A Spectroscopically Observed Iron Nitrosyl Intermediate in the Reduction of Nitrate by a Surface-Con
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Ghosh, Moumita↗
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Selective Stepwise Reduction of Nitrate and Nitrite to Dinitrogen or Ammonia
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Moore, Jewelianna M. (ORCID:0000000299017915)↗
Adaptive responses of Trichlorobacter lovleyi to nitrite detoxification reveal overlooked contributions of Geobacterales to nitrate ammonification
Abstract Poorly understood microorganisms “short-circuit” the nitrogen cycle via the dissimilatory nitrate reduction to ammonium to retain the element in agricultural lands and stimulate crop productivity. The prevalence of Geobacterales closely related to Trichlorobacter lovleyi in nitrate ammonification hotspots motivated us to investigate adaptive responses contributing to ammonification rates in the laboratory type strain T. lovleyi SZ. Here, we describe the identification of tightly regulated pathways for efficient nitrate foraging and respiration with acetate, an important intermediate of organic matter degradation that Geobacterales efficiently assimilate and oxidize. Challenging the established dogma that high carbon/nitrate ratios stimulate the reduction of nitrate to ammonium, T. lovleyi doubled rapidly across a wide range of ratios provided nitrate concentrations were low enough to prevent the accumulation of the toxic nitrite intermediate. Yet, excess electrons during hydrogenotrophic growth alleviated nitrite toxicity and stimulated the reduction of nitrate to ammonium even under conditions of severe acetate limitation. These findings underscore the importance of nitrite toxicity in the ammonification of nitrate by Geobacterales and provide much needed mechanistic understanding of microbial adaptations contributing to soil nitrogen conservation. This information is critical to enhance the predictive value of genomic-based traits in environmental surveys and to guide strategies for sustainable management of nitrogen fertilization as well as mitigation of green-house emissions and agrochemical leaching from agricultural lands.
Environmental Sciences & Ecology↗
Physiology and enzymology involved in denitrification by Shewanella putrefaciens
Nitrate reduction to N2O was investigated in batch cultures of Shewanella putrefaciens MR-1, MR-4, and MR-7. All three strains reduced nitrate to nitrite to N2O, and this reduction was coupled to growth, whereas ammonium accumulation was very low (0 to 1 micromol liter-1). All S. putrefaciens isolates were also capable of reducing nitrate aerobically; under anaerobic conditions, nitrite levels were three- to sixfold higher than those found under oxic conditions. Nitrate reductase activities (31 to 60 micromol of nitrite min-1 mg of protein-1) detected in intact cells of S. putrefaciens were equal to or higher than those seen in Escherichia coli LE 392. Km values for nitrate reduction ranged from 12 mM for MR-1 to 1.3 mM for MR-4 with benzyl viologen as an artifical electron donor. Nitrate and nitrite reductase activities in cell-free preparations were demonstrated in native gels by using reduced benzyl viologen. Detergent treatment of crude and membrane extracts suggested that the nitrate reductases of MR-1 and MR-4 are membrane bound. When the nitrate reductase in MR-1 was partially purified, three subunits (90, 70, and 55 kDa) were detected in denaturing gels. The nitrite reductase of MR-1 is also membrane bound and appeared as a 60-kDa band in sodium dodecyl sulfate-polyacrylamide gels after partial purification.
Nitrite Reductases/metabolism↗
Elucidating electrochemical nitrate and nitrite reduction over atomically-dispersed transition metal sites
Abstract Electrocatalytic reduction of waste nitrates (NO 3 − ) enables the synthesis of ammonia (NH 3 ) in a carbon neutral and decentralized manner. Atomically dispersed metal-nitrogen-carbon (M-N-C) catalysts demonstrate a high catalytic activity and uniquely favor mono-nitrogen products. However, the reaction fundamentals remain largely underexplored. Herein, we report a set of 14; 3 d -, 4 d -, 5 d - and f -block M-N-C catalysts. The selectivity and activity of NO 3 − reduction to NH 3 in neutral media, with a specific focus on deciphering the role of the NO 2 − intermediate in the reaction cascade, reveals strong correlations (R=0.9) between the NO 2 − reduction activity and NO 3 − reduction selectivity for NH 3 . Moreover, theoretical computations reveal the associative/dissociative adsorption pathways for NO 2 − evolution, over the normal M-N 4 sites and their oxo-form (O-M-N 4 ) for oxyphilic metals. This work provides a platform for designing multi-element NO 3 RR cascades with single-atom sites or their hybridization with extended catalytic surfaces.
