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Hassan MU, Guoqin H, Arif MS, Mubarik MS, Tang H, Xu H, Yang B, Zhou Q, Shakoor A. Can urea-coated fertilizers be an effective means of reducing greenhouse gas emissions and improving crop productivity? JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 367:121927. [PMID: 39079497 DOI: 10.1016/j.jenvman.2024.121927] [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: 12/11/2023] [Revised: 06/11/2024] [Accepted: 07/16/2024] [Indexed: 08/15/2024]
Abstract
Given the significance of nitrogen (N) as the most constraining nutrient in agro-ecosystems, it is crucial to develop an updated model for N fertilizers management to achieve higher crop yields while minimizing the negative impacts on the environment. Coated urea is touted as one of the most important controlled-release N fertilizers used in agriculture to reduce cropland emissions and improve nitrogen use efficiency (NUE) for optimal crop yields. The sustainability of coated urea depends on the trade-offs between crop productivity, NUE and greenhouse gas emissions (CO2, CH4 and N2O); however, role of various agro-edaphic factors in influencing these trade-offs remains unclear. To determine the effects of soil properties, climatic conditions, experimental conditions, and type of coated urea on greenhouse gas emissions, NH3 losses, crop productivity, and NUE, we conducted a meta-analysis using data from 76 peer-reviewed studies. Our results showed that the application of coated urea under field conditions contributed to a greater reduction in N2O emissions (-48.67%) and higher NUE (58.72%), but crop yields were not significant. Across different climate regions, subtropical monsoon climate showed a perceptible mitigation for CO2, CH4 and NH3 (-78.38%; -83.33%; -27.46%), while temperate climate reduced N2O emissions by -70.36%. For different crops, only rice demonstrated reduction in CO2, CH4, N2O and NH3 losses. On the other hand, our findings revealed a mitigating trade-off between CO2 and CH4 emissions on medium-textured soils and N2O emissions on fine-textured soils. A significant reduction in N2O and NH3 losses was evident when coated urea was applied to soils with a pH > 5.5. Interestingly, application of coated urea to soils with higher C/N ratios increased NH3 losses but showed a noticeable N2O reduction. We found that polymer-coated urea reduced CH4 and N2O emissions and NH3 losses at the expense of higher CO2 emissions. Moreover, application of a lower dose of coated urea (0-100 kg N ha-1) enhanced CO2 and CH4 mitigation, while N2O mitigation increased linearly with increasing dose of coated urea. Most importantly, our results showed that the application of coated urea leads to a large mismatch between NUE, crop yields and greenhouse gas mitigation. By and large, the application of coated urea did not correspond with higher crop yields despite significant reduction in the emissions and improved NUE. Overall, these results suggest that site-specific agro-edaphic conditions should be considered when applying coated urea to reduce these emissions and N volatilization losses for increasing NUE and crop yields.
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Affiliation(s)
- Muhammad Umair Hassan
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Huang Guoqin
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Muhammad Saleem Arif
- Department of Environmental Sciences, Government College University Faisalabad, Allama Iqbal Road, Faisalabad, 38000, Pakistan.
| | | | - Haiying Tang
- School of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Huifang Xu
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Binjuan Yang
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Quan Zhou
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Awais Shakoor
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
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2
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Hiis EG, Vick SHW, Molstad L, Røsdal K, Jonassen KR, Winiwarter W, Bakken LR. Unlocking bacterial potential to reduce farmland N 2O emissions. Nature 2024; 630:421-428. [PMID: 38811724 PMCID: PMC11168931 DOI: 10.1038/s41586-024-07464-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/25/2024] [Indexed: 05/31/2024]
Abstract
Farmed soils contribute substantially to global warming by emitting N2O (ref. 1), and mitigation has proved difficult2. Several microbial nitrogen transformations produce N2O, but the only biological sink for N2O is the enzyme NosZ, catalysing the reduction of N2O to N2 (ref. 3). Although strengthening the NosZ activity in soils would reduce N2O emissions, such bioengineering of the soil microbiota is considered challenging4,5. However, we have developed a technology to achieve this, using organic waste as a substrate and vector for N2O-respiring bacteria selected for their capacity to thrive in soil6-8. Here we have analysed the biokinetics of N2O reduction by our most promising N2O-respiring bacterium, Cloacibacterium sp. CB-01, its survival in soil and its effect on N2O emissions in field experiments. Fertilization with waste from biogas production, in which CB-01 had grown aerobically to about 6 × 109 cells per millilitre, reduced N2O emissions by 50-95%, depending on soil type. The strong and long-lasting effect of CB-01 is ascribed to its tenacity in soil, rather than its biokinetic parameters, which were inferior to those of other strains of N2O-respiring bacteria. Scaling our data up to the European level, we find that national anthropogenic N2O emissions could be reduced by 5-20%, and more if including other organic wastes. This opens an avenue for cost-effective reduction of N2O emissions for which other mitigation options are lacking at present.
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Affiliation(s)
- Elisabeth G Hiis
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Silas H W Vick
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Lars Molstad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Kristine Røsdal
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Wilfried Winiwarter
- International Institute for Applied Systems Analysis, Laxenburg, Austria
- Institute of Environmental Engineering, University of Zielona Góra, Zielona Góra, Poland
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
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3
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He G, Chen G, Xie Y, Swift CM, Ramirez D, Cha G, Konstantinidis KT, Radosevich M, Löffler FE. Sustained bacterial N 2O reduction at acidic pH. Nat Commun 2024; 15:4092. [PMID: 38750010 PMCID: PMC11096178 DOI: 10.1038/s41467-024-48236-x] [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: 01/12/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024] Open
Abstract
Nitrous oxide (N2O) is a climate-active gas with emissions predicted to increase due to agricultural intensification. Microbial reduction of N2O to dinitrogen (N2) is the major consumption process but microbial N2O reduction under acidic conditions is considered negligible, albeit strongly acidic soils harbor nosZ genes encoding N2O reductase. Here, we study a co-culture derived from acidic tropical forest soil that reduces N2O at pH 4.5. The co-culture exhibits bimodal growth with a Serratia sp. fermenting pyruvate followed by hydrogenotrophic N2O reduction by a Desulfosporosinus sp. Integrated omics and physiological characterization revealed interspecies nutritional interactions, with the pyruvate fermenting Serratia sp. supplying amino acids as essential growth factors to the N2O-reducing Desulfosporosinus sp. Thus, we demonstrate growth-linked N2O reduction between pH 4.5 and 6, highlighting microbial N2O reduction potential in acidic soils.
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Affiliation(s)
- Guang He
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
| | - Gao Chen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
- Center for Environmental Biotechnology, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
| | - Yongchao Xie
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Cynthia M Swift
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
- Center for Environmental Biotechnology, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
| | - Diana Ramirez
- Department of Microbiology, The University of Tennessee Knoxville, Knoxville, TN, 37996, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Gyuhyon Cha
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | | | - Mark Radosevich
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
| | - Frank E Löffler
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA.
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA.
- Center for Environmental Biotechnology, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA.
- Department of Microbiology, The University of Tennessee Knoxville, Knoxville, TN, 37996, USA.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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4
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Sun Y, Yin Y, He G, Cha G, Ayala-del-Río HL, González G, Konstantinidis KT, Löffler FE. pH selects for distinct N 2O-reducing microbiomes in tropical soil microcosms. ISME COMMUNICATIONS 2024; 4:ycae070. [PMID: 38808123 PMCID: PMC11131594 DOI: 10.1093/ismeco/ycae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 04/27/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024]
Abstract
Nitrous oxide (N2O), a greenhouse gas with ozone destruction potential, is mitigated by the microbial reduction to dinitrogen catalyzed by N2O reductase (NosZ). Bacteria with NosZ activity have been studied at circumneutral pH but the microbiology of low pH N2O reduction has remained elusive. Acidic (pH < 5) tropical forest soils were collected in the Luquillo Experimental Forest in Puerto Rico, and microcosms maintained with low (0.02 mM) and high (2 mM) N2O assessed N2O reduction at pH 4.5 and 7.3. All microcosms consumed N2O, with lag times of up to 7 months observed in microcosms with 2 mM N2O. Comparative metagenome analysis revealed that Rhodocyclaceae dominated in circumneutral microcosms under both N2O feeding regimes. At pH 4.5, Peptococcaceae dominated in high-N2O, and Hyphomicrobiaceae in low-N2O microcosms. Seventeen high-quality metagenome-assembled genomes (MAGs) recovered from the N2O-reducing microcosms harbored nos operons, with all eight MAGs derived from acidic microcosms carrying the Clade II type nosZ and lacking nitrite reductase genes (nirS/K). Five of the eight MAGs recovered from pH 4.5 microcosms represent novel taxa indicating an unexplored N2O-reducing diversity exists in acidic tropical soils. A survey of pH 3.5-5.7 soil metagenome datasets revealed that nosZ genes commonly occur, suggesting broad distribution of N2O reduction potential in acidic soils.
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Affiliation(s)
- Yanchen Sun
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Present address: Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Yongchao Yin
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Present address: Department of Biology, Antimicrobial Discovery Center, Northeastern University, Boston, MA 02148, United States
| | - Guang He
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
| | - Gyuhyon Cha
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | | | - Grizelle González
- USDA Forest Service, International Institute of Tropical Forestry, San Juan 00926, Puerto Rico
| | | | - Frank E Löffler
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
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5
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Li Y, Muhammad R, Saba B, Xia H, Wang X, Wang J, Jiang C. Can the co-application of biochar and different inorganic nitrogen fertilizers repress N 2O emissions in acidic soil? ENVIRONMENTAL RESEARCH 2023; 231:116217. [PMID: 37245574 DOI: 10.1016/j.envres.2023.116217] [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: 03/28/2023] [Revised: 05/15/2023] [Accepted: 05/21/2023] [Indexed: 05/30/2023]
Abstract
The sole application of nitrogen (N) fertilizer with lower N2O emission potential or combined with biochar may help for mitigating N2O production. However, how biochar applied with various inorganic N fertilizers affected N2O emission in acidic soil remains unclear. Thus, we examined N2O emission, soil N dynamics and relating nitrifiers (i.e., ammonia-oxidizing archaea, AOA) in acidic soil. The study contained three N fertilizers (including NH4Cl, NaNO3, NH4NO3) and two biochar application rates (i.e., 0% and 0.5%). The results indicated that the alone application of NH4Cl produced more N2O. Meanwhile, the co-application of biochar and N fertilizers enhanced N2O emission as well, especially in the combined treatment of biochar and NH4NO3. Soil pH was decreased with the application of various N fertilizers, especially with NH4Cl, and the average decrease rate was 9.6%. Meanwhile, correlation analysis showed a negative relationship between N2O and pH, dramatically, which might indicate that the alteration of pH was one factor relating to N2O emission. However, there was no difference between the same N addition treatments with or without biochar on pH. Interestingly, in the combined treatment of biochar and NH4NO3, the lowest net nitrification rate and net mineralization rate appeared during days 16-23. Meanwhile, the highest emission rate of N2O in the same treatment also appeared during days 16-23. The accordance might indicate that N transformation alteration was another factor relating to N2O emissions. In addition, compared to NH4NO3 alone application, co-applied with biochar had a lower content of Nitrososphaera-AOA, which was a main contributor to nitrification. The study emphasizes the importance of using a suitable form of N fertilizers and further indicates that two factors, namely alteration of pH and N transformation rate, are related to N2O emission. Moreover, in future studies, it is necessary to explore the soil N dynamics controlled by microorganisms.
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Affiliation(s)
- Yuxuan Li
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Riaz Muhammad
- College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, PR China
| | - Babar Saba
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Hao Xia
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Xiangling Wang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China; The Key Laboratory of Oasis Ecoagriculture, Xinjiang Production and Construction Corps, Shihezi University, Shihezi, Xinjiang, 832000, PR China
| | - JiYuan Wang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Cuncang Jiang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China; The Key Laboratory of Oasis Ecoagriculture, Xinjiang Production and Construction Corps, Shihezi University, Shihezi, Xinjiang, 832000, PR China.
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6
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Ni G, Leung PM, Daebeler A, Guo J, Hu S, Cook P, Nicol GW, Daims H, Greening C. Nitrification in acidic and alkaline environments. Essays Biochem 2023; 67:753-768. [PMID: 37449414 PMCID: PMC10427799 DOI: 10.1042/ebc20220194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Abstract
Aerobic nitrification is a key process in the global nitrogen cycle mediated by microorganisms. While nitrification has primarily been studied in near-neutral environments, this process occurs at a wide range of pH values, spanning ecosystems from acidic soils to soda lakes. Aerobic nitrification primarily occurs through the activities of ammonia-oxidising bacteria and archaea, nitrite-oxidising bacteria, and complete ammonia-oxidising (comammox) bacteria adapted to these environments. Here, we review the literature and identify knowledge gaps on the metabolic diversity, ecological distribution, and physiological adaptations of nitrifying microorganisms in acidic and alkaline environments. We emphasise that nitrifying microorganisms depend on a suite of physiological adaptations to maintain pH homeostasis, acquire energy and carbon sources, detoxify reactive nitrogen species, and generate a membrane potential at pH extremes. We also recognize the broader implications of their activities primarily in acidic environments, with a focus on agricultural productivity and nitrous oxide emissions, as well as promising applications in treating municipal wastewater.
