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DOE OSTI2022

The quality of organic amendments affects soil microbiome and nitrogen-cycling bacteria in an organic farming system

Organic amendments are applied in organic farming systems to provide nutrients for crop uptake and to improve soil health. Compost is often favored over fresh manure for food safety reasons, while fresh manure can be a valuable source of readily available nitrogen (N). However, the potential for fresh versus composted manure to differentially affect soil microbial and N-cycling functional communities over multiple seasons remains unknown. We compared the effect of composted vs. fresh cattle manure on soil microbial communities using taxonomic and functional approaches. Soils were collected from field plots with three organic N treatments: control (no amendment), composted manure (compost, 224 kg/ha total N), and fresh manure (manure, 224 kg/ha total N) in an organic production system. Illumina amplicon sequencing was used to comprehensively assess the bacterial community (16S rRNA genes), fungal community (ITS), ureolytic community ( ureC ), chitinolytic community ( chiA ), bacterial ammonia oxidizers (AOB amoA ), and nitrite oxidizers ( Nitrospira nxrB ). The results showed that both compost and manure treatment significantly changed the soil microbial communities. Manure had a stronger effect than compost on soil bacterial and fungal community composition, as well as on the ureolytic and chitinolytic communities, while compost treated soils had higher microbial richness than manure treated soils. Both taxonomic and functional approaches showed that the microbial community was more responsive to fresh manure than to compost. Manure treated soil also had more complex microbial interactions than compost treated soil. The abundance and community composition of N-cycling functional groups often played more limited roles than soil chemical properties (soil organic carbon, extractable organic carbon, and pH) in driving N-cycling processes. Results from our study may guide strategies for the management of organic amendments in organic farming systems and provide insights into the linkages between soil microbial communities and soil function.

Ouyang, Yang↗

DOE OSTI2023

Structuring Nutrient Yields throughout Mississippi/Atchafalaya River Basin Using Machine Learning Approaches

To minimize the eutrophication pressure along the Gulf of Mexico or reduce the size of the hypoxic zone in the Gulf of Mexico, it is important to understand the underlying temporal and spatial variations and correlations in excess nutrient loads, which are strongly associated with the formation of hypoxia. This study’s objective was to reveal and visualize structures in high-dimensional datasets of nutrient yield distributions throughout the Mississippi/Atchafalaya River Basin (MARB). For this purpose, the annual mean nutrient concentrations were collected from thirty-three US Geological Survey (USGS) water stations scattered in the upper and lower MARB from 1996 to 2020. Eight surface water quality indicators were selected to make comparisons among water stations along the MARB over the past two decades. Principal component analysis (PCA) was used to comprehensively evaluate the nutrient yields across thirty-three USGS monitoring stations and identify the major contributing nutrient loads. The results showed that all samples could be analyzed using two main components, which accounted for 81.6% of the total variance. The PCA results showed that yields of orthophosphate (OP), silica (SI), nitrate–nitrites (NO 3 -NO 2 ), and total suspended sediment (TSS) are major contributors to nutrient yields. It also showed that land-planted crops, density of population, domestic and industrial discharges, and precipitation are fundamental causes of excess nutrient loads in MARB. These factors are of great significance for the excess nutrient load management and pollution control of the Mississippi River. It was found that the average nutrient yields were stable within the sub-MARB area, but the large nitrogen yields in the upper MARB and the large phosphorus yields in the lower MARB were of great concern. t-distributed stochastic neighbor embedding (t-SNE) revealed interesting nonlinear and local structures in nutrient yield distributions. Clustering analysis (CA) showed the detailed development of similarities in the nutrient yield distribution. Moreover, PCA, t-SNE, and CA showed consistent clustering results. This study demonstrated that the integration of dimension reduction techniques, PCA, and t-SNE with CA techniques in machine learning are effective tools for the visualization of the structures of the correlations in high-dimensional datasets of nutrient yields and provide a comprehensive understanding of the correlations in the distributions of nutrient loads across the MARB.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Groundwater Depth Overrides Tree-Species Effects on the Structure of Soil Microbial Communities Involved in Nitrogen Cycling in Plantation Forests

