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Xu Z, Gao X, Li G, Nghiem LD, Luo W, Zhang F. Microbial Sources and Sinks of Nitrous Oxide during Organic Waste Composting. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:7367-7379. [PMID: 38644786 DOI: 10.1021/acs.est.3c10341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Composting is widely used for organic waste management and is also a major source of nitrous oxide (N2O) emission. New insight into microbial sources and sinks is essential for process regulation to reduce N2O emission from composting. This study used genome-resolved metagenomics to decipher the genomic structures and physiological behaviors of individual bacteria for N2O sources and sinks during composting. Results showed that several nosZ-lacking denitrifiers in feedstocks drove N2O emission at the beginning of the composting. Such emission became negligible at the thermophilic stage, as high temperatures inhibited all denitrifiers for N2O production except for those containing nirK. The nosZ-lacking denitrifiers were notably enriched to increase N2O production at the cooling stage. Nevertheless, organic biodegradation limited energy availability for chemotaxis and flagellar assembly to restrain nirKS-containing denitrifiers for nitrate reduction toward N2O sources but insignificantly interrupt norBC- and nosZ-containing bacteria (particularly nosZ-containing nondenitrifiers) for N2O sinks by capturing N2O and nitric oxide (NO) for energy production, thereby reducing N2O emission at the mature stage. Furthermore, nosZII-type bacteria included all nosZ-containing nondenitrifiers and dominated N2O sinks. Thus, targeted strategies can be developed to restrict the physiological behaviors of nirKS-containing denitrifiers and expand the taxonomic distribution of nosZ for effective N2O mitigation in composting.
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Affiliation(s)
- Zhicheng Xu
- Key Laboratory of Plant-Soil Interactions of Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xingzu Gao
- Key Laboratory of Plant-Soil Interactions of Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Guoxue Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Long D Nghiem
- Centre for Technology in Water and Wastewater, University of Technology Sydney, Ultimo 2007, NSW, Australia
| | - Wenhai Luo
- Key Laboratory of Plant-Soil Interactions of Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Fusuo Zhang
- Key Laboratory of Plant-Soil Interactions of Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
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2
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Zhong L, Li X, Sun Y, Xiao H, Tang Y, Wang R, Su X. Effects of microplastics on N 2O production and reduction potential in crop soils of northern China. CHEMOSPHERE 2024; 351:141256. [PMID: 38246503 DOI: 10.1016/j.chemosphere.2024.141256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/27/2023] [Accepted: 01/17/2024] [Indexed: 01/23/2024]
Abstract
Microplastics (MPs) pollution are found to be increasing in vegetable soils and potentially affecting N2O production and their associated pathways; however, its specific effects remain unclear. Here, we selected two common MPs, PE and PP at four different concentration levels of 0, 0.5, 1.5 and 3%, and conducted several incubation experiments aiming to explore soil bacterial and fungal N2O production. Results showed that the bacteria were the main contributors for the production of N2O, regardless of the absence or presence of MPs; and its contribution was decreased with increasing concentrations of PE and PP. The nosZ clade I and II genes were positively correlated with N2O reduction rates, indicating a combined regulation on soil N2O reduction. PE significantly inhibited the bacterial nitrification and denitrification, but did not affect the total N2O production rates; while PP significantly reduced both the bacterial and fungal N2O production rates. The resistance of fungal N2O production to MPs pollution was stronger than that of the bacterial N2O production. It highlights that the MPs pollution could reduce the potential of N2O production and reduction, and thus disturb soil nitrogen cycling system; while the inhibition on N2O production via bacteria and fungi varies with different types of MPs. This study is conducive to an improved and more comprehensive understanding of the ecological impacts of MPs within the agroecosystem.
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Affiliation(s)
- Lei Zhong
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, China.
| | - Xinhao Li
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Yuru Sun
- Beijing Construction Engineering Group Environmental Remediation Co., Ltd, National Engineering Laboratory for Site Remediation Technologies, Beijing, 100015, China
| | - Hui Xiao
- Institute of Agricultural Resources and Environment, Tianjin Academy of Agricultural Sciences, Tianjin, 300384, China
| | - Yafang Tang
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan, China
| | - Ruying Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Xiaoxuan Su
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing, 400715, China.
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3
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Mankad NP. Triazenide-supported [Cu 4S] structural mimics of Cu Z that mediate N 2O disproportionation rather than reduction. Chem Sci 2024; 15:1820-1828. [PMID: 38303935 PMCID: PMC10829023 DOI: 10.1039/d3sc05451a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/22/2023] [Indexed: 02/03/2024] Open
Abstract
As part of the nitrogen cycle, environmental nitrous oxide (N2O) undergoes the N2O reduction reaction (N2ORR) catalyzed by nitrous oxide reductase, a metalloenzyme whose catalytic active site is a tetranuclear copper-sulfide cluster (CuZ). On the other hand, heterogeneous Cu catalysts on oxide supports are known to mediate decomposition of N2O (deN2O) by disproportionation. In this study, a CuZ model system supported by triazenide ligands is characterized by X-ray crystallography, NMR and EPR spectroscopies, and electronic structure calculations. Although the triazenide-ligated Cu4(μ4-S) clusters are closely related to previous formamidinate derivatives, which differ only in replacement of a remote N atom for a CH group, divergent reactivity with N2O is observed. Whereas the formamidinate-ligated clusters were previously shown to mediate single-turnover N2ORR, the triazenide-ligated clusters are found to mediate deN2O, behavior that was previously unknown to natural or synthetic copper-sulfide clusters. The reaction pathway for deN2O by this model system, including previously unidentified transition state models for N2O activation in N-O cleavage and O-O coupling steps, are included. The divergent reactivity of these two related but subtly different systems point to key factors influencing behavior of Cu-based catalysts for N2ORR (i.e., CuZ) and deN2O (e.g., CuO/CeO2).
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Affiliation(s)
- Neal P Mankad
- Department of Chemistry, University of Illinois Chicago Chicago IL 60607 USA
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4
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Zhang F, Gu Z, Wang H, Wang R, Qing J, Xu X, Baoyin T, Zhong L, Rui Y, Li FY. Short term grazing increased growing-season N 2O production and decreased its reduction potential by reducing the abundance and expression of nosZ clade II gene in a semi-arid steppe. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168361. [PMID: 37944603 DOI: 10.1016/j.scitotenv.2023.168361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 10/23/2023] [Accepted: 11/04/2023] [Indexed: 11/12/2023]
Abstract
Understanding nitrous oxide (N2O) production as well as reduction in response to grazing and mowing is essential for designing better management strategies to improve sustainability of grassland ecosystems. We evaluated how four years of grazing or mowing altered N2O production and reduction potential, gene abundance, and expression of microbial functional groups pertinent to N2O production in situ on a typical grassland in Inner Mongolia. In our study, we found that grazing dramatically raised soil ammonium (NH4+-N) and nitrate (NO3--N) concentrations, AOB gene abundance and potential of N2O production through nitrification (NN2O) and denitrification (DN2O) in summer, but lessened the expression of nosZ clade II gene in all seasons. Mowing had minor effect on soil inorganic nitrogen (N) concentrations. Mowing diminished the quantity of denitrification genes (narG and nosZ), expression of nosZ and nosZ clade II genes, and DN2O concentration. The expression and abundance of nosZ clade II gene were related to DN2. These results suggested that short-term grazing could enhance N2O production potential in peak growing season, while the reduction in abundance and expression of nosZ calde II gene might be an important contributor to the enhanced N2O production of semi-arid typical steppe grasslands.