36 MATERIALS SCIENCE↗
Emerging Electrochemical Techniques for Probing Site Behavior in Single-Atom Electrocatalysts
Single-atom catalysts (SACs) have aroused tremendous interest over the past decade, particularly in the community of energy and environment-related electrocatalysis. A rapidly growing number of recent publications have recognized it as a promising candidate with maximum atomic utilization, distinct activity, and selectivity in comparison to bulk catalysts and nanocatalysts. However, the complexity of localized coordination environments and the dispersion of isolated sites lead to significant difficulties when it comes to gaining insight into the intrinsic behavior of electrocatalytic reactions. Furthermore, the low metal loadings of most SACs make conventional ensemble measurements less likely to be accurate on the subnanoscale. Thus, it remains challenging to probe the activity and properties of individual atomic sites by available commercial instruments and analytical methods. In spite of this, continuing efforts have lately focused on the development of advanced measurement methodologies, which are very useful to the fundamental understanding of SACs. There have recently been a number of in situ/operando techniques applied to SACs, such as electron microscopy, spectroscopy, and other analysis methods, which support relevant functions to identify the active sites and reaction intermediates and to investigate the dynamic behavior of localized structures of the catalytic sites. This Account aims to present recent electrochemical probing techniques which can be used to identify single-atomic catalytic sites within solid supports. First, we describe the basic principles of molecular probe methods for the study and analysis of electrocatalytic site behavior. In particular, the in situ probing technique enabled by surface interrogation scanning electrochemical microscopy (SISECM) can measure the active site density and kinetic rate with high resolution. An alternative electrochemical probing technique is further demonstrated on the basis of single-entity electrochemistry, which allows the unique electrochemical imaging of the size and catalytic rate of single atoms, molecules, and clusters. Next, the merits and limitations of different electrochemical techniques are then discussed, along with perspectives for future prospects. Apart from this, we further showcase the powerful capability of emerging electrochemical probing techniques for determining significant effects and properties of SACs for various electrocatalytic reactions, including oxygen reduction and evolution, hydrogen evolution, and nitrate reduction. Overall, electrochemical techniques with atomic resolution have greatly increased opportunities for observing, measuring, and understanding the surface and interface chemistry during energy conversion. In the future, it is anticipated that the development of electrochemical probing techniques will be advanced with innovative perspectives on the behavior and features of SACs. We hope that this Account can contribute in several ways to promoting the fundamental knowledge and technical progress of emerging electrochemical measurements for studying SACs.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Nitrate transport is independent of NADH and NAD(P)H nitrate reductases in barley seedlings
Barley (Hordeum vulgare L.) has NADH-specific and NAD(P)H-bispecific nitrate reductase isozymes. Four isogenic lines with different nitrate reductase isozyme combinations were used to determine the role of NADH and NAD(P)H nitrate reductases on nitrate transport and assimilation in barley seedlings. Both nitrate reductase isozymes were induced by nitrate and were required for maximum nitrate assimilation in barley seedlings. Genotypes lacking the NADH isozyme (Az12) or the NAD(P)H isozyme (Az70) assimilated 65 or 85%, respectively, as much nitrate as the wild type. Nitrate assimilation by genotype (Az12;Az70) which is deficient in both nitrate reductases, was only 13% of the wild type indicating that the NADH and NAD(P)H nitrate reductase isozymes are responsible for most of the nitrate reduction in barley seedlings. For all genotypes, nitrate assimilation rates in the dark were about 55% of the rates in light. Hypotheses that nitrate reductase has direct or indirect roles in nitrate uptake were not supported by this study. Induction of nitrate transporters and the kinetics of net nitrate uptake were the same for all four genotypes indicating that neither nitrate reductase isozyme has a direct role in nitrate uptake in barley seedlings.
