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Li S, Xie X, Li H, Xue D. Relationship between denitrification and anammox rates and N 2 production with substrate consumption and pH in a riparian zone. ENVIRONMENTAL TECHNOLOGY 2024; 45:2531-2540. [PMID: 36973186 DOI: 10.1080/09593330.2023.2177889] [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: 04/08/2022] [Accepted: 01/08/2023] [Indexed: 06/18/2023]
Abstract
Denitrification and anaerobic ammonium oxidation (anammox) are the key processes to quantitatively remove nitrate (NO3-) and balance the nitrogen (N) budget of the ecosystem. In this paper, a slurry-based 15N tracer approach was used to study the correlation and quantitative relation of substrate consumption and pH with rates of denitrification and anammox in a riparian zone. The results showed that the fastest rates of 0.93 µg N h-1 and 0.32 µg N h-1 for denitrification (Denitrif-N2) and anammox (Denitrif-N2), respectively. N2 produced by denitrification occupied 74.04% and produced by anammox occupied 25.96% of the total N2, proving denitrification is the dominant process to remove NO3-. The substrate content (NO3-, NH4+ and TOC) and pH varied during incubation and were significantly correlated with Dentrif-N2 and Anammox-N2. Nitrate and TOC as the substrates of denitrification demonstrated a significant correlation with Anammox-N2, which was associated with the products of denitrification involved in the anammox process. This proved a coupling of denitrification and anammox. A quantitative relationship was observed between Dentrif-N2 and Anammox-N2 in the range of 2.75-2.90 when TOC, NH4+ and NO3- consumption per unit mass or pH changed per unit. Nitrogen mass balance analysis showed that 1 mg N substrate (NO3-+NH4+) consumption in the denitrification and anammox can produce 1.05 mg N2 with a good linear relationship (r2 = 0.9334). This could be related to other processes that produced extra N2 in denitrification and anammox system.
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Affiliation(s)
- Shuangjian Li
- Tianjin Key Laboratory of Water Resources and Environment, Tianjin Normal University, Tianjin, People's Republic of China
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Xuefei Xie
- Tianjin Key Laboratory of Water Resources and Environment, Tianjin Normal University, Tianjin, People's Republic of China
| | - Hu Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Dongmei Xue
- Tianjin Key Laboratory of Water Resources and Environment, Tianjin Normal University, Tianjin, People's Republic of China
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Ganasamurthy S, Rex D, Samad MS, Richards KG, Lanigan GJ, Grelet GA, Clough TJ, Morales SE. Competition and community succession link N transformation and greenhouse gas emissions in urine patches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146318. [PMID: 34030223 DOI: 10.1016/j.scitotenv.2021.146318] [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: 10/07/2020] [Revised: 01/28/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
Nitrous oxide (N2O) is a strong greenhouse gas produced by biotic/abiotic processes directly linked to both fungal and prokaryotic communities that produce, consume or create conditions leading to its emission. In soils exposed to nitrogen (N) in the form of urea, an ecological succession is triggered resulting in a dynamic turnover of microbial populations. However, knowledge of the mechanisms controlling this succession and the repercussions for N2O emissions remain incomplete. Here, we monitored N2O production and fungal/prokaryotic community changes (via 16S and 18S amplicon sequencing) in soil microcosms exposed to urea. Contributions of microbes to emissions were determined using biological inhibitors. Results confirmed that urea leads to shifts in microbial community assemblages by selecting for certain microbial groups (fast growers) as dictated through life history strategies. Urea reduced overall community diversity by conferring dominance to specific groups at different stages in the succession. The diversity lost under urea was recovered with inhibitor addition through the removal of groups that were actively growing under urea indicating that species replacement is mediated in part by competition. Results also identified fungi as significant contributors to N2O emissions, and demonstrate that dominant fungal populations are consistently replaced at different stages of the succession. These successions were affected by addition of inhibitors which resulted in strong decreases in N2O emissions, suggesting that fungal contributions to N2O emissions are larger than that of prokaryotes.
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Affiliation(s)
- Syaliny Ganasamurthy
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
| | - David Rex
- Department of Soil and Physical Sciences, Lincoln University, Lincoln, New Zealand
| | - Md Sainur Samad
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand; Heinrich von Thünen-Institute, Institute for Biodiversity, Braunschweig, Germany
| | - Karl G Richards
- Teagasc, Environmental Research Centre, Johnstown Castle, Wexford, Ireland
| | - Gary J Lanigan
- Teagasc, Environmental Research Centre, Johnstown Castle, Wexford, Ireland
| | - Gwen-Aëlle Grelet
- Manaaki Whenua- Landcare Research, Land Use & Ecosystems Team, Gerald Street, PO, Box 69040, Lincoln 7640, New Zealand
| | - Timothy J Clough
- Department of Soil and Physical Sciences, Lincoln University, Lincoln, New Zealand.
| | - Sergio E Morales
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand.
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Aldossari N, Ishii S. Isolation of cold-adapted nitrate-reducing fungi that have potential to increase nitrate removal in woodchip bioreactors. J Appl Microbiol 2020; 131:197-207. [PMID: 33222401 DOI: 10.1111/jam.14939] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/12/2020] [Accepted: 11/17/2020] [Indexed: 11/27/2022]
Abstract
AIMS The aim of this study was to obtain cold-adapted denitrifying fungi that could be used for bioaugmentation in woodchip bioreactors to remove nitrate from agricultural subsurface drainage water. METHODS AND RESULTS We isolated a total of 91 nitrate-reducing fungal strains belonging to Ascomycota and Mucoromycota from agricultural soil and a woodchip bioreactor under relatively cold conditions (5 and 15°C). When these strains were incubated with 15 N-labelled nitrate, 29 N2 was frequently produced, suggesting the occurrence of co-denitrification (microbially mediated nitrosation). Two strains also produced 30 N2 , indicating their ability to reduce N2 O. Of the 91 nitrate-reducing fungal strains, fungal nitrite reductase gene (nirK) and cytochrome P450 nitric oxide reductase gene (p450nor) were detected by PCR in 34 (37%) and 11 (12%) strains, respectively. Eight strains possessed both nirK and p450nor, further verifying their denitrification capability. In addition, most strains degraded cellulose under denitrification condition. CONCLUSIONS Diverse nitrate-reducing fungi were isolated from soil and a woodchip bioreactor. These fungi reduced nitrate to gaseous N forms at relatively low temperatures. These cold-adapted, cellulose-degrading and nitrate-reducing fungi could support themselves and other denitrifiers in woodchip bioreactors. SIGNIFICANCE AND IMPACT OF THE STUDY The cold-adapted, cellulose-degrading and nitrate-reducing fungi isolated in this study could be useful to enhance nitrate removal in woodchip bioreactors under low-temperature conditions.
