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At least 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Optimal generation and isolation of attosecond pulses in an overdriven ionized medium

We identify optimal conditions for the generation and isolation of attosecond pulses in an overdriven ionized medium. In a high-pressure and highly ionized gas, the spatiotemporal wavefront rotation of a driving laser can be optimized, leading to complete spatial separation of successive attosecond bursts in the far field. The resulting isolated attosecond pulses (IAPs) are much more divergent such that they are spatially separated from the driving laser in the far field. We show that the time delay of near-field harmonic emission along the radial distance determines the divergence of the attosecond burst in the far field. Here, the generated IAPs are phase matched upon propagation in the second half of the gas medium. Validity of the generation scheme is tested at different carrier–envelope phases for a few-cycle laser pulse and by synthesizing the fundamental and its second harmonic field for a long-duration pulse.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Effects of physical, chemical, and biological ageing on the mineralization of pine wood biochar by a Streptomyces isolate

If biochar is to be used for carbon (C) management, we must understand how weathering or ageing affects biochar C mineralization. Here, we incubated aged and unaged eastern white pine wood biochar produced at 350 and 550°C with a Streptomyces isolate, a putative biochar-decomposing microbe. Ageing was accelerated via three different processes, namely, (a) physical ageing–subjecting biochar to alternating freeze-thaw and wet-dry cycles, (b) chemical ageing–treating biochar with concentrated hydrogen peroxide and (c) biological ageing–incubating biochar in the presence of nutrients and microorganisms. Elemental composition and surface chemistry (Fourier Transform Infrared spectroscopy) of biochar samples were compared before and after ageing. Biochar C mineralization between ageing treatments was significantly different in the case of 350°C biochar ( p value = 0.03). Among the 350°C biochars, physical ageing resulted in the greatest increase (by 103%) in biochar C mineralization ( p value = 0.05). However, in the case of 550°C biochar, ageing did not result in a significant change in biochar C mineralization ( p value = 0.40). Biochar C mineralization was positively correlated with an increase in O/C ratio post-ageing ( r s = 0.86, p value = 0.01). In the case of 350°C biochar, surface oxidation during ageing enhanced biochar degradation by the isolate. For 550°C biochar, however, ageing did not significantly increase biochar C mineralization, likely due to high condensed aromatic C content and lower surface oxidation during ageing. The results from our study suggest that low temperature aged biochar is more susceptible to biological degradation by soil microbes. These findings have implications for the use of biochar for long term C storage in soils.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Isolation and characterization of 24 phages infecting the plant growth-promoting rhizobacterium Klebsiella sp. M5al

Bacteriophages largely impact bacterial communities via lysis, gene transfer, and metabolic reprogramming and thus are increasingly thought to alter nutrient and energy cycling across many of Earth’s ecosystems. However, there are few model systems to mechanistically and quantitatively study phage-bacteria interactions, especially in soil systems. Here, we isolated, sequenced, and genomically characterized 24 novel phages infectingKlebsiellasp. M5al, a plant growth-promoting, nonencapsulated rhizosphere-associated bacterium, and compared many of their features against all 565 sequenced, dsDNAKlebsiellaphage genomes. Taxonomic analyses revealed that theseKlebsiellaphages belong to three known phage families (Autographiviridae,Drexlerviridae, andStraboviridae) and two newly proposed phage families (CandidatusMavericviridaeand Ca.Rivulusviridae). At the phage family level, we found that core genes were often phage-centric proteins, such as structural proteins for the phage head and tail and DNA packaging proteins. In contrast, genes involved in transcription, translation, or hypothetical proteins were commonly not shared or flexible genes. Ecologically, we assessed the phages’ ubiquity in recent large-scale metagenomic datasets, which revealed they were not widespread, as well as a possible direct role in reprogramming specific metabolisms during infection by screening their genomes for phage-encoded auxiliary metabolic genes (AMGs). Even though AMGs are common in the environmental literature, only one of our phage families,Straboviridae, contained AMGs, and the types of AMGs were correlated at the genus level. Host range phenotyping revealed the phages had a wide range of infectivity, infecting between 1–14 of our 22 bacterial strain panel that included pathogenicKlebsiellaandRaoultellastrains. This indicates that not all capsule-independent Klebsiella phages have broad host ranges. Together, these isolates, with corresponding genome, AMG, and host range analyses, help build theKlebsiellamodel system for studying phage-host interactions of rhizosphere-associated bacteria.

