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At least 127 records · Page 7

Synthetic communities as a model for determining interactions between a biofertilizer chassis organism and native microbial consortia

Biofertilizers are critical for sustainable agriculture because they can replace ecologically disruptive chemical fertilizers while improving the trajectory of soil and plant health. However, for improving deployment, the persistence of biofertilizers within native soil consortia must be elucidated and enhanced. In this study we characterized a high-throughput, modular, and automation-friendly in vitro approach to screen for biofertilizer persistence within soil-derived consortia after co-cultivation with stable synthetic soil microbial communities (SynComs) obtained through a top-down cultivation process. Here, we profiled ~1200 SynComs isolated from various soil sources and cultivated in divergent media types, and we detected significant phylogenetic diversity (e.g. Shannon index >4) and richness (observed richness >400) across these communities. We observed high reproducibility in SynCom community structure from common soil and media types, which provided a testbed for assessing biofertilizer persistence within representative native consortia. Furthermore, we demonstrated that the screening method described herein can be coupled with microbial engineering to efficiently identify soil-derived SynComs in which an engineered biofertilizer organism (i.e. Bacillus subtilis) persists. Accordingly, we discovered that B. subtilis persisted in ~10% of SynComs that generally followed the diversity–invasion principle. Additionally, our approach enabled analysis of the ecological impact of B. subtilis inoculation on SynCom structure and profile alterations in community diversity and richness associated with the presence of a genetically modified model bacterium. Ultimately, this work has established a modular pipeline that could be integrated into a variety of microbiology/microbiome-relevant workflows or related applications that would benefit from assessment of the persistence of a specific organism of interest and its interaction with native consortia.

biofertilizers↗

Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria

The bacterial colonization dynamics of plants can differ between phylogenetically similar bacterial strains and in the context of complex bacterial communities. Quantitative methods that can resolve closely related bacteria within complex communities can lead to a better understanding of plant–microbe interactions. However, current methods often lack the specificity to differentiate phylogenetically similar bacterial strains. In this study, we describe molecular strategies to study duckweed–associated bacteria. We first systematically optimized a bead-beating protocol to co-isolate nucleic acids simultaneously from duckweed and bacteria. We then developed a generic fingerprinting assay to detect bacteria present in duckweed samples. To detect specific duckweed–bacterium associations, we developed a genomics-based computational pipeline to generate bacterial strain-specific primers. These strain-specific primers differentiated bacterial strains from the same genus and enabled the detection of specific duckweed–bacterium associations present in a community context. Moreover, we used these strain-specific primers to quantify the bacterial colonization of duckweed by normalization to a plant reference gene and revealed differences in colonization levels between strains from the same genus. Lastly, confocal microscopy of inoculated duckweed further supported our PCR results and showed bacterial colonization of the duckweed root–frond interface and root interior. The molecular methods introduced in this work should enable the tracking and quantification of specific plant-microbe associations within plant-microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗

The Shifting Scales of Western U.S. Landfalling Atmospheric Rivers Under Climate Change

Atmospheric rivers (ARs) can be a boon and bane to water resource managers as they have the ability to replenish water reserves, but they can also generate million-to-billion-dollar flood damages. To investigate how anthropogenic climate change may influence AR characteristics in the coastal western United States by end century, we employ a suite of novel tools such as variable resolution in the Community Earth System Model (VR-CESM), the TempestExtremes AR detection algorithm, and the Ralph, Rutz, et al. (2019, https://doi.org/10.1175/BAMS-D-18-0023.1) AR category scale.We show that end-century ARs primarily shift from being “mostly or primarily beneficial” to “mostly or primarily hazardous” with a concomitant sharpening and intensification of winter season precipitation totals. Changes in precipitation totals are due to a significant increase in AR (+260%) rather than non-AR (+7%) precipitation, largely through increases in the most intense category of AR events and a decrease in the interval between landfalling ARs.

