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At least 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Online monitoring of lanthanide species with combined spectroscopy in flowing aqueous aerosol systems

Combined spectroscopic analysis through absorption and laser-induced breakdown spectroscopy (LIBS) was used to monitor Nd and Pr concentrations in a flowing aqueous system. A unique, online sampling approach was employed that allowed for an approximately closed analysis loop of liquids from a reservoir. Absorption spectroscopy was performed with an optical flow cell, and LIBS was performed on an aerosol stream. Multivariate calibrations based on combined absorption and LIBS signals were built for Nd and Pr and then used to monitor concentrations in mixed solutions in a series of spiking tests. In these tests, the concentrations of Nd and Pr in solution were intermittently changed while spectroscopic signals were monitored in real-time. The combined spectroscopic signals and multivariate models were successful in monitoring changing concentrations of lanthanide species with high accuracy and minimal latency. Root-mean squared error of predictions were 0.015 mol L −1 and 0.019 mol L −1 for Nd and Pr respectively, and these lanthanides were able to be monitored to an accuracy of < 0.2 wt%. This work demonstrates both the capabilities of a sampling system for online analysis of liquids and the capabilities of multimodal spectroscopic characterization for real-time, continuous tracking of species in potentially hazardous liquid systems.

absorbance spectroscopy↗
DOE OSTI2020

Observation of shock-front separation in multi-ion-species collisional plasma shocks

We observe shock-front separation and species-dependent shock widths in multi-ion-species collisional plasma shocks, which are produced by obliquely merging plasma jets of a He/Ar mixture (97% He and 3% Ar by initial number density) on the plasma liner experiment. Visible plasma emission near the He-I 587.6-nm and Ar-II 476.5–514.5-nm lines is simultaneously recorded by splitting a single visible image of the shock into two different fast-framing cameras with different narrow bandpass filters (589 ± 5 nm for observing the He-I line and 500 ± 25 nm for the Ar-II lines). For conditions in these experiments (pre-shock ion and electron densities ≈5×10 14 cm –3 , ion and electron temperatures of ≈2.2 eV, and relative plasma-merging speed of 22 km/s), the observationally inferred magnitude of He/Ar shock-front separation and the shock widths themselves are <1 cm, which correspond to ~50 post-shock thermal ion–ion mean free paths. These experimental length scales are in reasonable qualitative and quantitative agreement with results from 1D multi-fluid simulations using the CHICAGO code. However, we note there are differences between the experimentally inferred and simulation-predicted ionization states and line emission intensities, particularly in the post-shock region. Overall, the experimental and simulation results are consistent with theoretical predictions that the lighter He ions diffuse farther ahead within the overall shock front than the heavier Ar ions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Mutually magnetically insulated two-species Brillouin flow

In this work, we use the Brillouin flow analytic framework to examine the physics of Magnetically Insulated Transmission Lines (MITL). Here, we derive a model applicable to any particle species, including both positive and negative ions, in planar and cylindrical configurations. We then show how to self-consistently solve for two-species simultaneously, using magnetically insulated electrons and positive ions as an example. We require both layers to be spatially separated and magnetically insulated (mutually magnetically insulated); for a 7.5 cm gap with a 2 MV bias voltage, this condition requires magnetic fields in excess of 2.73 T. We see a close match between mutually insulated MITL performance and “superinsulated” (high degree of magnetic insulation) electron-only theory, as may be expected for these high magnetic fields. However, the presence of ions leads to several novel effects: (1) Opposite to electron-only theory, total electron currents increase rather than decrease as the degree of magnetic insulation becomes stronger. The common assumption of neglecting electrons for superinsulated MITL operation must be revisited when ions are present—we calculate up to 20× current enhancement. (2) The electron flow layer thickness increases up to double, due to ion space-charge enhancement. (3) The contributions from both ions and electrons to the MITL flow impedance are calculated. The flow impedance drops by over 50% when ions fill the gap, which can cause significant reflections at the load if not anticipated and degrade performance. Additional effects and results from the inclusion of the ion layer are discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Resistive drift wave turbulence and anomalous transport of multi-species plasma

Anomalous transport of multi-species plasma is considered with the generalized Hasegawa–Wakatani model. It is shown that the transport of all plasma species is described by fractional diffusion equations with the same effective diffusion coefficient. Strongly enhanced perturbations of heavy impurity density are found in long-living plasma flow vortices.

