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DOE OSTI2023

Synthesis and Characterization of Amorphous Lawsone Polymer Dots for Fluorescent Applications

In this work, a two-step hydrothermal/solvothermal process was developed to generate highly fluorescent lawsone polymer dots (LPDs) utilizing an inexpensive and abundant starting material, 2-hydroxy-1,4-napththoquinone (lawsone). This hydrothermal/solvothermal process produces LPDs that have excitation independent emission with well-defined electronic transitions. This two-step protocol provides a straightforward approach to remove unwanted small molecular fluorescence, which has plagued carbon dot systems, without the need for advanced chromatographic purification methods or steps. A series of spectroscopic, electrochemical, and theoretical experiments suggest that this process proceeds via a sequential dehydration and dehydrogenation pathway to cross-link the lawsone into a carbon dot structure. This polymerization process helps to stabilize and favor certain electronic transitions inherently present in the lawsone monomer. The generation of the LPDs results in a 2 order of magnitude increase in the emission intensity and a quantum yield of 37%. This behavior is likely the result of the cross-linked structure shielding these electronic states from deactivation caused by nonradiative processes such as vibrational coupling and excited state quenching from thermal deactivation and solvent collisions. This finding is consistent with a cross-linked enhanced emission (CEE) mechanism, as previously observed for other similar systems. The LPDs were then incorporated into a TiO2 photoanode and utilized as a photosensitizer in a dye-sensitized solar cell (DSSC) which showed an enhancement in photocurrent density over pure TiO2. We also prepared a derivative of the LPDs utilizing a diethylene triamine additive (nitrogen-doped lawsone polymer dots (N-LPDs)) using the same two-step protocol and demonstrated its potential as a fluorescence microscopy dye for imaging MDA-MB-231 cancer cells.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Chemical influence of ammonia on suppressing soot formation pathways

There is interest in mixing ammonia (NH3) with hydrocarbons, as this decreases overall CO2 emissions from the fuel mixture when burned. Co-firing NH3 with hydrocarbons like methane (CH4) also enables stable combustion over a larger set of operating conditions in engines and gas turbines than firing only NH3 permits. When NH3 is co-fired with hydrocarbons, the influence of NH3 on soot formation chemistry becomes relevant. In this work, soot concentrations in laminar nonpremixed co-flow flames of NH3/CH4 and N2/CH4 were analyzed using color-ratio pyrometry. The concentrations of combustion species (CH4, CO2, H2O, O2, C2H2, C6H6, HCN) across the different flames were also determined using on-line electron-impact mass spectrometry. The flames were also interrogated with 2D CFD simulations, which employ a detailed chemical mechanism tailored to capturing fuel-nitrogen chemistry. Addition of NH3 to CH4 flames was found to decrease soot concentrations more significantly than N2-addition (Fig. 1). The NH3/CH4 flames were found to have higher flame temperatures than the N2/CH4 flames, implying the suppression of soot afforded by NH3 is due to a chemical influence of NH3, as opposed to thermal or dilution effects. Based on experimental and simulated soot volume fractions and species concentrations, soot formation pathways affected by NH3 are postulated.

10 SYNTHETIC FUELS↗

DOE OSTI2020

Seasonal dynamics of core fungi in the switchgrass phyllosphere, and co-occurrence with leaf bacteria