Microbial communities found in soil ecosystems play important roles in decomposing organic materials and recycling nutrients. A clear understanding on how biotic and abiotic factors influence the microbial community and its functional role in ecosystems is fundamental to terrestrial biogeochemistry and plant production. The purpose of this study was to investigate microbial communities and functional genes involved in nitrogen cycling as a function of groundwater depth (deep and shallow), tree species (pine and eucalypt), and season (spring and fall). Soil fungal, bacterial, and archaeal communities were determined by length heterogeneity polymerase chain reaction (LH-PCR). Soil ammonia oxidation archaeal (AOA) amoA gene, ammonia oxidation bacterial (AOB) amoA gene, nitrite oxidoreductase nrxA gene, and denitrifying bacterial narG, nirK, nirS, and nosZ genes were further studied using PCR and denaturing gradient gel electrophoresis (DGGE). Soil fungal and bacterial communities remained similar between tree species and groundwater depths, respectively, regardless of season. Soil archaeal communities remained similar between tree species but differed between groundwater depths in the spring only. Archaeal amoA for nitrification and bacterial nirK and nosZ genes for denitrification were detected in DGGE, whereas bacterial amoA and nrxA for nitrification and bacterial narG and nirS genes for denitrification were undetectable. The detected nitrification and denitrification communities varied significantly with groundwater depth. There was no significant difference of nitrifying archaeal amoA or denitrifying nirK communities between different tree species regardless of season. The seasonal difference in microbial communities and functional genes involved in nitrogen cycling suggests microorganisms exhibit seasonal dynamics that likely impact relative rates of nitrification and denitrification.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Inclusion of Biological Targets in the Analysis of Electrical Characteristics of Non-Thermal Plasma Discharge

In Plasma Medicine studies, the effect of non-thermal plasma (NTP) on biological targets is typically correlated with the amount of stable reactive oxygen and nitrogen species produced in a liquid medium. The effect of NTP and the response of the biological target on cellular redox mechanisms is overlooked in these investigations. Additionally, the influence of electrical properties of cells on the physical properties of NTP is neglected. Therefore, we used a floating electrode dielectric barrier discharge plasma to explore the impact of cell structure, size, and viability of the biological target on the physical properties of NTP. Lissajous figures were used to determine circuit capacitance and energy per cycle during NTP exposure of different cell suspensions. We show that both, structural integrity and active enzymic processes of cells change the electrical properties of NTP. Correlations were also drawn between NTP-produced hydrogen peroxide and nitrite with measured capacitance. Our studies indicate that the observed changes between different cell suspensions may be due to a feedback loop between the biological target and the NTP source. In future studies, a more detailed analysis is needed to improve the control of clinical NTP devices.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Printed Potentiometric Nitrate Sensors for Use in Soil

Plant-available nitrogen, often in the form of nitrate, is an essential nutrient for plant growth. However, excessive nitrate in the environment and watershed has harmful impacts on natural ecosystems and consequently human health. A distributed network of nitrate sensors could help to quantify and monitor nitrogen in agriculture and the environment. Here, we have developed fully printed potentiometric nitrate sensors and characterized their sensitivity and selectivity to nitrate. Each sensor comprises an ion-selective electrode and a reference electrode that are functionalized with polymeric membranes. The sensitivity of the printed ion-selective electrodes was characterized by measuring their potential with respect to a commercial silver/silver chloride reference electrode in varying concentrations of nitrate solutions. The sensitivity of the printed reference electrodes to nitrate was minimized with a membrane containing polyvinyl butyral (PVB), sodium chloride, and sodium nitrate. Selectivity studies with sulphate, chloride, phosphate, nitrite, ammonium, calcium, potassium, and magnesium showed that high concentrations of calcium can influence sensor behavior. The printed ion-selective and reference electrodes were combined to form a fully printed sensor with sensitivity of −48.0 ± 3.3 mV/dec between 0.62 and 6200 ppm nitrate in solution and −47 ± 4.1 mV/dec in peat soil.