Physics↗
DOE OSTI2021

Linking species traits and demography to explain complex temperature responses across levels of organization

Significance Microbes regulate nutrient flux and carbon storage within ecosystems, making them essential to the global carbon cycle and ecosystem responses to climate change. Understanding how climate change will alter microbial communities and how this will feed back to influence the pace of climate change requires linking processes across levels of organization, from individual organisms to whole ecosystems. We show that the physical characteristics (traits) of protist species influence how their populations will respond to changes in temperature. These species-level temperature responses also alter the composition, dynamics, and functioning of whole microbial communities. Using traits to understand how complex, multilevel microbial processes change with temperature can help us anticipate possible consequences of rapid global climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Tuning the surface reactivity of oxides by peroxide species

The Mars–van Krevelen mechanism is the foundation for oxide-catalyzed oxidation reactions and relies on spatiotemporally separated redox steps. Herein, we demonstrate the tunability of this separation with peroxide species formed by excessively adsorbed oxygen, thereby modifying the catalytic activity and selectivity of the oxide. Using CuO as an example, we show that a surface layer of peroxide species acts as a promotor to significantly enhance CuO reducibility in favor of H 2 oxidation but conversely as an inhibitor to suppress CuO reduction against CO oxidation. Together with atomistic modeling, we identify that this opposite effect of the peroxide on the two oxidation reactions stems from its modification on coordinately unsaturated sites of the oxide surface. By differentiating the chemical functionality between lattice oxygen and peroxide, these results are closely relevant to a wide range of catalytic oxidation reactions using excessively adsorbed oxygen to activate lattice oxygen and tune the activity and selectivity of redox sites.

36 MATERIALS SCIENCE↗
DOE OSTI2023

A species’ response to spatial climatic variation does not predict its response to climate change

The dominant paradigm for assessing ecological responses to climate change assumes that future states of individuals and populations can be predicted by current, species-wide performance variation across spatial climatic gradients. However, if the fates of ecological systems are better predicted by past responses to in situ climatic variation through time, this current analytical paradigm may be severely misleading. Empirically testing whether spatial or temporal climate responses better predict how species respond to climate change has been elusive, largely due to restrictive data requirements. Here, we leverage a newly collected network of ponderosa pine tree-ring time series to test whether statistically inferred responses to spatial versus temporal climatic variation better predict how trees have responded to recent climate change. When compared to observed tree growth responses to climate change since 1980, predictions derived from spatial climatic variation were wrong in both magnitude and direction. This was not the case for predictions derived from climatic variation through time, which were able to replicate observed responses well. Future climate scenarios through the end of the 21st century exacerbated these disparities. These results suggest that the currently dominant paradigm of forecasting the ecological impacts of climate change based on spatial climatic variation may be severely misleading over decadal to centennial timescales.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Thermally unstable roosts influence winter torpor patterns in a threatened bat species

Abstract Many hibernating bats in thermally stable, subterranean roosts have experienced precipitous declines from white-nose syndrome (WNS). However, some WNS-affected species also use thermally unstable roosts during winter that may impact their torpor patterns and WNS susceptibility. From November to March 2017–19, we used temperature-sensitive transmitters to document winter torpor patterns of tricolored bats (Perimyotis subflavus) using thermally unstable roosts in the upper Coastal Plain of South Carolina. Daily mean roost temperature was 12.9 ± 4.9°C SD in bridges and 11.0 ± 4.6°C in accessible cavities with daily fluctuations of 4.8 ± 2°C in bridges and 4.0 ± 1.9°C in accessible cavities and maximum fluctuations of 13.8 and 10.5°C, respectively. Mean torpor bout duration was 2.7 ± 2.8 days and was negatively related to ambient temperature and positively related to precipitation. Bats maintained non-random arousal patterns focused near dusk and were active on 33.6% of tracked days. Fifty-one percent of arousals contained passive rewarming. Normothermic bout duration, general activity and activity away from the roost were positively related to ambient temperature, and activity away from the roost was negatively related to barometric pressure. Our results suggest ambient weather conditions influence winter torpor patterns of tricolored bats using thermally unstable roosts. Short torpor bout durations and potential nighttime foraging during winter by tricolored bats in thermally unstable roosts contrasts with behaviors of tricolored bats in thermally stable roosts. Therefore, tricolored bat using thermally unstable roosts may be less susceptible to WNS. More broadly, these results highlight the importance of understanding the effect of roost thermal stability on winter torpor patterns and the physiological flexibility of broadly distributed hibernating species.

