of litter-derived C into the mineral-associated soil C pool. In the field study, we sampled soils (0-5 cm) across six eastern US temperate forests, measuring microbial physiological traits, soil abiotic properties, and leaf litter chemistry. The analysis data are provided in two .csv files corresponding to either the lab experiment or field study. Both files contain data on litter chemistry, microbial physiological traits (growth and turnover rates, and carbon use efficiency [CUE]), and the mineral-associated soil C pool. The lab experiment dataset additionally contains litter-derived versus soil-derived soil C, respiration, and litter decomposition parameters. The field study dataset additionally contains site-level climatic information, ectomycorrhizal dominance of plots, and plot-level soil properties. Also provided is the R code and output reproducing the results in the related publication. Analyses were originally performed using R version 3.6.1 using the package "lavaan" and the packages listed on lines 5-7 in the file "data.R".

54 ENVIRONMENTAL SCIENCES↗

Sensor-based phenology from snowmelt experiment gradient, East River, Colorado, 2017 to 2020

The timing of snowmelt is a critical cue for the initiation of growth in mountain meadow ecosystems and can also impact the duration and magnitude of plant production. High frequency observations of species-level phenology are time consuming and require a high degree of expertise, and publicly available remote sensing products lack the necessary temporal resolution to assess fine-scale growing season dynamics. Near-surface sensing methods provide a middle ground with high temporal frequency and tractable spatial scales (from sub-meter to hillslope scale). This data package includes csv files of Normalized Difference Vegetation Index (NDVI) timeseries (SM_NDVI_dailymax.csv) and phenological thresholds (SM_NDVI_summary.csv) for sub-plots (1m2) and Green Chromatic Coordinate (GCC) phenological thresholds (SM_GCC_summary.csv) at the plot scale (10m x 14m). Location IDs associated with this data package are: ER-LM, WG-UM, WG-LS, ER-US, and XX-AL. Related data packages include: “Microclimate observations associated with snowmelt experiment gradient sites, East River, Colorado, 2017 to 2020” and “Colorado Elevation Gradient Snowmelt Manipulation Plant Phenology 2017-2018”.

54 ENVIRONMENTAL SCIENCES↗

Data for Zheng et al. (2025), "AquaMEND: Reconciling multiple impacts of salinization on soil carbon biogeochemistry"

Soil salinization, exacerbated by climate change, poses a global threat to coastal ecosystems and soil function. Salinity affects soil carbon cycling by directly impacting microbial activity and indirectly altering soil physicochemical properties, but current models inadequately represent these complexities. This dataset contains the observational and modeling data from Zheng et al. (2025), which described a process-based modeling framework that couples soil solution chemistry with microbial carbon cycling reactions to study the impacts of soil salinization. This conceptual model is implemented numerically into the open-source geochemical program PHREEQC 3.0 (Parkhurst and Appelo, 2013). This dataset consists of: - Figure2_AquaMEND_salinity_buffer: Contains model simulation outputs to assess the impact of three different cation exchange and surface complexation processes on salinity buffering (Fig. 2 from Zheng et al. 2025). - Figure3_Salinity_function: Contains salinity function fitting for literature data (Fig. 3 from Zheng et al. 2025). - Figure4_AquaMEND_microbial_mechanisms: Contains model simulation outputs for testing various microbial process-based hypotheses related to soil salinization, including microbial mortality, carbon use efficiency (CUE), extracellular enzyme activity, and other microbial mechanisms (Fig. 4 from Zheng et al. 2025). - Figure5_AquaMEND_Redox: Contains on model simulation outputs to evaluate shifts among key redox processes, such as aerobic respiration, sulfate reduction, and methanogenesis (Fig.5 from Zheng et al. 2025). - Figure6_AquaMEND_sorption: Contains on model simulation outputs for investigating the effects of salinity on dissolved organic matter (DOM) sorption and desorption processes (Fig. 6 from Zheng et al. 2025). - Figure7_AquaMEND_process_couple: Contains on model simulation outputs for exploring coupled biotic-abiotic processes and their interactions (Fig. 7 from Zheng et al. 2025). - data: Includes datasets used to develop salinity response functions and evaluate salinity buffering capacity. Datasets for MEND model calibration. - database: Contains the `.dat` file required by PHREEQC for model execution. - README.md: A Markdown plain text file describing the computational tools and directories. Files are a mixture of plain text CSV (comma-separated value) and plain text *.dat files written by the model; no special software is required to read them.