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Affiliation(s)
- Gaofeng Ni
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Pok Man Leung
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Anne Daebeler
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, Ceske Budejovice, Czechia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (Formerly AWMC), The University of Queensland, Brisbane, Queensland, Australia
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology (Formerly AWMC), The University of Queensland, Brisbane, Queensland, Australia
| | - Perran Cook
- School of Chemistry, Monash University, Melbourne, Victoria, Australia
| | - Graeme W Nicol
- Univ Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, Ecole Centrale de Lyon, Ampère, UMR5005, 69134 Ecully, France
| | - Holger Daims
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- The Comammox Research Platform, University of Vienna, Vienna, Austria
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Securing Antarctica's Environmental Future, Monash University, Melbourne, Victoria, Australia
- Centre to Impact AMR, Monash University, Melbourne, Victoria, Australia
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7
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Shaaban M, Hu R, Wu Y, Song L, Xu P. Soil pH management for mitigating N 2O emissions through nosZ (Clade I and II) gene abundance in rice paddy system. ENVIRONMENTAL RESEARCH 2023; 225:115542. [PMID: 36822538 DOI: 10.1016/j.envres.2023.115542] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 02/04/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Soil nitrous oxide (N2O) is produced by abiotic and biotic processes, but it is solely consumed by denitrifying microbes-encoded by nosZ genes. The nosZ gene includes two groups i.e. Clade I and Clade II, which are highly sensitive to pH. Managing pH of acidic soils can substantially influence soil N2O production or consumption through nosZ gene abundance. Nevertheless, the response of nosZ (Clade I and Clade II) to pH management needs elucidation in acidic soils. To clarify this research question, a pot experiment growing rice crop was conducted with three treatments: control (only soil), low dose of dolomite (LDD), and high dose of dolomite (HDD). The soil pH increased from 5.41 to 6.23 in the control, 6.5 in LDD and 6.8 in HDD treatment under flooded condition. The NH4+ and NO3- contents increased and reached the maximum at 30.4 and 21.5 mg kg-1, respectively, in HDD treatment under flooding condition. The contents of dissolved organic carbon and microbial biomass carbon showed a swift rise at midseason aeration and reached maximum at 30.7 and 101 mg kg-1 in the HDD treatment. Clade I, Clade II and 16S rRNA genes abundance increased with the onset of flooding, and occurred maximum in the HDD treatment. A peak in N2O emissions (5.96 μg kg-1 h-1) occurred at midseason events in the control when no dolomite was added. Dolomite application significantly (p ≤ 0.001) suppressed N2O emissions, and HDD treatment was more effective in reducing emissions. Pearson correlation, linear regressions and principal component analysis displayed that increased soil pH and Clade I and Clade II were the main controlling factors for N2O emission mitigation in acidic soil. This research demonstrates that ameliorating soil acidity with dolomite application is a potential option for the mitigation of N2O emissions.
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Affiliation(s)
- Muhammad Shaaban
- Department of Soil Science, FAS&T, Bahauddin Zakariya University, Multan, Pakistan.
| | - Ronggui Hu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China.
| | - Yupeng Wu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Ling Song
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, 610041 Chengdu, China
| | - Peng Xu
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, 610041 Chengdu, China
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Buchen-Tschiskale C, Well R, Flessa H. Tracing nitrogen transformations during spring development of winter wheat induced by 15N labeled cattle slurry applied with different techniques. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:162061. [PMID: 36758686 DOI: 10.1016/j.scitotenv.2023.162061] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 01/10/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Slurry application is often associated with considerable nitrogen (N) losses: ammonia (NH3), nitrous oxide (N2O) and a mostly unknown contribution of dinitrogen (N2) emission, as well as N leaching. Thus, an outdoor lysimeter experiment with growing winter wheat in undisturbed soil cores was set up to follow the transformation of cattle slurry 15NH4+ and soil 15NO3- using a double labeling approach. Slurry treatments included the following application techniques: a trailing hose with/without acidification, and open slot injection with/without nitrification inhibitor. The fertilizer application rate was 67 kg N ha-1. In addition to NH3 emissions, N2O and N2 emissions were measured, as well as N contents and 15N enrichment of soil N pools and plant compartments. The major gaseous loss pathway was NH3 with up to 8 kg N ha-1 following trailing hose application, while slot injection significantly reduced NH3-N losses. Regardless of the application technique, N2O emissions were low (up to 0.1 kg N2O-N ha-1), while N2 emissions reached up to 3 kg N ha-1. No effect on N leaching from topsoil was found. 15N plant uptake was greater in slot injection than trailing hose treatments. An effect of the nitrification inhibitor was visible in the nitrate contents, but not in gaseous N losses or N leaching from topsoil. Impacts of the application techniques on individual soil N pools were small. The 15N recovery offered a chance to map the short-term effects and was highest in the soil Nt pool (32 % to 48 % of 15N applied) with a greater contribution of microbial N than mineral N at beginning of stem elongation. Indications for high N immobilization was derived from the applied N balance approach. In the present case, slot injection scored as the best application technology based on the highest NH3 reduction, while N2 and N2O emissions were not enhanced.
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Affiliation(s)
- Caroline Buchen-Tschiskale
- Thünen Institute of Climate-Smart Agriculture, Federal Research Institute for Rural Areas, Forestry and Fisheries, Bundesallee 65, 38116 Braunschweig, Germany.
| | - Reinhard Well
- Thünen Institute of Climate-Smart Agriculture, Federal Research Institute for Rural Areas, Forestry and Fisheries, Bundesallee 65, 38116 Braunschweig, Germany
| | - Heinz Flessa
- Thünen Institute of Climate-Smart Agriculture, Federal Research Institute for Rural Areas, Forestry and Fisheries, Bundesallee 65, 38116 Braunschweig, Germany
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9
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Yin J, Cui W, Xu Y, Ma Y, Chen H, Guo J, Liu R, Chen Q. Understanding the relative contributions of fungi and bacteria led nitrous oxide emissions in an acidic soil amended with industrial waste. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 255:114727. [PMID: 37032574 DOI: 10.1016/j.ecoenv.2023.114727] [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: 08/29/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 06/19/2023]
Abstract
Amendment of fertilized arable soil with alkaline industrial waste has the potential to ameliorate soil acidification whilst also improving crop yield. Another co-benefit is nitrous oxide (N2O) emission abatement but the contribution of fungi and bacteria involved in this process remains unclear. Two incubation experiments were conducted to: 1) examine how amendment of acidic soils with a mixture of phosphorus tailings mixture and insoluble potassium-containing rocks (PT) affect N2O emissions and 2) understand the microbial mechanisms and relative contributions of fungi and bacteria responsible for N2O emissions. In the first incubation experiment, the four treatments consisted of: i) the study control, ii) urea, iii) PT amendment and iv) PT amendment plus urea. Results showed that the PT amendment significantly increased soil pH from 4.8 to above 6.0, and reduced N2O emissions by 65.7%. PT-amended soils had higher N2 emissions and faster O2 consumption. The PT amendment significantly increased extracellular enzyme activities of leucine aminopeptidase and N-Acetyl-β-glucosaminidase, while it significantly decreased activities of β-1, 4-glucosidase and β-cellobiosidase. Two antibiotics (cycloheximide and streptomycin) combined with substrate-induced respiration method were used in the second incubation experiment. Compared to soil with urea, urea with PT amendment raised soil bacteria-related N2O from 9.2% to 18.8% while decreasing fungi-related N2O from 50.5% to 43.2%. These findings suggest that the N2O emissions from acidic soils can be considerably mitigated by the application of alkaline industrial wastes. The contribution of fungi should be considered when designing and applying N2O mitigation strategies in acidic soils. DATA AVAILABILITY: Data will be made available on request.
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Affiliation(s)
- Junhui Yin
- Beijing Key Laboratory of Farmyard Soil Pollution Prevention-control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Wenjing Cui
- Beijing Key Laboratory of Farmyard Soil Pollution Prevention-control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Qingdao Agricultural University, Qingdao 266000, China
| | - Yumeng Xu
- Beijing Key Laboratory of Farmyard Soil Pollution Prevention-control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Yan Ma
- Beijing Key Laboratory of Farmyard Soil Pollution Prevention-control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510006, China
| | - Jingheng Guo
- Beijing Key Laboratory of Farmyard Soil Pollution Prevention-control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Rui Liu
- Beijing Key Laboratory of Farmyard Soil Pollution Prevention-control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
| | - Qing Chen
- Beijing Key Laboratory of Farmyard Soil Pollution Prevention-control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
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10
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Denitrification by Bradyrhizobia under Feast and Famine and the Role of the bc1 Complex in Securing Electrons for N 2O Reduction. Appl Environ Microbiol 2023; 89:e0174522. [PMID: 36662572 PMCID: PMC9972998 DOI: 10.1128/aem.01745-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Rhizobia living as microsymbionts inside nodules have stable access to carbon substrates, but also must survive as free-living bacteria in soil where they are starved for carbon and energy most of the time. Many rhizobia can denitrify, thus switch to anaerobic respiration under low O2 tension using N-oxides as electron acceptors. The cellular machinery regulating this transition is relatively well known from studies under optimal laboratory conditions, while little is known about this regulation in starved organisms. It is, for example, not known if the strong preference for N2O- over NO3- reduction in bradyrhizobia is retained under carbon limitation. Here, we show that starved cultures of a Bradyrhizobium strain with respiration rates 1 to 18% of well-fed cultures reduced all available N2O before touching provided NO3-. These organisms, which carry out complete denitrification, have the periplasmic nitrate reductase NapA but lack the membrane-bound nitrate reductase NarG. Proteomics showed similar levels of NapA and NosZ (N2O reductase), excluding that the lack of NO3- reduction was due to low NapA abundance. Instead, this points to a metabolic-level phenomenon where the bc1 complex, which channels electrons to NosZ via cytochromes, is a much stronger competitor for electrons from the quinol pool than the NapC enzyme, which provides electrons to NapA via NapB. The results contrast the general notion that NosZ activity diminishes under carbon limitation and suggest that bradyrhizobia carrying NosZ can act as strong sinks for N2O under natural conditions, implying that this criterion should be considered in the development of biofertilizers. IMPORTANCE Legume cropped farmlands account for substantial N2O emissions globally. Legumes are commonly inoculated with N2-fixing bacteria, rhizobia, to improve crop yields. Rhizobia belonging to Bradyrhizobium, the microsymbionts of several economically important legumes, are generally capable of denitrification but many lack genes encoding N2O reductase and will be N2O sources. Bradyrhizobia with complete denitrification will instead act as sinks since N2O-reduction efficiently competes for electrons over nitrate reduction in these organisms. This phenomenon has only been demonstrated under optimal conditions and it is not known how carbon substrate limitation, which is the common situation in most soils, affects the denitrification phenotype. Here, we demonstrate that bradyrhizobia retain their strong preference for N2O under carbon starvation. The findings add basic knowledge about mechanisms controlling denitrification and support the potential for developing novel methods for greenhouse gas mitigation based on legume inoculants with the dual capacity to optimize N2 fixation and minimize N2O emission.
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11
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Xu C, Wong VNL, Tuovinen A, Simojoki A. Effects of liming on oxic and anoxic N 2O and CO 2 production in different horizons of boreal acid sulfate soil and non-acid soil under controlled conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159505. [PMID: 36257417 DOI: 10.1016/j.scitotenv.2022.159505] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
In acid sulfate (AS) soils, organic rich topsoil and subsoil horizons with highly variable acidity and moisture conditions and interconnected reactions of sulfur and nitrogen make them potential sources of greenhouse gases (GHGs). Subsoil liming can reduce the acidification of sulfidic subsoils in the field. However, the mitigation of GHG production in AS subsoils by liming, and the mechanisms involved, are still poorly known. We limed samples from different horizons of AS and non-AS soils to study the effects of liming on the N2O and CO2 production during a 56-day oxic and subsequent 72-h anoxic incubation. Liming to pH ≥ 7 decreased oxic N2O production by 97-98 % in the Ap1 horizon, 38-50 % in the Bg1 horizon, and 34-36 % in the BC horizon, but increased it by 136-208 % in the C horizon, respectively. Liming decreased anoxic N2O production by 86-94 % and 78-91 % in Ap1 and Bg1 horizons, but increased it by 100-500 % and 50-162 % in BC and C horizons, respectively. Liming decreased N2O/(N2O + N2) in anoxic denitrification in most horizons of both AS and non-AS soils. Liming significantly increased the cumulative oxic and anoxic CO2 production in AS soil, but less so in non-AS soil due to the initial high soil pH. Higher carbon and nitrogen contents in AS soil compared to non-AS soil agreed with the respectively higher cumulative oxic N2O production in all horizons, and the higher CO2 production in the subsoil horizons of all lime treatments. Overall, liming reduced the proportion of N2O in the GHGs produced in most soil horizons under oxic and anoxic conditions but reduced the total GHG production (as CO2 equivalents) only in the Ap1 horizon of both soils. The results suggest that liming of subsoils may not always effectively mitigate GHG emissions due to concurrently increased CO2 production and denitrification.
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Affiliation(s)
- Chang Xu
- School of Earth, Atmosphere and Environment, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Vanessa N L Wong
- School of Earth, Atmosphere and Environment, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Anna Tuovinen
- Department of Agricultural Sciences, University of Helsinki, P. O. Box 56 (Biocenter 1, Viikinkaari 9), FI-00014, Finland
| | - Asko Simojoki
- Department of Agricultural Sciences, University of Helsinki, P. O. Box 56 (Biocenter 1, Viikinkaari 9), FI-00014, Finland.