Biodiversity & Conservation↗
DOE OSTI2020

Genomic Characterization of Newly Completed Genomes of Botulinum Neurotoxin-Producing Species from Argentina, Australia, and Africa

Botulinum neurotoxin-producing clostridia are diverse in the types of toxins they produce as well as in their overall genomic composition. They are globally distributed, with prevalent species and toxin types found within distinct geographic regions, but related strains containing the same toxin types may also be located on distinct continents. The mechanisms behind the spread of these bacteria and the independent movements of their bont genes may be understood through examination of their genetic backgrounds. The generation of 15 complete genomic sequences from bacteria isolated in Argentina, Australia, and Africa allows for a thorough examination of genome features, including overall relationships, bont gene cluster locations and arrangements, and plasmid comparisons, in bacteria isolated from various areas in the southern hemisphere. Insights gained from these examinations provide an understanding of the mechanisms behind the independent movements of these elements among distinct species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Microbial community dynamics in the soil-root continuum are linked with plant species turnover during secondary succession

Grazing exclusion and land abandonment are commonly adopted to restore degraded ecosystems in semiarid and arid regions worldwide. However, the temporal variation in the soil- versus root-associated microbiome over plant species turnover during secondary succession has rarely been quantified. Using the chronosequence restored from fenced grassland and abandoned farmlands on the Loess Plateau of China, we characterized the dynamics of the soil- and root-associated microbiome of host plant with different dominance statuses during secondary succession from 0 to 40 years. Our results revealed that the root microhabitat, the host plant and their interactions were the main contributors to the bacterial community shift (R 2 = 15.5%, 8.1%, and 22.3%, respectively), and plant interspecies replacement had a greater effect on the shift in the root-associated microbial community than intraspecies replacement did during succession. The root-associated bacterial community of pioneer plants was particularly responsive to succession, especially the endosphere community. Endosphere microbial diversity was positively correlated with host plant coverage change, and the diversity and abundance of taxon recruitment into the endosphere of pioneer plants from the surrounding environment decreased as succession progressed. The community assembly processes also indicated that the endosphere microbiota are strongly selected in younger host plants, whereas stochastic processes dominate in aged host plants. Our study provides evidence of the unique response of the root-associated microbiome to the replacement of plant species during secondary succession, and the function of endosphere microbes should be considered when studying plant–microbe feedback.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Occurrence and molecular characterization of Enterocytozoon bieneusi in wild and domestic animal species in Portugal

Abstract The phylum Microsporidia encompasses a diverse group of obligate, intracellular, and spore-forming organisms able to infect a wide range of animal hosts. Among them, Enterocytozoon bieneusi is the most frequently reported species in humans and animals. Little is known about the presence and epidemiology of E. bieneusi in wildlife. We investigated E. bieneusi occurrence and genetic diversity in wild and domestic mammals, through molecular-detection methods, from different regions across Portugal. A total of 756 samples were collected from 288, 242, and 226 wild carnivores, wild ungulates, and domestic animals, respectively. Overall, eight specimens were E. bieneusi-positive (1.1%, 8/756) obtained from five wild (Iberian lynx, Iberian wolf, red fox, stone marten, and wild boar) and one domestic (sheep) host. Nucleotide sequence analysis identified four genotypes of E. bieneusi, Type IV, Wildboar3, BEB6, and PtEbIX. Three of those genotypes belong to Groups 1 (Type IV and Wildboar3) and 2 (BEB6), which are known to contain genotypes capable of infecting a variety of hosts, including humans, highlighting their public health importance. PtEbIX belongs to the dog-specific Group 11. This study represents the first, largest, and most comprehensive molecular-based epidemiology survey carried out in Portugal in wild and domestic animals to date and the first worldwide identification of E. bieneusi in wolf species. Our study showed that wild carnivores and ungulates may act as reservoirs of zoonotic genotypes of E. bieneusi, establishing their role in maintaining the sylvatic cycle of this parasite while representing a potential source of infection for humans and domestic animals.