EARTH SCIENCE > AGRICULTURE > SOILS > SOIL SALINIT↗

Diurnal observations of basal stem CO2 efflux in three canopy dominant trees in the central Amazon

We explored mechanisms responsible for disturbance-induced shifts in carbon metabolism in forests north of Manaus, Brazil (S2º 38' 17", W60º 09' 25"), using data from a selective logging experiment (BIONTE). BIONTE (the BIOmass and NuTrient Experiment) selective logging treatments were initiated in the mid-1980s and comprised variable removal of commercial tree (not total) species basal area (T1 =32%, T2 = 42%, T3 = 69%), and control plots with no logging (T0). Raw data including tree base diameter (Db), CO2 concentration versus time inside a static stem chamber, and wood density were used to derive stem respiration rates (Rw), wood production rates (Pw), and wood carbon use efficiency (CUE). Changes in tree base diameter (Db; measured at 1.3 m height, or above the buttresses) was used to calculate wood production for individual trees (Pw). Wood density enabled calculation of stem growth rate in the same units as stem respiration (mmol C m-2 s-1). Four trees were randomly selected from five tree growth rate classes for each treatment block, for a total of 20 trees per treatment block, or 80 trees total from the BIONTE plots. Each of the 80 trees selected for the Rw study were outfitted with dendrometer bands (da Silva et al. 2002). Stem respiration was measured using the method described in Chambers et al. (2004). Briefly, an infra-red gas analyzer (LiCor 820) was operated as a closed dynamic chamber with a flow rate of 1.0 L min-1. Polyvinyl chloride (PVC) semi-cylindrical chambers (250–400 mL) were secured to the tree stem near the dendrometer bands using nylon straps. The measurement interval spanned 1–2 min, and the CO2 flux from the stem of each tree was quantified using the enclosed stem area and slope of the stem CO2 concentration versus time.

54 ENVIRONMENTAL SCIENCES↗

Communication Requirements for Price-Based Grid Coordination

Meeting ambitious goals for carbon reduction and supporting an electric grid with high levels of renewable energy supply will require significant flexibility from the demand side. This paper outlines a system architecture and communication technology infrastructure to enable dynamic pricing to be used to finely tune coordination between the grid and its customers. Taking a cue from the success of Internet architecture, this system — Price-Based Grid Coordination — emphasizes simplicity and universality. It enables a wide variety of ways for prices and other signals to pass from the grid to individual flexible loads, including multiple possible locations for the intelligence that combines price signals with device functional needs. The paper includes a reference data model to describe how information from the utility level can be conveyed to customer devices, but independent of any particular protocol. The paper also summarizes technology standards development needs, and reviews research needs to address the full spectrum of coordination scenarios.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Hanging String Cuts in SPR Caverns: Modeling Investigation and Comparison with Sonar Data

Investigation of leaching for oil sales includes looking closely at cavern geometries. Anomalous cavern "features" have been observed near the foot of some caverns subsequent to partial drawdowns. One potential mitigation approach to reducing further growth of preexisting features is based on the hypothesis that reducing the brine string length via a "string cue' would serve to move the zone associated with additional leaching to a location higher up in the cavern and thus away from the preexisting feature. Cutting of the hanging string is expected to provide a control of leaching depth that could be used to "smooth" existing features and thus reduce geomechanical instability in that region of the cavern. The SANSMIC code has been used to predict cavern geometry changes (i.e., the extent of cavern growth with depth) based on variable input parameters for four caverns: West Hackberry 11 (WH11), West Hackberry 113 (WH113), Big Hill 104 (BH104), Big Hill 114 (BH114). By comparing the initial sonar geometry with resultant geometries calculated by the SANSMIC code, conclusions may be drawn about the potential impact of these variables on future cavern growth. Ultimately, these conclusions can be used to assess possible mitigation strategies such as the potential advantage of cutting versus not cutting a brine string. This work has resulted in a recommendation that a hanging string cut of 80 ft in WH11 would be beneficial to future cavern geometry, while there would be little to no benefit to string cuts in the other three caverns investigated here. The WH11 recommendation was followed in 2019, resulting in an operational string cut. A sonar performed after the string cut showed no adverse leaching in the area of the preexisting flare, as expected from the results of the preliminary SANSMIC runs described in this report. Additional SANSMIC modeling of the actual amount of injected raw water resulted in good agreement with the post-cut sonar.

02 PETROLEUM↗

Description of SIS-AOP Result Format V1.0

Single Image SICD-Based Automatic Object Processing (SIS-AOP) is an automatic object identification tool for SAR imagery. It ingests a SAR image in standard SICD format, and it will run a suite of algorithms to cue possible vehicle detections, cull those detections and then ultimately label them either as detections only or possible expound to give a class-level ID or a vehicle-type ID. The SIS-AOP results are given in an XML (Extensible Markup Language) output format. This document defines the elements in the SISAOPR XML output format.

97 MATHEMATICS AND COMPUTING↗

Evaluating the economic impacts of using enzymatic membranes to optimize bicarbonate production and delivery to open raceway ponds

Gas sparging is the most commonly used method for delivering CO2 to algal cultures in Open Raceway Ponds (ORPs). While this method is well-tested and effective, these systems experience large amounts of outgassing to the surrounding atmosphere and often achieve carbon utilization efficiencies (CUE) lower than 30%. With such large losses, system are overdesigned to provide CO2 gas in extreme excess, resulting in increased capital and operational expenses. This research is focused on the development, testing, and implementation of a hydrogel membrane seeded with the enzyme carbonic anhydrase and designed to convert gaseous CO2 into aqueous bicarbonate and deliver this inorganic carbon (iC) directly to the algae pond. Despite increased capital expenses for the module, bicarbonate storage tank, and added pumps and infrastructure, preliminary results suggest that the membrane module has the potential to reduce the minimum biomass selling price by 35% by significantly reducing the operational expenditure for CO2.

