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Hou D, Meng X, Qin M, Zheng E, Chen P, Meng F, Zhang C. Nitrous oxide (N2O) emission characteristics of farmland (rice, wheat, and maize) based on different fertilization strategies. PLoS One 2024; 19:e0305385. [PMID: 38976672 PMCID: PMC11230557 DOI: 10.1371/journal.pone.0305385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/28/2024] [Indexed: 07/10/2024] Open
Abstract
Fertilizer application is the basis for ensuring high yield, high quality and high efficiency of farmland. In order to meet the demand for food with the increasing of population, the application of nitrogen fertilizer will be further increased, which will lead to problems such as N2O emission and nitrogen loss from farmland, it will easily deteriorate the soil and water environment of farmland, and will not conducive to the sustainable development of modern agriculture. However, optimizing fertilizer management is an important way to solve this problem. While, due to the differences in the study conditions (geographical location, environmental conditions, experimental design, etc.), leading to the results obtained in the literatures about the N2O emission with different nitrogen fertilizer application strategies have significant differences, which requiring further comprehensive quantitative analysis. Therefore, we analyzed the effects of nitrogen fertilizer application strategies (different fertilizer types and fertilizer application rates) on N2O emissions from the fields (rice, wheat and maize) based on the Meta-analysis using 67 published studies (including 1289 comparisons). For the three crops, inorganic fertilizer application significantly increased on-farm N2O emissions by 19.7-101.05% for all three; and organic fertilizer increased N2O emissions by 28.16% and 69.44% in wheat and maize fields, respectively, but the application of organic fertilizer in rice field significantly reduced N2O emissions by 58.1%. The results showed that overall, the application of inorganic fertilizers resulted in higher N2O emissions from farmland compared to the application of organic fertilizers. In addition, in this study, the average annual temperature, annual precipitation, soil type, pH, soil total nitrogen content, soil organic carbon content, and soil bulk weight were used as the main influencing factors of N2O emission under nitrogen fertilizer strategies, and the results of the study can provide a reference for the development of integrated management measures to control greenhouse gas emissions from agricultural soils.
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Affiliation(s)
- Dingmu Hou
- School of Hydraulic and Electric Power, Heilongjiang University, Harbin, China
| | - Xuanchen Meng
- School of Hydraulic and Electric Power, Heilongjiang University, Harbin, China
| | - Mengting Qin
- School of Hydraulic and Electric Power, Heilongjiang University, Harbin, China
| | - Ennan Zheng
- School of Hydraulic and Electric Power, Heilongjiang University, Harbin, China
| | - Peng Chen
- College of Hydrology and Water Resources, Hohai University, Nanjing, China
| | - Fanxiang Meng
- School of Hydraulic and Electric Power, Heilongjiang University, Harbin, China
| | - Chao Zhang
- College of Hydraulic Engineering, Zhejiang Tongji Vocational College of Science and Technology, Zhejiang, China
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2
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Kaviraj M, Kumar U, Snigdha A, Chatterjee S. Nitrate reduction to ammonium: a phylogenetic, physiological, and genetic aspects in Prokaryotes and eukaryotes. Arch Microbiol 2024; 206:297. [PMID: 38861039 DOI: 10.1007/s00203-024-04009-0] [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: 01/27/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/12/2024]
Abstract
The microbe-mediated conversion of nitrate (NO3-) to ammonium (NH4+) in the nitrogen cycle has strong implications for soil health and crop productivity. The role of prokaryotes, eukaryotes and their phylogeny, physiology, and genetic regulations are essential for understanding the ecological significance of this empirical process. Several prokaryotes (bacteria and archaea), and a few eukaryotes (fungi and algae) are reported as NO3- reducers under certain conditions. This process involves enzymatic reactions which has been catalysed by nitrate reductases, nitrite reductases, and NH4+-assimilating enzymes. Earlier reports emphasised that single-cell prokaryotic or eukaryotic organisms are responsible for this process, which portrayed a prominent gap. Therefore, this study revisits the similarities and uniqueness of mechanism behind NO3- -reduction to NH4+ in both prokaryotes and eukaryotes. Moreover, phylogenetic, physiological, and genetic regulation also shed light on the evolutionary connections between two systems which could help us to better explain the NO3--reduction mechanisms over time. Reports also revealed that certain transcription factors like NtrC/NtrB and Nit2 have shown a major role in coordinating the expression of NO3- assimilation genes in response to NO3- availability. Overall, this review provides a comprehensive information about the complex fermentative and respiratory dissimilatory nitrate reduction to ammonium (DNRA) processes. Uncovering the complexity of this process across various organisms may further give insight into sustainable nitrogen management practices and might contribute to addressing global environmental challenges.