NASA Discipline Number 61-10↗
Critical Roles of Chalcogenide Anion on Strengthening Stability of Ni 2 Mo 6 Te 8 for Almost Exclusive Electrocatalysts Nitrate to Ammonia Conversion
Electrochemical hydrogenation of nitrate to ammonia using renewable electricity is a promising route for sustainability but lacks catalysts that can deliver balanced selectivity, activity, and durability. For this work, a new family of noble metal-free and high-performing Chevrel phase Ni 2 Mo 6 T 8 (T = S, Se, and Te) catalysts that have similar structural and textural properties and differ presumably only in chalcogenide anion is systematically studied. The side-by-side comparisons allow the uncovering of the critical roles of chalcogenide anions in impacting kinetic activities and long-term durability. The incorporation of anions with larger size and smaller electronegativity from sulfide to selenide and telluride invokes stronger inhibition of the otherwise competing hydrogen evolution reaction (HER) and steers the hydrogenation toward the selective formation of ammonia, thus improving both Faradic selectivity and the turnover frequency to high levels of 99.4% and 21.5 s –1 , respectively, on the Ni 2 Mo 6 Te 8 catalyst. More significantly, the bulkier anion in the Ni 2 Mo 6 T 8 catalyst kinetically inhibited the intercalation of electrolyte cations, a major degradation mechanism in the catalyst family examined here and delivered several times improved durability. Therefore, this study introduces novel active motifs for selective nitrate reduction and provides insights into the catalyst degradation mechanism and practical ways to improve durability.
36 MATERIALS SCIENCE↗
Underpotential Deposition of 3D Transition Metals: Versatile Electrosynthesis of Single-Atom Catalysts on Oxidized Carbon Supports
Use of single-atom catalysts (SACs) has become a popular strategy for tuning activity and selectivity toward specific pathways. However, conventional SAC synthesis methods require high temperatures and pressures, complicated procedures, and expensive equipment. Recently, underpotential deposition (UPD) has been investigated as a promising alternative, yielding high-loading SAC electrodes under ambient conditions and within minutes. Yet only few studies have employed UPD to synthesize SACs, and all have been limited to UPD of Cu. In this work, a flexible UPD approach for synthesis of mono- and bi-metallic Cu, Fe, Co, and Ni SACs directly on oxidized, commercially available carbon electrodes is reported. The UPD mechanism is investigated using in situ X-ray absorption spectroscopy and, finally, the catalytic performance of a UPD-synthesized Co SAC is assessed for electrochemical nitrate reduction to ammonia. In conclusion, the findings expand upon the usefulness and versatility of UPD for SAC synthesis, with hopes of enabling future research toward realization of fast, reliable, and fully electrified SAC synthesis processes.
36 MATERIALS SCIENCE↗
PdCu Electrocatalysts for Selective Nitrate and Nitrite Reduction to Nitrogen
Electrocatalytic conversion of nitrate in waste can enable efficient waste remediation (NO 3 - to N 2 ) or waste valorization (NO 3 - to NH 4 + ) depending on the selectivity of the catalyst. Palladium and copper electrocatalysts typically exhibit ideal nitrate and nitrite binding properties, allowing for effective destruction of nitrate. However, rational steering of selectivity through material design remains a critical challenge for PdCu electrocatalyst. Here, we use the electrochemical underpotential deposition method to synthesize palladium nanocube electrocataysts with controlled copper surface coverage (e.g., partial and full copper coatings). We then examine the potential for NO 3 - destruction (conversion) and NO 2 - reduction reaction. We identify that partial copper-coated Pd nanocubes not only effectively facilitate the reduction of 95% of NO 3 - but also increase the reduction of NO 2 - to N 2 with 89% selectivity over 20 consecutive cycles (80 h). We also show that under these conditions, the Pd(100) surface facet is exposed. Complete copper-covered Pd nanocubes effectively facilitate the reduction of ~99% of NO 3 - . Complete coverage of copper; however, prevented exposure of Pd(100) surface facet, promoting the selective reduction of NO 2 - to NH 4 + with a 70% selectivity over 20 consecutive cycles (80 h). Density functional theory (DFT) calculations show that NO 3 - and NO 2 - adsorb more strongly on the Cu(100) surface compared to the Pd(100) surface, while the NO* intermediate generated from NO 3 - or NO 2 - reduction adsorbs more strongly on the Pd surface. Furthermore, barrier calculations show that NO* can readily migrate from the Cu domain to the Pd domain and that the N–N coupling barrier on Pd is significantly diminished at high NO* coverage. Together, these results suggest that the high N 2 selectivity observed on the PdCu electrocatalyst is caused by the spillover of NO* from the Cu domains to the Pd domains.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Increased replication of dissimilatory nitrate-reducing bacteria leads to decreased anammox bioreactor performance