Baumbauer, Carol L. (ORCID:0000000246747551)↗

DOE OSTI2024

Activity assays of NnlA homologs suggest the natural product N -nitroglycine is degraded by diverse bacteria

Linear nitramines (R–N(R′)NO 2 ; R′ = H or alkyl) are toxic compounds, some with environmental relevance, while others are rare natural product nitramines. One of these natural product nitramines is N -nitroglycine (NNG), which is produced by some Streptomyces strains and exhibits antibiotic activity towards Gram-negative bacteria. An NNG degrading heme enzyme, called NnlA, has recently been discovered in the genome of Variovorax sp. strain JS1663 ( Vs NnlA). Evidence is presented that NnlA and therefore, NNG degradation activity is widespread. To achieve this objective, we characterized and tested the NNG degradation activity of five Vs NnlA homologs originating from bacteria spanning several classes and isolated from geographically distinct locations. E. coli transformants containing all five homologs converted NNG to nitrite. Four of these five homologs were isolated and characterized. Each isolated homolog exhibited similar oligomerization and heme occupancy as Vs NnlA. Reduction of this heme was shown to be required for NnlA activity in each homolog, and each homolog degraded NNG to glyoxylate, NO 2 − and NH 4 + in accordance with observations of Vs NnlA. It was also shown that NnlA cannot degrade the NNG analog 2-nitroaminoethanol. The combined data strongly suggest that NnlA enzymes specifically degrade NNG and are found in diverse bacteria and environments. These results imply that NNG is also produced in diverse environments and NnlA may act as a detoxification enzyme to protect bacteria from exposure to NNG.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Data from: Niche differentiation of bacterial versus archaeal soil nitrifiers induced by ammonium inhibition along a management gradient

Soil nitrification, mediated mainly by ammonia oxidizing archaea (AOA) and bacteria (AOB), converts ammonium (NH4+) to nitrite (NO2−) and thence nitrate (NO3−). To better understand ecological differences between AOA and AOB, we investigated the nitrification kinetics of AOA and AOB under eight replicated cropped and unmanaged ecosystems (including two fertilized natural systems) along a long-term management intensity gradient in the upper U.S. Midwest. For five of eight ecosystems, AOB but not AOA exhibited Haldane kinetics (inhibited by high NH4+ additions), especially in perennial and successional systems. In contrast, AOA predominantly exhibited Michaelis-Menten kinetics, suggesting greater resistance to high nitrogen inputs than AOB. These responses suggest the potential for NH4+-induced niche differentiation between AOA and AOB. Additionally, long-term fertilization significantly enhanced maximum nitrification rates (Vmax) in the early successional systems for both AOA and AOB, but not in the deciduous forest systems. This was likely due to pH suppression of nitrification in the acidic forest soils, corroborated by a positive correlation of Vmax with soil pH but not with amoA gene abundance. Results also demonstrated that soil nitrification potentials were relatively stable, as there were no seasonal differences. Overall, results suggest that (1) NH4+ inhibition of AOB but not AOA could be another factor contributing to niche differentiation between AOA and AOB in soil, and (2) nitrification by both AOA and AOB can be significantly promoted by long-term nitrogen inputs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Effects of Lithium-ion Battery Recycling Wastes on Ammonia-Oxidizing Bacteria

Increased demand for lithium-ion batteries (LIB) necessitates development of effective recycling methods for critical battery materials. Oak Ridge National Laboratory (ORNL) is exploring membrane solvent extraction (MSX) for the hydrometallurgical recycling of LIB materials. In this study, waste from MSX was investigated for its impact on the ammonia-oxidizing organism, Nitrosomonas europaea—a model organism for nitrogen removal during wastewater treatment. It was found that Raffinate 4 from ORNL was inhibitory to the growth and nitrite production of N. europaea, likely due to its nickel content. Further investigation is currently underway.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2024

Collaborative Research Proposal: Time Resolved Optical Emissions Spectroscopy and Laser Induced Fluorescence Spectroscopy of Nanosecond Pulsed Discharges in a Gas-Liquid Water Film Reactor