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Affiliation(s)
- N Aldossari
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, MN, USA
| | - S Ishii
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, MN, USA.,BioTechnology Institute, University of Minnesota, Saint Paul, MN, USA
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Sebilo M, Aloisi G, Mayer B, Perrin E, Vaury V, Mothet A, Laverman AM. Controls on the Isotopic Composition of Nitrite (δ 15N and δ 18O) during Denitrification in Freshwater Sediments. Sci Rep 2019; 9:19206. [PMID: 31844081 PMCID: PMC6915737 DOI: 10.1038/s41598-019-54014-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 10/30/2019] [Indexed: 12/15/2022] Open
Abstract
The microbial reduction of nitrate, via nitrite into gaseous di-nitrogen (denitrification) plays a major role in nitrogen removal from aquatic ecosystems. Natural abundance stable isotope measurements can reveal insights into the dynamics of production and consumption of nitrite during denitrification. In this study, batch experiments with environmental bacterial communities were used to investigate variations of concentrations and isotope compositions of both nitrite and nitrate under anoxic conditions. To this end, denitrification experiments were carried out with nitrite or nitrate as sole electron acceptors at two substrate levels respectively. For experiments with nitrate as substrate, where the intermediate compound nitrite is both substrate and product of denitrification, calculations of the extent of isotope fractionation were conducted using a non-steady state model capable of tracing chemical and isotope kinetics during denitrification. This study showed that nitrogen isotope fractionation was lower during the use of nitrite as substrate (ε = −4.2 and −4.5‰ for both treatments) as compared to experiments where nitrite was produced as an intermediate during nitrate reduction (ε = −10 and −15‰ for both treatments). This discrepancy might be due to isotopic fractionation within the membrane of denitrifiers. Moreover, our results confirmed previously observed rapid biotic oxygen isotope exchange between nitrite and water.
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Affiliation(s)
- Mathieu Sebilo
- Sorbonne Université, CNRS, IEES, F-75005, Paris, France. .,CNRS/UNIV PAU & PAYS ADOUR/E2S UPPA, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux (IPREM), UMR 5254, 64000, Pau, France.
| | - Giovanni Aloisi
- Université de Paris, Institut de physique du globe de Paris, CNRS, 1 Rue Jussieu, 75005, Paris, France
| | - Bernhard Mayer
- Applied Geochemistry Group, Department of Geoscience, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada, T2N 1N4
| | - Emilie Perrin
- Sorbonne Université, CNRS, IEES, F-75005, Paris, France
| | | | | | - Anniet M Laverman
- Université de Rennes 1, CNRS, Ecobio, campus de Beaulieu, 263 avenue du Général Leclerc, 35042, Rennes Cédex, France
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Abbas T, Zhou H, Zhang Q, Li Y, Liang Y, Di H, Zhao Y. Anammox co-fungi accompanying denitrifying bacteria are the thieves of the nitrogen cycle in paddy-wheat crop rotated soils. ENVIRONMENT INTERNATIONAL 2019; 130:104913. [PMID: 31254866 DOI: 10.1016/j.envint.2019.104913] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/06/2019] [Accepted: 06/09/2019] [Indexed: 06/09/2023]
Abstract
Anammox bacteria are the key microbes after denitrifiers in the anaerobic environment. Nitrogen gap cannot be satisfied till date even with the advanced techniques, due to complex microbial network and different pathways. Recently, anaerobic fungi are the concerning point to investigate, which was previously ignored for a long time. Study was conducted with the aim of assessment of an individual and combined contribution of anammox, co-denitrification, and denitrification processes for N losses, under different organic-chemical fertilizers, i.e. 1) control _CK; 2) chemical fertilization _CF; 3) pig manure plus chemical fertilization _PMCF; and 4) straw returned plus chemical fertilization _SRCF). Hybrid techniques of 13C-DNA-Stable isotope and 15N isotopic tracer were used to discriminate the contribution of anammox-co-fungi using antibacterial and antifungal inhibitors. Results showed that fungi are the major culprit in N losses; the overall contribution rate by anammox-co-denitrification was 14.82-29.74%. While in case of individual N losses, fungi were dominating the N losses (3.51-25.60%, AB) than bacteria (7.50-21.80%, AF). The anammox and fungi have a positive correlation with each other's (r = 0.67), principal component analysis (PCA) and correlation analysis validate each other (anammox and fungi), and both showed the same type of attraction to the soil physicochemical properties. However, fungi did not show a significant relationship with NH+4-N (r = 0.38). A clone library of 13C-DNA-SIP was constructed, and results showed that denitrifying fungi were very likely belonges to the genera Agaricus, Aspergillus, Phycomyces, Saitoella, and Trichoderma. Conclusively, we propose that fertilization pattern can change anammox activity and abundance, but fungal activity and community structure undergo changes with organic amendments rather than inorganic fertilizers.
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Affiliation(s)
- Touqeer Abbas
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Zhejiang University, Hangzhou 310058, PR China
| | - Huifang Zhou
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Zhejiang University, Hangzhou 310058, PR China
| | - Qichun Zhang
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Zhejiang University, Hangzhou 310058, PR China.
| | - Yong Li
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Zhejiang University, Hangzhou 310058, PR China
| | - Yongchao Liang
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Zhejiang University, Hangzhou 310058, PR China
| | - Hongjie Di
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Zhejiang University, Hangzhou 310058, PR China
| | - Yuhua Zhao
- College of Life Science, Zhejiang University, Hangzhou 310058, PR China
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Yoon S, Song B, Phillips RL, Chang J, Song MJ. Ecological and physiological implications of nitrogen oxide reduction pathways on greenhouse gas emissions in agroecosystems. FEMS Microbiol Ecol 2019; 95:5488431. [DOI: 10.1093/femsec/fiz066] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 05/10/2019] [Indexed: 11/12/2022] Open
Abstract
ABSTRACT
Microbial reductive pathways of nitrogen (N) oxides are highly relevant to net emissions of greenhouse gases (GHG) from agroecosystems. Several biotic and abiotic N-oxide reductive pathways influence the N budget and net GHG production in soil. This review summarizes the recent findings of N-oxide reduction pathways and their implications to GHG emissions in agroecosystems and proposes several mitigation strategies. Denitrification is the primary N-oxide reductive pathway that results in direct N2O emissions and fixed N losses, which add to the net carbon footprint. We highlight how dissimilatory nitrate reduction to ammonium (DNRA), an alternative N-oxide reduction pathway, may be used to reduce N2O production and N losses via denitrification. Implications of nosZ abundance and diversity and expressed N2O reductase activity to soil N2O emissions are reviewed with focus on the role of the N2O-reducers as an important N2O sink. Non-prokaryotic N2O sources, e.g. fungal denitrification, codenitrification and chemodenitrification, are also summarized to emphasize their potential significance as modulators of soil N2O emissions. Through the extensive review of these recent scientific advancements, this study posits opportunities for GHG mitigation through manipulation of microbial N-oxide reductive pathways in soil.
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Affiliation(s)
- Sukhwan Yoon
- Department of Civil and Environmental Engineering, KAIST, 291 Daehakro, Yuseonggu, Daejeon 34141, South Korea
| | - Bongkeun Song
- Department of Biological Sciences, Virginia Institute of Marine Sciences, College of William and Mary, 1375 Greate Rd, Gloucester Point, VA 23062, USA
| | - Rebecca L Phillips
- Ecological Insights Corporation, 130 69th Street SE, Hazelton, ND 58544, USA
| | - Jin Chang
- Department of Civil and Environmental Engineering, KAIST, 291 Daehakro, Yuseonggu, Daejeon 34141, South Korea
| | - Min Joon Song
- Department of Civil and Environmental Engineering, KAIST, 291 Daehakro, Yuseonggu, Daejeon 34141, South Korea
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Zhang Y, Ding H, Zheng X, Ren X, Cardenas L, Carswell A, Misselbrook T. Land-use type affects N 2O production pathways in subtropical acidic soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 237:237-243. [PMID: 29486457 DOI: 10.1016/j.envpol.2018.02.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 01/10/2018] [Accepted: 02/15/2018] [Indexed: 06/08/2023]
Abstract
The change in land-use from woodland to crop production leads to increased nitrous oxide (N2O) emissions. An understanding of the main N2O sources in soils under a particular land can be a useful tool in developing mitigation strategies. To better understand the effect of land-use on N2O emissions, soils were collected from 5 different land-uses in southeast China: shrub land (SB), eucalyptus plantation (ET), sweet potato farmland (SP), citrus orchard (CO) and vegetable growing farmland (VE). A stable isotope experiment was conducted incubating soils from the different land use types at 60% water holding capacity (WHC), using 15NH4NO3 and NH415NO3 to determine the dominant N2O production pathway for the different land-uses. The average N2O emission rates for VE, CO and SP were 5.30, 4.23 and 3.36 μg N kg-1 dry soil d-1, greater than for SB and ET at 0.98 and 1.10 μg N kg-1 dry soil d-1, respectively. N2O production was dominated by heterotrophic nitrification for SB and ET, accounting for 51 and 50% of N2O emissions, respectively. However, heterotrophic nitrification was negligible (<8%) in SP, CO and VE, where autotrophic nitrification was a primary driver of N2O production, accounting for 44, 45 and 66% for SP, CO and VE, respectively. Denitrification was also an important pathway of N2O production across all land-uses, accounting for 35, 35, 49, 52 and 32% for SB, ET, SP, CO and VE respectively. Average N2O emission rates via autotrophic nitrification, denitrification and heterotrophic nitrification increased significantly with gross nitrification rates, NO3- contents and C:N ratios respectively, indicating that these were important factors in the N2O production pathways for these soils. These results contribute to our understanding and ability to predict N2O emissions from different land-uses in subtropical acidic soils and in developing potential mitigation strategies.