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Affiliation(s)
- Feifan Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Zhibin Gu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Hongyue Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Ruying Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Jinwu Qing
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Xingliang Xu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources, Chinese Academy of Sciences, Beijing 100101, China
| | - Taogetao Baoyin
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology & Environment, Inner Mongolia University, Hohhot 010021, China
| | - Lei Zhong
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China.
| | - Yichao Rui
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Frank Yonghong Li
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology & Environment, Inner Mongolia University, Hohhot 010021, China
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5
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Fujisawa K, Kataoka T, Terashima K, Kurihara H, de Santis Gonçalves F, Lehnert N. Coordinatively Unsaturated Nickel Nitroxyl Complex: Structure, Physicochemical Properties, and Reactivity toward Dioxygen. Molecules 2023; 28:6206. [PMID: 37687034 PMCID: PMC10489029 DOI: 10.3390/molecules28176206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
For its important roles in biology, nitrogen monoxide (·NO) has become one of the most studied and fascinating molecules in chemistry. ·NO itself acts as a "noninnocent" or "redox active" ligand to transition metal ions to give metal-NO (M-NO) complexes. Because of this uncertainty due to redox chemistry, the real description of the electronic structure of the M-NO unit requires extensive spectroscopic and theoretical studies. We previously reported the Ni-NO complex with a hindered N3 type ligand [Ni(NO)(L3)] (L3- denotes hydrotris(3-tertiary butyl-5-isopropyl-1-pyrazolyl)borate anion), which contains a high-spin (hs) nickel(II) center and a coordinated 3NO-. This complex is very stable toward dioxygen due to steric protection of the nickel(II) center. Here, we report the dioxygen reactivity of a new Ni-NO complex, [Ni(NO)(I)(L1″)], with a less hindered N2 type bis(pyrazolyl)methane ligand, which creates a coordinatively unsaturated ligand environment about the nickel center. Here, L1″ denotes bis(3,5-diisopropyl-1-pyrazolyl)methane. This complex is also described as a hs-nickel(II) center with a bound 3NO-, based on spectroscopic and theoretical studies. Unexpectedly, the reaction of [Ni(NO)(I)(L1″)] with O2 yielded [Ni(κ2-O2N)(L1″)2](I3), with the oxidation of both 3NO- and the I- ion to yield NO2- and I3-. Both complexes were characterized by X-ray crystallography, IR, and UV-Vis spectroscopy and theoretical calculations.
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Affiliation(s)
- Kiyoshi Fujisawa
- Department of Chemistry, Ibaraki University, Mito 310-8512, Ibaraki, Japan
| | - Taisei Kataoka
- Department of Chemistry, Ibaraki University, Mito 310-8512, Ibaraki, Japan
| | - Kohei Terashima
- Department of Chemistry, Ibaraki University, Mito 310-8512, Ibaraki, Japan
| | - Haruka Kurihara
- Department of Chemistry, Ibaraki University, Mito 310-8512, Ibaraki, Japan
| | - Felipe de Santis Gonçalves
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA;
| | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA;
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6
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Liu Y, Chatterjee S, Cutsail GE, Peredkov S, Gupta SK, Dechert S, DeBeer S, Meyer F. Cu 4S Cluster in "0-Hole" and "1-Hole" States: Geometric and Electronic Structure Variations for the Active Cu Z* Site of N 2O Reductase. J Am Chem Soc 2023; 145:18477-18486. [PMID: 37565682 PMCID: PMC10450684 DOI: 10.1021/jacs.3c04893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Indexed: 08/12/2023]
Abstract
The active site of nitrous oxide reductase (N2OR), a key enzyme in denitrification, features a unique μ4-sulfido-bridged tetranuclear Cu cluster (the so-called CuZ or CuZ* site). Details of the catalytic mechanism have remained under debate and, to date, synthetic model complexes of the CuZ*/CuZ sites are extremely rare due to the difficulty in building the unique {Cu4(μ4-S)} core structure. Herein, we report the synthesis and characterization of [Cu4(μ4-S)]n+ (n = 2, 2; n = 3, 3) clusters, supported by a macrocyclic {py2NHC4} ligand (py = pyridine, NHC = N-heterocyclic carbene), in both their 0-hole (2) and 1-hole (3) states, thus mimicking the two active states of the CuZ* site during enzymatic N2O reduction. Structural and electronic properties of these {Cu4(μ4-S)} clusters are elucidated by employing multiple methods, including X-ray diffraction (XRD), nuclear magnetic resonance (NMR), UV/vis, electron paramagnetic resonance (EPR), Cu/S K-edge X-ray emission spectroscopy (XES), and Cu K-edge X-ray absorption spectroscopy (XAS) in combination with time-dependent density functional theory (TD-DFT) calculations. A significant geometry change of the {Cu4(μ4-S)} core occurs upon oxidation from 2 (τ4(S) = 0.46, seesaw) to 3 (τ4(S) = 0.03, square planar), which has not been observed so far for the biological CuZ(*) site and is unprecedented for known model complexes. The single electron of the 1-hole species 3 is predominantly delocalized over two opposite Cu ions via the central S atom, mediated by a π/π superexchange pathway. Cu K-edge XAS and Cu/S K-edge XES corroborate a mixed Cu/S-based oxidation event in which the lowest unoccupied molecular orbital (LUMO) has a significant S-character. Furthermore, preliminary reactivity studies evidence a nucleophilic character of the central μ4-S in the fully reduced 0-hole state.
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Affiliation(s)
- Yang Liu
- Institute
of Inorganic Chemistry, University of Göttingen, Tammannstraße 4, 37077 Göttingen, Germany
| | - Sayanti Chatterjee
- Max
Planck Institute for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
| | - George E. Cutsail
- Max
Planck Institute for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
- Institute
of Inorganic Chemistry, University of Duisburg-Essen, Universitätsstraße 7, 45117 Essen, Germany
| | - Sergey Peredkov
- Max
Planck Institute for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
| | - Sandeep K. Gupta
- Institute
of Inorganic Chemistry, University of Göttingen, Tammannstraße 4, 37077 Göttingen, Germany
| | - Sebastian Dechert
- Institute
of Inorganic Chemistry, University of Göttingen, Tammannstraße 4, 37077 Göttingen, Germany
| | - Serena DeBeer
- Max
Planck Institute for Chemical Energy Conversion, Stiftstrasse 34−36, 45470 Mülheim an der Ruhr, Germany
| | - Franc Meyer
- Institute
of Inorganic Chemistry, University of Göttingen, Tammannstraße 4, 37077 Göttingen, Germany
- International
Center for Advanced Studies of Energy Conversion (ICASEC), University of Göttingen, Tammannstraße 6, 37077 Göttingen, Germany
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7
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Wang Y, Peng Y, Lv C, Xu X, Meng H, Zhou Y, Wang G, Lu Y. Quantitative discrimination of algae multi-impacts on N 2O emissions in eutrophic lakes: Implications for N 2O budgets and mitigation. WATER RESEARCH 2023; 235:119857. [PMID: 36924553 DOI: 10.1016/j.watres.2023.119857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
It is generally accepted that eutrophic lakes significantly contribute to nitrous oxide (N2O) emissions. However, how these emissions are affected by the formation, disappearance, and mechanisms of algal blooms in these lakes has not been systematically investigated. This study examined and determined the relative contribution of spatiotemporal N2O production pathways in hypereutrophic Lake Taihu. Synchronously, the multi-impacts of algae on N2O production and release potential were measured in the field and in microcosms using isotope ratios of oxygen (δ18O) and bulk nitrogen (δ15N) to N2O and to intramolecular 15N site preference (SP). Results showed that N2O production in Lake Taihu was derived from microbial effects (nitrification and incomplete denitrification) and water air exchanges. N2O production was also affected by the N2O reduction process. The mean dissolved N2O concentrations in the water column during the pre-outbreak, outbreak, and decay stages of algae accumulation were almost the same (0.05 μmol·L-1), which was 2-10 times higher than in lake areas algae was not accumulating. However, except for the central lake area, all surveyed areas (with and without accumulated algae) displayed strong release potential and acted as the emission source because of dissolved N2O supersaturation in the water column. The mean N2O release fluxes during the pre-outbreak, outbreak, and decay stages of algae accumulation areas were 17.95, 26.36, and 79.32 μmol·m-2·d-1, respectively, which were 2.0-7.5 times higher than the values in the non-algae accumulation areas. In addition, the decay and decomposition of algae released large amounts of nutrients and changed the physiochemical properties of the water column. Additionally, the increased algae biomass promoted N2O release and improved the proportion of N2O produced via denitrification process to being 9.8-20.4% microbial-derived N2O. This proportion became higher when the N2O consumption during denitrification was considered as evidenced by isotopic data. However, when the algae biomass was excessive in hypereutrophic state, the algae decomposition also consumed a large amount of oxygen, thus limiting the N2O production due to complete denitrification as well as due to the limited substrate supply of nitrate by nitrification in hypoxic or anoxic conditions. Further, the excessive algae accumulation on the water surface reduced N2O release fluxes via hindering the migration of the dissolved N2O into the atmosphere. These findings provide a new perspective and understanding for accurately evaluating N2O release fluxes driven by algae processes in eutrophic lakes.