Plant leaves harbor complex microbial communities that influence plant health and productivity. Nevertheless, a detailed understanding of phyllosphere community assembly and drivers is needed, particularly for phyllosphere fungi. Here, we investigated seasonal dynamics of epiphytic phyllosphere fungal communities in switchgrass ( Panicum virgatum L.), a focal bioenergy crop. We also leverage previously published data on switchgrass phyllosphere bacterial communities from the same experimental plants, allowing us to compare fungal and bacterial dynamics and explore inter-Domain network associations in the switchgrass phyllosphere. Overall, we found a strong impact of sampling date on fungal community composition, with multiple taxonomic levels exhibiting clear temporal patterns in relative abundance. In addition, leaf nitrogen concentration, leaf dry matter content, plant height, and minimum daily air temperature explained significant variation in phyllosphere fungal communities, likely due to their correlation with sampling date. Finally, among the core taxa, fungal-bacterial network associations were much more common than bacteria-bacteria associations, suggesting the importance of inter-Domain phylogenetic diversity in microbiome assembly. Although our findings highlight the complexity of phyllosphere microbiome assembly, the clear temporal patterns in lineage-specific fungal abundances give promise to the potential for accurately predicting shifts in fungal phyllosphere communities throughout the growing season, a key research priority for sustainable agriculture.

16S rRNA↗

DOE OSTI2025

Cryo-EM structure of a methanogen nitrogenase-PII protein supercomplex

Abstract Nitrogenases are metalloenzymes that catalyze the reduction of atmospheric dinitrogen to ammonia, sustaining the global nitrogen cycle. While bacterial nitrogenase has been extensively characterized, the architecture and regulation of archaeal nitrogenases remain unknown despite longstanding evidence of nitrogen fixation in methanogens. Here we report a 3.1 Å cryo-electron microscopy structure of a native nitrogenase–PII protein supercomplex from Methanosarcina acetivorans. The structure reveals an unprecedented assembly of three NifDK heterotetramers bridged by six NifI1,2 heterotrimeric PII complexes, which sterically block NifH association and lock the enzyme in an inactive state. The NifI complexes display asymmetric binding of ADP and 2-oxoglutarate, coupling nitrogenase inhibition directly to cellular energy and nitrogen status. Addition of 2-oxoglutarate and ATP releases the NifI complexes, stimulating a threefold increase in NifDK activity in vitro. This higher-order architecture uncovers a previously unrecognized regulatory strategy in methanogens, in which PII proteins drive nitrogenase oligomerization to control activity. The discovery that nitrogenase activity may be modulated through direct assembly into higher-order structures opens new avenues for exploring nitrogenase evolution, regulation, and biotechnological applications. One sentence summary Discovery of a nitrogenase-PII protein supercomplex in methanogens, uncovering a metabolite-gated assembly mechanism for nitrogenase inhibition.

Nitrogenase, Electron Transfer, Methanogen↗

DOE OSTI2023

Leaf gas exchange, spectral reflectance and leaf composition, BIONTE, Brazil, 2022

Leaf traits measured at the top of the canopy on 10 species at the BIONTE experimental plot T1B4SB3, near Manaus, Brazil, in August and September, 2022. The aim of this study was to test the relationship between leaf water use efficiency and wood density. Ten tree species located in close proximity of each other (within 50 meters) were selected and classified by wood density (low or high). Sampling was carried out on top-of-canopy leaves accessed by an articulated boom lift. Survey gas exchange measurement were performed on attached leaves at various times during the day. Following gas exchange, the leaf was harvested, and measured for spectral reflectance, leaf water content, leaf mass per area and leaf carbon content and leaf nitrogen content. Additional leaves other than those used for gas exchange were also harvested from different branches on the same tree for spectral reflectance and leaf trait measurements. Data in this data package is presented in csv files, with metadata in csv and descriptive experimental protocols as pdf. Gas exchange data and metadata meets the requirements of the ESS-DIVE reporting format for leaf gas exchange data and metadata.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Beyond Ammonia: Nitrogen–Element Bond Forming Reactions with Coordinated Dinitrogen

