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Physiological and Comparative Genomic Analysis of Arthrobacter sp. SRS-W-1-2016 Provides Insights on Niche Adaptation for Survival in Uraniferous Soils
Arthrobacter sp. strain SRS-W-1-2016 was isolated on high concentrations of uranium (U) from the Savannah River Site (SRS) that remains co-contaminated by radionuclides, heavy metals, and organics. SRS is located on the northeast bank of the Savannah River (South Carolina, USA), which is a U.S. Department of Energy (DOE) managed ecosystem left historically contaminated from decades of nuclear weapons production activities. Predominant contaminants within the impacted SRS environment include U and Nickel (Ni), both of which can be transformed microbially into less toxic forms via metal complexation mechanisms. Strain SRS-W-1-2016 was isolated from the uraniferous SRS soils on high concentrations of U (4200 μM) and Ni (8500 μM), but rapid growth was observed at much lower concentrations of 500 μM U and 1000 μM Ni, respectively. Microcosm studies established with strain SRS-W-1-2016 revealed a rapid decline in the concentration of spiked U such that it was almost undetectable in the supernatant by 72 h of incubation. Conversely, Ni concentrations remained unchanged, suggesting that the strain removed U but not Ni under the tested conditions. To obtain a deeper understanding of the metabolic potential, a draft genome sequence of strain SRS-W-1-2016 was obtained at a coverage of 90×, assembling into 93 contigs with an N50 contig length of 92,788 bases. The genomic size of strain SRS-W-1-2016 was found to be 4,564,701 bases with a total number of 4327 putative genes. An in-depth, genome-wide comparison between strain SRS-W-1-2016 and its four closest taxonomic relatives revealed 1159 distinct genes, representing 26.7% of its total genome; many associating with metal resistance proteins (e.g., for cadmium, cobalt, and zinc), transporter proteins, stress proteins, cytochromes, and drug resistance functions. Additionally, several gene homologues coding for resistance to metals were identified in the strain, such as outer membrane efflux pump proteins, peptide/nickel transport substrate and ATP-binding proteins, a high-affinity nickel-transport protein, and the spoT gene, which was recently implicated in bacterial resistance towards U. Detailed genome mining analysis of strain SRS-W-1-2016 also revealed the presence of a plethora of secondary metabolite biosynthetic gene clusters likely facilitating resistance to antibiotics, biocides, and metals. Additionally, several gene homologous for the well-known oxygenase enzyme system were also identified, potentially functioning to generate energy via the breakdown of organic compounds and thus enabling the successful colonization and natural attenuation of contaminants by Arthrobacter sp. SRS-W-1-2016 at the SRS site.
SRS Composite Analysis Monitoring Plan (FY2019 Model Validation)
Using a projected end-state date of 2065 (SRNS 2015b), the Savannah River Site (SRS) Composite Analysis (CA) modeling for each facility and waste site began on the inventory year assigned to it so that source depletion and radionuclide transport out of the system could be appropriately captured. Some SRS waste sites that have already achieved their end states (i.e. end-state inventories and end-state configuration) are currently contributing to the potential off-site public dose through source release, groundwater transport, discharge to on-site surface streams, and stream transport to the CA point of assessments (POAs). The inventory year assigned to these waste sites is 2002 or before. This means that SRS CA results from 2002 and beyond are a reasonable representation for these waste sites that have already achieved their end states and are currently contributing to the potential off-site public dose. The SRS Annual Environmental Report (AER) monitoring can differentiate and separate liquid pathway data allowing the data representing only waste sites at their end state to be produced. Because the SRS CA has projected reasonable end-state impacts from 2002 and beyond, and the AER monitoring can differentiate and separate operating and end-state contributions to annual liquid pathway release, an opportunity exists to use the AER monitoring data to validate the SRS CA model. The CA model validation program uses a graded and systematic approach for taking corrective action, starting with an SRS established administrative dose limit of 15 mrem/yr, below which no action is required. Based on the location of the 2010 SRS CA POAs, the only potential exposure pathway for the public is through surface water. The completion of the FY2019 CA model validation indicates that the SRS CA projected dose, while generally conservative, provides a reasonable representation of the maximum annual doses. These doses are well below the administrative limit; therefore, no additional action is required.