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Affiliation(s)
- Yiping Wang
- School of Water Resources and Hydropower Engineering, Wuhan University, Wuhan 430072, China; School of Environment, Nanjing Normal University, No.1, Wenyuan Road, Nanjing 210023, China; State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210029, China
| | - Yu Peng
- School of Environment, Nanjing Normal University, No.1, Wenyuan Road, Nanjing 210023, China
| | - Chengxu Lv
- School of Environment, Nanjing Normal University, No.1, Wenyuan Road, Nanjing 210023, China
| | - Xiaoguang Xu
- School of Environment, Nanjing Normal University, No.1, Wenyuan Road, Nanjing 210023, China.
| | - Han Meng
- School of Environment, Nanjing Normal University, No.1, Wenyuan Road, Nanjing 210023, China
| | - Yiwen Zhou
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Guoxiang Wang
- School of Environment, Nanjing Normal University, No.1, Wenyuan Road, Nanjing 210023, China
| | - Yongjun Lu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210029, China
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8
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Yu C, Qiao S, Zhou J. Sulfide-driven nitrous oxide recovery during the mixotrophic denitrification process. J Environ Sci (China) 2023; 125:443-452. [PMID: 36375927 DOI: 10.1016/j.jes.2021.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 06/16/2023]
Abstract
We propose a novel sulfide-driven process to recover N2O during the traditional denitrification process. The optimum initial sulfide concentration was 120 mg/L, and the N2O percentage in the gaseous products (N2O+N2) was up to 82.9%. Moreover, sulfide involved in denitrification processes could substitute for organic carbon as an electron donor, e.g., 1 g sulfide was equivalent to 0.5-2 g COD when sulfide was oxidized to sulfur and sulfate. The accumulation of N2O was mainly due to the inhibiting effect of sulfide on nitrous oxide reductase (N2OR), which was induced by the supply insufficiency of electrons from cytochrome c (cyt c) to N2OR. When the initial sulfide concentration was 120 mg/L, the N2OR activity was only 36.8% of its original level. According to the results of cyclic voltammetry, circular dichroism spectra and fluorescence spectra, significant changes in the conformations and protein structures of cyt c were caused by sulfide, and cyt c completely lost its electron transport capacity. This study provides a new concept for N2O recovery driven by sulfide in the denitrification process. In addition, the findings regarding the mechanism of the inhibition of N2OR activity have important implications both for reducing emissions of N2O and recovering N2O in the sulfide-driven denitrification process.
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Affiliation(s)
- Cong Yu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Sen Qiao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Jiti Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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9
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Bragança PMS, Carepo MSP, Pauleta SR, Pinter TBJ, Elia M, Cordas CM, Moura I, Pecoraro VL, Moura JJG. Incorporation of a molybdenum atom in a Rubredoxin-type Centre of a de novo-designed α 3DIV-L21C three-helical bundle peptide. J Inorg Biochem 2023; 240:112096. [PMID: 36603242 DOI: 10.1016/j.jinorgbio.2022.112096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/17/2022] [Accepted: 12/04/2022] [Indexed: 12/24/2022]
Abstract
The rational design and functionalization of small, simple, and stable peptides scaffolds is an attractive avenue to mimic catalytic metal-centres of complex proteins, relevant for the design of metalloenzymes with environmental, biotechnological and health impacts. The de novo designed α3DIV-L21C framework has a rubredoxin-like metal binding site and was used in this work to incorporate a Mo-atom. Thermostability studies using differential scanning calorimetry showed an increase of 4 °C in the melting temperature of the Mo-α3DIV-L21C when compared to the apo-α3DIV-L21C. Circular dichroism in the visible and far-UV regions corroborated these results showing that Mo incorporation provides stability to the peptide even though there were almost no differences observed in the secondary structure. A formal reduction potential of ∼ -408 mV vs. NHE, pH 7.6 was determined. Combining electrochemical results, EPR and UV-visible data we discuss the oxidation state of the molybdenum centre in Mo-α3DIV-L21C and propose that is mainly in a Mo (VI) oxidation state.
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Affiliation(s)
- Pedro M S Bragança
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; Microbial Stress Lab, UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Marta S P Carepo
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; Escola de Psicologia e Ciências da Vida, Departamento de Ciências da Vida, Universidade Lusófona de Humanidades e Tecnologias, Campo Grande, 1749-024 Lisboa, Portugal.
| | - Sofia R Pauleta
- Microbial Stress Lab, UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Tyler B J Pinter
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Maddalena Elia
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Cristina M Cordas
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Isabel Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Vincent L Pecoraro
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - José J G Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.
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10
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Behrendt U, Spanner T, Augustin J, Zak DH, Horn MA, Kolb S, Ulrich A. Consumption of N2O by Flavobacterium azooxidireducens sp. nov. Isolated from Decomposing Leaf Litter of Phragmites australis (Cav.). Microorganisms 2022; 10:microorganisms10112304. [PMID: 36422374 PMCID: PMC9697520 DOI: 10.3390/microorganisms10112304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/23/2022] Open
Abstract
Microorganisms acting as sinks for the greenhouse gas nitrous oxide (N2O) are gaining increasing attention in the development of strategies to control N2O emissions. Non-denitrifying N2O reducers are of particular interest because they can provide a real sink without contributing to N2O release. The bacterial strain under investigation (IGB 4-14T), isolated in a mesocosm experiment to study the litter decomposition of Phragmites australis (Cav.), is such an organism. It carries only a nos gene cluster with the sec-dependent Clade II nosZ and is able to consume significant amounts of N2O under anoxic conditions. However, consumption activity is considerably affected by the O2 level. The reduction of N2O was not associated with cell growth, suggesting that no energy is conserved by anaerobic respiration. Therefore, the N2O consumption of strain IGB 4-14T rather serves as an electron sink for metabolism to sustain viability during transient anoxia and/or to detoxify high N2O concentrations. Phylogenetic analysis of 16S rRNA gene similarity revealed that the strain belongs to the genus Flavobacterium. It shares a high similarity in the nos gene cluster composition and the amino acid similarity of the nosZ gene with various type strains of the genus. However, phylogenomic analysis and comparison of overall genome relatedness indices clearly demonstrated a novel species status of strain IGB 4-14T, with Flavobacterium lacus being the most closely related species. Various phenotypic differences supported a demarcation from this species. Based on these results, we proposed a novel species Flavobacterium azooxidireducens sp. nov. (type strain IGB 4-14T = LMG 29709T = DSM 103580T).
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Affiliation(s)
- Undine Behrendt
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
- Correspondence: (U.B.); (A.U.); Tel.: +49-33432-82460 (U.B.); +49-33432-82345 (A.U.)
| | - Tobias Spanner
- Institute of Microbiology, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Jürgen Augustin
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
| | - Dominik H. Zak
- Institute for Ecoscience, Aarhus University, C.F. Møllersvej, Bygning 1331, 8000 Aarhus, Denmark
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries Berlin, Müggelseedamm 301, D-12587 Berlin, Germany
| | - Marcus A. Horn
- Institute of Microbiology, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Steffen Kolb
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
| | - Andreas Ulrich
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
- Correspondence: (U.B.); (A.U.); Tel.: +49-33432-82460 (U.B.); +49-33432-82345 (A.U.)
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11
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Piper SEH, Casadevall C, Reisner E, Clarke TA, Jeuken LJC, Gates AJ, Butt JN. Photocatalytic Removal of the Greenhouse Gas Nitrous Oxide by Liposomal Microreactors. Angew Chem Int Ed Engl 2022; 61:e202210572. [PMID: 35951464 PMCID: PMC9825952 DOI: 10.1002/anie.202210572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Indexed: 01/11/2023]
Abstract
Nitrous oxide (N2 O) is a potent greenhouse and ozone-reactive gas for which emissions are growing rapidly due to increasingly intensive agriculture. Synthetic catalysts for N2 O decomposition typically contain precious metals and/or operate at elevated temperatures driving a desire for more sustainable alternatives. Here we demonstrate self-assembly of liposomal microreactors enabling catalytic reduction of N2 O to the climate neutral product N2 . Photoexcitation of graphitic N-doped carbon dots delivers electrons to encapsulated N2 O Reductase enzymes via a lipid-soluble biomolecular wire provided by the MtrCAB protein complex. Within the microreactor, electron transfer from MtrCAB to N2 O Reductase is facilitated by the general redox mediator methyl viologen. The liposomal microreactors use only earth-abundant elements to catalyze N2 O removal in ambient, aqueous conditions.