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Pizarro L, Magalhães C, Almeida CMR, Carvalho MDF, Semedo M. Cadmium effects on net N2O production by the deep-sea isolate Shewanella loihica PV-4. FEMS Microbiol Lett 2023; 370:fnad047. [PMID: 37279908 PMCID: PMC10337742 DOI: 10.1093/femsle/fnad047] [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: 01/31/2023] [Revised: 05/19/2023] [Accepted: 06/01/2023] [Indexed: 06/08/2023] Open
Abstract
Deep-sea mining may lead to the release of high concentrations of metals into the surrounding seabed, which can disturb important ecosystem functions provided by microbial communities. Among these, the production of N2O and its reduction to N2 is of great relevance since N2O is an important greenhouse gas. Metal impacts on net N2O production by deep-sea bacteria are, however, currently unexplored. Here, we evaluated the effects of cadmium (Cd) on net N2O production by a deep-sea isolate, Shewanella loihica PV-4. We performed a series of Cd exposure incubations in oxic conditions and determined N2O fluxes during induced anoxic conditions, as well as the relative expression of the nitrite reductase gene (nirK), preceding N2O production, and N2O reductase gene (nosZ), responsible for N2O reduction. Net N2O production by S. loihica PV-4 exposed to Cd was strongly inhibited when compared to the control treatment (no metal). Both nirK and nosZ gene expression were inhibited in reactors with Cd, but nirK inhibition was stronger, supporting the lower net N2O production observed with Cd. The Cd inhibition of net N2O production observed in this study poses the question whether other deep-sea bacteria would undergo the same effects. Future studies should address this question as well as its applicability to complex communities and other physicochemical conditions, which remain to be evaluated.
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Affiliation(s)
- Leonor Pizarro
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Faculty of Biotechnology, Catholic University of Portugal, Porto 4169-005, Portugal
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Department of Biology, Faculty of Sciences (FCUP), University of Porto, Porto 4169-007, Portugal
| | - C Marisa R Almeida
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Department of Chemistry and Biochemistry, Faculty of Sciences (FCUP), University of Porto, Porto 4169-007, Portugal
| | - Maria de Fátima Carvalho
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto 4050-313, Portugal
| | - Miguel Semedo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
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Mancia A, Chadwick DR, Waters SM, Krol DJ. Low N 2O emissions associated with sheep excreta deposition in temperate managed lowland grassland and extensively grazed hill pasture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:158070. [PMID: 35981583 DOI: 10.1016/j.scitotenv.2022.158070] [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: 05/06/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas (GHG) whose emission from soil can be enhanced by ruminant excretal returns in grasslands. The default (Tier 1) emission factors (EF3PRP; i.e. proportion of deposited nitrogen emitted as N2O) for ruminant excreta deposition are associated with a wide range of uncertainties and the development of country-specific (Tier 2) EF3PRP is encouraged. In Ireland, a Tier 2 EF3PRP has been developed for cattle excreta but no data are available for sheep. The aim of this study was to generate data to contribute to the derivation of a Tier 2 EF3PRP for sheep excreta, while assessing the effect of excreta type, grassland type and season of deposition on N2O emissions. An experiment was carried out on two sites in the west of Ireland: a managed lowland grassland (LOW) and an extensively grazed hill pasture (HILL), characterised by mineral and acid peat soils, respectively. For each season, four treatments were applied to the soil in a fully randomized block design: control (C), sheep urine (U), sheep dung (D), and artificial urine (AU). Nitrous oxide fluxes were assessed over a full year following each application of treatments, using a static chambers methodology. Results showed a brief initial peak following each application of U/AU in LOW but not in HILL. Cumulative N2O emissions were significantly higher from the lowland site. Average EF3PRP for combined excreta was negligible on both sites, thus lower than the IPCC Tier 1 EF3PRP. Causes of low emissions are likely to depend on site characteristics (e.g. soil acidity in HILL) and season of application (i.e. ammonia volatilisation in summer). This study showed very low N2O emissions from sheep excretal returns in Irish grasslands and highlighted the importance of developing Tier 2, animal-specific EF3PRP. More experimental grasslands should be assessed to confirm these results.
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Affiliation(s)
- Aude Mancia
- Teagasc, Crops, Land Use and Environment Programme, Johnstown Castle, Co. Wexford, Ireland; School of Natural Sciences, Bangor University, Bangor, UK; Teagasc, Animal and Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | | | - Sinéad M Waters
- Teagasc, Animal and Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - Dominika J Krol
- Teagasc, Crops, Land Use and Environment Programme, Johnstown Castle, Co. Wexford, Ireland.
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14
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Nie Y, Lau SYL, Tan X, Lu X, Liu S, Tahvanainen T, Isoda R, Ye Q, Hashidoko Y. Sphagnum capillifolium holobiont from a subarctic palsa bog aggravates the potential of nitrous oxide emissions. FRONTIERS IN PLANT SCIENCE 2022; 13:974251. [PMID: 36160957 PMCID: PMC9490422 DOI: 10.3389/fpls.2022.974251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
Melting permafrost mounds in subarctic palsa mires are thawing under climate warming and have become a substantial source of N2O emissions. However, mechanistic insights into the permafrost thaw-induced N2O emissions in these unique habitats remain elusive. We demonstrated that N2O emission potential in palsa bogs was driven by the bacterial residents of two dominant Sphagnum mosses especially of Sphagnum capillifolium (SC) in the subarctic palsa bog, which responded to endogenous and exogenous Sphagnum factors such as secondary metabolites, nitrogen and carbon sources, temperature, and pH. SC's high N2O emission activity was linked with two classes of distinctive hyperactive N2O emitters, including Pseudomonas sp. and Enterobacteriaceae bacteria, whose hyperactive N2O emitting capability was characterized to be dominantly pH-responsive. As the nosZ gene-harboring emitter, Pseudomonas sp. SC-H2 reached a high level of N2O emissions that increased significantly with increasing pH. For emitters lacking the nosZ gene, an Enterobacteriaceae bacterium SC-L1 was more adaptive to natural acidic conditions, and N2O emissions also increased with pH. Our study revealed previously unknown hyperactive N2O emitters in Sphagnum capillifolium found in melting palsa mound environments, and provided novel insights into SC-associated N2O emissions.
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Affiliation(s)
- Yanxia Nie
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Sharon Yu Ling Lau
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
- Sarawak Tropical Peat Research Institute, Kota Samarahan, Malaysia
| | - Xiangping Tan
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xiankai Lu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Suping Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Teemu Tahvanainen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Reika Isoda
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Qing Ye
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
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15
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A Dual Enrichment Strategy Provides Soil- and Digestate-Competent Nitrous Oxide-Respiring Bacteria for Mitigating Climate Forcing in Agriculture. mBio 2022; 13:e0078822. [PMID: 35638872 PMCID: PMC9239227 DOI: 10.1128/mbio.00788-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Manipulating soil metabolism through heavy inoculation with microbes is feasible if organic wastes can be utilized as the substrate for growth and vector as a fertilizer. This, however, requires organisms active in both digestate and soil (generalists). Here, we present a dual enrichment strategy to enrich and isolate such generalists among N2O-respiring bacteria (NRB) in soil and digestates, to be used as an inoculum for strengthening the N2O-reduction capacity of soils. The enrichment strategy utilizes sequential batch enrichment cultures alternating between sterilized digestate and soil as substrates, with each batch initiated with limited O2 and unlimited N2O. The cultures were monitored for gas kinetics and community composition. As predicted by a Lotka-Volterra competition model, cluster analysis identified generalist operational taxonomic units (OTUs) which became dominant, digestate/soil-specialists which did not, and a majority that were gradually diluted out. We isolated several NRBs circumscribed by generalist OTUs. Their denitrification genes and phenotypes predicted a variable capacity to act as N2O-sinks, while all genomes predicted broad catabolic capacity. The latter contrasts with previous attempts to enrich NRB by anaerobic incubation of unsterilized digestate only, which selected for organisms with a catabolic capacity limited to fermentation products. The two isolates with the most promising characteristics as N2O sinks were aPseudomonas sp. with a full-fledged denitrification-pathway and a Cloacibacterium sp. carrying only N2O reductase (clade II), and soil experiments confirmed their capacity to reduce N2O-emissions from soil. The successful enrichment of NRB with broad catabolic spectra suggests that the concept of dual enrichment should also be applicable for enrichment of generalists with traits other than N2O reduction.
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16
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Zheng Q, Ding J, Lin W, Yao Z, Li Q, Xu C, Zhuang S, Kou X, Li Y. The influence of soil acidification on N 2O emissions derived from fungal and bacterial denitrification using dual isotopocule mapping and acetylene inhibition. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 303:119076. [PMID: 35240268 DOI: 10.1016/j.envpol.2022.119076] [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: 09/12/2021] [Revised: 01/20/2022] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
Denitrification, as both origins and sinks of N2O, occurs extensively, and is of critical importance for regulating N2O emissions in acidified soils. However, whether soil acidification stimulates N2O emissions, and if so for what reason contributes to stimulate the emissions is uncertain and how the N2O fractions from fungal (ffD) and bacterial (fbD) denitrification change with soil pH is unclear. Thus, a pH gradient (6.2, 7.1, 8.7) was set via manipulating cropland soils (initial pH 8.7) in North China to illustrate the effect of soil acidification on fungal and bacterial denitrification after the addition of KNO3 and glucose. For source partitioning, we used and compared SP/δ18O mapping approach (SP/δ18O MAP) and acetylene inhibition technique combined isotope two endmember mixing model (AIT-IEM). The results showed significantly higher N2O emissions in the acidified soils (pH 6.2 and pH 7.1) compared with the initial soil (pH 8.7). The cumulative N2O emissions during the whole incubation period (15 days) ranged from 7.1 mg N kg-1 for pH 8.7-18.9 mg N kg-1 for pH 6.2. With the addition of glucose, relative to treatments without glucose, this emission also increased with the decrement of pH values, and were significantly stimulated. Similarly, the highest N2O emissions and N2O/(N2O + N2) ratios (rN2O) were observed in the pH 6.2 treatment. But the difference was the highest cumulative N2O + N2 emissions, which were recorded in the pH 7.1 treatment based on SP/δ18O MAP. Based on both approaches, ffD values slightly increased with the acidification of soil, and bacterial denitrification was the dominant pathway in all treatments. The SP/δ18O MAP data indicated that both the rN2O and ffD were lower compared to AIT-IEM. It has been known for long that low pH may lead to high rN2O of denitrification and ffD, but our documentation of a pervasive pH-control of rN2O and ffD by utilizing combined SP/δ18O MAP and AIT-IEM is new. The results of the evaluated N2O emissions by acidified soils are finely explained by high rN2O and enhanced ffD. We argue that soil pH management should be high on the agenda for mitigating N2O emissions in the future, particularly for regions where long-term excessive nitrogen fertilizer is likely to acidify the soils.
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Affiliation(s)
- Qian Zheng
- Key Laboratory of Dryland Agriculture, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Junjun Ding
- Key Laboratory of Dryland Agriculture, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Lin
- Environmental Stable Isotope Laboratory, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610213, China
| | - Zhipeng Yao
- Management Service Center of Shandong Binzhou National Agricultural Science and Technology Park, Binzhou, 256600, China
| | - Qiaozhen Li
- Key Laboratory of Dryland Agriculture, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chunying Xu
- Key Laboratory of Dryland Agriculture, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shan Zhuang
- Key Laboratory of Dryland Agriculture, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinyue Kou
- Key Laboratory of Dryland Agriculture, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuzhong Li
- Key Laboratory of Dryland Agriculture, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; Environmental Stable Isotope Laboratory, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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17
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Pessi IS, Viitamäki S, Virkkala AM, Eronen-Rasimus E, Delmont TO, Marushchak ME, Luoto M, Hultman J. In-depth characterization of denitrifier communities across different soil ecosystems in the tundra. ENVIRONMENTAL MICROBIOME 2022; 17:30. [PMID: 35690846 PMCID: PMC9188126 DOI: 10.1186/s40793-022-00424-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND In contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources of the greenhouse gas nitrous oxide (N2O). However, the microorganisms involved in the cycling of N2O in this system remain largely uncharacterized. Since tundra soils are variable sources and sinks of N2O, we aimed at investigating differences in community structure across different soil ecosystems in the tundra. RESULTS We analysed 1.4 Tb of metagenomic data from soils in northern Finland covering a range of ecosystems from dry upland soils to water-logged fens and obtained 796 manually binned and curated metagenome-assembled genomes (MAGs). We then searched for MAGs harbouring genes involved in denitrification, an important process driving N2O emissions. Communities of potential denitrifiers were dominated by microorganisms with truncated denitrification pathways (i.e., lacking one or more denitrification genes) and differed across soil ecosystems. Upland soils showed a strong N2O sink potential and were dominated by members of the Alphaproteobacteria such as Bradyrhizobium and Reyranella. Fens, which had in general net-zero N2O fluxes, had a high abundance of poorly characterized taxa affiliated with the Chloroflexota lineage Ellin6529 and the Acidobacteriota subdivision Gp23. CONCLUSIONS By coupling an in-depth characterization of microbial communities with in situ measurements of N2O fluxes, our results suggest that the observed spatial patterns of N2O fluxes in the tundra are related to differences in the composition of denitrifier communities.