Science & Technology - Other Topics↗
DOE OSTI2022

Excitations of static isolated fermions in the Higgs phase of gauge Higgs theory

A spectrum of localized excitations of isolated static fermions has been discovered in several different gauge Higgs theories. In lattice numerical simulations, we show that the charged elementary particles can have the spectrum of excitations in the Higgs phase of SU(3) gauge Higgs theory, q=2 Abelian Higgs theory, Landau-Ginzburg theory, and in chiral U(1) gauge Higgs theory. Possibly these excited states of the isolated fermions can be observed in ARPES studies of conventional superconductors. Also, we consider that similar kinds of excitations could exist in other gauge Higgs theories, such as the electroweak sector of the Standard Model.

Matsuyama, Kazue↗
DOE OSTI2020

Nuclear Criticality Safety Assessment of Criticality Control Containers without Moderation Control at the Waste Isolation Pilot Plant

The Waste Isolation Pilot Plant (WIPP) provides for safe, permanent disposal of government-owned transuranic (TRU) and TRU mixed wastes. Receipt and disposal of waste at the WIPP site began in March 1999. The Sandia report, Consideration of Nuclear Criticality When Disposing of Transuranic Waste at the Waste Isolation Pilot Plant, addressed potential nuclear criticality safety issues based on the projected inventory characteristics known at the time [1]. As designs for inventory, waste forms, and disposal packages have changed, new analyses have been performed, and updates have been made to address any potential effects to the WIPP safety basis. New analyses performed include Saylor 2017 [2] and Brickner 2019 [3], which address certain waste containers with specified loadings under post-closure conditions. Both examined several hypothetical scenarios and included analyses to bound (from a criticality potential standpoint) credible configurations that could occur at WIPP during the repository regulatory post-closure disposal time period for feature, event, and process (FEP) considerations—10,000 years. During this post-closure period at WIPP, the screening of FEPs is governed by the risk-based standards and implementing regulations of the US Environmental Protection Agency (EPA) (i.e., 40 CFR 191 and 40 CFR 194, respectively) [4,5]. An FEP screening can be based on either a low-consequence or low-probability rationale. A low-probability rationale includes either (a) a qualitative rationale that the FEP is not credible or (b) a quantitative demonstration that the probability is less than 10-4 in 104 years. In this evaluation, a qualitative lowprobability rationale of not credible is used by demonstrating that bounding configurations of the waste are not critical. The demonstration of subcriticality is through quantitative calculations, but a probability of criticality is not evaluated. Rather, the rationale for this evaluation is that bounding configurations with an effective neutron multiplication factor (keff) well below the upper subcriticality limit (USL) make criticality incredible. Reference [2] documented a nuclear criticality assessment of the WIPP repository for disposal of dilute surplus plutonium materials using the Dilute and Dispose Approach and packaging in criticality control overpacks (CCOs). The CCO is the waste disposal container recently designed to allow for up to 380 fissile gram equivalent (FGE) 239 Pu per drum, which is a higher fissile loading than typical waste containers. The CCO consists of a criticality control container (CCC) positioned by upper and lower plywood spacers within a standard 55 gal drum. The CCC is used to establish a geometry control for fissile materials during transportation and WIPP emplacement operations. The current WIPP waste acceptance criteria for CCO payloads limit beryllium to less than or equal to 1% by weight of the waste contents and require the waste form to be non-machine compacted. Reference [2] considered two scenario progressions—room closure from salt creep, hereafter referred to as the reconfigured dry scenario, and flooding with brine, hereafter referred to as the reconfigured wet scenario. The subsequent drying out of the reconfigured wet scenarios was also considered. For all scenarios, subcriticality was maintained when 50 g of B 4 C (acting as a neutron absorber) per CCC was intermixed within the plutonium disposition waste form. The analysis used a waste form description that limits the amount of moderation that could be present within the waste form (i.e., it limits the amount of water and polyethylene that could be present based on planned processing conditions). This