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Affiliation(s)
- Samuel E. H. Piper
- School of ChemistryUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Carla Casadevall
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Erwin Reisner
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Thomas A. Clarke
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Lars J. C. Jeuken
- Leiden Institute of ChemistryLeiden UniversityPO Box 95022300 RALeidenThe Netherlands
| | - Andrew J. Gates
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Julea N. Butt
- School of ChemistryUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK,School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
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12
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Piper SEH, Casadevall C, Reisner E, Clarke TA, Jeuken LJC, Gates AJ, Butt JN. Photocatalytic Removal of the Greenhouse Gas Nitrous Oxide by Liposomal Microreactors. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202210572. [PMID: 38529325 PMCID: PMC10962689 DOI: 10.1002/ange.202210572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Indexed: 11/11/2022]
Abstract
Nitrous oxide (N2O) is a potent greenhouse and ozone-reactive gas for which emissions are growing rapidly due to increasingly intensive agriculture. Synthetic catalysts for N2O decomposition typically contain precious metals and/or operate at elevated temperatures driving a desire for more sustainable alternatives. Here we demonstrate self-assembly of liposomal microreactors enabling catalytic reduction of N2O to the climate neutral product N2. Photoexcitation of graphitic N-doped carbon dots delivers electrons to encapsulated N2O Reductase enzymes via a lipid-soluble biomolecular wire provided by the MtrCAB protein complex. Within the microreactor, electron transfer from MtrCAB to N2O Reductase is facilitated by the general redox mediator methyl viologen. The liposomal microreactors use only earth-abundant elements to catalyze N2O removal in ambient, aqueous conditions.
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Affiliation(s)
- Samuel E. H. Piper
- School of ChemistryUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Carla Casadevall
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Erwin Reisner
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Thomas A. Clarke
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Lars J. C. Jeuken
- Leiden Institute of ChemistryLeiden UniversityPO Box 95022300 RALeidenThe Netherlands
| | - Andrew J. Gates
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Julea N. Butt
- School of ChemistryUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
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13
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Müller C, Zhang L, Zipfel S, Topitsch A, Lutz M, Eckert J, Prasser B, Chami M, Lü W, Du J, Einsle O. Molecular interplay of an assembly machinery for nitrous oxide reductase. Nature 2022; 608:626-631. [PMID: 35896743 DOI: 10.1038/s41586-022-05015-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/23/2022] [Indexed: 11/09/2022]
Abstract
Emissions of the critical ozone-depleting and greenhouse gas nitrous oxide (N2O) from soils and industrial processes have increased considerably over the last decades1-3. As the final step of bacterial denitrification, N2O is reduced to chemically inert N2 (refs. 1,4) in a reaction that is catalysed by the copper-dependent nitrous oxide reductase (N2OR) (ref. 5). The assembly of its unique [4Cu:2S] active site cluster CuZ requires both the ATP-binding-cassette (ABC) complex NosDFY and the membrane-anchored copper chaperone NosL (refs. 4,6). Here we report cryo-electron microscopy structures of Pseudomonas stutzeri NosDFY and its complexes with NosL and N2OR, respectively. We find that the periplasmic NosD protein contains a binding site for a Cu+ ion and interacts specifically with NosL in its nucleotide-free state, whereas its binding to N2OR requires a conformational change that is triggered by ATP binding. Mutually exclusive structures of NosDFY in complex with NosL and with N2OR reveal a sequential metal-trafficking and assembly pathway for a highly complex copper site. Within this pathway, NosDFY acts as a mechanical energy transducer rather than as a transporter. It links ATP hydrolysis in the cytoplasm to a conformational transition of the NosD subunit in the periplasm, which is required for NosDFY to switch its interaction partner so that copper ions are handed over from the chaperone NosL to the enzyme N2OR.
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Affiliation(s)
- Christoph Müller
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Sara Zipfel
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Annika Topitsch
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Marleen Lutz
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Johannes Eckert
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Benedikt Prasser
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Mohamed Chami
- BioEM Lab, Biozentrum, Universität Basel, Basel, Switzerland
| | - Wei Lü
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Juan Du
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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14
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Liu H, Li Y, Pan B, Zheng X, Yu J, Ding H, Zhang Y. Pathways of soil N 2O uptake, consumption, and its driving factors: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:30850-30864. [PMID: 35092587 DOI: 10.1007/s11356-022-18619-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Nitrous oxide (N2O) is an important greenhouse gas that plays a significant role in atmospheric photochemical reactions and contributes to stratospheric ozone depletion. Soils are the main sources of N2O emissions. In recent years, it has been demonstrated that soil is not only a source but also a sink of N2O uptake and consumption. N2O emissions at the soil surface are the result of gross N2O production, uptake, and consumption, which are co-occurring processes. Soil N2O uptake and consumption are complex biological processes, and their mechanisms are still worth an in-depth systematic study. This paper aimed to systematically address the current research progress on soil N2O uptake and consumption. Based on a bibliometric perspective, this study has highlighted the pathways of soil N2O uptake and consumption and their driving factors and measurement techniques. This systematic review of N2O uptake and consumption will help to further understand N transformations and soil N2O emissions.
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Affiliation(s)
- Hongshan Liu
- College of Earth Sciences, Jilin University, Chao'yang, Changchun, 130061, Jilin, People's Republic of China
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China
| | - Yuefen Li
- College of Earth Sciences, Jilin University, Chao'yang, Changchun, 130061, Jilin, People's Republic of China.
| | - Baobao Pan
- School of Agriculture and Food, The University of Melbourne, Parkville, 3010, VIC, Australia
| | - Xiangzhou Zheng
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China
| | - Juhua Yu
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China
| | - Hong Ding
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China
| | - Yushu Zhang
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China.
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15
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16
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Kroneck PMH. Nature's nitrite-to-ammonia expressway, with no stop at dinitrogen. J Biol Inorg Chem 2021; 27:1-21. [PMID: 34865208 PMCID: PMC8840924 DOI: 10.1007/s00775-021-01921-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022]
Abstract
Since the characterization of cytochrome c552 as a multiheme nitrite reductase, research on this enzyme has gained major interest. Today, it is known as pentaheme cytochrome c nitrite reductase (NrfA). Part of the NH4+ produced from NO2- is released as NH3 leading to nitrogen loss, similar to denitrification which generates NO, N2O, and N2. NH4+ can also be used for assimilatory purposes, thus NrfA contributes to nitrogen retention. It catalyses the six-electron reduction of NO2- to NH4+, hosting four His/His ligated c-type hemes for electron transfer and one structurally differentiated active site heme. Catalysis occurs at the distal side of a Fe(III) heme c proximally coordinated by lysine of a unique CXXCK motif (Sulfurospirillum deleyianum, Wolinella succinogenes) or, presumably, by the canonical histidine in Campylobacter jejeuni. Replacement of Lys by His in NrfA of W. succinogenes led to a significant loss of enzyme activity. NrfA forms homodimers as shown by high resolution X-ray crystallography, and there exist at least two distinct electron transfer systems to the enzyme. In γ-proteobacteria (Escherichia coli) NrfA is linked to the menaquinol pool in the cytoplasmic membrane through a pentaheme electron carrier (NrfB), in δ- and ε-proteobacteria (S. deleyianum, W. succinogenes), the NrfA dimer interacts with a tetraheme cytochrome c (NrfH). Both form a membrane-associated respiratory complex on the extracellular side of the cytoplasmic membrane to optimize electron transfer efficiency. This minireview traces important steps in understanding the nature of pentaheme cytochrome c nitrite reductases, and discusses their structural and functional features.
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Affiliation(s)
- Peter M H Kroneck
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
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17
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Nisbet EG, Dlugokencky EJ, Fisher RE, France JL, Lowry D, Manning MR, Michel SE, Warwick NJ. Atmospheric methane and nitrous oxide: challenges alongthe path to Net Zero. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200457. [PMID: 34565227 PMCID: PMC8473950 DOI: 10.1098/rsta.2020.0457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
The causes of methane's renewed rise since 2007, accelerated growth from 2014 and record rise in 2020, concurrent with an isotopic shift to values more depleted in 13C, remain poorly understood. This rise is the dominant departure from greenhouse gas scenarios that limit global heating to less than 2°C. Thus a comprehensive understanding of methane sources and sinks, their trends and inter-annual variations are becoming more urgent. Efforts to quantify both sources and sinks and understand latitudinal and seasonal variations will improve our understanding of the methane cycle and its anthropogenic component. Nationally declared emissions inventories under the UN Framework Convention on Climate Change (UNFCCC) and promised contributions to emissions reductions under the UNFCCC Paris Agreement need to be verified independently by top-down observation. Furthermore, indirect effects on natural emissions, such as changes in aquatic ecosystems, also need to be quantified. Nitrous oxide is even more poorly understood. Despite this, options for mitigating methane and nitrous oxide emissions are improving rapidly, both in cutting emissions from gas, oil and coal extraction and use, and also from agricultural and waste sources. Reductions in methane and nitrous oxide emission are arguably among the most attractive immediate options for climate action. This article is part of a discussion meeting issue 'Rising methane: is warming feeding warming? (part 1)'.