Electrical discharge plasma formed in contact with liquid water is of interest for a wide range of applications in chemical, biomedical, agricultural, electrical, and materials science and engineering. Such plasma reactors are of very timely importance since they also have significant disinfection capability by inactivating bacteria, viruses and other pathogens. Many types of plasma sources including those driven by AC, DC, RF, microwave, and pulsed electrical power supplies coupled to a wide range of different electrode configurations and reactor designs have been developed and explored which contact the plasma with liquid water. Recent roadmaps have recommended that further work is needed to develop our understanding of the fundamental chemical and physical process which occur at the interface of non-thermal plasma with liquid water solutions in order to advance this large diversity of applications which ultimately depend upon efficient production of key reactive chemical species. There is a wide range of interacting factors that affect the chemical reactions that occur in the plasma, in the liquid phase, and at the interface. These factors ultimately govern the key reactive chemical species formed and used in the various applications and they include a) the reactor design and input parameters, b) the discharge and transport processes, c) the plasma properties, and d) the resulting chemical reactions. For pulsed discharges, the power supply design and output parameters control the applied voltage, frequency, rise time, and width (duration) of the applied pulses. The reactor design involves specification of the gas-liquid contacting methods, electrode gap distance, reactor volume and shape, and gas and liquid flow rates achievable. The gas and liquid compositions as well as the liquid properties such as pH and conductivity are also of key importance in determination of the resulting chemical reactions. In addition, the important plasma properties include plasma gas temperature, electron density, electron energy (distribution), and size of the plasma channels which are all affected by the discharge and transport properties. Many studies have focused on specific aspects of these various processes. Of particular important and relevance to the proposed work is the utilization of nanosecond pulses to generate plasma in gas-liquid systems, liquid bubbles, underwater, and in gases. Recent advances in nanosecond pulses provide significant advantages in utilization with liquid water. For example, fast rise time and short pulses are less sensitive to water conductivity, such short pulses may provide advantages in fast temporal quenching of the plasma, and fundamental analysis of pulse properties, including pulse shape and width, may be facilitated by investigation of single filamentary fast pulses. Many studies have also dealt with the role of the gas composition on formation of reactive oxygen species (ROS) (i.e., hydroxyl radicals – ·OH, hydrogen peroxide – H 2 O 2 , various atomic oxygen species, ozone-O 3 , hydroperoxyl radicals HO 2 ·) and reactive nitrogen species (RNS) (i.e., nitrogen oxides – NO, NO 2 , N 2 O - collectively termed NO X , nitrite-NO 2 - , nitrate-NO 3 - , peroxynitrite-ONOO - ). The hydroxyl radical is the critical species in many chemical oxidation reactions for chemical degradation of toxic compounds in water and gases and for synthesis of some compounds. The mixture of various nitrogen oxide species is important for many biochemical and biological processes involved in biomedical and agricultural applications including disinfection and fertilizer production. The present proposal focuses on determination of the effects of time resolved electron density and hydroxyl radicals on plasma chemical reactions through collaboration with the Princeton Collaborative Low Temperature Plasma Research Facility (PCRF) at the Princeton Plasma Physics Laboratory (PPPL). In order to further investigate the role of the plasma generated electrons and hydroxyl radicals on the overall formation of the key species including hydrogen peroxide, hydroxyl radicals, and nitrogen oxides, the proposed work, thus seeks to determine high resolution time resolved electron density by optical emissions spectroscopy and time resolved hydroxyl radicals using laser induced fluorescence in the nanosecond discharge reactor. The combination of data on electron density and hydroxyl radical concentration will be utilized in the present work to more fully characterize the chemical reaction processes in this system and to advance the design, development, and operation of such chemical reactors for a wide range of applications.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2026

Project Development of an Electrochemical Denitration and Caustic Generation System for HLW Pretreatment at Hanford - 26350