analysis to evaluate increased limits on the amount of moderation that could be present was performed as a companion to Reference [2] to address concerns associated with verifying moisture and/or plastic contents of waste materials following packaging of dilute surplus plutonium in the CCO. To that end, this analysis used the models and methods from Reference [2] to evaluate a more generic base waste form consisting of water and polyethylene that is more similar (and nearly identical) to the generic waste forms utilized in other models/analyses supporting the TRU Package Transporter Model II (TRUPACTII) safety analysis [6] (all are without moderation controls). The waste form in this analysis uses a base mixture of 75% water and 25% polyethylene, the total amount of which is varied to determine the optimum moderation to fissile material (H/Pu) ratio. The fissile loading is maintained at up to 380 FGE 239 Pu (modeled as PuO 2 ) per CCO with an additional 545 g of beryllium (to bound the 1% by weight contents restriction) and 50 g of B 4 C intermixed per CCO. The beryllium content (1% by weight) is based on the total allowed waste weight (this does not include packaging and container weights). Figures ES-1 and ES-2 display summary results, showing that with this model including 50 g of B 4 C per CCO, the system keff remains under 0.85 for all moderator amounts and provides a significant margin against post-closure criticality under postulated bounding conditions for compaction. Figure ES-1 compares an infinite model with a room model at the initial emplacement spacing and under full radial compaction. Full radial compaction places each CCC in direct contact and does not credit any anticipated spacing associated with current post-closure geomechanical modeling of the repository [7]. The effects of variations in the H/Pu ratio were evaluated by varying the amount of the water/polyethylene component of the waste model, with fissile loading maintained at 380 239 Pu FGE. Similarly, Figure ES-2 illustrates how various amounts of B 4 C per CCO influence k eff at different radial compactions, all at the H/Pu ratio of 200 (in the room array model). Therefore, while the results from Saylor 2017 [2] modeled more realistic process limits associated with packaging of dilute surplus plutonium, this analysis demonstrates that limits on moderation (plastic and water content) are not necessary to ensure subcriticality in the WIPP repository, provided the requisite B 4 C absorber is present.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Improbability of Nuclear Criticality in Compacted Criticality Control Overpacks after Room Closure by Salt Creep at Waste Isolation Pilot Plant

Based on the rationale presented, nuclear criticality is improbable after salt creep causes compaction of criticality control overpacks (CCOs) disposed at the Waste Isolation Pilot Plant, an operating repository in bedded salt for the disposal of transuranic (TRU) waste from atomic energy defense activities. For most TRU waste, the possibility of post-closure criticality is exceedingly small either because the salt neutronically isolates TRU waste canisters or because closure of a disposal room from salt creep does not sufficiently compact the low mass of fissile material. The criticality potential has been updated here because of the introduction of CCOs, which may dispose up to 380 fissile gram equivalent plutonium-239 in each container. The criticality potential is evaluated through high-fidelity geomechanical modeling of a disposal room filled with CCOs during two representative conditions: (1) large salt block fall, and (2) gradual salt compaction (without brine seepage and subsequent gas generation to permit maximum room closure). Geomechanical models of rock fall demonstrate three tiers of CCOs are not greatly disrupted. Geomechanical models of gradual room closure from salt creep predict irregular arrays of closely packed CCOs after 1000 years, when room closure has asymptotically approached maximum compaction. Criticality models of spheres and cylinders of 380 fissile gram equivalent of plutonium (as oxide) at the predicted irregular spacing demonstrate that an array of CCOs is not critical when surrounded by salt and magnesium oxide, provided the amount of hydrogenous material shipped in the CCO (usually water and plastics) is controlled or boron carbide (a neutron poison) is mixed with the fissile contents.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Post-closure Nuclear Criticality Safety Evaluations for Disposition of Criticality Control Overpacks at the Waste Isolation Pilot Plant