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Affiliation(s)
- Euan G. Nisbet
- Department of Earth Sciences, Royal Holloway, University of London, Egham TW20 0EX, UK
- NCAS, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Edward J. Dlugokencky
- US National Oceanic and Atmospheric Administration, Global Monitoring Laboratory, 325 Broadway, Boulder, CO 80305, USA
| | - Rebecca E. Fisher
- Department of Earth Sciences, Royal Holloway, University of London, Egham TW20 0EX, UK
| | - James L. France
- Department of Earth Sciences, Royal Holloway, University of London, Egham TW20 0EX, UK
- British Antarctic Survey, Natural Environment Research Council, Cambridge CB3 0ET, UK
| | - David Lowry
- Department of Earth Sciences, Royal Holloway, University of London, Egham TW20 0EX, UK
| | - Martin R. Manning
- New Zealand Climate Change Research Institute, School of Geography Environment and Earth Studies, Victoria University of Wellington, Wellington, New Zealand
| | - Sylvia E. Michel
- Institute of Arctic and Antarctic Research, Univ. of Colorado, Boulder, CO 80309-0450, USA
| | - Nicola J. Warwick
- NCAS, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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18
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Deeba R, Chardon-Noblat S, Costentin C. Homogeneous molecular catalysis of the electrochemical reduction of N 2O to N 2: redox vs. chemical catalysis. Chem Sci 2021; 12:12726-12732. [PMID: 34703559 PMCID: PMC8494024 DOI: 10.1039/d1sc03044b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 08/24/2021] [Indexed: 12/20/2022] Open
Abstract
Homogeneous electrochemical catalysis of N2O reduction to N2 is investigated with a series of organic catalysts and rhenium and manganese bipyridyl carbonyl complexes. An activation-driving force correlation is revealed with the organic species characteristic of a redox catalysis involving an outer-sphere electron transfer from the radical anions or dianions of the reduced catalyst to N2O. Taking into account the previously estimated reorganization energy required to form the N2O radical anions leads to an estimation of the N2O/N2O˙− standard potential in acetonitrile electrolyte. The direct reduction of N2O at a glassy carbon electrode follows the same quadratic activation driving force relationship. Our analysis reveals that the catalytic effect of the mediators is due to a smaller reorganization energy of the homogeneous electron transfer than that of the heterogeneous one. The physical effect of “spreading” electrons in the electrolyte is shown to be unfavorable for the homogeneous reduction. Importantly, we show that the reduction of N2O by low valent rhenium and manganese bipyridyl carbonyl complexes is of a chemical nature, with an initial one-electron reduction process associated with a chemical reaction more efficient than the simple outer-sphere electron transfer process. This points to an inner-sphere mechanism possibly involving partial charge transfer from the low valent metal to the binding N2O and emphasizes the differences between chemical and redox catalytic processes. Homogeneous electrochemical catalysis of N2O reduction to N2 is investigated with a series of organic catalysts and rhenium and manganese bipyridyl carbonyl complexes.![]()
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Affiliation(s)
- Rana Deeba
- Univ Grenoble Alpes, DCM, CNRS 38000 Grenoble France
| | | | - Cyrille Costentin
- Univ Grenoble Alpes, DCM, CNRS 38000 Grenoble France .,Université de Paris 75013 Paris France
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19
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Jurgeleit R, Grimm-Lebsanft B, Flöser BM, Teubner M, Buchenau S, Senft L, Hoffmann J, Naumova M, Näther C, Ivanović-Burmazović I, Rübhausen M, Tuczek F. Catalytic Oxygenation of Hydrocarbons by Mono-μ-oxo Dicopper(II) Species Resulting from O-O Cleavage of Tetranuclear Cu I /Cu II Peroxo Complexes. Angew Chem Int Ed Engl 2021; 60:14154-14162. [PMID: 33856088 PMCID: PMC8251984 DOI: 10.1002/anie.202101035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/13/2021] [Indexed: 01/11/2023]
Abstract
One of the challenges of catalysis is the transformation of inert C-H bonds to useful products. Copper-containing monooxygenases play an important role in this regard. Here we show that low-temperature oxygenation of dinuclear copper(I) complexes leads to unusual tetranuclear, mixed-valent μ4 -peroxo [CuI /CuII ]2 complexes. These Cu4 O2 intermediates promote irreversible and thermally activated O-O bond homolysis, generating Cu2 O complexes that catalyze strongly exergonic H-atom abstraction from hydrocarbons, coupled to O-transfer. The Cu2 O species can also be produced with N2 O, demonstrating their capability for small-molecule activation. The binding and cleavage of O2 leading to the primary Cu4 O2 intermediate and the Cu2 O complexes, respectively, is elucidated with a range of solution spectroscopic methods and mass spectrometry. The unique reactivities of these species establish an unprecedented, 100 % atom-economic scenario for the catalytic, copper-mediated monooxygenation of organic substrates, employing both O-atoms of O2 .
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Affiliation(s)
- Ramona Jurgeleit
- Institute of Inorganic Chemistry, Christian-Albrechts-University of Kiel, Max-Eyth-Strasse 2, 24118, Kiel, Germany
| | - Benjamin Grimm-Lebsanft
- Institut für Nanostruktur- und Festkörperphysik, Center for Free Electron Laser Science (CFEL), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Benedikt Maria Flöser
- Institute of Inorganic Chemistry, Christian-Albrechts-University of Kiel, Max-Eyth-Strasse 2, 24118, Kiel, Germany.,Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mühlheim an der Ruhr, Germany
| | - Melissa Teubner
- Institut für Nanostruktur- und Festkörperphysik, Center for Free Electron Laser Science (CFEL), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Department of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52074, Aachen, Germany
| | - Sören Buchenau
- Institut für Nanostruktur- und Festkörperphysik, Center for Free Electron Laser Science (CFEL), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Laura Senft
- Department of Chemistry and Pharmacy, Friedrich-Alexander-University of Erlangen-Nürnberg, Egerlandstrasse 1, 91058, Erlangen, Germany
| | - Jonas Hoffmann
- Institute for Analytical and Organic Chemistry, University of Bremen, Leobener Strasse 7, 28359, Bremen, Germany.,MAPEX, Center for Materials and Processes, University of Bremen, Bibliothekstrasse 1, 28359, Bremen, Germany
| | - Maria Naumova
- DESY, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607, Hamburg, Germany
| | - Christian Näther
- Institute of Inorganic Chemistry, Christian-Albrechts-University of Kiel, Max-Eyth-Strasse 2, 24118, Kiel, Germany
| | - Ivana Ivanović-Burmazović
- Department of Chemistry and Pharmacy, Friedrich-Alexander-University of Erlangen-Nürnberg, Egerlandstrasse 1, 91058, Erlangen, Germany.,Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, Haus D, 81377, München, Germany
| | - Michael Rübhausen
- Institut für Nanostruktur- und Festkörperphysik, Center for Free Electron Laser Science (CFEL), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Felix Tuczek
- Institute of Inorganic Chemistry, Christian-Albrechts-University of Kiel, Max-Eyth-Strasse 2, 24118, Kiel, Germany
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20
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Jurgeleit R, Grimm‐Lebsanft B, Flöser BM, Teubner M, Buchenau S, Senft L, Hoffmann J, Naumova M, Näther C, Ivanović‐Burmazović I, Rübhausen M, Tuczek F. Katalytische Oxygenierung von Kohlenwasserstoffen durch Mono‐μ‐oxo‐Dikupfer(II)‐Spezies erzeugt durch O‐O‐Spaltung von tetranuklearen Cu
I
/Cu
II
‐Peroxo‐Komplexen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Ramona Jurgeleit
- Institute of Inorganic Chemistry Christian-Albrechts-University of Kiel Max-Eyth-Straße 2 24118 Kiel Deutschland
| | - Benjamin Grimm‐Lebsanft
- Institut für Nanostruktur- und Festkörperphysik Center for Free Electron Laser Science (CFEL) Universität Hamburg Luruper Chaussee 149 22761 Hamburg Deutschland
| | - Benedikt Maria Flöser
- Institute of Inorganic Chemistry Christian-Albrechts-University of Kiel Max-Eyth-Straße 2 24118 Kiel Deutschland
- Max Planck Institute for Chemical Energy Conversion Stiftstraße 34–36 45470 Mühlheim an der Ruhr Deutschland
| | - Melissa Teubner
- Institut für Nanostruktur- und Festkörperphysik Center for Free Electron Laser Science (CFEL) Universität Hamburg Luruper Chaussee 149 22761 Hamburg Deutschland
- Department of Inorganic Chemistry RWTH Aachen University Landoltweg 1 52074 Aachen Deutschland
| | - Sören Buchenau
- Institut für Nanostruktur- und Festkörperphysik Center for Free Electron Laser Science (CFEL) Universität Hamburg Luruper Chaussee 149 22761 Hamburg Deutschland
| | - Laura Senft
- Department of Chemistry and Pharmacy Friedrich-Alexander-University of Erlangen-Nürnberg Egerlandstraße 1 91058 Erlangen Deutschland
| | - Jonas Hoffmann
- Institute for Analytical and Organic Chemistry University of Bremen Leobener Straße 7 28359 Bremen Deutschland
- MAPEX, Center for Materials and Processes University of Bremen Bibliothekstrasse 1 28359 Bremen Deutschland
| | - Maria Naumova
- DESY, Deutsches Elektronen-Synchrotron (DESY) Notkestraße 85 22607 Hamburg Deutschland
| | - Christian Näther
- Institute of Inorganic Chemistry Christian-Albrechts-University of Kiel Max-Eyth-Straße 2 24118 Kiel Deutschland
| | - Ivana Ivanović‐Burmazović
- Department of Chemistry and Pharmacy Friedrich-Alexander-University of Erlangen-Nürnberg Egerlandstraße 1 91058 Erlangen Deutschland
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstraße 5–13, Haus D 81377 München Deutschland
| | - Michael Rübhausen
- Institut für Nanostruktur- und Festkörperphysik Center for Free Electron Laser Science (CFEL) Universität Hamburg Luruper Chaussee 149 22761 Hamburg Deutschland