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Affiliation(s)
- Igor S. Pessi
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
- Helsinki Institute of Sustainability Science (HELSUS), Yliopistonkatu 3, 00014 Helsinki, Finland
| | - Sirja Viitamäki
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - Anna-Maria Virkkala
- Woodwell Climate Research Center, 149 Woods Hole Road, Falmouth, MA 02540-1644 USA
- Department of Geosciences and Geography, University of Helsinki, Gustaf Hällströmin katu 2, 00014 Helsinki, Finland
| | - Eeva Eronen-Rasimus
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
- Marine Research Centre, Finnish Environment Institute (SYKE), Agnes Sjöbergin katu 2, 00790 Helsinki, Finland
| | - Tom O. Delmont
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d’Evry, Université Paris-Saclay, 91057 Evry, France
| | - Maija E. Marushchak
- Department of Biological and Environmental Science, University of Jyväskylä, 40014 Jyväskylä, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Miska Luoto
- Department of Geosciences and Geography, University of Helsinki, Gustaf Hällströmin katu 2, 00014 Helsinki, Finland
| | - Jenni Hultman
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
- Helsinki Institute of Sustainability Science (HELSUS), Yliopistonkatu 3, 00014 Helsinki, Finland
- Natural Resources Institute Finland (LUKE), Latokartanonkaari 9, 00790 Helsinki, Finland
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Bueno E, Mania D, Mesa S, Bedmar EJ, Frostegård Å, Bakken LR, Delgado MJ. Regulation of the Emissions of the Greenhouse Gas Nitrous Oxide by the Soybean Endosymbiont Bradyrhizobium diazoefficiens. Int J Mol Sci 2022; 23:1486. [PMID: 35163408 PMCID: PMC8836242 DOI: 10.3390/ijms23031486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 11/21/2022] Open
Abstract
The greenhouse gas nitrous oxide (N2O) has strong potential to drive climate change. Soils are a major source of N2O, with microbial nitrification and denitrification being the primary processes involved in such emissions. The soybean endosymbiont Bradyrhizobium diazoefficiens is a model microorganism to study denitrification, a process that depends on a set of reductases, encoded by the napEDABC, nirK, norCBQD, and nosRZDYFLX genes, which sequentially reduce nitrate (NO3-) to nitrite (NO2-), nitric oxide (NO), N2O, and dinitrogen (N2). In this bacterium, the regulatory network and environmental cues governing the expression of denitrification genes rely on the FixK2 and NnrR transcriptional regulators. To understand the role of FixK2 and NnrR proteins in N2O turnover, we monitored real-time kinetics of NO3-, NO2-, NO, N2O, N2, and oxygen (O2) in a fixK2 and nnrR mutant using a robotized incubation system. We confirmed that FixK2 and NnrR are regulatory determinants essential for NO3- respiration and N2O reduction. Furthermore, we demonstrated that N2O reduction by B. diazoefficiens is independent of canonical inducers of denitrification, such as the nitrogen oxide NO3-, and it is negatively affected by acidic and alkaline conditions. These findings advance the understanding of how specific environmental conditions and two single regulators modulate N2O turnover in B. diazoefficiens.
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Affiliation(s)
- Emilio Bueno
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain; (S.M.); (E.J.B.)
| | - Daniel Mania
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Aas, Norway; (D.M.); (Å.F.); (L.R.B.)
| | - Socorro Mesa
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain; (S.M.); (E.J.B.)
| | - Eulogio J. Bedmar
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain; (S.M.); (E.J.B.)
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Aas, Norway; (D.M.); (Å.F.); (L.R.B.)
| | - Lars R. Bakken
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Aas, Norway; (D.M.); (Å.F.); (L.R.B.)
| | - María J. Delgado
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain; (S.M.); (E.J.B.)
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19
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Mancia A, Chadwick DR, Waters SM, Krol DJ. Uncertainties in direct N 2O emissions from grazing ruminant excreta (EF 3PRP) in national greenhouse gas inventories. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 803:149935. [PMID: 34487900 DOI: 10.1016/j.scitotenv.2021.149935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/21/2021] [Indexed: 06/13/2023]
Abstract
Excreta deposition onto pasture, range and paddocks (PRP) by grazing ruminant constitute a source of nitrous oxide (N2O), a potent greenhouse gas (GHG). These emissions must be reported in national GHG inventories, and their estimation is based on the application of an emission factor, EF3PRP (proportion of nitrogen (N) deposited to the soil through ruminant excreta, which is emitted as N2O). Depending on local data available, countries use various EF3PRPs and approaches to estimate N2O emissions from grazing ruminant excreta. Based on ten case study countries, this review aims to highlight the uncertainties around the methods used to account for these emissions in their national GHG inventories, and to discuss the efforts undertaken for considering factors of variation in the calculation of emissions. Without any local experimental data, 2006 the IPCC default (Tier 1) EF3PRPs are still widely applied although the default values were revised in 2019. Some countries have developed country-specific (Tier 2) EF3PRP based on local field studies. The accuracy of estimation can be improved through the disaggregation of EF3PRP or the application of models; two approaches including factors of variation. While a disaggregation of EF3PRP by excreta type is already well adopted, a disaggregation by other factors such as season of excreta deposition is more difficult to implement. Empirical models are a potential method of considering factors of variation in the establishment of EF3PRP. Disaggregation and modelling requires availability of sufficient experimental and activity data, hence why only few countries have currently adopted such approaches. Replication of field studies under various conditions, combined with meta-analysis of experimental data, can help in the exploration of influencing factors, as long as appropriate metadata is recorded. Overall, despite standard IPCC methodologies for calculating GHG emissions, large uncertainties and differences between individual countries' accounting remain to be addressed.
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Affiliation(s)
- Aude Mancia
- Teagasc, Environment, Soils and Land Use Department, Johnstown Castle, Co. Wexford, Ireland; School of Natural Sciences, Bangor University, Bangor, Wales, UK; Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Athenry, Co. Galway, Ireland
| | - David R Chadwick
- School of Natural Sciences, Bangor University, Bangor, Wales, UK
| | - Sinéad M Waters
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Athenry, Co. Galway, Ireland
| | - Dominika J Krol
- Teagasc, Environment, Soils and Land Use Department, Johnstown Castle, Co. Wexford, Ireland.
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20
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Frostegård Å, Vick SHW, Lim NYN, Bakken LR, Shapleigh JP. Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N 2O emissions and nitrite accumulation in soil. THE ISME JOURNAL 2022; 16:26-37. [PMID: 34211102 PMCID: PMC8692524 DOI: 10.1038/s41396-021-01045-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/07/2021] [Accepted: 06/16/2021] [Indexed: 11/24/2022]
Abstract
Soil pH is a key controller of denitrification. We analysed the metagenomics/transcriptomics and phenomics of two soils from a long-term liming experiment, SoilN (pH 6.8) and un-limed SoilA (pH 3.8). SoilA had severely delayed N2O reduction despite early transcription of nosZ (mainly clade I), encoding N2O reductase, by diverse denitrifiers. This shows that post-transcriptionally hampered maturation of the NosZ apo-protein at low pH is a generic phenomenon. Identification of transcript reads of several accessory genes in the nos cluster indicated that enzymes for NosZ maturation were present across a range of organisms, eliminating their absence as an explanation for the failure to produce a functional enzyme. nir transcript abundances (for NO2- reductase) in SoilA suggest that low NO2- concentrations in acidic soils, often ascribed to abiotic degradation, are primarily due to biological activity. The accumulation of NO2- in neutral soil was ascribed to high nar expression (nitrate reductase). The -omics results revealed dominance of nirK over nirS in both soils while qPCR showed the opposite, demonstrating that standard primer pairs only capture a fraction of the nirK pool. qnor encoding NO reductase was strongly expressed in SoilA, implying an important role in controlling NO. Production of HONO, for which some studies claim higher, others lower, emissions from NO2- accumulating soil, was estimated to be ten times higher from SoilA than from SoilN. The study extends our understanding of denitrification-driven gas emissions and the diversity of bacteria involved and demonstrates that gene and transcript quantifications cannot always reliably predict community phenotypes.
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Affiliation(s)
- Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
| | - Silas H W Vick
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Natalie Y N Lim
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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21
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Wu L, Wang LK, Wei W, Song L, Ni BJ. Sulfur-driven autotrophic denitrification of nitric oxide for efficient nitrous oxide recovery. Biotechnol Bioeng 2021; 119:257-267. [PMID: 34693996 DOI: 10.1002/bit.27970] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/10/2021] [Accepted: 10/21/2021] [Indexed: 11/12/2022]
Abstract
Nitrous oxide (N2 O) was previously deemed as a potent greenhouse gas but is actually an untapped energy source, which can accumulate during the microbial denitrification of nitric oxide (NO). Compared with the organic electron donor required in heterotrophic denitrification, elemental sulfur (S0 ) is a promising electron donor alternative due to its cheap cost and low biomass yield in sulfur-driven autotrophic denitrification. However, no effort has been made to test N2 O recovery from sulfur-driven denitrification of NO so far. Therefore, in this study, batch and continuous experiments were carried out to investigate the NO removal performance and N2 O recovery potential via sulfur-driven NO-based denitrification under various Fe(II)EDTA-NO concentrations. Efficient energy recovery was achieved, as up to 35.5%-40.9% of NO was converted to N2 O under various NO concentrations. N2 O recovery from Fe(II)EDTA-NO could be enhanced by the low bioavailability of sulfur and the acid environment caused by sulfur oxidation. The NO reductase (NOR) and N2 O reductase (N2 OR) were inhibited distinctively at relatively low NO levels, leading to efficient N2 O accumulation, but were suppressed irreversibly at NO level beyond 15 mM in continuous experiments. Such results indicated that the regulation of NO at a relatively low level would benefit the system stability and NO removal capacity during long-term system operation. The continuous operation of the sulfur-driven Fe(II)EDTA-NO-based denitrification reduced the overall microbial diversity but enriched several key microbial community. Thauera, Thermomonas, and Arenimonas that are able to carry out sulfur-driven autotrophic denitrification became the dominant organisms with their relative abundance increased from 25.8% to 68.3%, collectively.
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Affiliation(s)
- Lan Wu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Li-Kun Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Wei Wei
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Lan Song
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Bing-Jie Ni
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales, Australia
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22
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Pokharel P, Chang SX. Biochar decreases the efficacy of the nitrification inhibitor nitrapyrin in mitigating nitrous oxide emissions at different soil moisture levels. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 295:113080. [PMID: 34186312 DOI: 10.1016/j.jenvman.2021.113080] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
Unprecedented increases in agricultural nitrous oxide (N2O) emissions in recent years have caused substantial environmental pollution that leads to ozone depletion and global warming. Application of biochar and/or nitrification inhibitors (NIs) has the potential to reduce N2O emissions; however, it is not clear how biochar application may affect the efficacy of NI in reducing nitrification rates, soil enzyme activities, and N2O emissions under different soil moisture regimes. We conducted a 60-day laboratory incubation experiment to study the effects of manure biochar and nitrapyrin (as a NI) on N2O emissions from a urea fertilized soil with either 60 (low) or 80% (high) water-filled pore space (WFPS). Nitrification rates were significantly affected by biochar × NI × WFPS and biochar × WFPS interactions. Biochar initially increased and then decreased the rates, resulting in 45.2 and 26.6% (P < 0.001 for both) overall reductions in low and high WFPS, respectively while NI reduced the rates only in the first 10 days at 60% WFPS. Biochar decreased (P < 0.001) and NI increased (P = 0.007) β-1,4-N-acetyl glucosaminidase activities while urease activities were increased (P < 0.001) by biochar across WFPS. Biochar had significant interaction with NI in cumulative N2O emissions with the efficacy of NI being reduced when co-applied with biochar. Cumulative N2O emissions were greater at high than at low WFPS; the emissions were decreased by biochar at 60% WFPS and NI at both 60 and 80% WFPS. We conclude that biochar reduces efficacy of nitrapyrin in mitigating N2O emissions and their effects on net nitrification rates, enzyme activities and N2O emissions are dependent on soil moisture level.
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Affiliation(s)
- Prem Pokharel
- 442Earth Sciences Building, Department of Renewable Resources, University of Alberta, Edmonton, T6G 2E3, Canada.
| | - Scott X Chang
- 442Earth Sciences Building, Department of Renewable Resources, University of Alberta, Edmonton, T6G 2E3, Canada.
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23
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Ramírez-Fernández L, Orellana LH, Johnston ER, Konstantinidis KT, Orlando J. Diversity of microbial communities and genes involved in nitrous oxide emissions in Antarctic soils impacted by marine animals as revealed by metagenomics and 100 metagenome-assembled genomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 788:147693. [PMID: 34029816 DOI: 10.1016/j.scitotenv.2021.147693] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 04/02/2021] [Accepted: 05/07/2021] [Indexed: 06/12/2023]
Abstract
Antarctic soils generally have low temperatures and limited availability of liquid water and nutrients. However, animals can increase the nutrient availability of ice-free areas by transferring nutrients from marine to terrestrial ecosystems, mainly through their excreta. In this study, we employed shotgun metagenomics and population genome binning techniques to study the diversity of microbial communities in Antarctic soils impacted by marine pinnipeds and birds relative to soils with no evident animal presence. We obtained ~285,000 16S rRNA gene-carrying metagenomic reads representing ~60 phyla and 100 metagenome-assembled genomes (MAGs) representing eight phyla. Only nine of these 100 MAGs represented previously described species, revealing that these soils harbor extensive novel diversity. Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant phyla in all samples, with Rhodanobacter being one of the most abundant genera in the bird-impacted soils. Further, the relative abundance of genes related to denitrification was at least double in soils impacted by birds than soils without animal influence. These results advance our understanding of the microbial populations and their genes involved in nitrous oxide emissions in ice-free coastal Antarctic soils impacted by marine animals and reveal novel microbial diversity associated with these ecosystems.
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Affiliation(s)
- Lia Ramírez-Fernández
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Luis H Orellana
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Eric R Johnston
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Julieta Orlando
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
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24
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Jonassen KR, Hagen LH, Vick SHW, Arntzen MØ, Eijsink VGH, Frostegård Å, Lycus P, Molstad L, Pope PB, Bakken LR. Nitrous oxide respiring bacteria in biogas digestates for reduced agricultural emissions. ISME JOURNAL 2021; 16:580-590. [PMID: 34489539 PMCID: PMC8776835 DOI: 10.1038/s41396-021-01101-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/10/2021] [Accepted: 08/19/2021] [Indexed: 11/17/2022]
Abstract
Inoculating agricultural soils with nitrous oxide respiring bacteria (NRB) can reduce N2O-emission, but would be impractical as a standalone operation. Here we demonstrate that digestates obtained after biogas production are suitable substrates and vectors for NRB. We show that indigenous NRB in digestates grew to high abundance during anaerobic enrichment under N2O. Gas-kinetics and meta-omic analyses showed that these NRB’s, recovered as metagenome-assembled genomes (MAGs), grew by harvesting fermentation intermediates of the methanogenic consortium. Three NRB’s were isolated, one of which matched the recovered MAG of a Dechloromonas, deemed by proteomics to be the dominant producer of N2O-reductase in the enrichment. While the isolates harbored genes required for a full denitrification pathway and could thus both produce and sequester N2O, their regulatory traits predicted that they act as N2O sinks in soil, which was confirmed experimentally. The isolates were grown by aerobic respiration in digestates, and fertilization with these NRB-enriched digestates reduced N2O emissions from soil. Our use of digestates for low-cost and large-scale inoculation with NRB in soil can be taken as a blueprint for future applications of this powerful instrument to engineer the soil microbiome, be it for enhancing plant growth, bioremediation, or any other desirable function.