An engineering-scale electrochemical processing skid is proposed to perform the denitration of Hanford tank waste, which would help to mitigate a key process concern with the direct feed processing of the Hanford Tank Waste Treatment and Immobilization Plant (WTP). The reduction of nitrates and organic compounds in the waste feed will directly reduce hazardous NOx and ammonia gases generated during the vitrification process, which in turn will aid in addressing potential regulatory and safety challenges associated with processing large volumes of tank waste. This paper highlights the past legacy work, project layout, accomplishments from Phase 1 and research and development envisioned for Phase 2. An innovative electrochemical denitration and caustic generation (EDCGe) process was demonstrated for the pretreatment of tank waste at the Savannah River Site (SRS) in the early 2000s. The denitration electrolyzer, off-gas abatement system, and caustic generator electrolyzer are being developed with the intent that the denitration electrolyzer will convert nitrate and nitrite anions to nitrogen gas while also yielding other gaseous byproducts, which may include N2O, NH3, VOCs, and H2. The gaseous byproducts will be managed via a tandem off-gas catalyst-bed treatment system. The caustic generation electrolyzer will recycle NaOH from the feed to produce a clean caustic stream for use within the batching tanks at Hanford, aiding in the preparation of waste for WTP. The reduction in hazardous emissions and improved waste treatment processes provides a robust solution for nuclear waste management, contributing to environmental safety and regulatory compliance. The EDCGe technology is being adapted, modified, and updated for the preparation of the Direct Feed-High Level Waste (DF-HLW) flowsheet at Hanford. Phase 1 demonstrated a bench-scale proof-of-concept for reactions involving the denitration electrolyzer and gas phase abatement of ammonia. The electrochemical technology is drawing on the scientific outcomes that were reported in the legacy work. The results from Phase 1 demonstrated the viability of the EDCGe system in reducing the nitrogen species of simple non-radioactive waste simulants. Commercially available alloys used as electrode materials and membranes are being studied for the denitration and caustic generation electrolyzers. The continuation of this project holds promise for broader applications, such as energy-efficient ammonia production, and contributes significant advancements in nuclear waste management. Additional material discovery has been investigated into ceramic Na super ion conductive (NaSICON) materials and off-gas abatement catalyst discovery. NaSICON is of interest for selective transport of Na within the electrolyzers to make a clean caustic stream. Future integration and optimization efforts, informed by Phase 1 results and ongoing research, will continue to drive advancements in nuclear waste management technology. The technology developed for the EDCGe treatment of tank waste will also have broader potential to inform other fields, such as energy-efficient ammonia production, as well as ammonia abatement catalysis through the lessons learned in electrochemical nitrate reduction. The applications and benefits of this research extend beyond Hanford and the Savannah River Site, supported by a collaborative team of scientists and engineers from national labs, academia, and industry, ensuring a comprehensive approach to solving complex waste treatment challenges. The team is leveraging advanced electrochemical technologies, machine learning, novel catalysts tailored for gaseous nitrogen species, and cutting-edge reactor systems to enhance the process efficiency and effectiveness of the denitration process.

Rodene, Dylan [Savannah River National Laboratory ↗

DOE OSTI2024

Synergizing Fe 2 O 3 Nanoparticles on Single Atom Fe‐N‐C for Nitrate Reduction to Ammonia at Industrial Current Densities

The electrochemical reduction of nitrates (NO 3 − ) enables a pathway for the carbon neutral synthesis of ammonia (NH 3 ), via the nitrate reduction reaction (NO 3 RR), which has been demonstrated at high selectivity. However, to make NH 3 synthesis cost-competitive with current technologies, high NH 3 partial current densities (j NH3 ) must be achieved to reduce the levelized cost of NH 3 . Here, the high NO 3 RR activity of Fe-based materials is leveraged to synthesize a novel active particle-active support system with Fe 2 O 3 nanoparticles supported on atomically dispersed Fe–N–C. The optimized 3×Fe 2 O 3 /Fe–N–C catalyst demonstrates an ultrahigh NO 3 RR activity, reaching a maximum j NH3 of 1.95 A cm −2 at a Faradaic efficiency (FE) for NH 3 of 100% and an NH 3 yield rate over 9 mmol hr −1 cm −2 . Operando XANES and post-mortem XPS reveal the importance of a pre-reduction activation step, reducing the surface Fe 2 O 3 (Fe 3+ ) to highly active Fe 0 sites, which are maintained during electrolysis. Durability studies demonstrate the robustness of both the Fe 2 O 3 particles and Fe–N x sites at highly cathodic potentials, maintaining a current of −1.3 A cm −2 over 24 hours. This work exhibits an effective and durable active particle-active support system enhancing the performance of the NO 3 RR, enabling industrially relevant current densities and near 100% selectivity.