| | - Felix Tuczek
- Institute of Inorganic Chemistry Christian-Albrechts-University of Kiel Max-Eyth-Straße 2 24118 Kiel Deutschland
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21
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Salas A, Cabrera JJ, Jiménez-Leiva A, Mesa S, Bedmar EJ, Richardson DJ, Gates AJ, Delgado MJ. Bacterial nitric oxide metabolism: Recent insights in rhizobia. Adv Microb Physiol 2021; 78:259-315. [PMID: 34147187 DOI: 10.1016/bs.ampbs.2021.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nitric oxide (NO) is a reactive gaseous molecule that has several functions in biological systems depending on its concentration. At low concentrations, NO acts as a signaling molecule, while at high concentrations, it becomes very toxic due to its ability to react with multiple cellular targets. Soil bacteria, commonly known as rhizobia, have the capacity to establish a N2-fixing symbiosis with legumes inducing the formation of nodules in their roots. Several reports have shown NO production in the nodules where this gas acts either as a signaling molecule which regulates gene expression, or as a potent inhibitor of nitrogenase and other plant and bacteria enzymes. A better understanding of the sinks and sources of NO in rhizobia is essential to protect symbiotic nitrogen fixation from nitrosative stress. In nodules, both the plant and the microsymbiont contribute to the production of NO. From the bacterial perspective, the main source of NO reported in rhizobia is the denitrification pathway that varies significantly depending on the species. In addition to denitrification, nitrate assimilation is emerging as a new source of NO in rhizobia. To control NO accumulation in the nodules, in addition to plant haemoglobins, bacteroids also contribute to NO detoxification through the expression of a NorBC-type nitric oxide reductase as well as rhizobial haemoglobins. In the present review, updated knowledge about the NO metabolism in legume-associated endosymbiotic bacteria is summarized.
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Affiliation(s)
- Ana Salas
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Juan J Cabrera
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain; School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Andrea Jiménez-Leiva
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Socorro Mesa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - David J Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Andrew J Gates
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - María J Delgado
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain.
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22
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Deeba R, Molton F, Chardon-Noblat S, Costentin C. Effective Homogeneous Catalysis of Electrochemical Reduction of Nitrous Oxide to Dinitrogen at Rhenium Carbonyl Catalysts. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01197] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Rana Deeba
- DCM, CNRS, Université Grenoble Alpes, 38000 Grenoble, France
| | - Florian Molton
- DCM, CNRS, Université Grenoble Alpes, 38000 Grenoble, France
| | | | - Cyrille Costentin
- DCM, CNRS, Université Grenoble Alpes, 38000 Grenoble, France
- Université de Paris, 75013 Paris, France
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23
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Rathnayaka SC, Mankad NP. Coordination chemistry of the Cu Z site in nitrous oxide reductase and its synthetic mimics. Coord Chem Rev 2021; 429:213718. [PMID: 33692589 PMCID: PMC7939133 DOI: 10.1016/j.ccr.2020.213718] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Atmospheric nitrous oxide (N2O) has garnered significant attention recently due to its dual roles as an ozone depletion agent and a potent greenhouse gas. Anthropogenic N2O emissions occur primarily through agricultural disruption of nitrogen homeostasis causing N2O to build up in the atmosphere. The enzyme responsible for N2O fixation within the geochemical nitrogen cycle is nitrous oxide reductase (N2OR), which catalyzes 2H+/2e- reduction of N2O to N2 and H2O at a tetranuclear active site, CuZ. In this review, the coordination chemistry of CuZ is reviewed. Recent advances in the understanding of biological CuZ coordination chemistry is discussed, as are significant breakthroughs in synthetic modeling of CuZ that have emerged in recent years. The latter topic includes both structurally faithful, synthetic [Cu4(µ4-S)] clusters that are able to reduce N2O, as well as dicopper motifs that shed light on reaction pathways available to the critical CuI-CuIV cluster edge of CuZ. Collectively, these advances in metalloenzyme studies and synthetic model systems provide meaningful knowledge about the physiologically relevant coordination chemistry of CuZ but also open new questions that will pose challenges in the near future.
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Affiliation(s)
- Suresh C. Rathnayaka
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St., Chicago, IL 60607, United States
| | - Neal P. Mankad
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St., Chicago, IL 60607, United States
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24
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Guo X, Liu J, Liu D, Yang Z, Xiao S, Lorke A. Density currents reduce nitrous oxide emissions in a tributary bay of Three Gorges Reservoir. WATER RESEARCH 2021; 190:116750. [PMID: 33373947 DOI: 10.1016/j.watres.2020.116750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/09/2020] [Accepted: 12/13/2020] [Indexed: 06/12/2023]
Abstract
Reservoirs are a significant source of the potent greenhouse gas nitrous oxide (N2O), but there are few data on N2O in the world's largest reservoirs and limited understanding of the factors controlling their emission rates. Here we analyzed high-resolution measurements of dissolved N2O concentrations and fluxes in a typical tributary bay of Three Gorges Reservoir. The surface water was oversaturated in N2O during both low and high water level (8.6 -16.4 nmol/L, 107% - 180% saturation) and N2O fluxes varied nearly tenfold (0.2 and 1.6 μmol/(m2 h)). Dissolved N2O concentrations were characterized by pronounced vertical gradients, which were controlled by bidirectional density currents. The river water with high concentrations entered the bay as an underflow along the riverbed, the upper part of the water column was formed by intrusive backwater of Three Gorges Reservoir having significantly lower N2O concentrations. In consequence, the N2O emission potential of the impoundment was reduced compared to pre-impoundment conditions. These results reveal the importance of hydraulic conditions on N2O emission from large reservoirs and suggest that flow regulation can be a potential tool for mitigating greenhouse gas emissions from manmade impoundments.
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Affiliation(s)
- Xiaojuan Guo
- Hubei Field Observation and Scientific Research Stations for Water Ecosystem in Three Gorges Reservoir, China Three Gorges University, Yichang, China
| | - Jia Liu
- Hubei Field Observation and Scientific Research Stations for Water Ecosystem in Three Gorges Reservoir, China Three Gorges University, Yichang, China
| | - Defu Liu
- Hubei Field Observation and Scientific Research Stations for Water Ecosystem in Three Gorges Reservoir, China Three Gorges University, Yichang, China
| | - Zhengjian Yang
- Hubei Field Observation and Scientific Research Stations for Water Ecosystem in Three Gorges Reservoir, China Three Gorges University, Yichang, China.
| | - Shangbin Xiao
- Hubei Field Observation and Scientific Research Stations for Water Ecosystem in Three Gorges Reservoir, China Three Gorges University, Yichang, China.
| | - Andreas Lorke
- Hubei Field Observation and Scientific Research Stations for Water Ecosystem in Three Gorges Reservoir, China Three Gorges University, Yichang, China; Institute for Environmental Sciences, University of Koblenz-Landau, Landau, Germany
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25
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Wang LK, Chen X, Wei W, Xu Q, Sun J, Mannina G, Song L, Ni BJ. Biological Reduction of Nitric Oxide for Efficient Recovery of Nitrous Oxide as an Energy Source. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:1992-2005. [PMID: 33430585 DOI: 10.1021/acs.est.0c04037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Chemical absorption-biological reduction based on Fe(II)EDTA is a promising technology to remove nitric oxide (NO) from flue gases. However, limited effort has been made to enable direct energy recovery from NO through production of nitrous oxide (N2O) as a potential renewable energy rather than greenhouse gas. In this work, the enhanced energy recovery in the form of N2O via biological NO reduction was investigated by conducting short-term and long-term experiments at different Fe(II)EDTA-NO and organic carbon levels. The results showed both NO reductase and N2O reductase were inhibited at Fe(II)EDTA-NO concentration up to 20 mM, with the latter being inhibited more significantly, thus facilitating N2O accumulation. Furthermore, N2O accumulation was enhanced under carbon-limiting conditions because of electron competition during short-term experiments. Up to 47.5% of NO-N could be converted to gaseous N2O-N, representing efficient N2O recovery. Fe(II)EDTA-NO reduced microbial diversity and altered the community structure toward Fe(II)EDTA-NO-reducing bacteria-dominated culture during long-term experiments. The most abundant bacterial genus Pseudomonas, which was able to resist the toxicity of Fe(II)EDTA-NO, was significantly enriched, with its relative abundance increased from 1.0 to 70.3%, suggesting Pseudomonas could be the typical microbe for the energy recovery technology in NO-based denitrification.