The Waste Isolation Pilot Plant (WIPP) is a geological repository in southern New Mexico that provides for disposal of transuranic (TRU) wastes from atomic energy defense activities. The Sandia National Laboratories (Sandia) Report, Consideration of Nuclear Criticality When Disposing of Transuranic Waste at the Waste Isolation Pilot Plant, addresses nuclear criticality safety based on the projected inventory characteristics for the initial compliance certification application of WIPP in 1996. As the inventory, waste forms, and disposal package designs change, revised or new analyses are necessary to demonstrate acceptability for these configurations within the WIPP safety basis and compliance with 10,000-year post-closure standards of the US Environmental Protection Agency (EPA). Saylor and Scaglione evaluated criticality control overpacks (CCOs) in 2017 based on conservative assumptions for post-closure repository structural conditions with resulting effects on containers and container spacing, The Saylor and Scaglione evaluation of CCOs addressed a single waste configuration that represents the Surplus Plutonium Disposition Program’s dilute and dispose waste form and composition. This initial CCO study demonstrated that 50 grams of boron carbide (B 4 C) per CCO is sufficient to ensure post-closure criticality safety based on a well-mixed waste composition, and Oak Ridge National Laboratory (ORNL) subsequently determined that this amount of B 4 C does not require constraints on moisture or plastic present as moderator. The Saylor and Scaglione analysis conservatively assumes repository room closure that eliminates all space between fissile gram equivalent (FGE) 239 Pu masses. The close-packed array was selected based on limited availability of repository salt creep modeling results at that time. In 2019, Brickner provided additional evaluations for pipe overpack containers (POCs), building on the conservative basis provided by Saylor and Scaglione. Brickner’s 2019 analysis made use of new geomechanical data for post-closure spacing that rely on advances in repository modeling as documented in the work by Reedlunn and Bean. This current CCO evaluation for generic waste materials expands on earlier work performed at ORNL and includes evaluation of CCOs across a much broader range of possible waste compositions and geometries. This evaluation is intended to provide input for the required feature, event and process (FEP) screening to determine if post-closure criticality must be included as an event in the 10,000-year regulatory evaluation. As such, the approach to modeling post-closure criticality presented in this report has been coordinated with the Sandia team responsible for FEP screening. The resulting analysis supports disposition of fissile materials in the CCO containing up to 380 FGE 239 Pu and expands conditions acceptable for disposal of fissile material in CCOs. This evaluation builds on the methodology of Saylor and Scaglione and Brickner, using the most recently available geomechanical data for CCO spacing under salt creep compaction scenarios provided by Reedlunn and Bean. The broad range of fissile material configurations analyzed in this report are intended to account for configurations that may occur during the post-closure disposal time period, and it also includes waste configurations that are not physically possible to support analysis of conditions that influence neutron fluence.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2025

ZIPPER: Zonal isolation with plug and perf in enhanced reservoirs (Final Technical Report)