54 ENVIRONMENTAL SCIENCES↗

Differentiable Simulation of a Liquid Argon Time Projection Chamber

Liquid argon time projection chambers (LArTPCs) are widely used in particle detection for their tracking and calorimetric capabilities. The particle physics community actively builds and improves high-quality simulators for such detectors in order to develop physics analyses in a realistic setting. The ability of these simulators to mimic real, measured data is limited by the modeling of the physical detectors used for data collection. This modeling can be improved by performing dedicated calibration measurements. Conventional approaches calibrate individual detector parameters or processes one at a time. However, the impact of detector processes is entangled, making this a poor description of the underlying physics. We introduce a differentiable simulator that enables a gradient-based optimization, allowing for the first time a simultaneous calibration of all detector parameters. We describe the procedure of making a differentiable simulator, highlighting the challenges of retaining the physics quality of the standard, non-differentiable version while providing meaningful gradient information. We further discuss the advantages and drawbacks of using our differentiable simulator for calibration. Finally, we provide a starting point for extensions to our approach, including applications of the differentiable simulator to physics analysis pipelines.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Development of a high fidelity model of the CROCUS experimental reactor

Measurements of scalar flux distributions with fine spatial and energy resolutions are needed to remedy one of the validation shortcomings of the novel neutronics full core solvers, such as MPACT and nTRACER. While a very detailed resolution of the flux can be calculated with such codes, only a limited experimental data set is available to check their accuracy. Such type of measurements are on-going at the zero power reactor CROCUS, operated at the Laboratory for Reactor Physics and System Behaviours of the EPFL, thanks to the development of advanced miniature neutron detection systems. This kind of experimental data would provide the community with a suitable benchmark for the validation of high fidelity neutronics solvers. In parallel, a multi-physics solver for steady-state and transient analysis of nuclear reactors, named GeN-Foam, has been developed. Based on the finite-volume OpenFOAM library, GeN-Foam provides us with enough flexibility to analyze non-conventional reactor geometries such as that of CROCUS. While CROCUS heterogeneities cannot be modeled by MPACT and nTRACER for the moment, GeN-Foam offers a unique opportunity to build a high fidelity model which mimics these codes' method to reach sub-pin simulation resolution. This document aims at describing the work achieved to get from the existing GeN-Foam model of the CROCUS reactor based on a structured mesh and using the neutron diffusion, the first high-fidelity model using discrete ordinates method as an approximation to neutron transport and an unstructured mesh for inter lattice water gap description and sub-pin heterogeneous modeling. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Report from the Workshop on Xenon Detector $0\nu\beta\beta$ Searches: Steps Towards the Kilotonne Scale

These proceedings summarize the program and discussions of the ``Workshop on Xenon Detector $0\nu\beta\beta$ Searches: Steps Towards the Kilotonne Scale'' held on October 25-27 2023 at SLAC National Accelerator Laboratory. This workshop brought together experts from the communities of neutrinoless double-beta decay and dark matter detection, to discuss paths forward for the realization of monolithic experiments with xenon approaching the kilotonne scale.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Integration of SARS-CoV-2 testing and genomic sequencing into influenza sentinel surveillance in Uganda, January to December 2022

The Uganda Virus Research Institute, National Influenza Center laboratory integrated SARS-CoV-2 polymerase chain reaction testing and genomic sequencing into the influenza surveillance program that was established in 2007. A total of 7,698 nasopharyngeal/oropharyngeal (NP/OP) swab samples were collected and analyzed from ILI/SARI sentinel sites across the country from January to December 2022. All samples were tested for influenza and SARS-CoV-2. Of these, 252 (3.3%), 162 (2.1%), and 589 (7.7%) were positive for influenza A, influenza B, and SARS-CoV-2, respectively. Out of 414 influenza-positive samples, 122 (29.5%) were AH1pdm09, 130 (31.4%) were AH3, and 162 (39.1%) were B-Victoria. All SARS-CoV-2 sequenced samples were of the Omicron variant, with subvariants of concern known to evade the immune system being detected, such as BQ.1 and XBB.2. Other SARS-CoV-2 positive samples collected from other health centers in the community outside the surveillance sites were included into SARS-CoV-2 genomic sequencing with similar patterns with respect to variants. In all, the ILI/SARI surveillance system has shown to be an efficient, cost-effective, and sustainable program, providing a ready platform to monitor the circulation of SARS-CoV-2 in communities at the national level while remaining vigilant for the persistent threat of influenza. The integration of SARS-CoV-2 detection and genomic surveillance into the influenza surveillance program will strengthen the laboratory response capacity, as well as facilitate the timely release of SARS-CoV-2 genomic information to be used to complement the multiple response strategies for COVID-19 pandemic mitigation.