Toward Predictive RANS and SRS Computations of Turbulent External Flows of Practical Interest
In this work, we investigate the main challenges to prediction of turbulent external flows of practical interest with Reynolds-Averaged Navier–Stokes equations (RANS) and Scale-Resolving Simulation (SRS) models. This represents a crucial step toward further developing and establishing these formulations so they can be confidently utilized in engineering problems without reference data. The study initiates by identifying the major challenges to prediction. A literature review is performed to illustrate their effects in RANS and SRS computations. Afterward, we evaluate the impact of the challenges to prediction by analyzing representative statistically steady and unsteady flows with prominent RANS and SRS methods. These include multiple turbulent viscosity and second-moment RANS closures, and hybrid and bridging SRS models. The results demonstrate the potential of the selected SRS models to predict engineering flows. Yet, they also show the importance of considering the challenges to prediction during the setup and conduction of numerical experiments. These can suppress the advantages of using SRS formulations. The data also indicate that only SRS models can confidently predict statistically unsteady flows. In contrast, the results demonstrate that mean-flow quantities of statistically steady flows can be efficiently calculated with RANS closures, especially second-moment closures. Among the selected SRS methods, bridging models reveal better suited for prediction due to their ability to prevent commutation errors and enable the robust evaluation of numerical and modeling errors. This last property allows the use of a new validation technique that does not require reference data.
Analysis Results for Sub-Samples of SRS Tanks 30, 32, and 39 to Support Evaluations of the I-129 Inventory
In order to appropriately model and predict the chemical integrity and performance of cementitious materials used for waste immobilization at the Savannah River Site (SRS), it is critical to understand the I-129 solubility and distribution within the tank farm. Iodine in radioactive waste and in environmental media is typically highly mobile and long lived. Iodine is ubiquitous in SRS tank waste and waste forms. The iodine is assumed to be soluble and present at low levels in Performance Assessments (PAs) for SRS Tank Farms, and is one of the dose drivers in the PAs for both the SRS Salt Disposal Facility (SDF) and the H-Area Tank Farm (HTF). Analysis of tank waste samples is critical to understanding the Tank Farm iodine inventory and reducing disposal uncertainty. Higher than expected iodine levels have recently been observed in residual solids isolated from some SRS tanks prior to closure, indicating uncertainty regarding the chemical species involved. If the iodine inventory uncertainty is larger than anticipated, future work may be necessary to reduce the uncertainty. This memorandum satisfies a portion of the work scope identified in Task Plan SRNL-RP-2016-00651. A separate memorandum issued previously, reported historical unpublished I-129 data, a significant portion of which was below detectable analytical limits. This memorandum includes iodine and general chemical analysis results for six archived SRNL samples which were previously reported to have I-129 concentrations below detectable limits. Lower sample dilution factors were used for the current analyses in order to obtain concentrations above detection. The samples analyzed included surface and depth samples from SRS tanks 30, 32, and 39.
Model Validation for the FY2021 SRS Composite Analysis Monitoring Plan
Using a projected end-state date of 2065 (SRNS 2015b), the Savannah River Site (SRS) Composite Analysis (CA) modeling for each facility and waste site began on the inventory year assigned to it so that source depletion and radionuclide transport out of the system could be appropriately captured. Some SRS waste sites that have already achieved their end states (i.e., end-state inventories and end-state configuration) are currently contributing to the potential off-site public dose through source release, groundwater transport, discharge to on-site surface streams, and stream transport to the CA point of assessments (POAs). The inventory year assigned to these waste sites is 2002 or before. This means that SRS CA results from 2002 and beyond are a reasonable representation for these waste sites that have already achieved their end states and are currently contributing to the potential off-site public dose. The SRS Annual Environmental Report (AER) monitoring can differentiate and separate liquid pathway data allowing the data representing only waste sites at their end state to be produced. Because the SRS CA has projected reasonable end-state impacts from 2002 and beyond, and the AER monitoring can differentiate and separate operating and end-state contributions to annual liquid pathway release, an opportunity exists to use the AER monitoring data to validate the SRS CA model.