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Affiliation(s)
- Kjell Rune Jonassen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway.,VEAS WWTP, Slemmestad, Norway
| | - Live H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Silas H W Vick
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Pawel Lycus
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Lars Molstad
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Phillip B Pope
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway.,Faculty of Biosciences, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway.
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25
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Buessecker S, Zamora Z, Sarno AF, Finn DR, Hoyt AM, van Haren J, Urquiza Muñoz JD, Cadillo-Quiroz H. Microbial Communities and Interactions of Nitrogen Oxides With Methanogenesis in Diverse Peatlands of the Amazon Basin. Front Microbiol 2021; 12:659079. [PMID: 34267733 PMCID: PMC8276178 DOI: 10.3389/fmicb.2021.659079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/21/2021] [Indexed: 12/03/2022] Open
Abstract
Tropical peatlands are hotspots of methane (CH4) production but present high variation and emission uncertainties in the Amazon region. This is because the controlling factors of methane production in tropical peats are not yet well documented. Although inhibitory effects of nitrogen oxides (NOx) on methanogenic activity are known from pure culture studies, the role of NOx in the methane cycling of peatlands remains unexplored. Here, we investigated the CH4 content, soil geochemistry and microbial communities along 1-m-soil profiles and assessed the effects of soil NOx and nitrous oxide (N2O) on methanogenic abundance and activity in three peatlands of the Pastaza-Marañón foreland basin. The peatlands were distinct in pH, DOC, nitrate pore water concentrations, C/N ratios of shallow soils, redox potential, and 13C enrichment in dissolved inorganic carbon and CH4 pools, which are primarily contingent on H2-dependent methanogenesis. Molecular 16S rRNA and mcrA gene data revealed diverse and novel methanogens varying across sites. Importantly, we also observed a strong stratification in relative abundances of microbial groups involved in NOx cycling, along with a concordant stratification of methanogens. The higher relative abundance of ammonia-oxidizing archaea (Thaumarchaeota) in acidic oligotrophic peat than ammonia-oxidizing bacteria (Nitrospira) is noteworthy as putative sources of NOx. Experiments testing the interaction of NOx species and methanogenesis found that the latter showed differential sensitivity to nitrite (up to 85% reduction) and N2O (complete inhibition), which would act as an unaccounted CH4 control in these ecosystems. Overall, we present evidence of diverse peatlands likely differently affected by inhibitory effects of nitrogen species on methanogens as another contributor to variable CH4 fluxes.
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Affiliation(s)
- Steffen Buessecker
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Zacary Zamora
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Analissa F Sarno
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Damien Robert Finn
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Alison M Hoyt
- Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Joost van Haren
- Biosphere 2 Institute, University of Arizona, Oracle, AZ, United States.,Honors College, University of Arizona, Tucson, AZ, United States
| | - Jose D Urquiza Muñoz
- Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Jena, Germany.,Laboratory of Soil Research, Research Institute of Amazonia's Natural Resources, National University of the Peruvian Amazon, Iquitos, Peru.,School of Forestry, National University of the Peruvian Amazon, Iquitos, Peru
| | - Hinsby Cadillo-Quiroz
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Swette Center for Environmental Biotechnology, The Biodesign Institute, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
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26
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Suri N, Zhang Y, Gieg LM, Ryan MC. Denitrification Biokinetics: Towards Optimization for Industrial Applications. Front Microbiol 2021; 12:610389. [PMID: 34025593 PMCID: PMC8131540 DOI: 10.3389/fmicb.2021.610389] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 03/18/2021] [Indexed: 11/28/2022] Open
Abstract
Denitrification is a microbial process that converts nitrate (NO3–) to N2 and can play an important role in industrial applications such as souring control and microbially enhanced oil recovery (MEOR). The effectiveness of using NO3– in souring control depends on the partial reduction of NO3– to nitrite (NO2–) and/or N2O while in MEOR complete reduction of NO3– to N2 is desired. Thauera has been reported as a dominant taxon in such applications, but the impact of NO3– and NO2– concentrations, and pH on the kinetics of denitrification by this bacterium is not known. With the goal of better understanding the effects of such parameters on applications such as souring and MEOR, three strains of Thauera (K172, NS1 and TK001) were used to study denitrification kinetics when using acetate as an electron donor. At low initial NO3– concentrations (∼1 mmol L–1) and at pH 7.5, complete NO3– reduction by all strains was indicated by non-detectable NO3– concentrations and near-complete recovery (> 97%) of the initial NO3-N as N2 after 14 days of incubation. The relative rate of denitrification by NS1 was low, 0.071 mmol L–1 d–1, compared to that of K172 (0.431 mmol L–1 d–1) and TK001 (0.429 mmol L–1 d–1). Transient accumulation of up to 0.74 mmol L–1 NO2– was observed in cultures of NS1 only. Increased initial NO3– concentrations resulted in the accumulation of elevated concentrations of NO2– and N2O, particularly in incubations with K172 and NS1. Strain TK001 had the most extensive NO3– reduction under high initial NO3– concentrations, but still had only ∼78% of the initial NO3-N recovered as N2 after 90 days of incubation. As denitrification proceeded, increased pH substantially reduced denitrification rates when values exceeded ∼ 9. The rate and extent of NO3– reduction were also affected by NO2– accumulation, particularly in incubations with K172, where up to more than a 2-fold rate decrease was observed. The decrease in rate was associated with decreased transcript abundances of denitrification genes (nirS and nosZ) required to produce enzymes for reduction of NO2– and N2O. Conversely, high pH also contributed to the delayed expression of these gene transcripts rather than their abundances in strains NS1 and TK001. Increased NO2– concentrations, N2O levels and high pH appeared to cause higher stress on NS1 than on K172 and TK001 for N2 production. Collectively, these results indicate that increased pH can alter the kinetics of denitrification by Thauera strains used in this study, suggesting that liming could be a way to achieve partial denitrification to promote NO2– and N2O production (e.g., for souring control) while pH buffering would be desirable for achieving complete denitrification to N2 (e.g., for gas-mediated MEOR).
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Affiliation(s)
- Navreet Suri
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Yuan Zhang
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Lisa M Gieg
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - M Cathryn Ryan
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
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27
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Shakoor A, Shahzad SM, Chatterjee N, Arif MS, Farooq TH, Altaf MM, Tufail MA, Dar AA, Mehmood T. Nitrous oxide emission from agricultural soils: Application of animal manure or biochar? A global meta-analysis. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 285:112170. [PMID: 33607561 DOI: 10.1016/j.jenvman.2021.112170] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/29/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Organic amendments (animal manure and biochar) to agricultural soils may enhance soil organic carbon (SOC) contents, improve soil fertility and crop productivity but also contribute to global warming through nitrous oxide (N2O) emission. However, the effects of organic amendments on N2O emissions from agricultural soils seem variable among numerous research studies and remains uncertain. Here, eighty-five publications (peer-reviewed) were selected to perform a meta-analysis study. The results of this meta-analysis study show that the application of animal manure enhanced N2O emissions by 17.7%, whereas, biochar amendment significantly mitigated N2O emissions by 19.7%. Moreover, coarse textured soils increased [lnRR‾ = 182.6%, 95% confidence interval (CI) = 151.4%, 217.7%] N2O emission after animal manure, in contrast, N2O emission mitigated by 7.0% from coarse textured soils after biochar amendment. In addition, this study found that 121-320 kg N ha-1 and ⩽ 30 T ha-1 application rates of animal manure and biochar mitigated N2O emissions by 72.3% and 22.5%, respectively. Soil pH also played a vital role in regulating the N2O emissions after organic amendments. Furthermore, > 10 soil C: N ratios increased N2O emissions by 121.4% and 27.6% after animal and biochar amendments, respectively. Overall, animal manure C: N ratios significantly enhanced N2O emissions, while, biochar C: N ratio had not shown any effect on N2O emissions. Overall, average N2O emission factors (EFs) for animal manure and biochar amendments were 0.46% and -0.08%, respectively. Thus, the results of this meta-analysis study provide scientific evidence about how organic amendments such as animal manure and biochar regulating the N2O emission from agricultural soils.
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Affiliation(s)
- Awais Shakoor
- Department of Environment and Soil Sciences, University of Lleida, Avinguda Alcalde Rovira Roure 191, 25198, Lleida, Spain.
| | - Sher Muhammad Shahzad
- Department of Soil and Environmental Sciences, College of Agriculture, University of Sargodha, Sargodha, 40100, Punjab, Pakistan
| | | | - Muhammad Saleem Arif
- Department of Environmental Sciences & Engineering, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Taimoor Hassan Farooq
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Muhammad Mohsin Altaf
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Ecology and Environment, Hainan University, Haikou, 570228, PR China
| | - Muhammad Aammar Tufail
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige, 38010, Italy; Department of Civil, Environmental and Mechanical Engineering, University of Trento, 38123, Trento, Italy
| | - Afzal Ahmed Dar
- School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xian, China
| | - Tariq Mehmood
- College of Environment, Hohai University, 210098, Nanjing, China
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28
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Duffner C, Wunderlich A, Schloter M, Schulz S, Einsiedl F. Strategies to Overcome Intermediate Accumulation During in situ Nitrate Remediation in Groundwater by Hydrogenotrophic Denitrification. Front Microbiol 2021; 12:610437. [PMID: 33763037 PMCID: PMC7982820 DOI: 10.3389/fmicb.2021.610437] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/15/2021] [Indexed: 11/13/2022] Open
Abstract
Bioremediation of polluted groundwater is one of the most difficult actions in environmental science. Nonetheless, the clean-up of nitrate polluted groundwater may become increasingly important as nitrate concentrations frequently exceed the EU drinking water limit of 50 mg L-1, largely due to intensification of agriculture and food production. Denitrifiers are natural catalysts that can reduce increasing nitrogen loading of aquatic ecosystems. Porous aquifers with high nitrate loading are largely electron donor limited and additionally, high dissolved oxygen concentrations are known to reduce the efficiency of denitrification. Therefore, denitrification lag times (time prior to commencement of microbial nitrate reduction) up to decades were determined for such groundwater systems. The stimulation of autotrophic denitrifiers by the injection of hydrogen into nitrate polluted regional groundwater systems may represent a promising remediation strategy for such environments. However, besides high costs other drawbacks, such as the transient or lasting accumulation of the cytotoxic intermediate nitrite or the formation of the potent greenhouse gas nitrous oxide, have been described. In this article, we detect causes of incomplete denitrification, which include environmental factors and physiological characteristics of the underlying bacteria and provide possible mitigation approaches.
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Affiliation(s)
- Clara Duffner
- Chair of Soil Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- Research Unit Comparative Microbiome Analysis, Helmholtz Center Munich, Neuherberg, Germany
| | - Anja Wunderlich
- Chair of Hydrogeology, TUM Department of Civil, Geo and Environmental Engineering, Technical University of Munich, Munich, Germany
| | - Michael Schloter
- Chair of Soil Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- Research Unit Comparative Microbiome Analysis, Helmholtz Center Munich, Neuherberg, Germany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Center Munich, Neuherberg, Germany
| | - Florian Einsiedl
- Chair of Hydrogeology, TUM Department of Civil, Geo and Environmental Engineering, Technical University of Munich, Munich, Germany
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Hetz SA, Horn MA. Burkholderiaceae Are Key Acetate Assimilators During Complete Denitrification in Acidic Cryoturbated Peat Circles of the Arctic Tundra. Front Microbiol 2021; 12:628269. [PMID: 33613495 PMCID: PMC7892595 DOI: 10.3389/fmicb.2021.628269] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/18/2021] [Indexed: 01/23/2023] Open
Abstract
Cryoturbated peat circles (pH 4) in the Eastern European Tundra harbor up to 2 mM pore water nitrate and emit the greenhouse gas N2O like heavily fertilized agricultural soils in temperate regions. The main process yielding N2O under oxygen limited conditions is denitrification, which is the sequential reduction of nitrate/nitrite to N2O and/or N2. N2O reduction to N2 is impaired by pH < 6 in classical model denitrifiers and many environments. Key microbes of peat circles are important but largely unknown catalysts for C- and N-cycling associated N2O fluxes. Thus, we hypothesized that the peat circle community includes hitherto unknown taxa and is essentially unable to efficiently perform complete denitrification, i.e., reduce N2O, due to a low in situ pH. 16S rRNA analysis indicated a diverse active community primarily composed of the bacterial class-level taxa Alphaproteobacteria, Acidimicrobiia, Acidobacteria, Verrucomicrobiae, and Bacteroidia, as well as archaeal Nitrososphaeria. Euryarchaeota were not detected. 13C2- and 12C2-acetate supplemented anoxic microcosms with endogenous nitrate and acetylene at an in situ near pH of 4 were used to assess acetate dependent carbon flow, denitrification and N2O production. Initial nitrate and acetate were consumed within 6 and 11 days, respectively, and primarily converted to CO2 and N2, suggesting complete acetate fueled denitrification at acidic pH. Stable isotope probing coupled to 16S rRNA analysis via Illumina MiSeq amplicon sequencing identified acetate consuming key players of the family Burkholderiaceae during complete denitrification correlating with Rhodanobacter spp. The archaeal community consisted primarily of ammonia-oxidizing Archaea of Nitrososphaeraceae, and was stable during the incubation. The collective data indicate that peat circles (i) host acid-tolerant denitrifiers capable of complete denitrification at pH 4-5.5, (ii) other parameters like carbon availability rather than pH are possible reasons for high N2O emissions in situ, and (iii) Burkholderiaceae are responsive key acetate assimilators co-occurring with Rhodanobacter sp. during denitrification, suggesting both organisms being associated with acid-tolerant denitrification in peat circles.