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Affiliation(s)
- Yushu Zhang
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, PR China; Sustainable Agricultural Sciences, Rothamsted Research, Devon, EX20 2SB, UK.
| | - Hong Ding
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, PR China
| | - Xiangzhou Zheng
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, PR China
| | - Xiangyun Ren
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, PR China
| | - Laura Cardenas
- Sustainable Agricultural Sciences, Rothamsted Research, Devon, EX20 2SB, UK
| | - Alison Carswell
- Sustainable Agricultural Sciences, Rothamsted Research, Devon, EX20 2SB, UK
| | - Tom Misselbrook
- Sustainable Agricultural Sciences, Rothamsted Research, Devon, EX20 2SB, UK.
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Posmanik R, Nejidat A, Dahan O, Gross A. Seasonal and soil-type dependent emissions of nitrous oxide from irrigated desert soils amended with digested poultry manures. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 593-594:91-98. [PMID: 28342421 DOI: 10.1016/j.scitotenv.2017.03.115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/10/2017] [Accepted: 03/11/2017] [Indexed: 06/06/2023]
Abstract
Expansion of dryland agriculture requires intensive supplement of organic fertilizers to improve the fertility of nutrient-poor desert soils. The environmental impact of organic supplements in hot desert climates is not well understood. We report on seasonal emissions of nitrous oxide (N2O) from sand and loess soils, amended with limed and non-limed anaerobic digestate of poultry manure in the Israeli Negev desert. All amended soils had substantially higher N2O emissions, particularly during winter applications, compared to unammended soils. Winter emissions from amended loess (10-175mgN2Om-2day-1) were markedly higher than winter emissions from amended sand (2-7mgN2Om-2day-1). Enumeration of marker genes for nitrification and denitrification suggested that both have contributed to N2O emissions according to prevailing environmental conditions. Lime treatment of digested manure inhibited N2O emissions regardless of season or soil type, thus reducing the environmental impact of amending desert soils with manure digestate.
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Affiliation(s)
- Roy Posmanik
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990, Israel
| | - Ali Nejidat
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990, Israel.
| | - Ofer Dahan
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990, Israel
| | - Amit Gross
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990, Israel.
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Rohe L, Well R, Lewicka-Szczebak D. Use of oxygen isotopes to differentiate between nitrous oxide produced by fungi or bacteria during denitrification. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1297-1312. [PMID: 28556299 DOI: 10.1002/rcm.7909] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 05/23/2017] [Accepted: 05/23/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Fungal denitrifiers can contribute substantially to N2 O emissions from arable soil and show a distinct site preference for N2 O (SP(N2 O)). This study sought to identify another process-specific isotopic tool to improve precise identification of N2 O of fungal origin by mass spectrometric analysis of the N2 O produced. METHODS Three pure bacterial and three fungal species were incubated under denitrifying conditions in treatments with natural abundance and stable isotope labelling to analyse the N2 O produced. Combining different applications of isotope ratio mass spectrometry enabled us to estimate the oxygen (O) exchange accelerated by denitrifying enzymes and the ongoing microbial pathway in parallel. This experimental set-up allowed the determination of δ18 O(N2 O) values and isotopic fractionation of O, as well as SP(N2 O) values, as a perspective to differentiate between microbial denitrifiers. RESULTS Oxygen exchange during N2 O production was lower for bacteria than for fungi, differed between species, and depended also on incubation time. Apparent O isotopic fractionation during denitrification was in a similar range for bacteria and fungi, but application of the fractionation model indicated that different enzymes in bacteria and fungi were responsible for O exchange. This difference was associated with different isotopic fractionation for bacteria and fungi. CONCLUSIONS δ18 O(N2 O) values depend on isotopic fractionation and isotopic fractionation may differ between processes and organism groups. By comparing SP(N2 O) values, O exchange and the isotopic signature of precursors, we propose here a novel tool for differentiating between different sources of N2 O.
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Affiliation(s)
- Lena Rohe
- Thünen Institute of Climate-Smart Agriculture, Braunschweig, Germany
| | - Reinhard Well
- Thünen Institute of Climate-Smart Agriculture, Braunschweig, Germany
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Terada A, Sugawara S, Hojo K, Takeuchi Y, Riya S, Harper WF, Yamamoto T, Kuroiwa M, Isobe K, Katsuyama C, Suwa Y, Koba K, Hosomi M. Hybrid Nitrous Oxide Production from a Partial Nitrifying Bioreactor: Hydroxylamine Interactions with Nitrite. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:2748-2756. [PMID: 28164698 DOI: 10.1021/acs.est.6b05521] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The goal of this study was to elucidate the mechanisms of nitrous oxide (N2O) production from a bioreactor for partial nitrification (PN). Ammonia-oxidizing bacteria (AOB) enriched from a sequencing batch reactor (SBR) were subjected to N2O production pathway tests. The N2O pathway test was initiated by supplying an inorganic medium to ensure an initial NH4+-N concentration of 160 mg-N/L, followed by 15NO2- (20 mg-N/L) and dual 15NH2OH (each 17 mg-N/L) spikings to quantify isotopologs of gaseous N2O (44N2O, 45N2O, and 46N2O). N2O production was boosted by 15NH2OH spiking, causing exponential increases in mRNA transcription levels of AOB functional genes encoding hydroxylamine oxidoreductase (haoA), nitrite reductase (nirK), and nitric oxide reductase (norB) genes. Predominant production of 45N2O among N2O isotopologs (46% of total produced N2O) indicated that coupling of 15NH2OH with 14NO2- produced N2O via N-nitrosation hybrid reaction as a predominant pathway. Abiotic hybrid N2O production was also observed in the absence of the AOB-enriched biomass, indicating multiple pathways for N2O production in a PN bioreactor. The additional N2O pathway test, where 15NH4+ was spiked into 400 mg-N/L of NO2- concentration, confirmed that the hybrid N2O production was a dominant pathway, accounting for approximately 51% of the total N2O production.