active support↗

DOE OSTI2024

Community structure and function during periods of high performance and system upset in a full-scale mixed microalgal wastewater resource recovery facility

Microalgae have the potential to exceed current nutrient recovery limits from wastewater, enabling water resource recovery facilities (WRRFs) to achieve increasingly stringent effluent permits. The use of photobioreactors (PBRs) and the separation of hydraulic retention and solids residence time (HRT/SRT) further enables increased biomass in a reduced physical footprint while allowing operational parameters (e.g., SRT) to select for desired functional communities. However, as algal technology transitions to full-scale, there is a need to understand the effect of operational and environmental parameters on complex microbial dynamics among mixotrophic microalgae, bacterial groups, and pests (i.e., grazers and pathogens) and to implement robust process controls for stable long-term performance. Here, we examine a full-scale, intensive WRRF utilizing mixed microalgae for tertiary treatment in the US (EcoRecover, Clearas Water Recovery Inc.) during a nine-month monitoring campaign. We investigated the temporal variations in microbial community structure (18S and 16S rRNA genes), which revealed that stable system performance of the EcoRecover system was marked by a low-diversity microalgal community (D INVSIMPSON = 2.01) dominated by Scenedesmus sp. (MRA = 55 %-80 %) that achieved strict nutrient removal (effluent TP < 0.04 mg·L -1 ) and steady biomass concentration (TSS monthly avg . = 400–700 mg·L −1 ). Operational variables including pH, alkalinity, and influent ammonium (NH 4 + ), correlated positively (p < 0.05, method = Spearman) with algal community during stable performance. Further, the use of these parameters as operational controls along with N/P loading and SRT allowed for system recovery following upset events. Importantly, the presence or absence of bacterial nitrification did not directly impact algal system performance and overall nutrient recovery, but partial nitrification (potentially resulting from NO 2 − accumulation) inhibited algal growth and should be considered during long-term operation. The microalgal communities were also adversely affected by zooplankton grazers (ciliates, rotifers) and fungal parasites (Aphelidium), particularly during periods of upset when algal cultures were experiencing culture turnover or stress conditions (e.g., nitrogen limitation, elevated temperature). Altogether, the active management of system operation in order to maintain healthy algal cultures and high biomass productivity can result in significant periods (>4 months) of stable system performance that achieve robust nutrient recovery, even in winter months in northern latitudes (WI, USA).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2022

Nitrogen Metabolism in Pseudomonas putida : Functional Analysis Using Random Barcode Transposon Sequencing

Pseudomonas putida KT2440 has long been studied for its diverse and robust metabolisms, yet many genes and proteins imparting these growth capacities remain uncharacterized. Using pooled mutant fitness assays, we identified genes and proteins involved in the assimilation of 52 different nitrogen containing compounds. To assay amino acid biosynthesis, 19 amino acid drop-out conditions were also tested. From these 71 conditions, significant fitness phenotypes were elicited in 672 different genes including 100 transcriptional regulators and 112 transport-related proteins. We divide these conditions into 6 classes, and propose assimilatory pathways for the compounds based on this wealth of genetic data. To complement these data, we characterize the substrate range of three promiscuous aminotransferases relevant to metabolic engineering efforts in vitro. So we examine the specificity of five transcriptional regulators, explaining some fitness data results and exploring their potential to be developed into useful synthetic biology tools. In addition, we use manifold learning to create an interactive visualization tool for interpreting our BarSeq data, which will improve the accessibility and utility of this work to other researchers.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds