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Affiliation(s)
- Megha Kaviraj
- ICAR- National Rice Research Institute, Cuttack, 753006, Odisha, India.
- The University of Burdwan, Burdwan, 713104, West Bengal, India.
| | - Upendra Kumar
- ICAR- National Rice Research Institute, Cuttack, 753006, Odisha, India.
| | - Alisha Snigdha
- Siksha 'O' Anusandhan University, Bhubaneswar, 751003, Odisha, India
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3
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Zhou J, Deng W, Wu J, Xiang H, Shen X, Lin JG, Hong Y. Respiration and growth of Paracoccus denitrificans R-1 with nitrous oxide as an electron acceptor. Microbiol Spectr 2024; 12:e0381123. [PMID: 38647341 DOI: 10.1128/spectrum.03811-23] [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: 10/31/2023] [Accepted: 03/22/2024] [Indexed: 04/25/2024] Open
Abstract
In the nitrogen biogeochemical cycle, the reduction of nitrous oxide (N2O) to N2 by N2O reductase, which is encoded by nosZ gene, is the only biological pathway for N2O consumption. In this study, we successfully isolated a strain of denitrifying Paracoccus denitrificans R-1 from sewage treatment plant sludge. This strain has strong N2O reduction capability, and the average N2O reduction rate was 5.10 ± 0.11 × 10-9 µmol·h-1·cell-1 under anaerobic condition in a defined medium. This reduction was accompanied by the stoichiometric consumption of acetate over time when N2O served as the sole electron acceptor and the reduction can yield energy to support microbial growth, suggesting that microbial N2O reduction is related to the energy generation process. Genomic analysis showed that the gene cluster encoding N2O reductase of P. denitrificans R-1 was composed of nosR, nosZ, nosD, nosF, nosY, nosL, and nosZ, which was identified as that in other strains in clade I. Respiratory inhibitors test indicated that the pathway of electron transport for N2O reduction was different from that of the traditional electron transport chain for aerobic respiration. Cu2+, silver nanoparticles, O2, and acidic conditions can strongly inhibit the reduction, whereas NO3- or NH4+ can promote it. These findings suggest that modular N2O reduction of P. denitrificans R-1 is linked to the electron transport and energy conservation, and dissimilatory N2O reduction is a form of microbial anaerobic respiration. IMPORTANCE Nitrous oxide (N2O) is a potent greenhouse gas and contributor to ozone layer destruction, and atmospheric N2O has increased steadily over the past century due to human activities. The release of N2O from fixed N is almost entirely controlled by microbial N2O reductase activities. Here, we investigated the ability to obtain energy for the growth of Paracoccus denitrificans R-1 by coupling the oxidation of various electron donors to N2O reduction. The modular N2O reduction process of denitrifying microorganism not only can consume N2O produced by itself but also can consume the external N2O generated from biological or abiotic pathways under suitable condition, which should be critical for controlling the release of N2O from ecosystems into the atmosphere.