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Affiliation(s)
- Akihiko Terada
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology , 2-24-16 Naka, Koganei, Tokyo 184-8588 Japan
| | - Sho Sugawara
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology , 2-24-16 Naka, Koganei, Tokyo 184-8588 Japan
| | - Keisuke Hojo
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology , 2-24-16 Naka, Koganei, Tokyo 184-8588 Japan
| | - Yuki Takeuchi
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology , 2-24-16 Naka, Koganei, Tokyo 184-8588 Japan
| | - Shohei Riya
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology , 2-24-16 Naka, Koganei, Tokyo 184-8588 Japan
| | - Willie F Harper
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology , 2-24-16 Naka, Koganei, Tokyo 184-8588 Japan
- Department of Systems Engineering and Management, Air Force Institute of Technology , Dayton, Ohio, United States
| | - Tomoko Yamamoto
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology , 2-24-16 Naka, Koganei, Tokyo 184-8588 Japan
| | - Megumi Kuroiwa
- Department of Environmental and Natural Resource Sciences, Tokyo University of Agriculture and Technology , Saiwai-cho Fuchu, Tokyo, Japan
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo , Yayoi, Bunkyo, Tokyo, Japan
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University , Bunkyo, Tokyo, Japan
| | - Kazuo Isobe
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo , Yayoi, Bunkyo, Tokyo, Japan
| | - Chie Katsuyama
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University , Bunkyo, Tokyo, Japan
| | - Yuichi Suwa
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University , Bunkyo, Tokyo, Japan
| | - Keisuke Koba
- Department of Environmental and Natural Resource Sciences, Tokyo University of Agriculture and Technology , Saiwai-cho Fuchu, Tokyo, Japan
| | - Masaaki Hosomi
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology , 2-24-16 Naka, Koganei, Tokyo 184-8588 Japan
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Toyoda S, Yoshida N, Koba K. Isotopocule analysis of biologically produced nitrous oxide in various environments. MASS SPECTROMETRY REVIEWS 2017; 36:135-160. [PMID: 25869149 DOI: 10.1002/mas.21459] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 01/13/2015] [Accepted: 01/13/2015] [Indexed: 06/04/2023]
Abstract
Natural abundance ratios of isotopocules, molecules that have the same chemical constitution and configuration, but that only differ in isotope substitution, retain a record of a compound's origin and reactions. A method to measure isotopocule ratios of nitrous oxide (N2 O) has been established by using mass analysis of molecular ions and fragment ions. The method has been applied widely to environmental samples from the atmosphere, ocean, fresh water, soils, and laboratory-simulation experiments. Results show that isotopocule ratios, particularly the 15 N-site preference (difference between isotopocule ratios 14 N15 N16 O/14 N14 N16 O and 15 N14 N16 O/14 N14 N16 O), have a wide range that depends on their production and consumption processes. Observational and laboratory studies of N2 O related to biological processes are reviewed and discussed to elucidate complex material cycles of this trace gas, which causes global warming and stratospheric ozone depletion. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:135-160, 2017.
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Affiliation(s)
- Sakae Toyoda
- Department of Environmental Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502, Japan
| | - Naohiro Yoshida
- Department of Environmental Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502, Japan
- Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Keisuke Koba
- Institute of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-City, Tokyo 183-8509, Japan
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12
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Phillips RL, Song B, McMillan AMS, Grelet G, Weir BS, Palmada T, Tobias C. Chemical formation of hybrid di-nitrogen calls fungal codenitrification into question. Sci Rep 2016; 6:39077. [PMID: 27976694 PMCID: PMC5157039 DOI: 10.1038/srep39077] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/17/2016] [Indexed: 11/09/2022] Open
Abstract
Removal of excess nitrogen (N) can best be achieved through denitrification processes that transform N in water and terrestrial ecosystems to di-nitrogen (N2) gas. The greenhouse gas nitrous oxide (N2O) is considered an intermediate or end-product in denitrification pathways. Both abiotic and biotic denitrification processes use a single N source to form N2O. However, N2 can be formed from two distinct N sources (known as hybrid N2) through biologically mediated processes of anammox and codenitrification. We questioned if hybrid N2 produced during fungal incubation at neutral pH could be attributed to abiotic nitrosation and if N2O was consumed during N2 formation. Experiments with gas chromatography indicated N2 was formed in the presence of live and dead fungi and in the absence of fungi, while N2O steadily increased. We used isotope pairing techniques and confirmed abiotic production of hybrid N2 under both anoxic and 20% O2 atmosphere conditions. Our findings question the assumptions that (1) N2O is an intermediate required for N2 formation, (2) production of N2 and N2O requires anaerobiosis, and (3) hybrid N2 is evidence of codenitrification and/or anammox. The N cycle framework should include abiotic production of N2.
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Affiliation(s)
| | - Bongkeun Song
- Dept. of Biological Sciences, Virginia Institute of Marine Science, Gloucester Point, Virginia, USA
| | | | - Gwen Grelet
- Landcare Research, Gerald Street, Lincoln, New Zealand
| | - Bevan S Weir
- Landcare Research, Gerald Street, Lincoln, New Zealand
| | | | - Craig Tobias
- Dept. of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
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13
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Xi D, Bai R, Zhang L, Fang Y. Contribution of Anammox to Nitrogen Removal in Two Temperate Forest Soils. Appl Environ Microbiol 2016; 82:4602-4612. [PMID: 27208117 PMCID: PMC4984287 DOI: 10.1128/aem.00888-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/17/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Anaerobic ammonium oxidation with nitrite reduction to dinitrogen (termed anammox) has been reported to be an important process for removing fixed nitrogen (N) in marine ecosystems and in some agricultural and wetland soils. However, its importance in upland forest soils has never been quantified. In this study, we evaluated the occurrence of anammox activity in two temperate forest soils collected from northeastern China. With (15)N-labeled NO3 (-) incubation, we found that the combined potential of the N2 production rates of anammox and codenitrification ranged from 0.01 ± 0.01 to 1.2 ± 0.18 nmol N per gram of soil per hour, contributing 0.5% to 14.4% of the total N2 production along the soil profile. Denitrification was the main pathway of N2 production and accounted for 85.6% to 99.5% of the total N2 production. Further labeling experiments with (15)NH4 (+) and (15)NO2 (-) indicated that codenitrification was present in the mixed forest soil. Codenitrification and anammox accounted for 2% to 12% and 1% to 7% of the total N2 production, respectively. Two anammox species, "Candidatus Brocadia fulgida" and "Candidatus Jettenia asiatica," were detected in this study but in very low abundance (as indicated by the hzsB gene). Our results demonstrated that the anammox process occurs in forest soils, but the contribution to N2 loss might be low in these ecosystems. More research is necessary to determine the activities of different N2 releasing pathways in different forest soils. IMPORTANCE In this study, we examined the anammox activity in temperate upland forest soils using the (15)N isotope technique. We found that the anammox process contributed little to the N2 production rate in the studied forest soil. Two anammox organisms, "Candidatus Brocadia fulgida" and "Candidatus Jettenia asiatica," were detected. In addition, we found that codenitrification was another N2 production pathway in forest soils. Our results could contribute to the understanding of soil gaseous N losses and microbial controls in forest soils.