Background: Anaerobic ammonium oxidation (anammox) is a biological process employed to remove reactive nitrogen from wastewater. While a substantial body of literature describes the performance of anammox bioreactors under various operational conditions and perturbations, few studies have resolved the metabolic roles of their core microbial community members. Results: Here, we used metagenomics to study the microbial community of a laboratory-scale anammox bioreactor from inoculation, through a performance destabilization event, to robust steady-state performance. Metabolic analyses revealed that nutrient acquisition from the environment is selected for in the anammox community. Dissimilatory nitrate reduction to ammonium (DNRA) was the primary nitrogen removal pathway that competed with anammox. Increased replication of bacteria capable of DNRA led to the out-competition of anammox bacteria, and the loss of the bioreactor's nitrogen removal capacity. These bacteria were highly associated with the anammox bacterium and considered part of the core microbial community. Conclusions: Our findings highlight the importance of metabolic interdependencies related to nitrogen- and carbon-cycling within anammox bioreactors and the potentially detrimental effects of bacteria that are otherwise considered core microbial community members.
59 BASIC BIOLOGICAL SCIENCES↗
Robust Oxygen‐Vacancy‐Engineered Co(OH) 2 /Cu Heterostructures Boost Nitrate Electroreduction to Ammonia beyond 2 A cm −2
Electrocatalytic nitrate reduction reaction (NO 3 RR) presents a sustainable paradigm for green NH 3 synthesis and NO 3 − wastewater valorization. However, overcoming sluggish NO 3 RR kinetics under industrial-current operation persists as a critical challenge. Herein, robust oxygen vacancy-enriched heterostructures (O v -Co(OH) 2 /Cu) are engineered through in situ electrochemical reconstruction. By coupling Cu-mediated NO 3 − -to-NO 2 − conversion with O v -Co(OH) 2 -accelerated NO 2 − -to-NH 3 transformation, this heterostructured system delivers an unprecedented NH 3 yield rate of 167.8 mg h −1 cm −2 and 97.7% Faradaic efficiency at >2 A cm −2 , while maintaining exceptional current tolerance over 25 h. Operando spectroscopic characterizations and theoretical calculations reveal that the introduction of O v in Co(OH) 2 synergistically accelerates water dissociation to ensure continuous hydrogen supply and optimizes *NOOH adsorption, reducing the energy barrier for the rate-limiting step (*NO 2 to *NOOH). To demonstrate practical viability, a membrane-electrode-assembly electrolyzer integrating NO 3 RR with glycerol oxidation reaction achieves highly effective co-production of NH 3 and formate alongside wastewater treatment. In conclusion, this work offers new insights into the rational design of electrocatalysts through in situ reconstruction-induced vacancy engineering for scalable and practical NO 3 RR applications.
ammonia synthesis↗
Multi-omics reveals nitrogen dynamics associated with soil microbial blooms during snowmelt
Snowmelt triggers a soil microbial bloom and crash that affects nitrogen (N) export in high-elevation watersheds. The mechanisms underlying these microbial dynamics are uncertain, making soil nitrogen processes difficult to predict as snowpack declines globally. Here, integration of genome-resolved metagenomics, metatranscriptomics and metabolomics in a high-elevation watershed revealed ecologically distinct soil microorganisms linked across the snowmelt time-period by their unique nitrogen cycling capacities. The molecular properties and transformations of dissolved organic N suggested that degradation or recycling of microbial biomass provided N for biosynthesis during the microbial bloom. Winter-adapted Bradyrhizobia spp. oxidized amino acids anaerobically and had the highest gene expression for denitrification during the microbial bloom. A pulse of nitrate was driven by spring-adapted Nitrososphaerales after snowmelt, but dissimilatory nitrate reduction to ammonia (DNRA) gene expression indicated significant nitrate retention potential. These findings inform our understanding of nitrogen cycling in environments sensitive to snowpack decline due to global change.