59 BASIC BIOLOGICAL SCIENCES↗

Bioenergy Cropping Reduces the Spatiotemporal Scaling of Soil Bacterial Biodiversity

Widespread bioenergy cropping can transform landscapes, strongly affecting biodiversity. However, the impact of bioenergy cropping on the spatiotemporal scaling of soil biodiversity remains virtually unknown, despite its profound implications for the functioning of the ecological community. Here, we investigated how bioenergy cropping influenced the spatiotemporal scaling of soil bacterial biodiversity in marginal soils (sandy loam and clay loam soils) in Oklahoma, USA. We detected strong, significant species-time-area relationships (STARs) and phylogenetic-time-area relationships (PTARs) in bacterial communities and their lineages, suggesting that STARs and PTARs exist in microbial ecology within the studied system. Also, spatiotemporal scaling rates (the slopes of STAR and PTAR models) varied substantially among bacterial lineages and were positively correlated with their 16S rRNA gene copy numbers, a genomic trait indicative of microbial growth potentials. Strikingly, bioenergy cropping significantly reduced spatiotemporal scaling rates by 6.8%-14.1%, with a more pronounced reduction observed in sandy loam soils, where those rates were significantly lower than in clay loam soils. The heterogeneity of soil phosphorus and carbon resulted in variations in bacterial spatiotemporal scaling rates. Collectively, our findings suggest that bioenergy cropping may alleviate rapid shifts in soil biodiversity across space and time, thereby stabilizing soil biodiversity and supporting its role as part of sustainable land management and climate mitigation strategies.

bacterial diversity↗

Ants disperse seeds farther in habitat patches with corridors

Habitat fragmentation impacts ecosystems worldwide through habitat loss, reduced connectivity, and edge effects. Yet, these landscape factors are often confounded, leaving much to be investigated about their relative effects, especially on species interactions. In a landscape experiment, we investigated the consequences of connectivity and edge effects for seed dispersal by ants. We found that ants dispersed seeds farther in habitat patches connected by corridors, but only in patch centers. We did not see an effect on the total number of seeds moved or the rate ants detected seeds. Furthermore, we did not see any differences in ant community composition across patch types, suggesting that shifts in ant behavior or other factors increased ant seed dispersal in patches connected by corridors. Long-distance seed dispersal by ants that requires an accumulation of short-distance dispersal events over generations may be an underappreciated mechanism through which corridors increase plant diversity.

60 APPLIED LIFE SCIENCES↗

Determination of Solar System R-Process Abundances using ENDF/B-VIII.0 and TENDL-2015 libraries

Recent multi-messenger detection of the binary neutron star merger (GW170817) energized the astrophysical community and encouraged further research for determination of nuclear physics observables. Comprehensive studies of atomic nuclei in the cosmos provide an opportunity for investigating these astrophysical phenomena and acquiring complementary information on stellar nucleosynthesis processes that can be verified using the latest nuclear data. Evaluated Nuclear Data File (ENDF) libraries contain complete collections of reaction cross sections over the energy range relevant to astrophysics, fission yields and decay data. These data collections have been used worldwide in nuclear science, industry and national security applications. There is great interest in exploring the ENDF/B-VIII.0 and TALYS Evaluated Nuclear Data Library (TENDL-2015) for nuclear astrophysics purposes and comparing findings with the Karlsruhe Astrophysical Database of Nucleosynthesis in Stars (KADoNiS). The Maxwellian-averaged cross sections (MACS) and astrophysical reaction rates have been calculated using the ENDF/B-VIII.0 and TENDL-2015 evaluated data sets. The calculated cross sections were combined with the solar system abundances and fitted using the classical model of stellar nucleosynthesis. Astrophysical rapid- and slow-neutron capture, r- and s-process, respectively, abundances were obtained from present data and compared with available values. Further analysis of MACS reveals potential evaluated libraries data deficiencies and a strong need for new measurements. The current results demonstrate a large nuclear astrophysics potential of evaluated libraries and mutually beneficial relations between nuclear industry and research e orts.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Performance of SK-Gd’s Upgraded Real-time Supernova Monitoring System