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Affiliation(s)
- Dan Xi
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- Qingyuan Forest CERN, Shenyang, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Ren Bai
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Limei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing, China
| | - Yunting Fang
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- Qingyuan Forest CERN, Shenyang, China
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14
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Higgins SA, Welsh A, Orellana LH, Konstantinidis KT, Chee-Sanford JC, Sanford RA, Schadt CW, Löffler FE. Detection and Diversity of Fungal Nitric Oxide Reductase Genes (p450nor) in Agricultural Soils. Appl Environ Microbiol 2016; 82:2919-2928. [PMID: 26969694 PMCID: PMC4959062 DOI: 10.1128/aem.00243-16] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 03/03/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Members of the Fungi convert nitrate (NO3 (-)) and nitrite (NO2 (-)) to gaseous nitrous oxide (N2O) (denitrification), but the fungal contributions to N loss from soil remain uncertain. Cultivation-based methodologies that include antibiotics to selectively assess fungal activities have limitations, and complementary molecular approaches to assign denitrification potential to fungi are desirable. Microcosms established with soils from two representative U.S. Midwest agricultural regions produced N2O from added NO3 (-) or NO2 (-) in the presence of antibiotics to inhibit bacteria. Cultivation efforts yielded 214 fungal isolates belonging to at least 15 distinct morphological groups, 151 of which produced N2O from NO2 (-) Novel PCR primers targeting the p450nor gene, which encodes the nitric oxide (NO) reductase responsible for N2O production in fungi, yielded 26 novel p450nor amplicons from DNA of 37 isolates and 23 amplicons from environmental DNA obtained from two agricultural soils. The sequences shared 54 to 98% amino acid identity with reference P450nor sequences within the phylum Ascomycota and expand the known fungal P450nor sequence diversity. p450nor was detected in all fungal isolates that produced N2O from NO2 (-), whereas nirK (encoding the NO-forming NO2 (-) reductase) was amplified in only 13 to 74% of the N2O-forming isolates using two separate nirK primer sets. Collectively, our findings demonstrate the value of p450nor-targeted PCR to complement existing approaches to assess the fungal contributions to denitrification and N2O formation. IMPORTANCE A comprehensive understanding of the microbiota controlling soil N loss and greenhouse gas (N2O) emissions is crucial for sustainable agricultural practices and addressing climate change concerns. We report the design and application of a novel PCR primer set targeting fungal p450nor, a biomarker for fungal N2O production, and demonstrate the utility of the new approach to assess fungal denitrification potential in fungal isolates and agricultural soils. These new PCR primers may find application in a variety of biomes to assess the fungal contributions to N loss and N2O emissions.
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Affiliation(s)
- Steven A Higgins
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Allana Welsh
- Department of Geology, University of Illinois, Urbana, Illinois, USA
| | - Luis H Orellana
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | | | - Robert A Sanford
- Department of Geology, University of Illinois, Urbana, Illinois, USA
| | - Christopher W Schadt
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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15
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Braker G, Conrad R. Diversity, structure, and size of N(2)O-producing microbial communities in soils--what matters for their functioning? ADVANCES IN APPLIED MICROBIOLOGY 2016; 75:33-70. [PMID: 21807245 DOI: 10.1016/b978-0-12-387046-9.00002-5] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Nitrous oxide (N(2)O) is mainly generated via nitrification and denitrification processes in soils and subsequently emitted into the atmosphere where it causes well-known radiative effects. How nitrification and denitrification are affected by proximal and distal controls has been studied extensively in the past. The importance of the underlying microbial communities, however, has been acknowledged only recently. Particularly, the application of molecular methods to study nitrifiers and denitrifiers directly in their habitats enabled addressing how environmental factors influence the diversity, community composition, and size of these functional groups in soils and whether this is of relevance for their functioning and N(2)O production. In this review, we summarize the current knowledge on community-function interrelationships. Aerobic nitrification (ammonia oxidation) and anaerobic denitrification are clearly under different controls. While N(2)O is an obligatory intermediate in denitrification, its production during ammonia oxidation depends on whether nitrite, the end product, is further reduced. Moreover, individual strains vary strongly in their responses to environmental cues, and so does N(2)O production. We therefore conclude that size and structure of both functional groups are relevant with regard to production and emission of N(2)O from soils. Diversity affects on function, however, are much more difficult to assess, as it is not resolved as yet how individual nitrification or denitrification genotypes are related to N(2)O production. More research is needed for further insights into the relation of microbial communities to ecosystem functions, for instance, how the actively nitrifying or denitrifying part of the community may be related to N(2)O emission.
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Affiliation(s)
- Gesche Braker
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, Marburg, Germany.
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16
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Chen H, Mothapo NV, Shi W. Soil moisture and pH control relative contributions of fungi and bacteria to N2O production. MICROBIAL ECOLOGY 2015; 69:180-191. [PMID: 25190581 DOI: 10.1007/s00248-014-0488-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 08/25/2014] [Indexed: 06/03/2023]
Abstract
Fungal N(2)O production has been progressively recognized, but its controlling factors remain unclear. This study examined the impacts of soil moisture and pH on fungal and bacterial N(2)O production in two ecosystems, conventional farming and plantation forestry. Four treatments, antibiotic-free soil and soil amended with streptomycin, cycloheximide, or both were used to determine N(2)O production of fungi versus bacteria. Soil moisture and pH effects were assessed under 65-90 % water-filled pore space (WFPS) and pH 4.0-9.0, respectively. Irrespective of antibiotic treatments, soil N(2)O fluxes peaked at 85-90 % WFPS and pH 7.0 or 8.0, indicating that both fungi and bacteria preferred more anoxic and neutral or slightly alkaline conditions in producing N(2)O. However, compared with bacteria, fungi contributed more to N(2)O production under sub-anoxic and acidic conditions. Real-time polymerase chain reaction of 16S, ITS rDNA, and denitrifying genes for quantifications of bacteria, fungi, and denitrifying bacteria, respectively, showed that fungi were more abundant at acidic pH, whereas total and denitrifying bacteria favored neutral conditions. Such variations in the abundance appeared to be related to the pH effects on the relative fungal and bacterial contribution to N(2)O production.
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Affiliation(s)
- Huaihai Chen
- Department of Soil Science, North Carolina State University, Raleigh, NC, 27695, USA
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17
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Harter J, Krause HM, Schuettler S, Ruser R, Fromme M, Scholten T, Kappler A, Behrens S. Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community. THE ISME JOURNAL 2014; 8:660-674. [PMID: 24067258 PMCID: PMC3930306 DOI: 10.1038/ismej.2013.160] [Citation(s) in RCA: 210] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 08/09/2013] [Accepted: 08/14/2013] [Indexed: 11/08/2022]
Abstract
Nitrous oxide (N2O) contributes 8% to global greenhouse gas emissions. Agricultural sources represent about 60% of anthropogenic N2O emissions. Most agricultural N2O emissions are due to increased fertilizer application. A considerable fraction of nitrogen fertilizers are converted to N2O by microbiological processes (that is, nitrification and denitrification). Soil amended with biochar (charcoal created by pyrolysis of biomass) has been demonstrated to increase crop yield, improve soil quality and affect greenhouse gas emissions, for example, reduce N2O emissions. Despite several studies on variations in the general microbial community structure due to soil biochar amendment, hitherto the specific role of the nitrogen cycling microbial community in mitigating soil N2O emissions has not been subject of systematic investigation. We performed a microcosm study with a water-saturated soil amended with different amounts (0%, 2% and 10% (w/w)) of high-temperature biochar. By quantifying the abundance and activity of functional marker genes of microbial nitrogen fixation (nifH), nitrification (amoA) and denitrification (nirK, nirS and nosZ) using quantitative PCR we found that biochar addition enhanced microbial nitrous oxide reduction and increased the abundance of microorganisms capable of N2-fixation. Soil biochar amendment increased the relative gene and transcript copy numbers of the nosZ-encoded bacterial N2O reductase, suggesting a mechanistic link to the observed reduction in N2O emissions. Our findings contribute to a better understanding of the impact of biochar on the nitrogen cycling microbial community and the consequences of soil biochar amendment for microbial nitrogen transformation processes and N2O emissions from soil.