Bioaugmentation of an Engineered Metal Treatment Wetland with Cupriavidus SRS
There are many chemical methods to remediate copper (Cu) from the environment. However, the use of microorganisms has been identified to be cheaper and more efficient in remediating toxic compounds in a method known as bioremediation. A microorganism, Cupriavidus SRS, is a metal resistant, rod shaped, gram negative bacteria that was isolated from a location with heavy metal contamination. As a predator this isolate has the ability to attack gram-negative and gram-positive bacteria. It is highly tolerant to Cu, and the isolates growth initiation is stimulated by Cu. Wang et al. (2015) determined that efflux pump activity is one of the most important mechanisms of heavy metal tolerance and the Cupriavidus genus demonstrates this behavior. In this study, Cupriavidus SRS will be inoculated to sediment and water from an area with high concentrations of Cu and zinc, to determine the ability of the isolate to grow and survive in a high level Cu wetland as well as the bioremoval efficiency. The H-02 wetland in the AL1 outfall area is an engineered wetland that was constructed to utilize natural processes associated with sediments and microbial communities to remove contaminants from waste waters at the Savannah River Site. Specifically, this wetland treats the building processes and runoff form the Tritium Processing Facility in H-area to prevent Cu and Zn from entering the water before the contaminants go in the Savannah River. Distributions of Cu and Zn follow organic matter levels with higher densities along the shoreline showing that metal concentrations correlate with organic matter content. Cupriavidus SRS Growth: Cupriavidus SRS was isolated at the Savannah River Site from an area with heavy metal contamination. Cultures were grown in R2A medium at 25 deg. C and shaken at 80 rpm for liquid cultures for 5 days. Sediment and Water Collection: All samples were collected from the AL1 Outfall area within the Department of Energy's Savannah River Site. Sediment cores, organic layer samples, and water samples were collected from the Inlet and Outlet cells in triplicate. Only water samples were collected from the basin. Cell Pellet: After centrifugation at 10,000 RPM for 10 minutes the supernatant was removed. 1 mL of phosphate buffer saline was added to the tube, vortexed, and recentrifuged. Inoculation of Sediment and Water: All samples were done in triplicate, vortexed after inoculation, and put on the shaker for 72 hours. Day 0 begins when the samples are removed from the shaker. Experimental Set-Up: All samples were done in triplicate. All sediment samples were centrifuged at 7500 RPM for 10 minutes on Day 0 and Day 5. All the sediment and water samples were filtered with a 0.2 μm nylon filters to obtain approximately 10 mL of supernatant on Day 0 and Day 3. pH was taken 24, 48, and 72 hours after the samples had been on the shaker. Plate Count: Plate counts were done on Day 0 and Day 3 to determine Cupriavidus SRS growth following a quantitative counting method from Seely et al. (1972). This project is ongoing and the goal is to determine if Cupriavidus SRS has the ability to uptake excess Cu out of the environment. These could be some possible results for the experiment: - The isolate uptakes too much Cu, dies, and releases Cu back into the environment. - The isolate is able to uptake Cu, continue to live, but chemically changes the environment introducing new problems. - The isolate is able to uptake Cu, continue to live, and does not disrupt the environment with toxic chemical changes.
Squeezed Light Stimulated Raman Scattering (SRS) Microscopy for Bioenergy Applications
Stimulated Raman scattering (SRS) microscopy using picosecond near-IR pulses have provided a great penetration depth with reduced fluorescence interference when imaging biological samples for bioenergy applications. These tools have provided insight into 1) tracking the degradation of chemical composites in biomass feedstocks to investigate the recalcitrant factors during the deconstruction processes, 2) monitoring the production of chemicals in photosynthetic plants and wood-digesting microorganisms, and 3) probing plant-bacteria interactions. However, the above processes are usually slow and require continuous imaging for an extended period. This is challenging for classic SRS because the laser power needed to achieve enough sensitivity causes photodamage in the samples during such long experiments. Quantum-squeezed light with reduced noise in the intensity quadrature can improve the sensitivity of classic SRS microscopy beyond the shot noise limit. The successful squeezing of one of the picosecond pulses in the above SRS will improve sensitivity and reduce photodamage, greatly expanding the range of studies available to SRS microscopy.
Scalable Reasoning System (SRS)
SRS is a web-based and mobile toolkit for information visualization and collaboration. It includes server-side components in the form of web services that provide analytical functions such as data clustering and temporal analysis. The SRS client is accessed via a web browser and uses asynchronous javascript and XML (AJAX) to interact with and visualize the results of these web services. Users of SRS can query data sources that are connected to the SRS backend, and query results are presented in the form of coordinated visual displays in a web browser that depict temporal, topical, and spatial relationships in the results. SRS also includes an early stage graphical reasoning diagram interface that helps analysts express and test hypotheses. This software was developed with funding from the Science and Technology Directorate of the U.S. Department of Homeland Security.
SRS Computer Animation and Drive Train System
The spinning rocket simulator (SRS) is an ongoing project at Oral Roberts University. The goal of the SRS is to gather crucial data concerning a spinning rocket under thrust for the purpose of analysis and correction of the coning motion experienced by this type of spacecraft maneuver. The computer animation simulates a virtual, scale model of the component of the SRS that represents the spacecraft itself. This component is known as the (VSM), or virtual spacecraft model. During actual physical simulation, this component of the SRS will experience a coning. The goal of the animation is to cone the VSM within that range to accurately represent the motion of the actual simulator. The drive system of the SRS is the apparatus that turns the actual simulator. It consists of a drive motor, motor mount and chain to power the simulator into motion. The motor mount is adjustable and rigid for high torque application. A digital stepper motor controller actuates the main drive motor for linear acceleration. The chain transfers power from the motor to the simulator via sprockets on both ends.