Figueiredo, Ana M. (ORCID:0000000226236340)↗
DOE OSTI2025

Stable hypermutators revealed by the genomic landscape of genes involved in genome stability among yeast species

Mutator phenotypes are short-lived due to the rapid accumulation of deleterious mutations. Yet, recent observations reveal that certain fungi can undergo prolonged accelerated evolution after losing genes involved in DNA repair. Here, we surveyed 1,154 yeast genomes representing nearly all known yeast species of the subphylum Saccharomycotina (phylum Ascomycota) to examine the relationship between reduced gene repertoires broadly associated with genome stability functions (e.g., DNA repair, cell cycle) and elevated evolutionary rates. We identified three distantly related lineages—encompassing 12% of species—that had both the most streamlined sets of genes involved in genome stability (specifically DNA repair) and the highest evolutionary rates in the entire subphylum. Two of these “faster-evolving lineages” (FELs)—a subclade within the order Pichiales and the Wickerhamiella/Starmerella (W/S) clade (order Dipodascales)—are described here for the first time, while the third corresponds to a previously documented Hanseniaspora FEL. Examination of genome stability gene repertoires revealed a set of genes predominantly absent in these three FELs, suggesting a potential role in the observed acceleration of evolutionary rates. In the W/S clade, genomic signatures are consistent with a substantial mutational burden, including pronounced A|T bias and endogenous DNA damage. Interestingly, we found that the W/S clade also contains DNA repair genes possibly acquired through horizontal gene transfer, including a photolyase of bacterial origin. These findings highlight how hypermutators can persist across macroevolutionary timescales, potentially linked to the loss of genes related with genome stability, with horizontal gene transfer as a possible avenue for partial functional compensation.

DNA repair↗
DOE OSTI2022

Protoplast fusion in Bacillus species produces frequent, unbiased, genome-wide homologous recombination

Abstract In eukaryotes, fine-scale maps of meiotic recombination events have greatly advanced our understanding of the factors that affect genomic variation patterns and evolution of traits. However, in bacteria that lack natural systems for sexual reproduction, unbiased characterization of recombination landscapes has remained challenging due to variable rates of genetic exchange and influence of natural selection. Here, to overcome these limitations and to gain a genome-wide view on recombination, we crossed Bacillus strains with different genetic distances using protoplast fusion. The offspring displayed complex inheritance patterns with one of the parents consistently contributing the major part of the chromosome backbone and multiple unselected fragments originating from the second parent. Our results demonstrate that this bias was in part due to the action of restriction–modification systems, whereas genome features like GC content and local nucleotide identity did not affect distribution of recombination events around the chromosome. Furthermore, we found that recombination occurred uniformly across the genome without concentration into hotspots. Notably, our results show that species-level genetic distance did not affect genome-wide recombination. This study provides a new insight into the dynamics of recombination in bacteria and a platform for studying recombination patterns in diverse bacterial species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Metagenomics harvested genus-specific single-stranded DNA-annealing proteins improve and expand recombineering in Pseudomonas species

The widespread Pseudomonas genus comprises a collection of related species with remarkable abilities to degrade plastics and polluted wastes and to produce a broad set of valuable compounds, ranging from bulk chemicals to pharmaceuticals. Pseudomonas possess characteristics of tolerance and stress resistance making them valuable hosts for industrial and environmental biotechnology. However, efficient and high-throughput genetic engineering tools have limited metabolic engineering efforts and applications. To improve their genome editing capabilities, we first employed a computational biology workflow to generate a genus-specific library of potential single-stranded DNA-annealing proteins (SSAPs). Assessment of the library was performed in different Pseudomonas using a high-throughput pooled recombinase screen followed by Oxford Nanopore NGS analysis. Among different active variants with variable levels of allelic replacement frequency (ARF), efficient SSAPs were found and characterized for mediating recombineering in the four tested species. New variants yielded higher ARFs than existing ones in Pseudomonas putida and Pseudomonas aeruginosa, and expanded the field of recombineering in Pseudomonas taiwanensisand Pseudomonas fluorescens. These findings will enhance the mutagenesis capabilities of these members of the Pseudomonas genus, increasing the possibilities for biotransformation and enhancing their potential for synthetic biology applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A broad-host-range event detector: expanding and quantifying performance between Escherichia coli and Pseudomonas species

Modern microbial biodesign relies on the principle that well-characterized genetic parts can be reused and reconfigured for different functions. However, this paradigm has only been successful in a limited set of hosts, mostly comprised from common lab strains of Escherichia coli . It is clear that new applications such as chemical sensing and event logging in complex environments will benefit from new host chassis. This study quantitatively compared how the same chemical event logger performed across four strains and three different microbial species. An integrase-based sensor and memory device was operated by two representative soil Pseudomonads— Pseudomonas fluorescens SBW25 and Pseudomonas putida DSM 291. Quantitative comparisons were made between these two non-traditional hosts and two benchmark E. coli chassis including the probiotic Nissle 1917 and common cloning strain DH5α. The performance of sensor and memory components changed according to each host, such that a clear chassis effect was observed and quantified. These results were obtained via fluorescence from reporter proteins that were transcriptionally fused to the integrase and downstream recombinant region and via data-driven kinetic models. The Pseudomonads proved to be acceptable chassis for the operation of this event logger, which outperformed the common E. coli DH5α in many ways. This study advances an emerging frontier in synthetic biology that aims to build broad-host-range devices and understand the context by which different species can execute programmable genetic operations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Species Separation and Hydrogen Streaming upon Shock Release from Polystyrene under Inertial Confinement Fusion Conditions