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Affiliation(s)
- Johannes Harter
- Geomicrobiology and Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Tuebingen, Germany
| | - Hans-Martin Krause
- Geomicrobiology and Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Tuebingen, Germany
| | - Stefanie Schuettler
- Geomicrobiology and Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Tuebingen, Germany
| | - Reiner Ruser
- Fertilisation and Soil Matter Dynamics, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Markus Fromme
- Department of Geography, Soil Science and Geomorphology, University of Tuebingen, Tuebingen, Germany
| | - Thomas Scholten
- Department of Geography, Soil Science and Geomorphology, University of Tuebingen, Tuebingen, Germany
| | - Andreas Kappler
- Geomicrobiology and Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Tuebingen, Germany
| | - Sebastian Behrens
- Geomicrobiology and Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Tuebingen, Germany.
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18
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Butterbach-Bahl K, Baggs EM, Dannenmann M, Kiese R, Zechmeister-Boltenstern S. Nitrous oxide emissions from soils: how well do we understand the processes and their controls? Philos Trans R Soc Lond B Biol Sci 2013; 368:20130122. [PMID: 23713120 PMCID: PMC3682742 DOI: 10.1098/rstb.2013.0122] [Citation(s) in RCA: 651] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Although it is well established that soils are the dominating source for atmospheric nitrous oxide (N2O), we are still struggling to fully understand the complexity of the underlying microbial production and consumption processes and the links to biotic (e.g. inter- and intraspecies competition, food webs, plant–microbe interaction) and abiotic (e.g. soil climate, physics and chemistry) factors. Recent work shows that a better understanding of the composition and diversity of the microbial community across a variety of soils in different climates and under different land use, as well as plant–microbe interactions in the rhizosphere, may provide a key to better understand the variability of N2O fluxes at the soil–atmosphere interface. Moreover, recent insights into the regulation of the reduction of N2O to dinitrogen (N2) have increased our understanding of N2O exchange. This improved process understanding, building on the increased use of isotope tracing techniques and metagenomics, needs to go along with improvements in measurement techniques for N2O (and N2) emission in order to obtain robust field and laboratory datasets for different ecosystem types. Advances in both fields are currently used to improve process descriptions in biogeochemical models, which may eventually be used not only to test our current process understanding from the microsite to the field level, but also used as tools for up-scaling emissions to landscapes and regions and to explore feedbacks of soil N2O emissions to changes in environmental conditions, land management and land use.
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Affiliation(s)
- Klaus Butterbach-Bahl
- Karlsruhe Institute of Technology, Institute for Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU), Kreuzeckbahnstrasse 19, Garmisch-Partenkirchen 82467, Germany.
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19
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Co-occurring anammox, denitrification, and codenitrification in agricultural soils. Appl Environ Microbiol 2012; 79:168-76. [PMID: 23087029 DOI: 10.1128/aem.02520-12] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anammox and denitrification mediated by bacteria are known to be the major microbial processes converting fixed N to N(2) gas in various ecosystems. Codenitrification and denitrification by fungi are additional pathways producing N(2) in soils. However, fungal codenitrification and denitrification have not been well investigated in agricultural soils. To evaluate bacterial and fungal processes contributing to N(2) production, molecular and (15)N isotope analyses were conducted with soil samples collected at six different agricultural fields in the United States. Denitrifying and anammox bacterial abundances were measured based on quantitative PCR (qPCR) of nitrous oxide reductase (nosZ) and hydrazine oxidase (hzo) genes, respectively, while the internal transcribed spacer (ITS) of Fusarium oxysporum was quantified to estimate the abundance of codenitrifying and denitrifying fungi. (15)N tracer incubation experiments with (15)NO(3)(-) or (15)NH(4)(+) addition were conducted to measure the N(2) production rates from anammox, denitrification, and codenitrification. Soil incubation experiments with antibiotic treatments were also used to differentiate between fungal and bacterial N(2) production rates in soil samples. Denitrifying bacteria were found to be the most abundant, followed by F. oxysporum based on the qPCR assays. The potential denitrification rates by bacteria and fungi ranged from 4.118 to 42.121 nmol N(2)-N g(-1) day(-1), while the combined potential rates of anammox and codenitrification ranged from 2.796 to 147.711 nmol N(2)-N g(-1) day(-1). Soil incubation experiments with antibiotics indicated that fungal codenitrification was the primary process contributing to N(2) production in the North Carolina soil. This study clearly demonstrates the importance of fungal processes in the agricultural N cycle.
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20
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Prendergast-Miller MT, Baggs EM, Johnson D. Nitrous oxide production by the ectomycorrhizal fungi Paxillus involutus and Tylospora fibrillosa. FEMS Microbiol Lett 2011; 316:31-5. [DOI: 10.1111/j.1574-6968.2010.02187.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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21
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Kool DM, Van Groenigen JW, Wrage N. Source Determination of Nitrous Oxide Based on Nitrogen and Oxygen Isotope Tracing. Methods Enzymol 2011; 496:139-60. [DOI: 10.1016/b978-0-12-386489-5.00006-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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22
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23
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Seo DC, DeLaune RD. Fungal and bacterial mediated denitrification in wetlands: influence of sediment redox condition. WATER RESEARCH 2010; 44:2441-2450. [PMID: 20122708 DOI: 10.1016/j.watres.2010.01.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Revised: 01/05/2010] [Accepted: 01/07/2010] [Indexed: 05/28/2023]
Abstract
Fungal and bacterial denitrification rates were determined under a range of redox conditions in sediment from a Louisiana swamp forest used for wastewater treatment. Sediment was incubated in microcosms at 6 Eh levels (-200, -100, 0, +100, +250 and +400 mV) ranging from strongly reducing to moderately oxidizing conditions. Denitrification was determined using the substrate-induced respiration (SIR) inhibition and acetylene inhibition methods. Cycloheximide (C15H23NO4) was used as the fungal inhibitor and streptomycin (C21H39N7O12) as the bacterial inhibitor. At Eh values of +250 mV and +400 mV, denitrification rates by fungi and bacteria were 34.3-35.1% and 1.46-1.59% of total denitrification, respectively, indicating that fungi were responsible for most of the denitrification under aerobic or weakly reducing conditions. On the other hand, at Eh -200 mV, denitrification rates of fungi and bacteria were 17.6% and 64.9% of total denitrification, respectively, indicating that bacteria were responsible for most of the denitrification under strongly reducing conditions. Results show fungal denitrification was dominant under moderately reducing to weakly oxidizing conditions (Eh>+250 mV), whereas bacterial denitrification was dominant under strongly reducing condition (Eh<-100 mV). At Eh values between -100 to +100 mV, denitrification by fungi and bacteria were 37.9-43.2% and 53.0-51.1% of total denitrification, respectively, indicating that both bacteria and fungi contributed significantly to denitrification under these redox conditions. Because N2O is an important gaseous denitrification product in sediment, fungal denitrification could be of greater ecological significance under aerobic or moderately reducing conditions contributing to greenhouse gas emission and global warming potential (GWP).