Bioremediation of copper in sediments from a constructed wetland ex situ with the novel bacterium Cupriavidus basilensis SRS
The H-02 constructed wetland was designed to remove metals (primarily copper and zinc) to treat building process water and storm water runoff from multiple sources associated with the Tritium Facility at the DOE-Savannah River Site, Aiken, SC. The concentration of Cu and Zn in the sediments has increased over the lifetime of the wetland and is a concern. A bioremediation option was investigated at the laboratory scale utilizing a newly isolated bacterium of the copper metabolizing genus Cupriavidus isolated from Tim’s Branch Creek, a second-order stream that eventually serves as a tributary to the Savannah River, contaminated with uranium and other metals including copper, nickel, and mercury. Cupriavidus basilensis SRS is a rod-shaped, gram-negative bacterium which has been shown to have predatory tendencies. The isolate displayed resistance to the antibiotics ofloxacin, tetracycline, ciprofloxacin, select fungi, as well as Cu 2+ and Zn 2+ . Subsequent ribosomal sequencing demonstrated a 100% confidence for placement in the genus Cupriavidus and a 99.014% match to the C. basilensis type strain. When H-02 wetland samples were inoculated with Cupriavidus basilensis SRS samples showed significant (p < 0.05) decrease in Cu 2+ concentrations and variability in Zn 2+ concentrations. Over the 72-h incubation there were no significant changes in the inoculate densities (10 6 –10 8 cells/ML) indicating Cupriavidus basilensis SRS resiliency in this environment. This research expands our understanding of the Cupriavidus genus and demonstrates the potential for Cupriavidus basilensis SRS to bioremediate sites impacted with heavy metals, most notably copper.
Maxdose-SR and popdose-SR routine release atmospheric dose models used at SRS
MAXDOSE-SR and POPDOSE-SR are used to calculate dose to the offsite Reference Person and to the surrounding Savannah River Site (SRS) population respectively following routine releases of atmospheric radioactivity. These models are currently accessed through the Dose Model Version 2014 graphical user interface (GUI). MAXDOSE-SR and POPDOSE-SR are personal computer (PC) versions of MAXIGASP and POPGASP, which both resided on the SRS IBM Mainframe. These two codes follow U.S. Nuclear Regulatory Commission (USNRC) Regulatory Guides 1.109 and 1.111 (1977a, 1977b). The basis for MAXDOSE-SR and POPDOSE-SR are USNRC developed codes XOQDOQ (Sagendorf et. al 1982) and GASPAR (Eckerman et. al 1980). Both of these codes have previously been verified for use at SRS (Simpkins 1999 and 2000). The revisions incorporated into MAXDOSE-SR and POPDOSE-SR Version 2014 (hereafter referred to as MAXDOSE-SR and POPDOSE-SR unless otherwise noted) were made per Computer Program Modification Tracker (CPMT) number Q-CMT-A-00016 (Appendix D). Version 2014 was verified for use at SRS in Dixon (2014).
Review of Mercury in the SRS Tank Waste Storage and Treatment Processes for Applicability to Hanford Waste Processing
The Savannah River Site (SRS) and Hanford produced large quantities of plutonium and other radioisotopes. The separations processes recovered plutonium and produced large quantities of High- Level Waste (HLW) that accumulated at each site in large, underground storage tanks. SRS has been retrieving the stored HLW, pretreating the waste for immobilization, and immobilizing the waste in glass or grout waste forms since the mid-1990s. Treatment of the waste at Hanford is expected to start in the early 2020s. Mercury is present in both the SRS and Hanford tank waste. SRS has recently completed an evaluation of mercury speciation throughout the tank waste treatment and immobilization flowsheet. This study was reviewed to determine what information from the study can be applied to the Hanford tank waste treatment program.
Preliminary Design of Mu2E Spill Regulation System (SRS)
Direct μ→e conversion requires resonant extraction of a stream of pulsed beam, comprised of short micro-bunches (pulses) from the Delivery ring (DR) to the Mu2e target. Experimental needs and radiation protection apply strict re-quirements on the beam quality control and regulation of the spill. The objective of the Spill Regulation System (SRS) is to maintain the intensity uniformity of a stream of ~25k pulses as 1e12 protons are extracted at 590.08 kHz over a 43 ms spill period. To meet the specified perfor-mance, two regulation elements will be driven simultane-ously: a family of three zero-harmonic quadrupoles (tune ramp quads) and a RF Knock-Out (RFKO) system. The SRS will use two separate control loops to control each regulation element simultaneously. It will be critical to co-ordinate the SRS processes within the machine cycle and within each spill interval. The SRS has been designed to have a total Gain-Bandwidth product of 10 kHz, which can be used to mitigate several sources of ripple in the spill pro-file.