The functionalization of coordinated dinitrogen to form nitrogen-element bonds en route to nitrogen-containing molecules is a long-standing challenge in chemical synthesis. The strong triple bond and the non-polarity of the N 2 molecule pose thermodynamic and kinetic challenges for promoting reactivity. Although heterogeneous, homogeneous and biological catalysts are all known for catalytic nitrogen fixation to ammonia, the catalytic synthesis of more complicated nitrogen-containing organic molecules has far less precedent. Examples of silyl radical additions to coordinated nitrogen to form silylamines stands as the lone example of a catalytic reaction involving N 2 to form a product other than ammonia. Our review surveys the field of molecular transition metal complexes, as well as recent boron examples for the formation of nitrogen-element bonds. Emphasis is placed on the coordination and activation modes of N 2 in the various metal compounds from across the transition series and how these structures can rationally inform reactivity studies. Over the past few decades, the field has evolved from the addition of carbon electrophiles in a manner similar to protonation reactions to more organometallic-inspired reactivity including insertions, 1,2-additions and cycloadditions. Various N–C, N–Si and N–B bond-forming reactions have been discovered highlighting that the challenge for catalytic chemistry is not in the reactivity of coordinated dinitrogen but rather removal of the functionalized ligand from the coordination sphere of the metal.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Insights into Sustainable Nitrogen Fixation by Gas-phase Spectroscopic Measurements and Global Modeling of Reaction Intermediates in Humid Nitrogen Plasma

In this article, there is growing interest in reacting molecular nitrogen and water to sustainably synthesize fixed forms of nitrogen such as ammonia. In particular, low-temperature plasmas can activate these relatively inert feedstocks at or near room temperature without a catalyst. However, because of the enhanced reactivity and nonequilibrium chemistry, a diverse range of products is formed, and the underlying reaction mechanisms are exceedingly complex. In this work, we studied a simplified reactor consisting of a gaseous plasma containing controlled mixtures of nitrogen gas and water vapor. Densities of key chemical species such as N, H, OH, NH, and NO were measured by emission and laser-based spectroscopy as a function of the relative humidity. A global model was constructed and the reaction network was validated by comparing calculated species densities with experiments. We discover that N, a key initial intermediate for ammonia, strongly decreases in the presence of water vapor, and as a result, ammonia formation becomes limited at high relative humidity. This decrease is surprisingly not because N itself reacts, but because one of its main sources, an excited molecular nitrogen state, is reacted away. In addition, oxidation pathways for nitrogen, which lead to NO and related products, are found to be favored over reduction pathways because the corresponding reverse reactions are less significant. Together, this understanding helps explain previously reported observations of selectivity toward nitrogen oxides over ammonia, particularly at higher relative humidities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences

Ammonia-oxidizing microorganisms (AOM) contribute to one of the largest nitrogen fluxes in the global nitrogen budget. Four distinct lineages of AOM: ammonia-oxidizing archaea (AOA), beta- and gamma-proteobacterial ammonia-oxidizing bacteria (β-AOB and γ-AOB) and complete ammonia oxidizers (comammox), are thought to compete for ammonia as their primary nitrogen substrate. In addition, many AOM species can utilize urea as an alternative energy and nitrogen source through hydrolysis to ammonia. How the coordination of ammonia and urea metabolism in AOM influences their ecology remains poorly understood. Here we use stable isotope tracing, kinetics and transcriptomics experiments to show that representatives of the AOM lineages employ distinct regulatory strategies for ammonia or urea utilization, thereby minimizing direct substrate competition. The tested AOA and comammox species preferentially used ammonia over urea, while β-AOB favoured urea utilization, repressed ammonia transport in the presence of urea and showed higher affinity for urea than for ammonia. Characterized γ-AOB co-utilized both substrates. Furthermore, these results reveal contrasting niche adaptation and coexistence patterns among the major AOM lineages.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Microbial community response to a decade of simulated global changes depends on the plant community