Among multimessenger observations of the next Galactic core-collapse supernova, Super-Kamiokande (SK) plays a critical role in detecting the emitted supernova neutrinos, determining the direction to the supernova (SN), and notifying the astronomical community of these observations in advance of the optical signal. In 2022, SK has increased the gadolinium dissolved in its water target (SK-Gd) and has achieved a Gd concentration of 0.033%, resulting in enhanced neutron detection capability, which in turn enables more accurate determination of the supernova direction. Accordingly, SK-Gd’s real-time supernova monitoring system has been upgraded. SK_SN Notice, a warning system that works together with this monitoring system, was released on 2021 December 13, and is available through GCN Notices. When the monitoring system detects an SN-like burst of events, SK_SN Notice will automatically distribute an alarm with the reconstructed direction to the supernova candidate within a few minutes. In this paper, we present a systematic study of SK-Gd’s response to a simulated Galactic SN. Assuming a supernova situated at 10 kpc, neutrino fluxes from six supernova models are used to characterize SK-Gd’s pointing accuracy using the same tools as the online monitoring system. The pointing accuracy is found to vary from 3° to 7° depending on the models. However, if the supernova is closer than 10 kpc, SK_SN Notice can issue an alarm with three-degree accuracy, which will benefit follow-up observations by optical telescopes with large fields of view.

Core-collapse supernovae↗

Measurements of soil protist richness and community composition are influenced by primer pair, annealing temperature, and bioinformatics choices

ABSTRACT Protists are a diverse and understudied group of microbial eukaryotic organisms especially in terrestrial environments. Advances in molecular methods are increasing our understanding of the distribution and functions of these creatures; however, there is a vast array of choices researchers make including barcoding genes, primer pairs, PCR settings, and bioinformatic options that can impact the outcome of protist community surveys. Here, we tested four commonly used primer pairs targeting the V4 and V9 regions of the 18S rRNA gene using different PCR annealing temperatures and processed the sequences with different bioinformatic parameters in 10 diverse soils to evaluate how primer pair, amplification parameters, and bioinformatic choices influence the composition and richness of protist and non-protist taxa using Illumina sequencing. Our results showed that annealing temperature influenced sequencing depth and protist taxon richness for most primer pairs, and that merging forward and reverse sequencing reads for the V4 primer pairs dramatically reduced the number of sequences and taxon richness of protists. The data sets of primers that targeted the same 18S rRNA gene region (e.g., V4 or V9) had similar protist community compositions; however, data sets from primers targeting the V4 18S rRNA gene region detected a greater number of protist taxa compared to those prepared with primers targeting the V9 18S rRNA region. There was limited overlap of protist taxa between data sets targeting the two different gene regions (80/549 taxa). Together, we show that laboratory and bioinformatic choices can substantially affect the results and conclusions about protist diversity and community composition using metabarcoding. IMPORTANCE Ecosystem functioning is driven by the activity and interactions of the microbial community, in both aquatic and terrestrial environments. Protists are a group of highly diverse, mostly unicellular microbes whose identity and roles in terrestrial ecosystem ecology have been largely ignored until recently. This study highlights the importance of choices researchers make, such as primer pair, on the results and conclusions about protist diversity and community composition in soils. In order to better understand the roles protist taxa play in terrestrial ecosystems, biases in methodological and analytical choices should be understood and acknowledged.