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Affiliation(s)
- Jiaxian Zhou
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, China
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Wenfang Deng
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, China
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, China
| | - Hua Xiang
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, China
| | - Xiaomei Shen
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, China
| | - Jih-Gaw Lin
- Institute of Environmental Engineering, National Yangming Chiao Tung University, Hsinchu City, Taiwan
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, China
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4
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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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5
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Lee KK, Liu S, Crocker K, Huggins DR, Tikhonov M, Mani M, Kuehn S. Functional regimes define the response of the soil microbiome to environmental change. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.584851. [PMID: 38559185 PMCID: PMC10980070 DOI: 10.1101/2024.03.15.584851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The metabolic activity of soil microbiomes plays a central role in carbon and nitrogen cycling. Given the changing climate, it is important to understand how the metabolism of natural communities responds to environmental change. However, the ecological, spatial, and chemical complexity of soils makes understanding the mechanisms governing the response of these communities to perturbations challenging. Here, we overcome this complexity by using dynamic measurements of metabolism in microcosms and modeling to reveal regimes where a few key mechanisms govern the response of soils to environmental change. We sample soils along a natural pH gradient, construct >1500 microcosms to perturb the pH, and quantify the dynamics of respiratory nitrate utilization, a key process in the nitrogen cycle. Despite the complexity of the soil microbiome, a minimal mathematical model with two variables, the quantity of active biomass in the community and the availability of a growth-limiting nutrient, quantifies observed nitrate utilization dynamics across soils and pH perturbations. Across environmental perturbations, changes in these two variables give rise to three functional regimes each with qualitatively distinct dynamics of nitrate utilization over time: a regime where acidic perturbations induce cell death that limits metabolic activity, a nutrient-limiting regime where nitrate uptake is performed by dominant taxa that utilize nutrients released from the soil matrix, and a resurgent growth regime in basic conditions, where excess nutrients enable growth of initially rare taxa. The underlying mechanism of each regime is predicted by our interpretable model and tested via amendment experiments, nutrient measurements, and sequencing. Further, our data suggest that the long-term history of environmental variation in the wild influences the transitions between functional regimes. Therefore, quantitative measurements and a mathematical model reveal the existence of qualitative regimes that capture the mechanisms and dynamics of a community responding to environmental change.
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Affiliation(s)
- Kiseok Keith Lee
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL 60637, USA
- Center for Living Systems, The University of Chicago, Chicago, IL 60637, USA
| | - Siqi Liu
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA
| | - Kyle Crocker
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL 60637, USA
- Center for Living Systems, The University of Chicago, Chicago, IL 60637, USA
| | - David R. Huggins
- USDA-ARS, Northwest Sustainable Agroecosystems Research Unit, Pullman, WA 99164, USA
| | - Mikhail Tikhonov
- Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Madhav Mani
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
- National Institute for Theory and Mathematics in Biology, Northwestern University and The University of Chicago, Chicago, IL
| | - Seppe Kuehn
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL 60637, USA
- National Institute for Theory and Mathematics in Biology, Northwestern University and The University of Chicago, Chicago, IL
- Center for Living Systems, The University of Chicago, Chicago, IL 60637, USA
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6
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Awala SI, Gwak JH, Kim Y, Jung MY, Dunfield PF, Wagner M, Rhee SK. Nitrous oxide respiration in acidophilic methanotrophs. Nat Commun 2024; 15:4226. [PMID: 38762502 PMCID: PMC11102522 DOI: 10.1038/s41467-024-48161-z] [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: 01/03/2024] [Accepted: 04/22/2024] [Indexed: 05/20/2024] Open
Abstract
Aerobic methanotrophic bacteria are considered strict aerobes but are often highly abundant in hypoxic and even anoxic environments. Despite possessing denitrification genes, it remains to be verified whether denitrification contributes to their growth. Here, we show that acidophilic methanotrophs can respire nitrous oxide (N2O) and grow anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen. We study two strains that possess N2O reductase genes: Methylocella tundrae T4 and Methylacidiphilum caldifontis IT6. We show that N2O respiration supports growth of Methylacidiphilum caldifontis at an extremely acidic pH of 2.0, exceeding the known physiological pH limits for microbial N2O consumption. Methylocella tundrae simultaneously consumes N2O and CH4 in suboxic conditions, indicating robustness of its N2O reductase activity in the presence of O2. Furthermore, in O2-limiting conditions, the amount of CH4 oxidized per O2 reduced increases when N2O is added, indicating that Methylocella tundrae can direct more O2 towards methane monooxygenase. Thus, our results demonstrate that some methanotrophs can respire N2O independently or simultaneously with O2, which may facilitate their growth and survival in dynamic environments. Such metabolic capability enables these bacteria to simultaneously reduce the release of the key greenhouse gases CO2, CH4, and N2O.