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Affiliation(s)
- Dong Cheol Seo
- Department of Oceanography and Coastal Sciences, School of the Coast and Environment, Louisiana State University, Baton Rouge, LA 70803, USA
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24
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Kool DM, Wrage N, Oenema O, Harris D, Van Groenigen JW. The 18O signature of biogenic nitrous oxide is determined by O exchange with water. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:104-108. [PMID: 19061209 DOI: 10.1002/rcm.3859] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To effectively mitigate emissions of the greenhouse gas nitrous oxide (N(2)O) it is essential to understand the biochemical pathways by which it is produced. The (18)O signature of N(2)O is increasingly used to characterize these processes. However, assumptions on the origin of the O atom and resultant isotopic composition of N(2)O that are based on reaction stoichiometry may be questioned. In particular, our deficient knowledge on O exchange between H(2)O and nitrogen oxides during N(2)O production complicates the interpretation of the (18)O signature of N(2)O.Here we studied O exchange during N(2)O formation in soil, using a novel combination of (18)O and (15)N tracing. Twelve soils were studied, covering soil and land-use variability across Europe. All soils demonstrated the significant presence of O exchange, as incorporation of O from (18)O-enriched H(2)O into N(2)O exceeded their maxima achievable through reaction stoichiometry. Based on the retention of the enrichment ratio of (18)O and (15)N of NO(3)(-) into N(2)O, we quantified O exchange during denitrification. Up to 97% (median 85%) of the N(2)O-O originated from H(2)O instead of from the denitrification substrate NO(3)(-).We conclude that in soil, the main source of atmospheric N(2)O, the (18)O signature of N(2)O is mainly determined by H(2)O due to O exchange between nitrogen oxides and H(2)O. This also challenges the assumption that the O of N(2)O originates from O(2) and NO(3)(-), in ratios reflecting reaction stoichiometry.
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Affiliation(s)
- D M Kool
- Alterra, Wageningen University and Research Centre, Wageningen, The Netherlands.
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25
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Spott O, Stange CF. A new mathematical approach for calculating the contribution of anammox, denitrification and atmosphere to an N2 mixture based on a 15N tracer technique. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:2398-406. [PMID: 17582623 DOI: 10.1002/rcm.3098] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Denitrification and anaerobic ammonium oxidation (anammox) have been identified as biotic key processes of N2 formation during global nitrogen cycling. Based on the principle of a 15N tracer technique, new analytical expressions have been derived for a calculation of the fractions of N2 simultaneously released by anammox and denitrification. An omnipresent contamination with atmospheric N2 is also taken into account and is furthermore calculable in terms of a fraction. Two different mathematical approaches are presented which permit a precise calculation of the contribution of anammox, denitrification, and atmosphere to a combined N2 mixture. The calculation is based on a single isotopic analysis of a sampled N2 mixture and the determination of the 15N abundance of nitrite and nitrate (simplified approach) or of ammonium, nitrite, and nitrate (comprehensive approach). Calculations are even processable under conditions where all basal educts of anammox and denitrification (ammonium, nitrite, and nitrate) are differently enriched in 15N. An additional determination of concentrations of dissolved N compounds is unnecessary. Finally, the presented approach is transferable to studies focused on terrestrial environments where N2 is formed by denitrification and simultaneously by codenitrification or chemodenitrification.
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Affiliation(s)
- Oliver Spott
- UFZ, Helmholtz Centre for Environmental Research - UFZ, Department of Soil Physics, Theodor-Lieser-Strasse 4, 06120 Halle/Saale, Germany.
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Wallenstein MD, Myrold DD, Firestone M, Voytek M. Environmental controls on denitrifying communities and denitrification rates: insights from molecular methods. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2006; 16:2143-52. [PMID: 17205893 DOI: 10.1890/1051-0761(2006)016[2143:ecodca]2.0.co;2] [Citation(s) in RCA: 187] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The advent of molecular techniques has improved our understanding of the microbial communities responsible for denitrification and is beginning to address their role in controlling denitrification processes. There is a large diversity of bacteria, archaea, and fungi capable of denitrification, and their community composition is structured by long-term environmental drivers. The range of temperature and moisture conditions, substrate availability, competition, and disturbances have long-lasting legacies on denitrifier community structure. These communities may differ in physiology, environmental tolerances to pH and O2, growth rate, and enzyme kinetics. Although factors such as O2, pH, C availability, and NO3- pools affect instantaneous rates, these drivers act through the biotic community. This review summarizes the results of molecular investigations of denitrifier communities in natural environments and provides a framework for developing future research for addressing connections between denitrifier community structure and function.
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Affiliation(s)
- Matthew D Wallenstein
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara 80524, USA.
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Takaya N. Dissimilatory nitrate reduction metabolisms and their control in fungi. J Biosci Bioeng 2005; 94:506-10. [PMID: 16233342 DOI: 10.1016/s1389-1723(02)80187-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2002] [Accepted: 08/26/2002] [Indexed: 10/27/2022]
Abstract
Most fungi grow under aerobic conditions by generating ATP through oxygen respiration. However, they alternatively express two pathways of dissimilatory nitrate reduction in response to environmental oxygen tension when the oxygen supply is insufficient. The fungus Fusarium oxysporum expressed the pathway of respiratory nitrate denitrification that is catalyzed by the sequential reactions of nitrate reductase and nitrite reductase. These enzymes are coupled with ATP generation through the respiratory chain and produce nitric oxide. Fungal nitric oxide reductase uses NADH as the direct electron donor in contrast to bacterial systems and thus might function in regeneration of NAD+ and detoxification of the toxic radical, nitric oxide. Another pathway of nitrate dissimilation by fungi reduces nitrate to ammonium and couples acetogenic reaction with substrate-level phosphorylation. This metabolic mechanism is also in feature of a variety of fungi and it is called ammonia fermentation. Thus, fungi adapt to various aerated conditions using these pathways of nitrate dissimilation in addition to conventional oxygen respiration.
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Affiliation(s)
- Naoki Takaya
- Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.
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Sameshima-Saito R, Chiba K, Minamisawa K. New method of denitrification analysis of bradyrhizobium field isolates by gas chromatographic determination of (15)N-labeled N(2). Appl Environ Microbiol 2004; 70:2886-91. [PMID: 15128547 PMCID: PMC404451 DOI: 10.1128/aem.70.5.2886-2891.2004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2003] [Accepted: 01/22/2004] [Indexed: 11/20/2022] Open
Abstract
To evaluate the denitrification abilities of many Bradyrhizobium field isolates, we developed a new (15)N-labeled N(2) detection methodology, which is free from interference from atmospheric N(2) contamination. (30)N(2) ((15)N(15)N) and (29)N(2) ((15)N(14)N) were detected as an apparent peak by a gas chromatograph equipped with a thermal conductivity detector with N(2) gas having natural abundance of (15)N (0.366 atom%) as a carrier gas. The detection limit was 0.04% (30)N(2), and the linearity extended at least to 40% (30)N(2). When Bradyrhizobium japonicum USDA110 was grown in cultures anaerobically with (15)NO(3)(-), denitrification product ((30)N(2)) was detected stoichiometrically. A total of 65 isolates of soybean bradyrhizobia from two field sites in Japan were assayed by this method. The denitrification abilities were partly correlated with filed sites, Bradyrhizobium species, and the hup genotype.