Biotechnology & Applied Microbiology↗

The NREL Sensor Laboratory: Status and Future Directions for Hydrogen Detection

The NREL Hydrogen Sensor Laboratory was commissioned in 2010 as a resource for the national and international hydrogen community to ensure the availability and proper use of hydrogen sensors. Since then, the Sensor Laboratory has provided unbiased verification of hydrogen sensor performance for sensor developers, end-users, and regulatory agencies and has also provided active support for numerous code and standards development organizations. Although sensor performance assessment remains a core capability, the mission of the NREL Sensor Laboratory has expanded toward a more holistic approach regarding the role of hydrogen detection and its implementation strategy for both assurance of facility safety as well as for process control applications. Active monitoring for detection of unintended releases has been identified by the NFPA 2 Storage Task Group as a viable approach for improving facility safety and lowering setbacks. The current research program for the Sensor Laboratory addresses both conventional and advanced developing detection strategies in response to the emerging large-scale markets, such as those envisioned by H2@Scale. These emerging hydrogen applications may require alternative detection strategies that supplement and may ultimately supplant the use of traditional sensors for monitoring hydrogen releases. Research focus areas for the NREL Sensor Laboratory now encompasses the characterization of released hydrogen behavior to optimize detection strategies for both indoor and outdoor applications, advanced methods of hydrogen leak detection such as hydrogen wide area monitoring approaches for large scale and distributed applications, the incorporation of active monitoring as a risk reduction strategy to improve safety at hydrogen facilities, and continuing support of hydrogen safety codes and standards. In addition to assurance of safety, detection will be critical for process control applications, such as hydrogen fuel quality verification for fuel cell vehicle applications and for monitoring and controlling of hydrogen-natural gas blend composition.

codes and standards↗

Fermi -LAT follow-up observations in seven years of real-time high-energy neutrino alerts

The realtime program for high-energy neutrino track events detected by the IceCube South Pole Neutrino Observatory releases alerts to the astronomical community with the goal of identifying electromagnetic counterparts to astrophysical neutrinos. Gamma-ray observations from theFermi-Large Area Telescope (LAT) enabled the identification of the flaring gamma-ray blazar TXS 0506+056 as a likely counterpart to the neutrino event IC-170922A. By continuously monitoring the gamma-ray sky,Fermi-LAT plays a key role in the identification of candidate counterparts to realtime neutrino alerts. In this paper, we present theFermi-LAT strategy for following up high-energy neutrino alerts applied to seven years of IceCube data. Right after receiving an alert, a search is performed in order to identify gamma-ray activity from known and newly detected sources that are positionally consistent with the neutrino localization. In this work, we study the population of blazars found in coincidence with high-energy neutrinos and compare them to the full population of gamma-ray blazars detected byFermi-LAT. We also evaluate the relationship between the neutrino and gamma-ray luminosities, finding different trends between the two blazar classes BL Lacs and flat-spectrum radio quasars.

Astronomy & Astrophysics↗

The direct and indirect drivers shaping RNA viral communities in grassland soil

Recent studies have revealed diverse RNA viral communities in soils. Yet, how environmental factors influence soil RNA viruses remains largely unknown. Here, we recovered RNA viral communities from 24 metatranscriptomes sequenced from grassland soils managed under a range of environmental conditions including 1) water content: 100% and 25% water holding capacity, 2) plant presence: planted with tall wheatgrass (Thinopyrum ponticum) and bare soil, 3) cultivar type: Alkar and Jose, and 4) soil depth: 0-5 cm and 15-25 cm. The recovered RNA viral communities were novel with nearly one-third of the RNA viral contigs uniquely detected in the studied grassland. The classified RNA viral contigs are mostly known as eukaryotic RNA viruses (74.7%) belonging to Phyla Duplornaviricota, Kitrinoviricota, Lenarviricota, and Pisuviricota. Eukaryotic RNA viruses of Family Mitoviridae as well as their natural hosts, Fungi, are one of the most dominant taxa. Consistent with the results of nonmetric multidimensional scaling analysis, the four environmental conditions (water content, plant presence, cultivar, and soil depth) significantly influence the assemblages of soil RNA viral communities as suggested by the correlation analysis and the random forest algorithm. The modularity analysis of the factor network and the structural equation modeling further support the hierarchical associations among the four environmental factors and the community factors representing the co-existing eukaryotic, prokaryotic, and RNA viral communities. The soil water content, plant presence, and type of cultivar demonstrate a significant positive impact on eukaryotic RNA viral richness directly as well as indirectly on eukaryotic RNA viral abundance via influencing the co-existing eukaryotic members in this soil. Our data also provide statistical support for the negative influence of soil depth on soil eukaryotic richness and abundances resulting in its indirect impact on soil eukaryotic RNA viral communities. This study provides field-relevant information on how environmental and community factors collectively shape soil RNA communities and contribute to ecological understanding of RNA viral survival under various environmental conditions and virus-host interactions in soil.