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Affiliation(s)
- Samuel Imisi Awala
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
- Center for Ecology and Environmental Toxicology, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Joo-Han Gwak
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - Yongman Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - Man-Young Jung
- Interdisciplinary Graduate Programme in Advance Convergence Technology and Science, Jeju National University, Jeju, Republic of Korea
- Department of Science Education, Jeju National University, Jeju, Republic of Korea
- Jeju Microbiome Center, Jeju National University, Jeju, Republic of Korea
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea.
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7
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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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8
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Chen B, Guo L, Tang J, Li Y, Li C. Comprehensive impacts of different integrated rice-animal co-culture systems on rice yield, nitrogen fertilizer partial factor productivity and nitrogen losses: A global meta-analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:169994. [PMID: 38232823 DOI: 10.1016/j.scitotenv.2024.169994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/28/2023] [Accepted: 01/05/2024] [Indexed: 01/19/2024]
Abstract
Integrated rice-animal co-culture (IRAC) is an ecological agricultural system combining rice cultivation with animal farming, which holds significant implications for food security and agriculture sustainable development. However, the comprehensive impacts of the co-culture on rice yield, nitrogen (N) losses, and N fertilizer partial factor productivity (NPFP) remain elusive and may vary under different environmental conditions and N management. Here, we conducted a meta-analysis of data from various IRAC systems on a global scale, including 371, 298, and 115 sets of data for rice yield, NPFP, and N losses, respectively. The results showed that IRAC could significantly increase rice yield (by 3.47 %) and NPFP (by 4.26 %), and reduce N2O emissions (by 16.69 %), NH3 volatilization (by 11.03 %), N runoff (by 17.72 %), and N leaching (by 19.10 %). Furthermore, there were significant differences in rice yield, NPFP, and N loss among different IRAC systems, which may be ascribed to variations in regional climate, soil variables, and N fertilizer management practices. The effect sizes of rice yield and NPFP were notably correlated with the rate and frequency of N application and the soil clay content. Moreover, a higher amount of precipitation corresponded to a larger effect size on rice NPFP. N2O emissions were closely associated with mean annual air temperature, annual precipitation, N application frequency, soil pH level, soil organic matter content, soil clay content, and soil bulk density. However, NH3 volatilization, N runoff, and N leaching exhibited no correlation with either the environmental conditions or the N management. Multivariate regression analysis further demonstrated that the soil clay content and N application rate are pivotal in predicting the effect sizes of rice yield, NPFP, and N2O emissions under IRAC. Specifically, IRAC with a low N application rate in soils with a high clay content could augment the effect size to increase rice NPFP and yield and reduce N2O emissions. In conclusion, IRAC offers a potent strategy to optimize rice yield and NPFP as well as mitigate N losses.
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Affiliation(s)
- Binpeng Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River/College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Lijin Guo
- International Magnesium Institute, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 3550002, PR China
| | - Jichao Tang
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River/College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yanshi Li
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River/College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Chengfang Li
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River/College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
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9
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Zhang H, Adalibieke W, Ba W, Butterbach-Bahl K, Yu L, Cai A, Fu J, Yu H, Zhang W, Huang W, Jian Y, Jiang W, Zhao Z, Luo J, Deng J, Zhou F. Modeling denitrification nitrogen losses in China's rice fields based on multiscale field-experiment constraints. GLOBAL CHANGE BIOLOGY 2024; 30:e17199. [PMID: 38385944 DOI: 10.1111/gcb.17199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/23/2024]
Abstract
Denitrification plays a critical role in soil nitrogen (N) cycling, affecting N availability in agroecosystems. However, the challenges in direct measurement of denitrification products (NO, N2 O, and N2 ) hinder our understanding of denitrification N losses patterns across the spatial scale. To address this gap, we constructed a data-model fusion method to map the county-scale denitrification N losses from China's rice fields over the past decade. The estimated denitrification N losses as a percentage of N application from 2009 to 2018 were 11.8 ± 4.0% for single rice, 12.4 ± 3.7% for early rice, and 11.6 ± 3.1% for late rice. The model results showed that the spatial heterogeneity of denitrification N losses is primarily driven by edaphic and climatic factors rather than by management practices. In particular, diffusion and production rates emerged as key contributors to the variation of denitrification N losses. These findings humanize a 38.9 ± 4.8 kg N ha-1 N loss by denitrification and challenge the common hypothesis that substrate availability drives the pattern of N losses by denitrification in rice fields.