Shock release from inertial confinement fusion (ICF) shells poses a great challenge to single-fluid hydrodynamic equations, especially for describing materials composed of different ion species. This has been evidenced by a recent experiment [Haberberger et al., Phys. Rev. Lett. 123, 235001 (2019)], in which low-density plasmas ( 10 19 to 10 20 cm – 3 ) are measured to move far ahead of what radiation-hydrodynamic simulations predict. To understand such experimental observations, in this work we have performed large-scale nonequilibrium molecular-dynamics simulations of shock release in polystyrene (CH) at experimental conditions. These simulations revealed that upon shock releasing from the back surface of a CH foil, hydrogen can stream out of the bulk of the foil due to its mass being lighter than carbon. This released hydrogen, exhibiting a much broader velocity distribution than carbon, forms low-density plasmas moving in nearly constant velocities ahead of the in-flight shell, which is in quantitative agreement with the experimental measurements. Such kinetic effect of species separation is currently missing in single-fluid radiation-hydrodynamics codes for ICF simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Assessing the exposure of three diving bird species to offshore wind areas on the U.S. Atlantic Outer Continental Shelf using satellite telemetry

Abstract Aim The United States Atlantic Outer Continental Shelf (OCS) has considerable offshore wind energy potential. Capturing that resource is part of a broader effort to reduce CO 2 emissions. While few turbines have been constructed in U.S. waters, over a dozen currently planned offshore wind projects have the potential to displace marine birds, potentially leading to effective habitat loss. We focused on three diving birds identified in Europe to be vulnerable to displacement. Our research aimed to determine their potential exposure to areas designated or proposed for offshore wind development along the Atlantic OCS. Methods Satellite tracking technology was used to determine the spatial and temporal use and movement patterns of Surf Scoters ( Melanitta perspicillata ), Red‐throated Loons ( Gavia stellata ) and Northern Gannets ( Morus bassanus ), and calculate their exposure to each offshore wind area. We tagged 236 adults in 2012–2015 on the Atlantic OCS from New Jersey to North Carolina; an additional 147 birds tagged in previous tracking studies were integrated into our analyses. Tracking data were analysed in two‐week intervals using dynamic Brownian bridge movement models to develop composite spatial utilization distributions. For each species, these distributions were then used to calculate the spatio‐temporal exposure to each offshore wind area. Results Surf Scoters and Red‐throated Loons were exposed to offshore wind areas almost exclusively during migration because these species were distributed among coastal and inshore waters during winter months. In contrast, Northern Gannets ranged over a much larger area, reaching farther offshore and south in winter, thus exhibited the greatest exposure to extant offshore wind areas. Conclusions Results of this study provide better understanding of how diving birds use current and potential future offshore wind areas on the Atlantic OCS, and can inform permitting, risk assessment and pre‐ and post‐construction impact assessments of offshore energy infrastructure.

Stenhouse, Iain J.↗
DOE OSTI2020

The functional roles of species in metacommunities, as revealed by metanetwork analyses of bird–plant frugivory networks

Abstract Understanding how biodiversity and interaction networks change across environmental gradients is a major challenge in ecology. We integrated metacommunity and metanetwork perspectives to test species’ functional roles in bird–plant frugivory interactions in a fragmented forest landscape in Southwest China, with consequences for seed dispersal. Availability of fruit resources both on and under trees created vertical feeding stratification for frugivorous birds. Bird–plant interactions involving birds feeding only on‐the‐tree or both on and under‐the‐tree (shared) had a higher centrality and contributed more to metanetwork organisation than interactions involving birds feeding only under‐the‐tree. Moreover, bird–plant interactions associated with large‐seeded plants disproportionately contributed to metanetwork organisation and centrality. Consequently, on‐the‐tree and shared birds contributed more to metanetwork organisation whereas under‐the‐tree birds were more involved in local processes. We would expect that species’ roles in the metanetwork will translate into different conservation values for maintaining functioning of seed‐dispersal networks.

Li, Hai‐Dong↗