Modern multistage hydraulic stimulation treatments in cased wellbores require an effective method of isolating stages between treatments. A commonly used method in the oil and gas industry, plug and perf, is not currently viable for Enhanced Geothermal Systems (EGS) due to limitations of a critical component of the system – the ball drop (flow through) frac plug. Commercially available ball drop frac plugs do not meet the temperature or wellbore diameter requirements needed for use in EGS stimulations. For example, one particular drillable bridge and frac plug line from a large tool developer is only rated to 175 °C, while another is only available up to casing sizes of 5 ½” and rated up to 204 °C. We developed, prototyped, and field tested an upgraded ball drop frac plug to meet the requirements of EGS stimulations, including high-temperature (225+ °C), differential pressure (6000+ psi), and wellbore diameters ranging from 6 5/8” to 10 5/8”. We focused on designs and materials to optimize drillability, a key cost driver in plug and perf systems. The primary objective was to upgrade a drillable frac plug (currently rated to a temperature of 175°C and a pressure of 10,000 psi in 7” casing) to withstand temperatures of 225+°C. The upgraded frac plug was tested in the laboratory as well as in a field trial at a geothermal field. Engineering design and fabrication of the new plug was completed in 2019. Lab testing, validation, and qualification of the plug was completed in 2020. Ultimately the plug was successfully run during a multistage stimulation treatment in a fully horizontal EGS well in 2022. Prior to this project, a ball-drop, flow-through stimulation plug had never been used in a geothermal well. At the conclusion of this project, three different types of zonal isolation plugs were evaluated under full-scale operating conditions across 16 stimulation treatment stages in a first-of-a-kind EGS project called Project Red. This trial included the newly designed high-temperature, large-diameter plug. The plugs met all of 5 the technical requirements for commercial viability. Project Red has since been fully commissioned and is generating electricity on the Nevada grid - the first EGS project to successfully deliver power to the grid in the US.

15 GEOTHERMAL ENERGY↗
DOE OSTI2025

Five PMI Isolates from Populus Deltoides and Populus Trichocarpa

Five bacterial isolates were isolated from the roots of poplar trees (Populus deltoides and P. trichocarpa), which are model organisms and a main focus of the Plant-Microbe Interfaces (PMI) project at ORNL. These strains belong to genera are not well represented and give a more complete view of the microbial community and bacterial interactions with poplar trees. These strains will support future studies and contribute to the broader PMI goal of understanding microbe-microbe and plant-microbe interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Two-dimensional heteronuclear single quantum coherence (HSQC) NMR spectra of lignin isolated from Populus trichocarpa residues after CELF pretreatment and CBP fermentation

Here we present a curated dataset of a series of two-dimensional heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra of lignin isolated from a woody energy crop (Populus trichocarpa) residues after co-solvent enhanced lignocellulosic fractionation (CELF) pretreatment and consolidated bioprocessing (CBP) process. The natural poplar variant GW-9947 from the Center for Bioenergy Innovation (CBI) was used. The poplar was knife milled and passed through a 1 mm sieve. The CELF pretreatment was performed in a Parr autoclave reactor with 7.5 wt % solids loading, 0.5 wt% H2SO4 as catalyst at 150°C with 15, 25 and 30 minutes, respectively. Tetrahydrofuran was added in a 1:1 mass ratio with water as the pretreatment solvent. The residues from CELF pretreatment were then subjected to CBP using the bacterium C. thermocellum DSM 1313. CBP fermentations were performed at 60 °C in a shaker at 50 grams/L solids loadings. Lignin was isolated from the pretreated samples after ball-milling in a porcelain jar with ceramic balls via Retsch PM 200 at 580 rpm for 2.5 h followed by enzymatic hydrolysis in acetate buffer (pH 4.8, 50 °C) for 48 h. The lignin samples were characterized using 13C–1H HSQC experiments which were performed in a Bruker Avance III HD 500 MHz NMR spectrometer operating at a frequency of 125.12 MHz for the 13C nucleus. A standard Bruker pulse sequence was used on a Prodigy platform cryoprobe. The dry lignin samples were dissolved in deuterated dimethylsulfoxide for HSQC experiments. The spectra were acquired under the following acquisition conditions: 210 ppm spectral width in F1 (13C) dimension with 256 data points and 11 ppm spectral width in F2 (1H) dimension with 1024 data points, a 90° pulse, a one bond C–H coupling constant of 145 Hz, a 1.0 s pulse delay, and 64 scans. All the data was processed using the TopSpin 3.6 software (Bruker BioSpin). The NMR spectra provides structural characteristics information about lignin remaining in solids after CELF (150 °C with 15, 25 and 30 minutes) process and C. thermocellum CBP.