Sorensen, Patrick O↗
The global anaerobic metabolism regulator fnr is necessary for the degradation of food dyes and drugs by Escherichia coli
ABSTRACT The microbiome is an underappreciated contributor to intestinal drug metabolism with broad implications for drug efficacy and toxicity. While considerable progress has been made toward identifying the gut bacterial genes and enzymes involved, the role of environmental factors in shaping their activity remains poorly understood. Here, we focus on the gut bacterial reduction of azo bonds (R-N = N-R’), found in diverse chemicals in both food and drugs. Surprisingly, the canonical azoR gene in Escherichia coli was dispensable for azo bond reduction. Instead, azoreductase activity was controlled by the fumarate and nitrate reduction ( fnr ) regulator, consistent with a requirement for the anoxic conditions found within the gastrointestinal tract. Paired transcriptomic and proteomic analysis of the fnr regulon revealed that in addition to altering the expression of multiple reductases, FNR is necessary for the metabolism of L-Cysteine to hydrogen sulfide, enabling the degradation of azo bonds. Furthermore, we found that FNR indirectly regulates this process through the small noncoding regulatory RNA fnrS . Taken together, these results show how gut bacteria sense and respond to their intestinal environment to enable the metabolism of chemical groups found in both dietary and pharmaceutical compounds. IMPORTANCE This work has broad relevance due to the ubiquity of dyes containing azo bonds in food and drugs. We report that azo dyes can be degraded by human gut bacteria through both enzymatic and nonenzymatic mechanisms, even from a single gut bacterial species. Furthermore, we revealed that environmental factors, oxygen, and L-Cysteine control the ability of E. coli to degrade azo dyes due to their impacts on bacterial transcription and metabolism. These results open up new opportunities to manipulate the azoreductase activity of the gut microbiome through the manipulation of host diet, suggest that azoreductase potential may be altered in patients suffering from gastrointestinal disease, and highlight the importance of studying bacterial enzymes for drug metabolism in their natural cellular and ecological context.
59 BASIC BIOLOGICAL SCIENCES↗
Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development
Interactions between plant roots and rhizosphere bacteria modulate nitrogen (N)-cycling processes and create habitats rich in low molecular weight compounds (exudates) and complex organic molecules (decaying root litter) compared to those of bulk soil. Microbial N-cycling is regulated by edaphic conditions and genes from many interconnected metabolic pathways, but most studies of soil N-cycling gene expression have focused on single pathways. Currently, we lack a comprehensive understanding of the interplay between soil N-cycling gene regulation, spatial habitat, and time. We present results from a replicated time series of soil metatranscriptomes; we followed gene expression of multiple N transformations in four soil habitats (rhizosphere, detritusphere, rhizo-detritusphere, and bulk soil) during active root growth for the annual grass, Avena fatua. The presence of root litter and living roots significantly altered the trajectories of N-cycling gene expression. Upregulation of assimilatory nitrate reduction in the rhizosphere suggests that rhizosphere bacteria were actively competing with roots for nitrate. Simultaneously, ammonium assimilatory pathways were upregulated in both rhizosphere and detritusphere soil, which could have limited N availability to plants. The detritusphere supported dissimilatory processes DNRA and denitrification. Expression of nitrification genes was dominated by three phylotypes of Thaumarch aeota and was upregulated in bulk soil. Unidirectional ammonium assimilation and its regulatory genes (GS/GOGAT) were upregulated near relatively young roots and highly decayed root litter, suggesting N may have been limiting in these habitats (GS/GOGAT is typically activated under N limitation). In conclusion, our comprehensive analysis indicates that differences in carbon and inorganic N availability control contemporaneous transcription of N-cycling pathways in soil habitats.