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Affiliation(s)
- Li-Kun Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Xueming Chen
- College of Environment and Resources, Fuzhou University, Fujian 350116, PR China
| | - Wei Wei
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Qiuxiang Xu
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Jing Sun
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Giorgio Mannina
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
- Engineering Department, Palermo University, Viale delle Scienze, ed. 8, 90128 Palermo, Italy
| | - Lan Song
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, PR China
| | - Bing-Jie Ni
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
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26
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Ghosh AC, Duboc C, Gennari M. Synergy between metals for small molecule activation: Enzymes and bio-inspired complexes. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213606] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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27
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Zhang L, Bill E, Kroneck PMH, Einsle O. A [3Cu:2S] cluster provides insight into the assembly and function of the Cu Z site of nitrous oxide reductase. Chem Sci 2021; 12:3239-3244. [PMID: 34164092 PMCID: PMC8179356 DOI: 10.1039/d0sc05204c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Nitrous oxide reductase (N2OR) is the only known enzyme reducing environmentally critical nitrous oxide (N2O) to dinitrogen (N2) as the final step of bacterial denitrification. The assembly process of its unique catalytic [4Cu:2S] cluster CuZ remains scarcely understood. Here we report on a mutagenesis study of all seven histidine ligands coordinating this copper center, followed by spectroscopic and structural characterization and based on an established, functional expression system for Pseudomonas stutzeri N2OR in Escherichia coli. While no copper ion was found in the CuZ binding site of variants H129A, H130A, H178A, H326A, H433A and H494A, the H382A variant carried a catalytically inactive [3Cu:2S] center, in which one sulfur ligand, SZ2, had relocated to form a weak hydrogen bond to the sidechain of the nearby lysine residue K454. This link provides sufficient stability to avoid the loss of the sulfide anion. The UV-vis spectra of this cluster are strikingly similar to those of the active enzyme, implying that the flexibility of SZ2 may have been observed before, but not recognized. The sulfide shift changes the metal coordination in CuZ and is thus of high mechanistic interest. Variants of all seven histidine ligands of the [4Cu:2S] active site of nitrous oxide reductase mostly result in loss of the metal site. However, a H382A variant retains a [3Cu:2S] cluster that hints towards a structural flexibility also present in the intact site.![]()
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Affiliation(s)
- Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg im Breisgau Germany
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion Stiftstr. 34-36 D-45470 Mülheim an der Ruhr Germany
| | | | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg im Breisgau Germany
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28
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Chen H, Zeng L, Wang D, Zhou Y, Yang X. Recent advances in nitrous oxide production and mitigation in wastewater treatment. WATER RESEARCH 2020; 184:116168. [PMID: 32683143 DOI: 10.1016/j.watres.2020.116168] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/17/2020] [Accepted: 07/10/2020] [Indexed: 05/21/2023]
Abstract
Nitrous oxide (N2O) emitted from wastewater treatment plants has caused widespread concern. Over the past decade, people have made tremendous efforts to discover the microorganisms responsible for N2O production, elucidate metabolic pathways, establish production models and formulate mitigation strategies. The ultimate goal of all these efforts is to shed new light on how N2O is produced and how to reduce it, and one of the best ways is to find key opportunities by integrating the information obtained. This review article critically evaluates the knowledge gained in the field within a decade, especially in N2O production microbiology, biochemistry, models and mitigation strategies, with a focus on denitrification. Previous research has greatly deepened the understanding of the N2O generation mechanism, but further efforts are still needed due to the lack of standardized methodology for establishing N2O mitigation strategies in full-scale systems. One of the challenges seems to be to convert the denitrification process from a net N2O source into an effective sink, which is recommended as a key opportunity to reduce N2O production in this review.
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Affiliation(s)
- Hongbo Chen
- College of Environment and Resources, Xiangtan University, Xiangtan 411105, China.
| | - Long Zeng
- College of Environment and Resources, Xiangtan University, Xiangtan 411105, China
| | - Dongbo Wang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China.
| | - Yaoyu Zhou
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong, China
| | - Xiao Yang
- Korea Biochar Research Center, O-Jeong Eco-Resilience Institute & Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, South Korea
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29
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Carreira C, Nunes RF, Mestre O, Moura I, Pauleta SR. The effect of pH on Marinobacter hydrocarbonoclasticus denitrification pathway and nitrous oxide reductase. J Biol Inorg Chem 2020; 25:927-940. [PMID: 32851479 DOI: 10.1007/s00775-020-01812-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/12/2020] [Indexed: 11/27/2022]
Abstract
Increasing atmospheric concentration of N2O has been a concern, as it is a potent greenhouse gas and promotes ozone layer destruction. In the N-cycle, release of N2O is boosted upon a drop of pH in the environment. Here, Marinobacter hydrocarbonoclasticus was grown in batch mode in the presence of nitrate, to study the effect of pH in the denitrification pathway by gene expression profiling, quantification of nitrate and nitrite, and evaluating the ability of whole cells to reduce NO and N2O. At pH 6.5, accumulation of nitrite in the medium occurs and the cells were unable to reduce N2O. In addition, the biochemical properties of N2O reductase isolated from cells grown at pH 6.5, 7.5 and 8.5 were compared for the first time. The amount of this enzyme at acidic pH was lower than that at pH 7.5 and 8.5, pinpointing to a post-transcriptional regulation, though pH did not affect gene expression of N2O reductase accessory genes. N2O reductase isolated from cells grown at pH 6.5 has its catalytic center mainly as CuZ(4Cu1S), while that from cells grown at pH 7.5 or 8.5 has it as CuZ(4Cu2S). This study evidences that an in vivo secondary level of regulation is required to maintain N2O reductase in an active state.
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Affiliation(s)
- Cíntia Carreira
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal
- Biological Chemistry Lab, LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal
| | - Rute F Nunes
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal
| | - Olga Mestre
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal
| | - Isabel Moura
- Biological Chemistry Lab, LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal
| | - Sofia R Pauleta
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal.
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30
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Rathnayaka SC, Hsu CW, Johnson BJ, Iniguez SJ, Mankad NP. Impact of Electronic and Steric Changes of Ligands on the Assembly, Stability, and Redox Activity of Cu 4(μ 4-S) Model Compounds of the Cu Z Active Site of Nitrous Oxide Reductase (N 2OR). Inorg Chem 2020; 59:6496-6507. [PMID: 32309936 DOI: 10.1021/acs.inorgchem.0c00564] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Model compounds have been widely utilized in understanding the structure and function of the unusual Cu4(μ4-S) active site (CuZ) of nitrous oxide reductase (N2OR). However, only a limited number of model compounds that mimic both structural and functional features of CuZ are available, limiting insights about CuZ that can be gained from model studies. Our aim has been to construct Cu4(μ4-S) clusters with tailored redox activity and chemical reactivity via modulating the ligand environment. Our synthetic approach uses dicopper(I) precursor complexes (Cu2L2) that assemble into a Cu4(μ4-S)L4 cluster with the addition of an appropriate sulfur source. Here, we summarize the features of the ligands L that stabilize precursor and Cu4(μ4-S) clusters, along with the alternative products that form with inappropriate ligands. The precursors are more likely to rearrange to Cu4(μ4-S) clusters when the Cu(I) ions are supported by bidentate ligands with 3-atom bridges, but steric and electronic features of the ligand also play crucial roles. Neutral phosphine donors have been found to stabilize Cu4(μ4-S) clusters in the 4Cu(I) oxidation state, while neutral nitrogen donors could not stabilize Cu4(μ4-S) clusters. Anionic formamidinate ligands have been found to stabilize Cu4(μ4-S) clusters in the 2Cu(I):2Cu(II) and 3Cu(I):1Cu(II) states, with both the formation of the dicopper(I) precursors and subsequent assembly of clusters being governed by the steric factor at the ortho positions of the N-aryl substituents. Phosphaamidinates, which combine a neutral phosphine donor and an anionic nitrogen donor in the same ligand, form multinuclear Cu(I) clusters unless the negative charge is valence-trapped on nitrogen, in which case the resulting dicopper precursor is unable to rearrange to a multinuclear cluster. Taken together, the results presented in this study provide design criteria for successful assembly of synthetic model clusters for the CuZ active site of N2OR, which should enable future insights into the chemical behavior of CuZ.