Lignin structure, HSQC, poplar, CELF, CBP, CBI↗
DOE OSTI2024

Heteronuclear single quantum coherence (HSQC) NMR spectra of lignin isolated from switchgrass residues after fermentation with milling

Here we present a curated dataset of two-dimensional heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra of lignin isolated from a herbaceous energy crop (Panicum virgatum L.). The lowland variant “Timber” switchgrass from Ernst seeds was used. The switchgrass was knife milled and passed through a 2 mm sieve prior to consolidated bioprocessing (CBP) process. Switchgrass was suspended in Milli-Q water and autoclaved for 90 min on liquid cycles. The residues after autoclaving were then subjected to CBP using coculture of Clostridium thermocellum (C. thermocellum DSM 1313 (LL1004)) and Thermoanaerobacterium thermosaccarolyticum ( T. thermosaccharolyticum HG-8 ATCC 31960 (LL1244)). Once-fermented and twice-fermented (FF) switchgrass were subjected to ball and disc milling in bioreactors at 55 °C and 60, 48 grams/L solids loadings for primary and secondary fermentation respectively. When fermentations were completed, the residual solids were rinsed with milli-Q water. Lignin was isolated from the pretreated residues after ball-milling in a porcelain jar with ceramic balls via Retsch PM 200 at 600 rpm for 2 h followed by enzymatic hydrolysis in acetate buffer (pH 4.8, 50 °C) for 48 h. The dry lignin samples were dissolved in deuterated dimethyl sulfoxide (d6) and characterized using 13C–1H HSQC in a Bruker Avance III HD 500-MHz NMR spectrometer. A standard Bruker pulse sequence (hsqcetgpsisp.2) was used on a Prodigy platform cryoprobe. The spectra were acquired with the following acquisition conditions: 230 ppm spectral width in F1 (13C) dimension with 256 data points and 12 ppm spectral width in F2 (1H) dimension with 2048 data points, a 90° pulse, with a C–H coupling constant of 145 Hz, a 1.0 s pulse delay, and 64 scans. Spectra were processed using the Bruker TopSpin 3.6 software.

Lignin, HSQC, Switchgrass, CBP , Ball mill, Disc m↗
DOE OSTI2021

Hidden Processes During Seasonal Isolation of a High-Altitude Watershed

Biogeochemical processes capable of altering global carbon systems occur frequently in Earth’s Critical Zone–the area spanning from vegetation canopy to saturated bedrock–yet many of these phenomena are difficult to detect. Observation of these processes is limited by the seasonal inaccessibility of remote ecosystems, such as those in mountainous, snow- and ice-dominated areas. This isolation leads to a distinct gap in biogeochemical knowledge that ultimately affects the accuracy and confidence with which these ecosystems can be computationally modeled for the purpose of projecting change under different climate scenarios. To examine a high-altitude, headwater ecosystem’s role in methanogenesis, sulfate reduction, and groundwater-surface water exchange, water samples were continuously collected from the river and hyporheic zones (HZ) during winter isolation in the East River (ER), CO watershed. Measurements of continuously collected ER surface water revealed up to 50 μM levels of dissolved methane in July through September, while samples from 12 cm deep in the hyporheic zone at the same location showed a spring to early summer peak in methane with a strong biogenic signature (<65 μM, δ13C-CH4, -60.76‰) before declining. Continuously collected δ 18 O-H 2 O and δ 2 H-H 2 O isotopes from the water column exhibited similar patterns to discrete measurements, while samples 12 cm deep in the hyporheic zone experienced distinct fluctuations in δ 18 O-H 2 O, alluding to significant groundwater interactions. Continuously collected microbial communities in the river in the late fall and early winter revealed diverse populations that reflect the taxonomic composition of ecologically similar river systems, including taxa indicative of methane cycling in this system. These measurements captured several biogeochemical components of the high-altitude watershed in response to seasonality, strengthening our understanding of these systems during the winter months.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Leptospira borgpetersenii serovar Hardjo and Leptospira santarosai serogroup Pyrogenes isolated from bovine dairy herds in Puerto Rico