Global changes such as increased drought and atmospheric nitrogen deposition perturb both the microbial and plant communities that mediate terrestrial ecosystem functioning. However, few studies consider how microbial responses to global changes may be influenced by interactions with plant communities. To begin to address the role of microbial–plant interactions, we tested the hypothesis that the response of microbial communities to global change depends on the plant community. We characterized bacterial and fungal communities from 395 plant litter samples taken from the Loma Ridge Global Change Experiment, a decade-long global change experiment in Southern California that manipulates rainfall and nitrogen levels across two adjacent ecosystems, a grassland and a coastal sage scrubland. The differences in bacterial and fungal composition between ecosystems paralleled distinctions in plant community composition. In addition to the direct main effects, the global change treatments altered microbial composition in an ecosystem-dependent manner, in support of our hypothesis. The interaction between the drought treatment and ecosystem explained nearly 5% of the variation in bacterial community composition, similar to the variation explained by the ecosystem-independent effects of drought. Unexpectedly, we found that the main effect of drought was approximately four times as strong on bacterial composition as that of nitrogen addition, which did not alter fungal or plant composition. Overall, the findings underscore the importance of considering plant–microbe interactions when considering the transferability of the results of global change experiments across ecosystems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Nitrogen-Fixing Gamma Proteobacteria Azotobacter vinelandii—A Blueprint for Nitrogen-Fixing Plants?

The availability of fixed nitrogen limits overall agricultural crop production worldwide. The so-called modern “green revolution” catalyzed by the widespread application of nitrogenous fertilizer has propelled global population growth. It has led to imbalances in global biogeochemical nitrogen cycling, resulting in a “nitrogen problem” that is growing at a similar trajectory to the “carbon problem”. As a result of the increasing imbalances in nitrogen cycling and additional environmental problems such as soil acidification, there is renewed and increasing interest in increasing the contributions of biological nitrogen fixation to reduce the inputs of nitrogenous fertilizers in agriculture. Interestingly, biological nitrogen fixation, or life’s ability to convert atmospheric dinitrogen to ammonia, is restricted to microbial life and not associated with any known eukaryotes. It is not clear why plants never evolved the ability to fix nitrogen and rather form associations with nitrogen-fixing microorganisms. Perhaps it is because of the large energy demand of the process, the oxygen sensitivity of the enzymatic apparatus, or simply failure to encounter the appropriate selective pressure. Whatever the reason, it is clear that this ability of crop plants, especially cereals, would transform modern agriculture once again. Successfully engineering plants will require creating an oxygen-free niche that can supply ample energy in a tightly regulated manner to minimize energy waste and ensure the ammonia produced is assimilated. Nitrogen-fixing aerobic bacteria can perhaps provide a blueprint for engineering nitrogen-fixing plants. This short review discusses the key features of robust nitrogen fixation in the model nitrogen-fixing aerobe, gamma proteobacteria Azotobacter vinelandii, in the context of the basic requirements for engineering nitrogen-fixing plants.

Microbiology↗

DOE OSTI2022

Nitrogen increases early‐stage and slows late‐stage decomposition across diverse grasslands

1. To evaluate how increased anthropogenic nutrient inputs alter carbon cycling in grasslands, we conducted a litter decomposition study across 20 temperate grasslands on three continents within the Nutrient Network, a globally distributed nutrient enrichment experiment 2. We determined the effects of addition of experimental nitrogen (N), phosphorus (P) and potassium plus micronutrient (K μ ) on decomposition of a common tree leaf litter in a long-term study (maximum of 7 years; exact deployment period varied across sites). The use of higher order decomposition models allowed us to distinguish between the effects of nutrients on early- versus late-stage decomposition. 3. Across continents, the addition of N (but not other nutrients) accelerated early-stage decomposition and slowed late-stage decomposition, increasing the slowly decomposing fraction by 28% and the overall litter mean residence time by 58%. 4. Synthesis. Using a novel, long-term cross-site experiment, we found widespread evidence that N enhances the early stages of above-ground plant litter decomposition across diverse and widespread temperate grassland sites but slows late-stage decomposition. These findings were corroborated by fitting the data to multiple decomposition models and have implications for N effects on soil organic matter formation. For example, following N enrichment, increased microbial processing of litter substrates early in decomposition could promote the production and transfer of low molecular weight compounds to soils and potentially enhance the stabilization of mineral-associated organic matter. By contrast, by slowing late-stage decomposition, N enrichment could promote particulate organic matter (POM) accumulation. Such hypotheses deserve further testing.