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Affiliation(s)
- Stefanie A Hetz
- Institute of Microbiology, Leibniz University Hannover, Hannover, Germany
| | - Marcus A Horn
- Institute of Microbiology, Leibniz University Hannover, Hannover, Germany
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30
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Rhizobia: highways to NO. Biochem Soc Trans 2021; 49:495-505. [PMID: 33544133 DOI: 10.1042/bst20200989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 02/02/2023]
Abstract
The interaction between rhizobia and their legume host plants conduces to the formation of specialized root organs called nodules where rhizobia differentiate into bacteroids which fix atmospheric nitrogen to the benefit of the plant. This beneficial symbiosis is of importance in the context of sustainable agriculture as legumes do not require the addition of nitrogen fertilizer to grow. Interestingly, nitric oxide (NO) has been detected at various steps of the rhizobium-legume symbiosis where it has been shown to play multifaceted roles. Both bacterial and plant partners are involved in NO synthesis in nodules. To better understand the role of NO, and in particular the role of bacterial NO, at all steps of rhizobia-legumes interaction, the enzymatic sources of NO have to be elucidated. In this review, we discuss different enzymatic reactions by which rhizobia may potentially produce NO. We argue that there is most probably no NO synthase activity in rhizobia, and that instead the NO2- reductase nirK, which is part of the denitrification pathway, is the main bacterial source of NO. The nitrate assimilation pathway might contribute to NO production but only when denitrification is active. The different approaches to measure NO in rhizobia are also addressed.
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31
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Wang J, Cui W, Che Z, Liang F, Wen Y, Zhan M, Dong X, Jin W, Dong Z, Song H. Effects of synthetic nitrogen fertilizer and manure on fungal and bacterial contributions to N 2O production along a soil acidity gradient. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 753:142011. [PMID: 32890881 DOI: 10.1016/j.scitotenv.2020.142011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 06/11/2023]
Abstract
Reactive nitrogen (Nr) input often induces soil acidification, which may in turn affect bacterial and fungal nitrogen (N) transformations in soil and nitrous oxide (N2O) emissions. However, the interactive effects of soil acidity and Nr on the contributions of bacteria and fungi to N2O emissions remain unclear. We conducted a field experiment to assess the effects of anthropogenic Nr forms (i.e., synthetic N fertilizer and manure) on bacterial and fungal N2O emissions along a soil acidity gradient (soil pH = 6.8, 6.1, 5.2, and 4.2). The abundances and structure of bacterial and fungal communities were analyzed by real-time polymerase chain reaction and high-throughput sequencing techniques, respectively. Soil acidification reduced bacterial but increased fungal contributions to N2O production, corresponding respectively to changes in bacterial and fungal abundance. It also altered bacterial and fungal community structures and soil chemical properties, such as dissolved organic carbon and ammonia concentrations. Structural equation modeling (SEM) analyses showed that the soil properties and fungal community were the most important factors determining bacterial and fungal contributions to N2O emissions, respectively. The fertilizer form markedly affected N2O emissions from bacteria but not from fungi. Compared with synthetic N fertilizer, manure significantly lowered the bacterial contribution to N2O emissions in the soils with pH of 5.2 and 4.2. The manure application significantly increased soil pH but reduced nitrate concentration. The fertilizer form did not significantly alter the bacterial and fungal community structures. The SEM revealed that the fertilizer form affected the bacterial contribution to N2O production by changing the soil chemical properties. Together, these results indicated that soil acidification enhanced fungal dominance for N2O emission, and manure application has limited effects on fungal N2O emission, highlighting the challenges for mitigation of soil N2O emissions under future acid deposition and N enrichment scenarios.
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Affiliation(s)
- Jun Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Wenli Cui
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Zhao Che
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Fei Liang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Yongkang Wen
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Meimei Zhan
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Xiao Dong
- School of Engineering, Anhui Agricultural University, Hefei 230036, China
| | - Wenjun Jin
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Zhaorong Dong
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - He Song
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China.
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32
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Shakoor A, Shahbaz M, Farooq TH, Sahar NE, Shahzad SM, Altaf MM, Ashraf M. A global meta-analysis of greenhouse gases emission and crop yield under no-tillage as compared to conventional tillage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 750:142299. [PMID: 33182198 DOI: 10.1016/j.scitotenv.2020.142299] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/05/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
No-tillage (NT) practice is extensively adopted with aims to improve soil physical conditions, carbon (C) sequestration and to alleviate greenhouse gases (GHGs) emissions without compromising crop yield. However, the influences of NT on GHGs emissions and crop yields remains inconsistent. A global meta-analysis was performed by using fifty peer-reviewed publications to assess the effectiveness of soil physicochemical properties, nitrogen (N) fertilization, type and duration of crop, water management and climatic zones on GHGs emissions and crop yields under NT compared to conventional tillage (CT) practices. The outcome reveals that compared to CT, NT increased CO2, N2O, and CH4 emissions by 7.1, 12.0, and 20.8%, respectively. In contrast, NT caused up to 7.6% decline in global warming potential as compared to CT. However, absence of difference in crop yield was observed both under NT and CT practices. Increasing N fertilization rates under NT improved crop yield and GHGs emission up to 23 and 58%, respectively, compared to CT. Further, NT practices caused an increase of 16.1% CO2 and 14.7% N2O emission in the rainfed areas and up to 54.0% CH4 emission under irrigated areas as compared to CT practices. This meta-analysis study provides a scientific basis for evaluating the effects of NT on GHGs emissions and crop yields, and also provides basic information to mitigate the GHGs emissions that are associated with NT practice.
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Affiliation(s)
- Awais Shakoor
- Department of Environment and Soil Sciences, University of Lleida, Avinguda Alcalde Rovira Roure 191, 25198 Lleida, Spain.
| | - Muhammad Shahbaz
- Centre for Environmental and Climate Research, Lund University, 223 62 Lund, Sweden
| | - Taimoor Hassan Farooq
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Najam E Sahar
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Sher Muhammad Shahzad
- Department of Soil and Environmental Sciences, College of Agriculture, University of Sargodha, Sargodha 40100, Punjab, Pakistan
| | - Muhammad Mohsin Altaf
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Ecology and Environment, Hainan University, Haikou 570228, PR China
| | - Muhammad Ashraf
- Department of Soil Science, Faculty of Agriculture, Bahauddin Zakariya University, Multan, Punjab, Pakistan
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Pandey CB, Kumar U, Kaviraj M, Minick KJ, Mishra AK, Singh JS. DNRA: A short-circuit in biological N-cycling to conserve nitrogen in terrestrial ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 738:139710. [PMID: 32544704 DOI: 10.1016/j.scitotenv.2020.139710] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/21/2020] [Accepted: 05/23/2020] [Indexed: 06/11/2023]
Abstract
This paper reviews dissimilatory nitrate reduction to ammonium (DNRA) in soils - a newly appreciated pathway of nitrogen (N) cycling in the terrestrial ecosystems. The reduction of NO3- occurs in two steps; in the first step, NO3- is reduced to NO2-; and in the second, unlike denitrification, NO2- is reduced to NH4+ without intermediates. There are two sets of NO3-/NO2- reductase enzymes, i.e., Nap/Nrf and Nar/Nir; the former occurs on the periplasmic-membrane and energy conservation is respiratory via electron-transport-chain, whereas the latter is cytoplasmic and energy conservation is both respiratory and fermentative (Nir, substrate-phosphorylation). Since, Nir catalyzes both assimilatory- and dissimilatory-nitrate reduction, the nrfA gene, which transcribes the NrfA protein, is treated as a molecular-marker of DNRA; and a high nrfA/nosZ (N2O-reductase) ratio favours DNRA. Recently, several crystal structures of NrfA have been presumed to producee N2O as a byproduct of DNRA via the NO (nitric-oxide) pathway. Meta-analyses of about 200 publications have revealed that DNRA is regulated by oxidation state of soils and sediments, carbon (C)/N and NO2-/NO3- ratio, and concentrations of ferrous iron (Fe2+) and sulfide (S2-). Under low-redox conditions, a high C/NO3- ratio selects for DNRA while a low ratio selects for denitrification. When the proportion of both C and NO3- are equal, the NO2-/NO3- ratio modulates partitioning of NO3-, and a high NO2-/NO3- ratio favours DNRA. A high S2-/NO3- ratio also promotes DNRA in coastal-ecosystems and saline sediments. Soil pH, temperature, and fine soil particles are other factors known to influence DNRA. Since, DNRA reduces NO3- to NH4+, it is essential for protecting NO3- from leaching and gaseous (N2O) losses and enriches soils with readily available NH4+-N to primary producers and heterotrophic microorganisms. Therefore, DNRA may be treated as a tool to reduce ground-water NO3- pollution, enhance soil health and improve environmental quality.
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Affiliation(s)
- C B Pandey
- ICAR-Central Arid Zone Research Institute, Jodhpur 342003, Rajasthan, India.
| | - Upendra Kumar
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India.
| | - Megha Kaviraj
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India
| | - K J Minick
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - A K Mishra
- International Rice Research Institute, New Delhi 110012, India
| | - J S Singh
- Ecosystem Analysis Lab, Centre of Advanced Study in Botany, Banaras Hindu University (BHU), Varanasi 221005, India
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Bennett SP, Torres MJ, Soriano-Laguna MJ, Richardson DJ, Gates AJ, Le Brun NE. nosX is essential for whole-cell N 2O reduction in Paracoccus denitrificans but not for assembly of copper centres of nitrous oxide reductase. MICROBIOLOGY-SGM 2020; 166:909-917. [PMID: 32886603 PMCID: PMC7660919 DOI: 10.1099/mic.0.000955] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas that is produced naturally as an intermediate during the process of denitrification carried out by some soil bacteria. It is consumed by nitrous oxide reductase (N2OR), the terminal enzyme of the denitrification pathway, which catalyses a reduction reaction to generate dinitrogen. N2OR contains two important copper cofactors (CuA and CuZ centres) that are essential for activity, and in copper-limited environments, N2OR fails to function, contributing to rising levels of atmospheric N2O and a major environmental challenge. Here we report studies of nosX, one of eight genes in the nos cluster of the soil dwelling α-proteobaterium Paraccocus denitrificans. A P. denitrificans ΔnosX deletion mutant failed to reduce N2O under both copper-sufficient and copper-limited conditions, demonstrating that NosX plays an essential role in N2OR activity. N2OR isolated from nosX-deficient cells was found to be unaffected in terms of the assembly of its copper cofactors, and to be active in in vitro assays, indicating that NosX is not required for the maturation of the enzyme; in particular, it plays no part in the assembly of either of the CuA and CuZ centres. Furthermore, quantitative Reverse Transcription PCR (qRT-PCR) studies showed that NosX does not significantly affect the expression of the N2OR-encoding nosZ gene. NosX is a homologue of the FAD-binding protein ApbE from Pseudomonas stutzeri, which functions in the flavinylation of another N2OR accessory protein, NosR. Thus, it is likely that NosX is a system-specific maturation factor of NosR, and so is indirectly involved in maintaining the reaction cycle of N2OR and cellular N2O reduction.
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Affiliation(s)
- Sophie P Bennett
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Maria J Torres
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Manuel J Soriano-Laguna
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - David J Richardson
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Andrew J Gates
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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35
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Zhuge YY, Shen XY, Liu YD, Shapleigh J, Li W. Application of acidic conditions and inert-gas sparging to achieve high-efficiency nitrous oxide recovery during nitrite denitrification. WATER RESEARCH 2020; 182:116001. [PMID: 32544733 DOI: 10.1016/j.watres.2020.116001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/21/2020] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
Nitrogen removal with energy recovery through denitrification dependent N2O production is garnering recent attention due to its cost advantages. The most effective current method requires alternating COD and nitrite to achieve high N2O production making it incompatible with typical wastewaters and consequently difficult to use in most settings. The work described here introduces a robust and highly efficient N2O recovery approach which has the potential to work with wastewaters containing COD and nitrite simultaneously. This method relies on low pH incubation and inert gas sparging (IGS) to shift a community of mainly N2 producing nitrite denitrifiers to a community that accumulates N2O when incubated in the absence of IGS. Before experiencing IGS, samples from activated sludge incubated at a pH of 4.5 and 6.0 only achieved a maximum N2O production efficiency (PE_N2O) of ∼26%. After IGS the PE_N2O values increased to ∼97.5% and ∼80.2% for samples from these same pH 4.5 and pH 6.0 reactors, respectively. IGS did not lead to N2O production in a pH 7.5 bioreactor. Meta-omics analysis revealed that IGS resulted in an increase in bacteria utilizing the clade I nitrous oxide reductase (nosZI) relative to bacteria utilizing the clade II nitrous oxide reductase (nosZII). This likely results from IGS flushing out N2O leaving nitrite as the principal nitrogen oxide available for respiration, favoring nosZI utilizing bacteria which are more likely to be complete denitrifiers. Metatranscriptomic analysis suggested that the high PE_N2O values that occurred after stopping IGS result from the NO generated by chemodenitrification accumulating to levels that inactivate [4Fe:4S] clusters in the NosR protein essential for N2O reduction in the nosZI denitrifiers. This study provides an efficient and straightforward method for N2O recovery, widening the options for energy recovery from nitrogen-based wastes.