Leptospirosis is one of the most common zoonotic diseases in the world and endemic in the Caribbean Islands. Bovine leptospirosis is an important reproductive disease. Globally, cattle are recognized as a reservoir host for L. borgpetersenii serovar Hardjo, which is transmitted via urine, semen, and uterine discharges, and can result in abortion and poor reproductive performance. The dairy industry in Puerto Rico comprises up to 25% of agriculture-related income and is historically the most financially important agricultural commodity on the island. In this study, we report the isolation of two different pathogenic Leptospira species, from two different serogroups, from urine samples collected from dairy cows in Puerto Rico: L. borgpetersenii serogroup Sejroe serovar Hardjo and L. santarosai serogroup Pyrogenes. Recovered isolates were classified using whole-genome sequencing, serotyping with reference antisera and monoclonal antibodies, and immunoblotting. These results demonstrate that dairy herds in Puerto Rico can be concurrently infected with more than one species and serovar of Leptospira, and that bacterin vaccines and serologic diagnostics should account for this when applying intervention and diagnostic strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Characterization of Senecavirus A Isolates Collected From the Environment of U.S. Sow Slaughter Plants

Vesicular disease caused by Senecavirus A (SVA) is clinically indistinguishable from foot-and-mouth disease (FMD) and other vesicular diseases of swine. When a vesicle is observed in FMD-free countries, a costly and time-consuming foreign animal disease investigation (FADI) is performed to rule out FMD. Recently, there has been an increase in the number of FADIs and SVA positive samples at slaughter plants in the U.S. The objectives of this investigation were to: (1) describe the environmental burden of SVA in sow slaughter plants; (2) determine whether there was a correlation between PCR diagnostics, virus isolation (VI), and swine bioassay results; and (3) phylogenetically characterize the genetic diversity of contemporary SVA isolates. Environmental swabs were collected from three sow slaughter plants (Plants 1-3) and one market-weight slaughter plant (Plant 4) between June to December 2020. Of the 426 samples taken from Plants 1-3, 304 samples were PCR positive and 107 were VI positive. There was no detection of SVA by PCR or VI at Plant 4. SVA positive samples were most frequently found in the summer (78.3% June-September, vs. 59.4% October-December), with a peak at 85% in August. Eighteen PCR positive environmental samples with a range of C t values were selected for a swine bioassay: a single sample infected piglets ( n = 2). A random subset of the PCR positive samples was sequenced; and phylogenetic analysis demonstrated co-circulation and divergence of two genetically distinct groups of SVA. These data demonstrate that SVA was frequently found in the environment of sow slaughter plants, but environmental persistence and diagnostic detection was not indicative of whether a sampled was infectious to swine. Consequently, a more detailed understanding of the epidemiology of SVA and its environmental persistence in the marketing chain is necessary to reduce the number of FADIs and aide in the development of control measures to reduce the spread of SVA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Restoration of Geographically Isolated Wetlands: An Amphibian-Centric Review of Methods and Effectiveness