Nutrient Network (NutNet)↗

DOE OSTI2023

SPRUCE Sphagnum Phytobiome Responses to Whole Ecosystem Warming and Elevated Atmospheric CO2 in July, 2017-2021

This dataset reports the carbon (C) and nitrogen (N) isotopic composition of Sphagnum moss tissue collected from the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experimental site within the Marcell Experimental Forest in northern Minnesota, USA. Tissues were collected inside the SPRUCE experimental study plot, where air and peat warming are combined in whole-ecosystem warming treatments, from 2019-2021. Additionally, rates of nitrogen fixation and methane oxidation measured for Sphagnum from 2017, 2019, and 2021. Sphagnum tissue % water content was measured at all timepoints. This dataset was used to conduct analyses within Petro et al (2023). Sphagnum C and N concentrations and 13C and 15N isotopic natural abundance were determined for three replicate Sphagnum tissue samples collected from inside the SPRUCE enclosures in July 2019-2021. Elemental and isotope analyses were conducted at the University of Georgia – Center for Applied Isotope Studies (CAIS; https://cais.uga.edu/). Plant elemental analysis was performed by the micro-Dumas method, while isotopic natural abundance was measured by isotope ratio mass spectrometry. 13C natural abundance is expressed as the per mille (‰) deviation from the Pee Dee Belemnite standard (PDB) 13C:12C ratio (δ13C), while 15N natural abundance is expressed as the ‰ deviation from the N2 atmospheric 15N:14N ratio (δ15N). Rates of nitrogen fixation and methane oxidation were measured using serum bottle incubations performed with Sphagnum collected inside the SPRUCE enclosures in July 2017, 2019, and 2021. Rates were calculated according to the amount of 15N-N2 or 13C-CH4 (methane) incorporated into the Sphagnum tissue or incubation headspace over the 48-hour intion period. In 2017, incubations were performed in growth chambers set to the temperature of the experimental plots during Sphagnum sampling. In 2019 and 2021, the incubations were performed directly inside the experimental plots. The 13C and 15N isotopic natural abundance data and rate measurements presented in this dataset provide insight into the impacts of whole-ecosystem warming and elevated atmospheric carbon dioxide (CO2) on N and C cycling within the Sphagnum phytobiome. This dataset contains two data files in comma-separate values (*.csv) format. Additional metadata are provided: two data dictionaries and a file-level metadata file in comma-separate values (.csv) format and a user guide in PDF (*.pdf) format. Additional datasets on NH4-N availability, porewater concentrations of CH4 and CO2, and Sphagnum groundcover within the SPRUCE experimental plots are available. These are outlined in the Related Datasets section in the user guide.

delta 13 carbon↗

DOE OSTI2023

Roots selectively decompose litter to mine nitrogen and build new soil carbon

Abstract Plant–microbe interactions in the rhizosphere shape carbon and nitrogen cycling in soil organic matter (SOM). However, there is conflicting evidence on whether these interactions lead to a net loss or increase of SOM. In part, this conflict is driven by uncertainty in how living roots and microbes alter SOM formation or loss in the field. To address these uncertainties, we traced the fate of isotopically labelled litter into SOM using root and fungal ingrowth cores incubated in a Miscanthus x giganteus field. Roots stimulated litter decomposition, but balanced this loss by transferring carbon into aggregate associated SOM. Further, roots selectively mobilized nitrogen from litter without additional carbon release. Overall, our findings suggest that roots mine litter nitrogen and protect soil carbon.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

The collaborative effects of intrinsic and extrinsic impurities in low RRR SRF cavities