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Affiliation(s)
- Reiko Sameshima-Saito
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan
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Immoos CE, Chou J, Bayachou M, Blair E, Greaves J, Farmer PJ. Electrocatalytic Reductions of Nitrite, Nitric Oxide, and Nitrous Oxide by Thermophilic Cytochrome P450 CYP119 in Film-Modified Electrodes and an Analytical Comparison of Its Catalytic Activities with Myoglobin. J Am Chem Soc 2004; 126:4934-42. [PMID: 15080699 DOI: 10.1021/ja038925c] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Previous investigations of nitrite and nitric oxide reduction by myoglobin in surfactant film modified electrodes characterized several distinct steps in the denitrification pathway, including isolation of a nitroxyl adduct similar to that proposed in the P450nor catalytic cycle. To investigate the effect of the axial ligand on these biomimetic reductions, we report here a comparison of the electrocatalytic activity of myoglobin (Mb) with a thermophilic cytochrome P450 CYP119. Electrocatalytic nitrite reduction by CYP119 is very similar to that by Mb: two catalytic waves at analogous potentials are observed, the first corresponding to the reduction of nitric oxide, the second to the production of ammonia. CYP119 is a much more selective catalyst, giving almost exclusively ammonia during the initial half-hour of reductive electrolysis of nitrite. More careful investigations of specific steps in the catalytic cycle show comparable rates of nitrite dehydration and almost identical potentials and lifetimes for ferrous nitroxyl intermediate (Fe(II)-NO(-)) in CYP119 and Mb. The catalytic efficiency of nitric oxide reduction is reduced for CYP119 as compared to Mb, attributable to both a lower affinity of the protein for NO and a decreased rate of N-N coupling. Isotopic labeling studies show ammonia incorporation into nitrous oxide produced during nitrite reduction, as has been termed co-denitrification for certain bacterial and fungal nitrite reductases. Mb has a much higher co-denitrification activity than CYP119. Conversely, CYP119 is shown to be slightly more efficient at the two-electron reduction of N(2)O to N(2). These results suggest that thiolate ligation does not significantly alter the catalytic reactivity, but the dramatic difference in product distribution may suggest an important role for protein stability in the selectivity of biocatalysts.
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Affiliation(s)
- Chad E Immoos
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
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Gutiérrez MM, Amorebieta VT, Estiú GL, Olabe JA. The electrophilic reactions of pentacyanonitrosylferrate(II) with hydrazine and substituted derivatives. Catalytic reduction of nitrite and theoretical prediction of eta(1)-, eta(2)-N(2)O bound intermediates. J Am Chem Soc 2002; 124:10307-19. [PMID: 12197734 DOI: 10.1021/ja025995v] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The electrophilic reactivity of the pentacyanonitrosylferrate(II) ion, [Fe(CN)(5)NO](2)(-), toward hydrazine (Hz) and substituted hydrazines (MeHz, 1,1-Me(2)Hz, and 1,2-Me(2)Hz) has been studied by means of stoichiometric and kinetic experiments (pH 6-10). The reaction of Hz led to N(2)O and NH(3), with similar paths for MeHz and 1,1-Me(2)Hz, which form the corresponding amines. A parallel path has been found for MeHz, leading to N(2)O, N(2), and MeOH. The reaction of 1,2-Me(2)Hz follows a different route, characterized by azomethane formation (MeNNMe), full reduction of nitrosyl to NH(3), and intermediate detection of [Fe(CN)(5)NO](3)(-). In the above reactions, [Fe(CN)(5)H(2)O](3)(-) was always a product, allowing the system to proceed catalytically for nitrite reduction, an issue relevant in relation to the behavior of the nitrite and nitric oxide reductase enzymes. The mechanism comprises initial reversible adduct formation through the binding of the nucleophile to the N-atom of nitrosyl. The adducts decompose through OH(-) attack giving the final products, without intermediate detection. Rate constants for the adduct-formation steps (k = 0.43 M(-)(1) s(-)(1), 25 degrees C for Hz) decrease with methylation by about an order of magnitude. Among the different systems studied, one-, two-, and multielectron reductions of bound NO(+) are analyzed comparatively, with consideration of the role of NO, HNO (nitroxyl), and hydroxylamine as bound intermediates. A DFT study (B3LYP) of the reaction profile allows one to characterize intermediates in the potential hypersurface. These are the initial adducts, as well as their decomposition products, the eta(1)- and eta(2)-linkage isomers of N(2)O.
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Affiliation(s)
- María M Gutiérrez
- Department of Chemistry, Facultad de Ciencias Exactas, Universidad Nacional de Mar del Plata, Funes y Roca, Mar del Plata B7602AYL, Argentina
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Kumon Y, Sasaki Y, Kato I, Takaya N, Shoun H, Beppu T. Codenitrification and denitrification are dual metabolic pathways through which dinitrogen evolves from nitrate in Streptomyces antibioticus. J Bacteriol 2002; 184:2963-8. [PMID: 12003936 PMCID: PMC135070 DOI: 10.1128/jb.184.11.2963-2968.2002] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We screened actinomycete strains for dinitrogen (N(2))-producing activity and discovered that Streptomyces antibioticus B-546 evolves N(2) and some nitrous oxide (N(2)O) from nitrate (NO(3)(-)). Most of the N(2) that evolved from the heavy isotope ([(15)N]NO(3)(-)) was (15)N(14)N, indicating that this nitrogen species consists of two atoms, one arising from NO(3)(-) and the other from different sources. This phenomenon is similar to codenitrification in fungi. The strain also evolved less, but significant, amounts of (15)N(15)N from [(15)N]NO(3)(-) in addition to (15)N(15)NO with concomitant cell growth. Prior to the production of N(2) and N(2)O, NO(3)(-) was rapidly reduced to nitrite (NO(2)(-)) accompanied by distinct cell growth, showing that the actinomycete strain is a facultative anaerobe that depends on denitrification and nitrate respiration for anoxic growth. The cell-free activities of denitrifying enzymes could be reconstituted, supporting the notion that the (15)N(15)N and (15)N(15)NO species are produced by denitrification from NO(3)(-) via NO(2)(-). We therefore demonstrated a unique system in an actinomycete that produces gaseous nitrogen (N(2) and N(2)O) through both denitrification and codenitrification. The predominance of codenitrification over denitrification along with oxygen tolerance is the key feature of nitrate metabolism in this actinomycete.
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Affiliation(s)
- Yasuyuki Kumon
- Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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Abstract
Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.
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Affiliation(s)
- W G Zumft
- Lehrstuhl für Mikrobiologie, Universität Fridericiana, Karlsruhe, Germany
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Affiliation(s)
- Bruce A. Averill
- E. C. Slater Institute, University of Amsterdam, Plantage Muidergracht 12, 1018 TV Amsterdam, The Netherlands
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Usuda K, Toritsuka N, Matsuo Y, Kim DH, Shoun H. Denitrification by the fungus Cylindrocarpon tonkinense: anaerobic cell growth and two isozyme forms of cytochrome P-450nor. Appl Environ Microbiol 1995; 61:883-9. [PMID: 7793922 PMCID: PMC167353 DOI: 10.1128/aem.61.3.883-889.1995] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We examined the denitrification system of the fungus Cylindrocapon tonkinense and found several properties distinct from those of the denitrification system of Fusarium oxysporum. C. tonkinense could form N2O from nitrite under restricted aeration but could not reduce nitrate by dissimilatory metabolism. Nitrite-dependent N2O formation and/or cell growth during the anaerobic culture was not affected by further addition of ammonium ions but was suppressed by respiration inhibitors such as rotenone or antimycin, suggesting that denitrification plays a physiological role in respiration. Dissimilatory nitrite reductase and nitric oxide reductase (Nor) activities could not be detected in cell extracts of the denitrifying cells. The Nor activity was purified and found to depend upon two isoenzymes of Cytochrome P-450nor (P-450nor), which were designated P-450nor1 and P-450nor2. These isozymes differed in the N-terminal amino acid sequence, isoelectric point, specificity to the reduced pyridine nucleotide (NADH or NADPH), and the reactivity to the antibody to P-450nor of F. oxysporum. the difference between the specificities to NADH and NADPH suggests that P-450nor1 and P-450nor2 play different roles in anaerobic energy acquisition.
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Affiliation(s)
- K Usuda
- Institute of Applied Biochemistry, University of Tsukuba, Ibaraki, Japan
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