The ammonia-oxidizing bacterium Nitrosomonas europaea has been widely recognized as an important player in the nitrogen cycle as well as one of the most abundant members in microbial communities for the treatment of industrial or sewage wastewater. Its natural metabolic versatility and extraordinary ability to degrade environmental pollutants (e.g., aromatic hydrocarbons such as benzene and toluene) enable it to thrive under various harsh environmental conditions. Constraint-based metabolic models constructed from genome sequences enable quantitative insight into the central and specialized metabolism within a target organism. These genome-scale models have been utilized to understand, optimize, and design new strategies for improved bioprocesses. Reduced modeling approaches have been used to elucidate Nitrosomonas europaea metabolism at a pathway level. However, genome-scale knowledge about the simultaneous oxidation of ammonia and pollutant metabolism of N . europaea remains limited. Here, we describe the reconstruction, manual curation, and validation of the genome-scale metabolic model for N . europaea , i GC535. This reconstruction is the most accurate metabolic model for a nitrifying organism to date, reaching an average prediction accuracy of over 90% under several growth conditions. The manually curated model can predict phenotypes under chemolithotrophic and chemolithoorganotrophic conditions while oxidating methane and wastewater pollutants. Calculated flux distributions under different trophic conditions show that several key pathways are affected by the type of carbon source available, including central carbon metabolism and energy production.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

WHONDRS Summer 2019 Sampling Campaign: Global River Corridor Surface Water FTICR-MS, NPOC, TN, Anions, Stable Isotopes, Bacterial Abundance, and Dissolved Inorganic Carbon (v8)

The WHONDRS Summer 2019 Sampling (S19S) Campaign collected samples in 97 globally distributed river corridor systems between July and September 2019. Surficial streambed sediments were collected at three locations within each site (upstream, midstream, and downstream). Surface water was collected at the downstream site. This dataset includes a portion of the data types produced from the surface water samples and does not include any results from the sediment. Sediment data can be found at https://data.ess-dive.lbl.gov/view/doi:10.15485/1729719. The S19S campaign was designed with the science community to ask questions associated with links among core/transient metabolomes, microbial metabolism, biogeochemical function, and physical properties of watershed and river corridor systems. This data package was originally published in March 2020. It was updated in October 2020 (v2, new and modified files), July 2021 (v3, new and modified files), January 2023 (v4, new and modified files), February 2023 (v5, new and modified files), August 2023 (v6, new and modified files), July 2025 (v7,new and modified files), and August 2026 (v8, new and modified files). Version 8 includes major restructuring of the files and their formats. See the change history section in readme for more details. In addition to a readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset contains (1) readme, (2) data dictionary, (3) file level metadata, (4) sampling protocol, (5) a data checks report, (6) field metadata, (7) international generic sample number (IGSN) mapping file, (8) joint genome institute (JGI) mapping file, and (9) a folder of sample data. The sample data folder contains (1) dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC) and FTICR methods, (2) dissolved inorganic carbon (DIC), (3) stable water isotopes (O and H), (4) specific conductivity, (5) total dissolved nitrogen (TN), (6) anions, (7) flow cytometry bacterial abundance data, (8) laboratory methods, and (9) a folder containing unaligned, peak-picked high resolution characterization of dissolved organic matter from sediment via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL, https://www.pnnl.gov/environmental-molecular-sciences-laboratory), and (12) a folder containing processed FTICR-MS data. All files are .msa, .txt, .spx, .xml, .csv, .pdf, .txt, .html, .jpg, or .jpeg.

18-O↗

DOE OSTI2021

Data from: "Responses of alpine plant communities to climate warming"