09 BIOMASS FUELS↗

Human RNome Project draft human RNome sequence of GM12878, B-cell line, obtained by mass-spectrometry sequencing, long-read sequencing and short-read sequencing.

Here we report the first draft of the human RNome sequence, a reference map of RNA chemical modifications in a human B-cell line. RNA carries a diverse repertoire of chemical modifications that regulate gene expression, cellular function, and responses to physiological and pathological cues. Yet, unlike the genome, no reference map of RNA modifications is available for any human cell. To generate this resource, the Human RNome Project Consortium analyzed a shared RNA preparation from the well-characterized GM12878 B-cell line using short-read sequencing, long-read direct RNA sequencing, and mass spectrometry, generating more than 7.1 billion sequencing reads spanning approximately 1.2 trillion nucleotides. The resulting maps of the human RNome reveal that RNA modifications are organized according to function, transcript architecture, and cellular identity. Modifications concentrate at functional centers of ribosomal and transfer RNAs, follow the canonical topology of N6-methyladenosine in coding transcripts, and form coordinated hotspots in immune regulatory genes. This first reference human RNome provides a foundation for understanding how RNA chemistry shapes cellular identity, human disease, and the development of RNA-based therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗

The regulation of the cell wall by glycosylphosphatidylinositol-anchored proteins in Arabidopsis

A polysaccharides-based cell wall covers the plant cell, shaping it and protecting it from the harsh environment. Cellulose microfibrils constitute the cell wall backbone and are embedded in a matrix of pectic and hemicellulosic polysaccharides and glycoproteins. Various environmental and developmental cues can regulate the plant cell wall, and diverse glycosylphosphatidylinositol (GPI)-anchored proteins participate in these regulations. GPI is a common lipid modification on eukaryotic proteins, which covalently tethers the proteins to the membrane lipid bilayer. Catalyzed by a series of enzymic complexes, protein precursors are post-translationally modified at their hydrophobic carboxyl-terminus in the endomembrane system and anchored to the lipid bilayer through an oligosaccharidic GPI modification. Ultimately, mature proteins reach the plasma membrane via the secretory pathway facing toward the apoplast and cell wall in plants. In Arabidopsis, more than three hundred GPI-anchored proteins (GPI-APs) have been predicted, and many are reported to be involved in diverse regulations of the cell wall. In this review, we summarize GPI-APs involved in cell wall regulation. GPI-APs are proposed to act as structural components of the cell wall, organize cellulose microfibrils at the cell surface, and during cell wall integrity signaling transduction. Besides regulating protein trafficking, the GPI modification is potentially governed by a GPI shedding system that cleaves and releases the GPI-anchored proteins from the plasma membrane into the cell wall.

59 BASIC BIOLOGICAL SCIENCES↗

Shifting Trade-offs: Finding the Sustainable Nexus of Hydropower and Environmental Flows in the San Joaquin River Watershed, California

Environmental flow management in watersheds with multi-objective reservoirs is often presented as an additional constraint to an already strained and over-allocated stream system. Nevertheless, environmental flow legislation and regulatory policies are increasingly being developed and implemented globally. In California, USA, recent legislative and regulatory policies place environmental flows at the forefront of the state’s water management objectives; however, the increased reliance on hydropower to support climate change mitigation goals may complicate efforts on both issues. This study modelled alternative environmental flow strategies in the major tributaries to the San Joaquin River in California. Strategies included detailed water management rules for hydropower production, flood control, and water deliveries, and three methodological approaches to environmental flow releases: minimum instream flows (“baseline”) year-round, 40% of full natural flow (FNF) during the spring runoff season and minimum releases the remainder of the year, and functional flows year-round. Results show that environmental flow strategies affect downstream flow releases in each of the San Joaquin’s four sub-basins differently depending on infrastructure capacity, water management objectives, and hydrologic year types. While hydropower production was comparable or declined in the Stanislaus, Tuolumne, and Merced basins, functional flow and 40% FNF strategies increased hydropower production in the Upper San Joaquin basin by 11%. Uncontrolled spill of high flow events decreased when high flow releases were based on hydrologic cues rather than exclusively on flood storage capacity. Water deliveries were reduced in all years regardless of environmental flow strategy. The 40% FNF and functional flow strategies both increased water released to the river relative to baseline, but in different ways. The functional flow strategy allocated water in a holistic approach that enhanced ecological functions in all years, but particularly in moderate and wet years. In contrast, the 40% FNF strategy provided increased flows relative to baseline and some ecological benefit in dry years, but less ecological benefit in other years. This study shows that alternative environmental flow strategies will have different and important trade-offs for integrated water management, and may mutually benefit seemingly conflicting objectives.

13 HYDRO ENERGY↗