SRS Defense Waste Processing Facility - the Nation's Only Operating Vitrification Facility - Completes 20 Years of Radioactive Operations - 17407
Savannah River Remediation (SRR) is the current Liquid Waste contractor at the U.S. Department of Energy's (DOE) Savannah River Site (SRS), located near Aiken, South Carolina, and operates the Defense Waste Processing Facility (DWPF), along with the other SRS liquid waste facilities. The DWPF, the nation's only operating vitrification facility, completed 20 years of radioactive operations in 2016. During this period, DWPF has safely treated the high-level liquid waste at this DOE facility since radioactive operations began with the first transfer of sludge waste feed to DWPF on March 12, 1996. A little over a month later, on April 29, 1996, the first radioactive canister was poured. DWPF poured its 4,000. canister of vitrified waste on December 31, 2015. As of September 30, 2016, DWPF has removed approximately 59.9 million curies from the liquid waste system at SRS and placed them in 4,106 canisters. SRS has operationally closed 8 high-level waste tanks. The DWPF melter has poured nearly 7.14 million kg of molten glass, and the facility has used only two melters in its lifetime. Melter 1 poured 1,339 canisters (1996-2002), while melter 2 to date (September 30, 2016) has poured 2,767 canisters (2003-present). Melter 2 continues to safely and efficiently operate. In order to achieve these accomplishments, the facility has chronicled a history of continued operational improvements such as the installation of bubblers in the melter to increase production, incorporation of glass compositions to achieve higher waste loadings, and improvements to melter design to extend melter life. As SRR moves forward to the next 20 years, continued improvements as well as maintaining the aging infrastructure through a proactive system health program are key priorities. This paper chronicles 20 years of challenges, improvements and accomplishments, and discusses future operations and infrastructure upgrades including implementation of a key flowsheet change to significantly reduce hydrogen generation in the Chemical Process Cell. (authors)
A simple method of measuring the effective SRS coefficient in single-mode optical fibres and its applicability limits
This paper describes techniques for measuring the SRS coefficient in a wide spectral range, including the region of small Stokes shifts. A simple, approximate method is proposed for evaluating the SRS coefficient near a gain peak. Spectral dependences of the SRS coefficient are presented for various telecom fibres. (nonlinear optical phenomena)
Bioaugmentation of an Engineered Metal Treatment Wetland with Cupriavidus SRS
Cupriavidus SRS is a metal resistant, rod shaped, gram negative bacteria that was isolated from a location with heavy metal contamination at the Department of Energy’s Savannah River Site in Aiken, South Carolina. This isolate has also been able to demonstrate antibiotic resistance and predatory behavior to other microorganisms, giving it a competitive advantage. The effect of bioaugmentation with Cupriavidus SRS and copper (Cu) uptake is not well understood, although multiple studies have analyzed this effect with other metal resistant bacteria. In this study, sediment from the AL1 outfall area will be inoculated with Cupriavidus SRS to analyze the effectiveness of the degradation of Cu.
Determining the Release of Radionuclides from SRS Tank 12H Waste Residual Solids Following Tank Closure
Eight High Level Waste (HLW) tanks used to store radioactive waste slurries have been emptied and closed at the Savannah River Site (SRS). Performance Analyses (PA) modeling of the release of radionuclides from residual waste solids in these tanks into the environment over extended time periods indicated the most likely risk drivers for environmental contamination. Radionuclide leaching studies were desired to provide additional information regarding the residual waste solubility assumptions used in the models. This report serves to provide equilibrium solubility data for several radionuclides identified as risk drivers and adds to the database of solubility values reported in the previous analogous study with Tank 18F solids. Pore water leaching studies were conducted on actual SRS Tank 12H residual waste solids to support Liquid Waste tank closure efforts and closed tank Performance Analyses. Tank 12H was exposed to extensive mechanical cleaning, caustic aluminum dissolution, and oxalic acid chemical cleaning prior to closure. The methodology utilized for leach testing was developed during previous testing. Slurries of tank residual solids and grout-representative solids in simulated grout pore water solutions (based on SRS groundwater compositions) with pH and E h values expected during the aging of the closed waste tank were produced. The soluble concentrations of selected radionuclides were analyzed versus time to confirm equilibrium conditions were achieved. These are the first leach studies conducted on waste tank residuals exposed to these cleaning conditions.