The superconducting radio-frequency (SRF) community has shown that introducing certain impurities into high-purity niobium can improve quality factors and accelerating gradients. We question why some impurities improve RF performance while others hinder it. The purpose of this study is to characterize the impurity profile of niobium with a low residual resistance ratio (RRR) and correlate these impurities with the RF performance of low RRR cavities so that the mechanism of impurity-based improvements can be better understood and improved upon. The combination of RF testing and material analysis reveals a microscopic picture of why low RRR cavities experience low temperature-dependent BCS resistance behavior more prominently than their high RRR counterparts. We performed surface treatments, low temperature baking and nitrogen-doping, on low RRR cavities to evaluate how the intentional addition of oxygen and nitrogen to the RF layer further improves performance through changes in the mean free path and impurity profile. The results of this study have the potential to unlock a new understanding on SRF materials and enable the next generation of SRF surface treatments.

43 PARTICLE ACCELERATORS↗

DOE OSTI2023

The Collaborative Effects of Intrinsic and Extrinsic Impurities in Low RRR SRF Cavities

43 PARTICLE ACCELERATORS↗

DOE OSTI2023

The Collaborative Effects of Intrinsic and Extrinsic Impurities in Low RRR SRF Cavities

The SRF community has shown that introducing certain impurities into high-purity niobium can improve quality factors and accelerating gradients. We question why some impurities improve RF performance while others hinder it. The purpose of this study is to characterize the impurity profile of niobium coupons with a low residual resistance ratio (RRR) and correlate these impurities with the RF performance of low RRR cavities so that the mechanism of impurity-based improvements can be better understood and improved upon. The combination of RF testing and material analysis reveals a microscopic picture of why low RRR cavities experience low BCS resistance behavior more prominently than their high RRR counterparts. We performed surface treatments, low temperature baking and nitrogen-doping, on low RRR cavities to evaluate how the intentional addition of oxygen and nitrogen to the RF layer further improves performance through changes in the mean free path and impurity profile. Th e results of this study have the potential to unlock a new understanding on SRF materials and enable the next generation of high Q/high gradient surface treatments.

Howard, K.↗

DOE OSTI2023

The Collaborative Effects of Intrinsic and Extrinsic Impurities in Low RRR SRF Cavities

The SRF community has shown that introducing certain impurities into high-purity niobium can improve quality factors and accelerating gradients. We question why some impurities improve RF performance while others hinder it. The purpose of this study is to characterize the impurity profile of niobium coupons with a low residual resistance ratio (RRR) and correlate these impurities with the RF performance of low RRR cavities so that the mechanism of impurity-based improvements can be better understood and improved upon. The combination of RF testing and material analysis reveals a microscopic picture of why low RRR cavities experience low BCS resistance behavior more prominently than their high RRR counterparts. We performed surface treatments, low temperature baking and nitrogen-doping, on low RRR cavities to evaluate how the intentional addition of oxygen and nitrogen to the RF layer further improves performance through changes in the mean free path and impurity profile. The results of this study have the potential to unlock a new understanding on SRF materials and enable the next generation of high Q/high gradient surface treatments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Bulk density, grain size, carbon, and nitrogen content of floodplain fine sediment along the East River, Colorado collected from 2014 to 2017

The dataset is comprised of grain size, bulk density, carbon and nitrogen content of soils sampled on the floodplain of the East River 4 to 11 km downstream of Gothic, CO near Crested Butte. This dataset was collected to characterize the sedimentological properties and carbon inventory of the East River floodplain. The data help quantify the flux and storage of sediment and carbon between the East River and the alluvial floodplain bounding the river. The samples were collected between 2014 and 2017. The soil samples come from a total of 156 locations and were sampled in the upper 40 to 60 cm of the floodplain and in abandoned channel segments or oxbows. Not all samples were analyzed for all properties, but 26 samples were analyzed for bulk density, full particle size distribution, carbon, and nitrogen content. An additional 48 samples were analyzed for particle size fraction greater than and less than 2 mm and total organic content determined by loss on ignition. The dataset is comprised of a total of six separate data files based on the sample type and analysis and another file lists the sample identifications and locations of samples with a complete suite of analyses.

54 ENVIRONMENTAL SCIENCES↗