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Affiliation(s)
- Yang-Yang Zhuge
- National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Xun-Yu Shen
- National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Yong-di Liu
- National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
| | | | - Wei Li
- National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China.
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36
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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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37
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Yin C, Fan X, Yan G, Chen H, Ye M, Ni L, Peng H, Ran W, Zhao Y, Li T, Wakelin SA, Liang Y. Gross N 2O Production Process, Not Consumption, Determines the Temperature Sensitivity of Net N 2O Emission in Arable Soil Subject to Different Long-Term Fertilization Practices. Front Microbiol 2020; 11:745. [PMID: 32411109 PMCID: PMC7198778 DOI: 10.3389/fmicb.2020.00745] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 03/30/2020] [Indexed: 11/20/2022] Open
Abstract
Chronic amendment of agricultural soil with synthetic nitrogen fertilization and/or livestock manure has been demonstrated to enhance the feedback intensity of net N2O emission to temperature variation (i.e., temperature sensitivity, TS). Yet few studies have explored the relevance of changes in underlying gross N2O production and consumption processes toward explaining this phenomenon, in particular for the latter. Furthermore, the microbe-based mechanisms associated with the variation of N2O consumption process remain largely unexplored. To address this knowledge gap, a temperature- (15, 25, and 35°C) and moisture-controlled (50% water holding capacity) microcosm incubation experiment was established using an arable soil subject to long-term addition of synthetic fertilizer (NPK), a mixture of synthetic fertilizer with livestock manure (MNPK), or with no fertilizer treatment (CT). Over the incubation time period, the C2H2 inhibition method was adopted to monitor reaction rates of gross N2O production and consumption; the population sizes and community structures of nosZI- and nosZII-N2O reducers were analyzed using quantitative PCR (Q-PCR) and terminal restriction fragment length polymorphism (T-RFLP). The results indicated that only NPK significantly increased the TS of net N2O emission, and gross N2O consumption process consistently occurred under all treatment combinations (temperature and fertilization) at each sampling time point. The responses of gross N2O production and consumption processes to temperature elevation exhibited fertilization- and sampling time-dependent pattern, and the higher net N2O production TS in the NPK treatment was underlain by its higher TS of gross production process and insensitivity of gross consumption process to temperature. The size and structure of nosZII-N2O reducers, as well as the community structure of nosZI-N2O reducers, were positively correlated with variation of gross N2O production and consumption rates across all fertilization regimes. NosZII-N2O reducer abundance was less responsive to temperature change, and its community structure less susceptible to fertilization, as compared with nosZI-N2O reducers. Overall, our results demonstrate that the TS of the gross N2O production process, not gross consumption, is the key step regulating the TS of net N2O production, and both nosZI- and nosZII-N2O clades are likely active N2O reducers in the tested soil.
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Affiliation(s)
- Chang Yin
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, China
| | - Xiaoping Fan
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, China
| | - Guochao Yan
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, China
| | - Hao Chen
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, China
| | - Mujun Ye
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, China
| | - Liang Ni
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, China
| | - Hongyun Peng
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, China
| | - Wei Ran
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yuhua Zhao
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Tingqiang Li
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, China
| | - Steven A Wakelin
- New Zealand Forest Research Institute Limited (Scion), Christchurch, New Zealand
| | - Yongchao Liang
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, China
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Aamer M, Shaaban M, Hassan MU, Guoqin H, Ying L, Hai Ying T, Rasul F, Qiaoying M, Zhuanling L, Rasheed A, Peng Z. Biochar mitigates the N 2O emissions from acidic soil by increasing the nosZ and nirK gene abundance and soil pH. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 255:109891. [PMID: 32063300 DOI: 10.1016/j.jenvman.2019.109891] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/25/2019] [Accepted: 11/18/2019] [Indexed: 06/10/2023]
Abstract
Nitrous oxide (N2O) is a pervasive greenhouse gas, and soil management practices greatly affect its release into the atmosphere. Soil pH management (particularly increasing the pH) using biochar can seriously affect soil N2O emissions. The current incubation experiment was conducted to explore the response of N2O emissions from acidic soils using various doses of biochar. Soil with a pH of 5.48 was treated with rice straw biochar at different doses (0%, 1% and 2%) and incubated with 60% water-filled pore spaces (WFPS). The experiment was conducted in a completely randomized design (CRD) with three replications. The soil N2O emissions, pH, NH4+-N, NO3--N, microbial biomass carbon (MBC), and nosZ and nirK gene abundance were determined at various intervals throughout the study. The biochar application (2%) increased the soil pH (from 5.48 to 6.11), triggered the transformation of nitrogen, and augmented the abundance of nosZ and nirK genes. Higher magnitudes of cumulative soil N2O emissions (48.60 μg kg-1) were noted in the control (no biochar) compared to 1% (28.10 μg kg-1) and 2% (14.50 μg kg-1) biochar application. The 2% biochar application more effectively decreased the soil N2O emissions, mainly because of the increased nosZ and nirK gene abundance at higher soil pH levels. The findings suggest that the amelioration of acidic soil with rice straw biochar can considerably control soil N2O emissions by elevating the soil pH and the abundance of nosZ and nirK genes.
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Affiliation(s)
- Muhammad Aamer
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Muhammad Shaaban
- Department of Soil Science, Bahauddin Zakariya University, Multan, Pakistan
| | | | - Huang Guoqin
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Liu Ying
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China
| | - Tang Hai Ying
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China
| | - Fahd Rasul
- Department of Agronomy, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Ma Qiaoying
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China
| | - Li Zhuanling
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China
| | - Adnan Rasheed
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhang Peng
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China
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39
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Hénault C, Bourennane H, Ayzac A, Ratié C, Saby NPA, Cohan JP, Eglin T, Gall CL. Management of soil pH promotes nitrous oxide reduction and thus mitigates soil emissions of this greenhouse gas. Sci Rep 2019; 9:20182. [PMID: 31882900 PMCID: PMC6934481 DOI: 10.1038/s41598-019-56694-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 12/15/2019] [Indexed: 11/29/2022] Open
Abstract
While concerns about human-induced effects on the Earth's climate have mainly concentrated on carbon dioxide (CO2) and methane (CH4), reducing anthropogenic nitrous oxide (N2O) flux, mainly of agricultural origin, also represents an opportunity for substantial mitigation. To develop a solution that induces neither the transfer of nitrogen pollution nor decreases agricultural production, we specifically investigated the last step of the denitrification pathway, the N2O reduction path, in soils. We first observed that this path is mainly driven by soil pH and is progressively inhibited when pH is lower than 6.8. During field experiments, we observed that liming acidic soils to neutrality made N2O reduction more efficient and decreased soil N2O emissions. As we estimated acidic fertilized soils to represent 37% [27-50%] of French soils, we calculated that liming could potentially decrease France's total N2O emissions by 15.7% [8.3-21.2%]. Nevertheless, due to the different possible other impacts of liming, we currently recommend that the deployment of this solution to mitigate N2O emission should be based on local studies that take into account agronomic, environmental and economic aspects.
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Affiliation(s)
- Catherine Hénault
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France.
- URSOLS, INRAE, 45075, Orléans, France.
| | | | | | | | | | - Jean-Pierre Cohan
- ARVALIS- Institut du Végétal Route de Châteaufort - RD 36 - ZA des Graviers, 91190, Villiers le Bacle, France
| | - Thomas Eglin
- ADEME, Direction Bioéconomie et Energies Renouvelables, Service Forêts, Alimentation et Bioéconomie, F-49000, Angers, France
| | - Cécile Le Gall
- TERRES INOVIA, Avenue Lucien Brétignières, 78850, Thiverval Grignon, France
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40
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Marsden KA, Holmberg JA, Jones DL, Charteris AF, Cárdenas LM, Chadwick DR. Nitrification represents the bottle-neck of sheep urine patch N 2O emissions from extensively grazed organic soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 695:133786. [PMID: 31422321 DOI: 10.1016/j.scitotenv.2019.133786] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 06/26/2019] [Accepted: 08/04/2019] [Indexed: 06/10/2023]
Abstract
Extensively grazed grasslands are understudied in terms of their contribution to greenhouse gas (GHG) emissions from livestock production. Mountains, moorlands and heath occupy 18% of the UK land area, however, in situ studies providing high frequency N2O emissions from sheep urine deposited to such areas are lacking. Organic soils typical of these regions may provide substrates for denitrification-related N2O emissions, however, acidic and anoxic conditions may inhibit nitrification (and associated emissions from nitrification and denitrification). We hypothesised urine N2O-N emission factors (EFs) would be lower than the UK country-specific and IPCC default value for urine, which is based on lowland measurements. Using automated GHG sampling chambers, N2O emissions were determined from real sheep urine (930 kg N ha-1) and artificial urine (920 kg N ha-1) applied in summer, and from an artificial urine treatment (1120 kg N ha-1) and a combined NO3- and glucose treatment (106 kg N ha-1; 213 kg C ha-1) in autumn. The latter treatment provided an assessment of the soils capacity for denitrification under non-substrate limiting conditions. The artificial urine-N2O EF was 0.01 ± 0.00% of the N applied in summer and 0.00 ± 0.00% of the N applied in autumn. The N2O EF for real sheep urine applied in summer was 0.01 ± 0.02%. A higher flux was observed in only one replicate of the real urine treatment, relating to one chamber where an increase in soil solution NO3- was observed. No lag phase in N2O emission was evident following application of the NO3- and glucose treatment, which emitted 0.69 ± 0.15% of the N applied. This indicates nitrification rates are the bottle-neck for N2O emissions in upland organic soils. We calculated the potential impact of using hill-grazing specific urine N2O EFs on the UK inventory of N2O emissions from sheep excreta, and found a reduction of ca. 43% in comparison to the use of a country-specific excretal EF.
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Affiliation(s)
- Karina A Marsden
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Jon A Holmberg
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Davey L Jones
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; UWA School of Agriculture and Environment, University of Western Australia, Crawley, WA 6009, Australia
| | - Alice F Charteris
- Sustainable Agriculture Sciences, Rothamsted Research, North Wyke, Okehampton, Devon EX20 2SB, UK
| | - Laura M Cárdenas
- Sustainable Agriculture Sciences, Rothamsted Research, North Wyke, Okehampton, Devon EX20 2SB, UK
| | - David R Chadwick
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
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41
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Shaaban M, Hu R, Wu Y, Younas A, Xu X, Sun Z, Jiang Y, Lin S. Mitigation of N 2O emissions from urine treated acidic soils by liming. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 255:113237. [PMID: 31541820 DOI: 10.1016/j.envpol.2019.113237] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/10/2019] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
Nitrous oxide (N2O) is a devastating greenhouse gas mainly released from soils to the atmosphere. Pasture soils, particularly acidic in nature, are large contributors of atmospheric N2O through deposition of urine-N. Devising strategies for reducing N2O emissions in acidic soils are the utmost need of the time. Therefore, the present study was carried out to investigate the possible efficacy of dolomite application to reduce N2O emissions from urine treated acidic soil. Application of urine to soil enlarged the production of NH4+-N, NO3--N, microbial biomass C (MBC) and dissolved organic C (DOC), resulting in higher N2O emissions as compared to the control (soil only). The highest N2O emission rate (1.35 μg N2O-N kg-1 h-1) and cumulative flux (408 μg N2O-N kg-1) occurred in urine only treated soil. Dolomite addition, especially higher application dose, greatly reduced N2O emissions through improved soil pH. The results suggest that increasing pH of acidic soils is a good applicable approach for reducing N2O emissions from urine-treated soils.
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Affiliation(s)
- Muhammad Shaaban
- Department of Soil Science, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Ronggui Hu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China.
| | - Yupeng Wu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Aneela Younas
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiangyu Xu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China; Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China
| | - Zheng Sun
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Yanbin Jiang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Shan Lin
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
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42
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Variations in Greenhouse Gas Fluxes in Response to Short-Term Changes in Weather Variables at Three Elevation Ranges, Wakiso District, Uganda. ATMOSPHERE 2019. [DOI: 10.3390/atmos10110708] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Weather conditions are among the major factors leading to the increasing greenhouse gas (GHG) fluxes from the agricultural soils. In this study, variations in the soil GHG fluxes with precipitation and soil temperatures at different elevation ranges in banana–coffee farms, in the Wakiso District, Uganda, were evaluated. The soil GHG fluxes were collected weekly, using the chamber method, and analyzed by using gas chromatography. Parallel soil temperature samples were collected by using a REOTEMP soil thermometer. Daily precipitation was measured with an automated weather station instrument installed on-site. The results showed that CO2, N2O, and CH4 fluxes were significantly different between the sites at different elevation ranges. Daily precipitation and soil temperatures significantly (p < 0.05) affected the soil GHG fluxes. Along an elevation gradient, daily precipitation and soil temperatures positively associated with the soil GHG fluxes. The combined factors of daily precipitation and soil temperatures also influence the soil GHG fluxes, but their effect was less than that of the single effects. Overall, daily precipitation and soil temperatures are key weather factors driving the soil GHG fluxes in time and space. This particular study suggests that agriculture at lower elevation levels would help reduce the magnitudes of the soil GHG fluxes. However, this study did not measure the soil GHG fluxes from the non-cultivated ecosystems. Therefore, future studies should focus on assessing the variations in the soil GHG fluxes from non-cultivated ecosystems relative to agriculture systems, at varying elevation ranges.