Geographically isolated wetlands provide a critical habitat for pond-breeding amphibians, a taxa of broad conservation concern. Global wetland loss and degradation has made restoration essential for amphibian conservation. Restoration goals typically include recovering the wetlands’ physiochemical, hydrological, and ecological functions. However, for pond-breeding amphibians, successful restoration should also result in sustained populations, which is difficult to assess and infrequently reported. In this paper, we review the available evidence that restoration of geographically isolated wetlands promotes pond-breeding amphibian occupancy and population persistence. We provide an overview of restoration practices addressing hydrology, vegetation, and ecological processes within these unique environments and across spatial scales. We then summarize the evidence, and discuss the limitations, for evaluating successful restoration within the context of amphibian conservation across these categories. Finally, we provide recommendations for researchers and practitioners to leverage prior successes and establish systematic data collection and dissemination. Moving restoration of wetlands for amphibian conservation forward will require more robust data collection and reporting.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Taxonomic Re-Evaluation and Genomic Comparison of Novel Extracellular Electron Uptake-Capable Rhodovulum visakhapatnamense and Rhodovulum sulfidophilum Isolates

Rhodovulum spp. are anoxygenic phototrophic purple bacteria with versatile metabolisms, including the ability to obtain electrons from minerals in their environment to drive photosynthesis, a relatively novel process called phototrophic extracellular electron uptake (pEEU). A total of 15 strains of Rhodovulum sulfidophilum were isolated from a marine estuary to observe these metabolisms in marine phototrophs. One representative strain, Rhodovulum sulfidophilum strain AB26, can perform phototrophic iron oxidation (photoferrotrophy) and couples carbon dioxide fixation to pEEU. Here, we reclassify two R. sulfidophilum isolates, strainAB26 and strain AB19, as Rhodovulum visakhapatnamense using taxonomic re-evaluation based on 16S and pufM phylogenetic analyses. The strain AB26 genome consists of 4,380,746 base-pairs, including two plasmids, and encodes 4296 predicted protein-coding genes. Strain AB26 contains 22 histidine kinases, 20 response regulators, and dedicates ~16% of its genome to transport. Transcriptomic data under aerobic, photoheterotrophy, photoautotrophy, and pEEU reveals how gene expression varies between metabolisms in a novel R. visakhapatnamense strain. Genome comparison led by transcriptomic data under pEEU reveals potential pEEU-relevant genes both unique to R. visakhapatnamense strains and shared within the R. sulfidophilum genomes. With these data we identify potential pEEU-important transcripts and how speciation may affect molecular mechanisms of pEEU in Rhodovulum species from the same environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

High Synteny and Sequence Identity between Genomes of Nitrosococcus oceani Strains Isolated from Different Oceanic Gyres Reveals Genome Economization and Autochthonous Clonal Evolution

The ammonia-oxidizing obligate aerobic chemolithoautotrophic gammaproteobacterium, Nitrosococcus oceani, is omnipresent in the world’s oceans and as such important to the global nitrogen cycle. We generated and compared high quality draft genome sequences of N. oceani strains isolated from the Northeast (AFC27) and Southeast (AFC132) Pacific Ocean and the coastal waters near Barbados at the interface between the Caribbean Sea and the North Atlantic Ocean (C-27) with the recently published Draft Genome Sequence of N. oceani Strain NS58 (West Pacific Ocean) and the complete genome sequence of N. oceani C-107, the type strain (ATCC 19707) isolated from the open North Atlantic, with the goal to identify indicators for the evolutionary origin of the species. The genomes of strains C–107, NS58, C-27, and AFC27 were highly conserved in content and synteny, and these four genomes contained one nearly sequence-identical plasmid. The genome of strain AFC132 revealed the presence of genetic inventory unknown from other marine ammonia-oxidizing bacteria such as genes encoding NiFe-hydrogenase and a non-ribosomal peptide synthetase (NRPS)-like siderophore biosynthesis module. Comparative genome analysis in context with the literature suggests that AFC132 represents a metabolically more diverse ancestral lineage to the other strains with C-107 and NS58 potentially being the youngest. The results suggest that the N. oceani species evolved by genome economization characterized by the loss of genes encoding catabolic diversity while acquiring a higher redundancy in inventory dedicated to nitrogen catabolism, both of which could have been facilitated by their rich complements of CRISPR/Cas and Restriction Modification systems.

59 BASIC BIOLOGICAL SCIENCES↗