Wu, Ruonan↗

Accelerated, scalable and reproducible AI-driven gravitational wave detection

The development of reusable artificial intelligence (AI) models for wider use and rigorous validation by the community promises to unlock new opportunities in multi-messenger astrophysics. Here we develop a workflow that connects the Data and Learning Hub for Science, a repository for publishing AI models, with the Hardware-Accelerated Learning (HAL) cluster, using funcX as a universal distributed computing service. Using this workflow, an ensemble of four openly available AI models can be run on HAL to process an entire month's worth (August 2017) of advanced Laser Interferometer Gravitational-Wave Observatory data in just seven minutes, identifying all four binary black hole mergers previously identified in this dataset and reporting no misclassifications. This approach combines advances in AI, distributed computing and scientific data infrastructure to open new pathways to conduct reproducible, accelerated, data-driven discovery. By combining a repository for artificial intelligence models and a supercomputing cluster, an entire month's worth of advanced LIGO data is analysed in just 7 min, finding all binary black hole mergers previously identified in this dataset and reporting no misclassifications.

79 ASTRONOMY AND ASTROPHYSICS↗

Decadal survival of tropical pioneer seeds in the soil seed bank is accompanied by fungal infection and dormancy release

Pioneer trees require high-light environments for successful seedling establishment. Consequently, seeds of these species often persist in the soil seed bank (SSB) for periods ranging from several weeks to decades. How they survive despite extensive pressure from seed predators and soil-borne pathogens remains an intriguing question. Here this study aims to test the hypotheses that decades-old seeds collected from the SSB in a lowland tropical forest remain viable by (i) escaping infection by fungi, which are major drivers of seed mortality in tropical soils, and/or (ii) maintaining high levels of seed dormancy and seed coat integrity when compared to inviable seeds. We collected seeds of Trema micrantha and Zanthoxylum ekmanii at Barro Colorado Island, Panama, from sites where adult trees previously occurred in the past 30 years. We used carbon dating to measure seed age and characterized seed coat integrity, seed dormancy and fungal communities. Viable seeds from the SSB ranged in age from 9 to 30 years for T. micrantha, and 5 to 33 years for Z. ekmanii. We found no evidence that decades-old seeds maintain high levels of seed dormancy or seed coat integrity. Fungi were rarely detected in fresh seeds (no soil contact), but phylogenetically diverse fungi were detected often in seeds from the SSB. Although fungal infections were more commonly detected in inviable seeds than in viable seeds, a lack of differences in fungal diversity and community composition between viable and inviable seeds suggested that viable seeds are not simply excluding fungal species to survive long periods in the SSB. Synthesis. Our findings reveal the importance of a previously understudied aspect of seed survival, where the impact of seed–microbial interactions may be critical to understand long-term persistence in the SSB.

54 ENVIRONMENTAL SCIENCES↗

NA-22 Write for Consortium Efforts

We are asked to look into the improvements for the measurement of Pu of a variety of material types (MT): MT41 (Pu-242, 20 – 60% enriched), MT42 (Pu-242 > 60% enrichment), and MT-82 (Np-237). Many of these are legacy items that were packaged years ago (Fig 1&2), and when the items are re-packaged for long-term storage, they must be re-measured using either NDA (nondestructive analysis methods or radiochemical methods. It is of interest to improve the NDA and radiochemistry to reduce the un-certainty in the measurements, as in the case of larger items (250 g to 2 kg items) the uncertainty in measurements makes it difficult to certify the mass of the material down to the 0.5 g accountability requirement per DOE orders by only doing NDA measurement. It would be of interest to look into methods to improve the detection of these materials, which would not only benefit the weapon manufacturing community, but also has the ability to significantly improve the non-proliferation community.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