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43
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Wang S, Zhao J, Huang T. High NO and N 2O accumulation during nitrite denitrification in lab-scale sequencing batch reactor: influencing factors and mechanism. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:34377-34387. [PMID: 31637614 DOI: 10.1007/s11356-019-06391-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/30/2019] [Indexed: 06/10/2023]
Abstract
Nitrous oxide (N2O) accumulation in biological nitrogen removal has drawn much attention in recent years; however, nitric oxide (NO) accumulation in denitrification was rarely studied. In this study, NO and N2O accumulation during nitrite denitrification in a lab-scale sequencing batch reactor (SBR) were investigated. Results showed that low pH (< 7) and high influent loading (> 360:90) (COD:NO2--N) caused serious NO and N2O accumulation. The maximal NO accumulation of 4.96 mg L-1 was observed at influent loading of 720:180 and the maximal N2O accumulation of 46.29 mg L-1 was found at pH of 6. The NO accumulation was far higher than the values reported in previous studies. In addition, the high NO accumulation could completely inhibit the activities of reductases involved in denitrification. High NO and N2O accumulation were mainly caused by significant free nitrous acid (FNA) and NO inhibition at low pH and high influent loading. There were significant differences on NO and N2O accumulation at different carbon to nitrogen (COD/N). Low COD/N (≤ 4) could mitigate NO accumulation, but led to high N2O accumulation. It is speculated that NO accumulation is related to the rapid denitrification with accumulated electron in anaerobic stage at high COD/N. N2O accumulation is attributed to intense electron competition at low COD/N. High dissolved oxygen (DO) of 4.04 mg L-1 was detected during NO detoxification in this experiment, which is speculated to be partly caused by NO dismutation.
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Affiliation(s)
- Sha Wang
- School of Environmental Science and Engineering, Chang'an University, Xi'an, 710064, Shaanxi, China
| | - Jianqiang Zhao
- School of Environmental Science and Engineering, Chang'an University, Xi'an, 710064, Shaanxi, China.
- Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Xi'an, 710064, Shaanxi, China.
| | - Ting Huang
- School of Architecture and Civil Engineering, Xi'an University of Science and Technology, Xi'an, 710054, Shaanxi, China
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44
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Biochar Enhances Nitrous Oxide Reduction in Acidic but Not in Near-Neutral pH Soil. SOIL SYSTEMS 2019. [DOI: 10.3390/soilsystems3040069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We quantified nitrous oxide (N2O) fluxes and total denitrification (N2O + N2) in an acidic (Ferralsol) and a near-neutral pH soil (Cambisol) to determine whether biochar’s alkalinization effect could be the mechanism inducing potential reductions in N2O fluxes. In Ferralsol, decreases in N2O emissions and in the N2O to N2O + N2 ratio were observed in both biochar and lime treatments. In Cambisol, neither biochar nor lime decreased N2O emissions, despite significantly increasing soil pH. The abundance and community structure of nosZ gene-bearing microorganisms indicated that gene abundances did not explain biochar effects, but a higher diversity of nosZ gene-bearing microorganisms correlated to lower total denitrification. Overall, our results suggest that biochar’s potential to decrease N2O emissions, through soil alkalinization, may be more effective in acidic soils.
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45
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Herold MB, Giles ME, Alexander CJ, Baggs EM, Daniell TJ. Variable response of nirK and nirS containing denitrifier communities to long-term pH manipulation and cultivation. FEMS Microbiol Lett 2019; 365:4875922. [PMID: 29471521 DOI: 10.1093/femsle/fny035] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/16/2018] [Indexed: 11/14/2022] Open
Abstract
Denitrification is a key process responsible for the majority of soil nitrous oxide (N2O) emissions but the influences of pH and cultivation on the soil denitrifier community remain poorly understood. We hypothesised that the abundance and community structure of the total bacterial community and bacterial denitrifiers would be pH sensitive and that nirK and nirS containing denitrifiers would differ in their responses to change in pH and cultivation. We investigated the effect of long-term pH-adjusted soils (ranging from pH 4.2 to 6.6) under different lengths of grass cultivation (one, two and three years of ley grass) on the general bacterial and denitrifier functional communities using 16S rRNA, nirK and nirS genes as markers. Denitrifier abundance increased with pH, and at pH below 4.7 there was a greater loss in nirS abundance per unit drop in pH than soils above this threshold pH. All community structures responded to changes in soil pH, while cultivation only influenced the community structure of nirK. These differences in denitrifier responses highlight the importance of considering both nirK and nirS gene markers for estimating denitrifier activity. Identifying such thresholds in response of the microbial community to changes in pH is essential to understanding impacts of management or environmental change.
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Affiliation(s)
- Miriam B Herold
- Ecological Sciences, The James Hutton Institute, Dundee, Perth and Kinross, DD2 5DA, UK.,Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Madeline E Giles
- Ecological Sciences, The James Hutton Institute, Dundee, Perth and Kinross, DD2 5DA, UK
| | - Colin J Alexander
- Biomathematics and Statistics Scotland, Dundee, Perth and Kinross, DD2 5DA, UK
| | - Elizabeth M Baggs
- The Royal (Dick) School of Veterinary Studies, Easter Bush Campus, Midlothian EH25 9RG University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Tim J Daniell
- Ecological Sciences, The James Hutton Institute, Dundee, Perth and Kinross, DD2 5DA, UK.,Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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46
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Han H, Song B, Song MJ, Yoon S. Enhanced Nitrous Oxide Production in Denitrifying Dechloromonas aromatica Strain RCB Under Salt or Alkaline Stress Conditions. Front Microbiol 2019; 10:1203. [PMID: 31275250 PMCID: PMC6593283 DOI: 10.3389/fmicb.2019.01203] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 05/13/2019] [Indexed: 11/25/2022] Open
Abstract
Salinity and pH have direct and indirect impacts on the growth and metabolic activities of microorganisms. In this study, the effects of salt and alkaline stresses on the kinetic balance between nitrous oxide (N2O) production and consumption in the denitrification pathway of Dechloromonas aromatica strain RCB were examined. N2O accumulated transiently only in insignificant amounts at low salinity (≤0.5% NaCl) and circumneutral pH (7.0 and 7.5). As compared to these control conditions, incubation at 0.7% salinity resulted in substantially longer lag phase and slower growth rate, along with the increase in the amounts of transiently accumulated N2O (15.8 ± 2.8 μmoles N2O-N/vessel). Incubation at pH 8.0 severely inhibited growth and resulted in permanent accumulation of 29.9 ± 1.3 μmoles N2O-N/vessel from reduction of 151 ± 20 μmoles NO3−/vessel. Monitoring of temporal changes in nirS1, nirS2, and nosZ transcription suggested that the nosZ/(nirS1+nirS2) ratios were indicative of whether N2O was produced or consumed at the time points where measurements were taken. The salt and alkaline stresses altered the N2O consumption kinetics of the resting D. aromatica cells with expressed nitrous oxide reductases. The N2O consumption rates of the cells subjected to the salt and alkaline stress conditions were significantly reduced from 0.84 ± 0.007 μmoles min−1 mg protein−1 of the control to 0.27 ± 0.02 μmoles min−1 mg protein−1 and 0.31 ± 0.03 μmoles min−1 mg protein−1, respectively, when the initial dissolved N2O concentration was 0.1 mM. As the rates of N2O production from NO2− reduction was not significantly affected by the stresses (0.45–0.55 μmoles min−1 mg protein−1), the N2O consumption rate was lower than the N2O production rate at the stress conditions, but not at the control condition. These results clearly indicate that the altered kinetics of expressed nitrous oxide reductase and the resultant disruption of kinetic balance between N2O production and consumption was another cause of enhanced N2O emission observed under the salt and alkaline stress conditions. These findings suggest that canonical denitrifiers may become a significant N2O source when faced with abrupt environmental changes.
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Affiliation(s)
- Heejoo Han
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Bongkeun Song
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Department of Biological Sciences, Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, VA, United States
| | - Min Joon Song
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Sukhwan Yoon
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
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47
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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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48
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Bennett SP, Soriano-Laguna MJ, Bradley JM, Svistunenko DA, Richardson DJ, Gates AJ, Le Brun NE. NosL is a dedicated copper chaperone for assembly of the Cu Z center of nitrous oxide reductase. Chem Sci 2019; 10:4985-4993. [PMID: 31183047 PMCID: PMC6530538 DOI: 10.1039/c9sc01053j] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/01/2019] [Indexed: 11/21/2022] Open
Abstract
Nitrous oxide reductase (N2OR) is the terminal enzyme of the denitrification pathway of soil bacteria that reduces the greenhouse gas nitrous oxide (N2O) to dinitrogen. In addition to a binuclear CuA site that functions in electron transfer, the active site of N2OR features a unique tetranuclear copper cluster bridged by inorganic sulfide, termed CuZ. In copper-limited environments, N2OR fails to function, resulting in truncation of denitrification and rising levels of N2O released by cells to the atmosphere, presenting a major environmental challenge. Here we report studies of nosL from Paracoccus denitrificans, which is part of the nos gene cluster, and encodes a putative copper binding protein. A Paracoccus denitrificans ΔnosL mutant strain had no denitrification phenotype under copper-sufficient conditions but failed to reduce N2O under copper-limited conditions. N2OR isolated from ΔnosL cells was found to be deficient in copper and to exhibit attenuated activity. UV-visible absorbance spectroscopy revealed that bands due to the CuA center were unaffected, while those corresponding to the CuZ center were significantly reduced in intensity. In vitro studies of a soluble form of NosL without its predicted membrane anchor showed that it binds one Cu(i) ion per protein with attomolar affinity, but does not bind Cu(ii). Together, the data demonstrate that NosL is a copper-binding protein specifically required for assembly of the CuZ center of N2OR, and thus represents the first characterised assembly factor for the CuZ active site of this key environmental enzyme, which is globally responsible for the destruction of a potent greenhouse gas.
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Affiliation(s)
- Sophie P Bennett
- Centre for Molecular and Structural Biochemistry , School of Chemistry , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Manuel J Soriano-Laguna
- Centre for Molecular and Structural Biochemistry , School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Justin M Bradley
- Centre for Molecular and Structural Biochemistry , School of Chemistry , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Dimitri A Svistunenko
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester CO4 3SQ , UK
| | - David J Richardson
- Centre for Molecular and Structural Biochemistry , School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Andrew J Gates
- Centre for Molecular and Structural Biochemistry , School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry , School of Chemistry , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK .
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49
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The Responses of Soil N2O Emissions to Residue Returning Systems: A Meta-Analysis. SUSTAINABILITY 2019. [DOI: 10.3390/su11030748] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background: Much attention has been focused on the influences of residue returning on N2O emissions. However, comprehensive quantification of the effect size on N2O emission following crop residue returning in subtropical, tropical and warm temperate conditions remains untested. Methods: To identify site-specific factors that influence N2O emission (kg N2O-N ha−1) in residue returning systems, we performed a meta-analysis involving 260 comparisons from 72 studies. Results: The data indicated that significant promoting effects were observed under residue returning by rotary tillage, no-tillage and mulch, whereas N2O release was significantly inhibited by 8% under residue returning by plough. For other contributors, the stimulatory and significant effects occurred in upland fields, under short- and medium-term residue returning durations, acidic/neutral soils, medium organic C and clay content. Nitrogen fertilizer application significantly stimulated N2O emission, even though application rate at 100–150 kg N ha−1 was inhibitory. Although a negative correlation between residue C/N ratio and N2O emission has been shown, residue returning could not reduce N2O emission with a higher C/N ratio and amount. Conclusions: Some options, such as converting residue returning methods, decreasing N fertilizer application rate, and regulating soil C/N ratio could be adopted to mitigate soil N2O emission following residue returning.
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Anderson CR, Peterson ME, Frampton RA, Bulman SR, Keenan S, Curtin D. Rapid increases in soil pH solubilise organic matter, dramatically increase denitrification potential and strongly stimulate microorganisms from the Firmicutes phylum. PeerJ 2018; 6:e6090. [PMID: 30581677 PMCID: PMC6295159 DOI: 10.7717/peerj.6090] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 11/08/2018] [Indexed: 01/13/2023] Open
Abstract
Rapid and transient changes in pH frequently occur in soil, impacting dissolved organic matter (DOM) and other chemical attributes such as redox and oxygen conditions. Although we have detailed knowledge on microbial adaptation to long-term pH changes, little is known about the response of soil microbial communities to rapid pH change, nor how excess DOM might affect key aspects of microbial N processing. We used potassium hydroxide (KOH) to induce a range of soil pH changes likely to be observed after livestock urine or urea fertilizer application to soil. We also focus on nitrate reductive processes by incubating microcosms under anaerobic conditions for up to 48 h. Soil pH was elevated from 4.7 to 6.7, 8.3 or 8.8, and up to 240-fold higher DOM was mobilized by KOH compared to the controls. This increased microbial metabolism but there was no correlation between DOM concentrations and CO2 respiration nor N-metabolism rates. Microbial communities became dominated by Firmicutes bacteria within 16 h, while few changes were observed in the fungal communities. Changes in N-biogeochemistry were rapid and denitrification enzyme activity (DEA) increased up to 25-fold with the highest rates occurring in microcosms at pH 8.3 that had been incubated for 24-hour prior to measuring DEA. Nitrous oxide reductase was inactive in the pH 4.7 controls but at pH 8.3 the reduction rates exceeded 3,000 ng N2-N g-1 h-1 in the presence of native DOM. Evidence for dissimilatory nitrate reduction to ammonium and/or organic matter mineralisation was observed with ammonium increasing to concentrations up to 10 times the original native soil concentrations while significant concentrations of nitrate were utilised. Pure isolates from the microcosms were dominated by Bacillus spp. and exhibited varying nitrate reductive potential.
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Affiliation(s)
- Craig R Anderson
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
| | - Michelle E Peterson
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
| | - Rebekah A Frampton
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
| | - Simon R Bulman
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
| | - Sandi Keenan
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
| | - Denis Curtin
- The New Zealand Institute for Plant & Food Research Limited, Lincoln Campus, Christchurch, New Zealand
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