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Affiliation(s)
- Suresh C Rathnayaka
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, United States
| | - Chia-Wei Hsu
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, United States
| | - Brittany J Johnson
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, United States
| | - Sarah J Iniguez
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, United States
| | - Neal P Mankad
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, United States
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31
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Carreira C, Dos Santos MMC, Pauleta SR, Moura I. Proton-coupled electron transfer mechanisms of the copper centres of nitrous oxide reductase from Marinobacter hydrocarbonoclasticus - An electrochemical study. Bioelectrochemistry 2020; 133:107483. [PMID: 32120320 DOI: 10.1016/j.bioelechem.2020.107483] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/13/2020] [Accepted: 02/13/2020] [Indexed: 11/16/2022]
Abstract
Reduction of N2O to N2 is catalysed by nitrous oxide reductase in the last step of the denitrification pathway. This multicopper enzyme has an electron transferring centre, CuA, and a tetranuclear copper-sulfide catalytic centre, "CuZ", which exists as CuZ*(4Cu1S) or CuZ(4Cu2S). The redox behaviour of these metal centres in Marinobacter hydrocarbonoclasticus nitrous oxide reductase was investigated by potentiometry and for the first time by direct electrochemistry. The reduction potential of CuA and CuZ(4Cu2S) was estimated by potentiometry to be +275 ± 5 mV and +65 ± 5 mV vs SHE, respectively, at pH 7.6. A proton-coupled electron transfer mechanism governs CuZ(4Cu2S) reduction potential, due to the protonation/deprotonation of Lys397 with a pKox of 6.0 ± 0.1 and a pKred of 9.2 ± 0.1. The reduction potential of CuA, in enzyme samples with CuZ*(4Cu1S), is controlled by protonation of the coordinating histidine residues in a two-proton coupled electron transfer process. In the cyclic voltammograms, two redox pairs were identified corresponding to CuA and CuZ(4Cu2S), with no additional signals being detected that could be attributed to CuZ*(4Cu1S). However, an enhanced cathodic signal for the activated enzyme was observed under turnover conditions, which is explained by the binding of nitrous oxide to CuZ0(4Cu1S), an intermediate species in the catalytic cycle.
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Affiliation(s)
- Cíntia Carreira
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal; Biological Chemistry Lab, LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Margarida M C Dos Santos
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Sofia R Pauleta
- Microbial Stress Lab, UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal. http://docentes.fct.unl.pt/srp/
| | - Isabel Moura
- Biological Chemistry Lab, LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal.
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32
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Li Q, Wang F, Yu Q, Yan W, Li X, Lv S. Dominance of nitrous oxide production by nitrification and denitrification in the shallow Chaohu Lake, Eastern China: Insight from isotopic characteristics of dissolved nitrous oxide. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 255:113212. [PMID: 31542667 DOI: 10.1016/j.envpol.2019.113212] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/05/2019] [Accepted: 09/06/2019] [Indexed: 06/10/2023]
Abstract
In recent decades, most lakes in Eastern China have suffered unprecedented nitrogen pollution, making them potential "hotspots" for N2O production and emission. Understanding the mechanisms of N2O production and quantifying emissions in these lakes is essential for assessing regional and global N2O budgets and for mitigating N2O emissions. Here, we measure isotopic compositions (δ15N-N2O and δ18O-N2O) and site preference (SP) of dissolved N2O in an attempt to differentiate the relative contribution of N2O production processes in the shallow, eutrophic Chaohu Lake, Eastern China. Our results show that the bulk isotope ratios for δ15N-N2O, δ18O-N2O, and SP were 5.8 ± 3.9‰, 29.3 ± 13.4‰, and 18.6 ± 3.2‰, respectively. More than 76.8% of the dissolved N2O was produced via microbial processes. Findings suggest that dissolved N2O is primarily produced via nitrification (between 27.3% and 48.0%) and denitrification (between 31.9% and 49.5%). In addition, isotopic data exhibit significant N2O consumption during denitrification. We estimate the average N2O emission rate (27.5 ± 26.0 μg N m-2 h-1), which is higher than that from rivers in the Changjiang River network (CRN). We scaled-up the regional N2O emission (from 1.98 Gg N yr-1 to 4.58 Gg N yr-1) using a N2O emission factor (0.51 ± 0.63%) for shallow lakes in the middle and lower region of the CRN. We suggest that beneficial circumstances for promoting complete denitrification may be helpful for reducing N2O production and emissions in fresh surface waters.
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Affiliation(s)
- Qingqian Li
- Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Fang Wang
- Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China.
| | - Qibiao Yu
- Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China.
| | - Weijin Yan
- Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xinyan Li
- Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Shucong Lv
- Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China.
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Wang Z, Chen C, Liu H, Hrynshpan D, Savitskaya T, Chen J, Chen J. Effects of carbon nanotube on denitrification performance of Alcaligenes sp. TB: Promotion of electron generation, transportation and consumption. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 183:109507. [PMID: 31386942 DOI: 10.1016/j.ecoenv.2019.109507] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/14/2019] [Accepted: 07/30/2019] [Indexed: 06/10/2023]
Abstract
Multi-walled carbon nanotubes (MWCNTs) promote biodegradation in water treatment, but the effect of MWCNT on denitrification under aerobic conditions is still unclear. This investigation focused on the denitrification performance of MWCNT and its toxic effects on Alcaligenes sp. TB which showed that 30 mg/L MWCNTs increased NO3- removal efficiency from 84% to 100% and decreased the NO2-and N2O accumulation rates by 36% and 17.5%, respectively. Nitrite reductase and nitrous oxide reductase activities were further increased by 19.5% and 7.5%, respectively. The mechanism demonstrated that electron generation (NADH yield) and electron transportation system activity increased by 14.5% and 104%, respectively. Cell membrane analysis found that MWCNT caused an increase in polyunsaturated fatty acids, which had positive effects on electron transportation and membrane fluidity at a low concentration of 96 mg/kg but caused membrane lipid peroxidation and impaired membrane integrity at a high concentration of 115 mg/L. These findings confirmed that MWCNT affects the activity of Alcaligenes sp. TB and consequently enhances denitrification performance.
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Affiliation(s)
- Zeyu Wang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Cong Chen
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Huan Liu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Dzmitry Hrynshpan
- Research Institute of Physical and Chemical Problems, Belarusian State University, Minsk, 220030, Belarus
| | - Tatsiana Savitskaya
- Research Institute of Physical and Chemical Problems, Belarusian State University, Minsk, 220030, Belarus
| | - Jianmeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Jun Chen
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou, 310021, PR China.
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Esmieu C, Orio M, Ménage S, Torelli S. Influence of Copper Coordination Spheres on Nitrous Oxide Reductase (N2Or) Activity of a Mixed-Valent Copper Complex Containing a {Cu2S} Core. Inorg Chem 2019; 58:11649-11655. [DOI: 10.1021/acs.inorgchem.9b01594] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Charlène Esmieu
- CEA-DRF-BIG-LCBM-BioCE, Univ. Grenoble Alpes, CNRS UMR 5249, 17 rue des Martyrs, 38054 Grenoble, France
| | - Maylis Orio
- Institut des Sciences Moléculaires de Marseille, Aix Marseille Université, CNRS, Centrale Marseille, ISM2 UMR 7313, 13097 Marseille, France
| | - Stéphane Ménage
- CEA-DRF-BIG-LCBM-BioCE, Univ. Grenoble Alpes, CNRS UMR 5249, 17 rue des Martyrs, 38054 Grenoble, France
| | - Stéphane Torelli
- CEA-DRF-BIG-LCBM-BioCE, Univ. Grenoble Alpes, CNRS UMR 5249, 17 rue des Martyrs, 38054 Grenoble, France
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