54 ENVIRONMENTAL SCIENCES↗
Intensified atomic utilization efficiency of single-atom catalysts for nitrate conversion via electrified nanoporous membrane
Conventional electrochemical reactors for nitrate reduction typically suffer from limited reaction efficiency when applied for real-world water treatment due to poor utilization of electrocatalytic active sites. Here, we applied nanoporous electrofiltration to intensify atomic utilization by incorporating single-atom catalysts into an electrified membrane for reducing low-concentration nitrate to ammonia under realistic water conditions. We enhance the exposure of single atoms in nanopores by coating the catalysts on a carbon nanotube–interwoven membrane framework. Electrofiltration intensifies the transport and adsorption of nitrate in confined nanopores with highly exposed single-atom active sites to enhance reduction. The membrane enables a superior ammonia turnover frequency of 15.1 grams of nitrogen per gram of metal per hour, up to four orders of magnitude higher than that reported in the literature, under both high removal efficiency and Faradaic efficiency of over 86% when treating influents with a low nitrate concentration of 100 milligrams of nitrogen per liter in a residence time on the order of seconds.
Science & Technology - Other Topics↗
Ammonia Electrosynthesis from Nitrate Using a Ruthenium–Copper Cocatalyst System: A Full Concentration Range Study
Electrochemical synthesis of ammonia via the nitrate reduction reaction (NO3RR) has been intensively researched as an alternative to the traditional Haber–Bosch process. Most research focuses on the low concentration range representative of the nitrate level in wastewater, leaving the high concentration range, which exists in nuclear and fertilizer wastes, unexplored. The use of a concentrated electrolyte (≥1 M) for higher rate production is hampered by poor hydrogen transfer kinetics. Herein, we demonstrate that a cocatalytic system of Ru/Cu 2 O catalyst enables NO3RR at 10.0 A in 1 M nitrate electrolyte in a 16 cm 2 flow electrolyzer, with 100% faradaic efficiency toward ammonia. Detailed mechanistic studies by deuterium labeling and operando Fourier transform infrared (FTIR) spectroscopy allow us to probe the hydrogen transfer rate and intermediate species on Ru/Cu 2 O. Ab initio molecular dynamics (AIMD) simulations reveal that adsorbed hydroxide on Ru nanoparticles increases the density of the hydrogen-bonded water network near the Cu 2 O surface, which promotes the hydrogen transfer rate. Finally, our work highlights the importance of engineering synergistic interactions in cocatalysts for addressing the kinetic bottleneck in electrosynthesis.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The intermediate in a nitrate-responsive ω-amidase pathway in plants may signal ammonium assimilation status
Abstract A metabolite of ammonium assimilation was previously theorized to be involved in the coordination of the overall nitrate response in plants. Here we show that 2-hydroxy-5-oxoproline, made by transamination of glutamine, the first product of ammonium assimilation, may be involved in signaling a plant’s ammonium assimilation status. In leaves, 2-hydroxy-5-oxoproline met four foundational requirements to be such a signal. First, when it was applied to foliage, enzyme activities of nitrate reduction and ammonium assimilation increased; the activities of key tricarboxylic acid cycle-associated enzymes that help to supply carbon skeletons for amino acid synthesis also increased. Second, its leaf pools increased as nitrate availability increased. Third, the pool size of its precursor, Gln, reflected ammonium assimilation rather than photorespiration. Fourth, it was widely conserved among monocots, dicots, legumes, and nonlegumes and in plants with C3 or C4 metabolism. Made directly from the first product of ammonium assimilation, 2-hydroxy-5-oxoproline acted as a nitrate uptake stimulant. When 2-hydroxy-5-oxoproline was provided to roots, the plant’s nitrate uptake rate approximately doubled. Plants exogenously provided with 2-hydroxy-5-oxoproline to either roots or leaves accumulated greater biomass. A model was constructed that included the proposed roles of 2-hydroxy-5-oxoproline as a signal molecule of ammonium assimilation status in leaves, as a stimulator of nitrate uptake by roots and nitrate downloading from the xylem. In summary, a glutamine metabolite made in the ω-amidase pathway stimulated nitrate uptake by roots and was likely to be a signal of ammonium assimilation status in leaves. A chemical synthesis method for 2-hydroxy-5-oxoproline was also developed.
59 BASIC BIOLOGICAL SCIENCES↗