The Alpine Treeline Warming Experiment (ATWE) was a common garden-climate manipulation experiment set up across an elevation gradient in Niwot Ridge, in the Front Range of the Colorado Rocky Mountains, USA. The project sought to learn more about the effects of climate change on alpine and subalpine ecosystems, namely tree species ranges and alpine plant communities. Plots were experimentally manipulated using infrared heaters set up to warm plots to temperatures comparable to those projected for the year 2100. Other treatments include watering, and a combination of watering and heating. Three sites were set up at different elevations to study three tree species, with the highest-elevation “Alpine” site ( ~3540 m) containing twenty additional plots to study alpine plant communities. Data in this package originate from these unseeded alpine plots. To evaluate soil nitrogen availability given site treatments, resin bags were deployed, removed, and extracted annually to produce ammonium and nitrate/nitrite readings.--------------------------------------------------Data files within this archive are in comma-separated-values (.csv) and Microsoft Excel (.xlsx) formats. .csvs can be read and opened by Microsoft Excel, R, or any other simple text-editing software, and .xlsx files can be opened using Microsoft Excel. Geospatial data associated with this package are in .kml and ESRI shapefile (.shp) formats. .kml files can be read using Google Earth or Google Maps, and shapefiles can be read with any software compatible with the file type, such as QGIS or ESRI’s ArcMap suite.Data files in this package - excluding “Winkler_2019_ALPO_inorganic_N_allyears.csv” - are provided in both Microsoft Excel and .csv formats, for added accessibility and flexibility in workflows. File contents are identical.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Temporal Study 2021-2022: Sample-Based Surface Water Chemistry and Organic Matter Characterization across Watersheds in the Yakima River Basin, Washington, USA (v3)

This dataset supports a broader study examining the drivers of temporal variability in sediment respiration rates in the Yakima River Basin. The dataset provides geochemistry and organic matter characterization data generated from samples collected at weekly or bi-weekly intervals at six sites across the Yakima River Basin in Washington, USA. Related sensor data will be published separately and can be used to link sediment respiration rates to biogeochemical processing rates. The data package was originally published in November 2022. It was updated in November 2023 (v2; modified files) and April 2025 (new and modified files). See the change history section in readme for more details. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) dissolved inorganic carbon (DIC), dissolved organic carbon (DOC; reported as non-purgeable organic carbon; NPOC), total nitrogen (TN), total suspended solids (TSS), and ions; (5) averaged values from water chemistry data; (6) surface water sampling protocol; (7) sensor protocol; (8) readme; (9) methods codes; (10) international generic sample number (IGSN) mapping file; and (11) folder of high resolution characterization of organic via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory). This folder contains two subfolders, one containing the .xml data files and the other containing instructions for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user's specific needs. All files are .csv, .pdf, .R, .ref, or .xml. We acknowledge the Yakama Nation as owners and caretakers of the lands where we collected our data. We thank the Confederated Tribes and Bands of the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Spatial Study 2021: Sample-Based Surface Water Chemistry and Organic Matter Characterization across Watersheds in the Yakima River Basin, Washington, USA (v3)

This dataset supports a broader study examining the drivers of spatial variability in sediment respiration rates in the Yakima River Basin. The dataset provides geochemistry and organic matter characterization data generated from samples collected during the same two-week period at 47 sites within multiple rivers throughout the Yakima River Basin in Washington, USA. Related sensor data are published at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1892054. This data package was originally published September 2022. It was updated May 2023 (modified files) and November 2024 (new and modified files). See the change history section in the readme for more details. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) dissolved inorganic carbon (DIC), dissolved organic carbon (DOC; reported as non-purgeable organic carbon; NPOC), total nitrogen (TN), total suspended solids (TSS), ions, and benzene polycarboxylic acid (BPCA) concentration and stable isotope data; (5) averaged values from water chemistry data; (6) surface water sampling protocol; (7) sensor protocol (8) readme; (9) methods codes; (10) international generic-sample number (IGSN) mapping file; and (11) folder of high resolution characterization of organic matter via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory). This folder contains two subfolders, one containing the .xml data files and the other containing instructions for using Formultitude (https://github.com/PNNL-Comp-Mass-Spec/Formultitude) and an R script to process the data based on the user's specific needs. All files are .csv, .pdf, .R, .ref, or .xml. We thank the United States Forest Service, Washington Department of Natural Resources, Washington Department of Fish and Wildlife, Washington State Parks, Confederated Tribes and Bands of the Yakama Nation, and Cowiche Canyon Conservancy for access to field locations where these samples were collected. We also thank the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

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