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Affiliation(s)
- Huayan Zhang
- Institute of Carbon Neutrality, Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Wulahati Adalibieke
- Institute of Carbon Neutrality, Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Wenxin Ba
- Institute of Carbon Neutrality, Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | | | - Longfei Yu
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, China
| | - Andong Cai
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jin Fu
- College of Geography and Remote Sensing, Hohai University, Nanjing, China
| | - Haoming Yu
- Institute of Carbon Neutrality, Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Wantong Zhang
- Institute of Carbon Neutrality, Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Weichen Huang
- Institute of Carbon Neutrality, Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Yiwei Jian
- Institute of Carbon Neutrality, Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Wenjun Jiang
- Institute of Carbon Neutrality, Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Zheng Zhao
- Institute of Ecological Environment Protection Research, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jiafa Luo
- AgResearch Ruakura, Hamilton, New Zealand
| | - Jia Deng
- Earth Systems Research Center, Institute for the Study of Earth, Oceans and Space, University of New Hampshire, Durham, New Hampshire, USA
| | - Feng Zhou
- Institute of Carbon Neutrality, Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, China
- College of Geography and Remote Sensing, Hohai University, Nanjing, China
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10
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Krichels AH, Jenerette GD, Shulman H, Piper S, Greene AC, Andrews HM, Botthoff J, Sickman JO, Aronson EL, Homyak PM. Bacterial denitrification drives elevated N 2O emissions in arid southern California drylands. SCIENCE ADVANCES 2023; 9:eadj1989. [PMID: 38055826 DOI: 10.1126/sciadv.adj1989] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
Soils are the largest source of atmospheric nitrous oxide (N2O), a powerful greenhouse gas. Dry soils rarely harbor anoxic conditions to favor denitrification, the predominant N2O-producing process, yet, among the largest N2O emissions have been measured after wetting summer-dry desert soils, raising the question: Can denitrifiers endure extreme drought and produce N2O immediately after rainfall? Using isotopic and molecular approaches in a California desert, we found that denitrifiers produced N2O within 15 minutes of wetting dry soils (site preference = 12.8 ± 3.92 per mil, δ15Nbulk = 18.6 ± 11.1 per mil). Consistent with this finding, we detected nitrate-reducing transcripts in dry soils and found that inhibiting microbial activity decreased N2O emissions by 59%. Our results suggest that despite extreme environmental conditions-months without precipitation, soil temperatures of ≥40°C, and gravimetric soil water content of <1%-bacterial denitrifiers can account for most of the N2O emitted when dry soils are wetted.
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Affiliation(s)
- Alexander H Krichels
- Environmental Sciences, University of California, Riverside, CA, USA
- Center for Conservation Biology, University of California, Riverside, CA, USA
- USDA Rocky Mountain Research Station, Albuquerque, NM, USA
| | - G Darrel Jenerette
- Center for Conservation Biology, University of California, Riverside, CA, USA
- Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Hannah Shulman
- Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA
- Microbiology and Plant Pathology, University of California, Riverside, CA, USA
| | - Stephanie Piper
- Botany and Plant Sciences, University of California, Riverside, CA, USA
- Houston Advanced Research Center, The Woodlands, TX, USA
| | - Aral C Greene
- Environmental Sciences, University of California, Riverside, CA, USA
| | - Holly M Andrews
- Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
- Geography, Development and Environment, University of Arizona, Tucson, AZ, USA
| | - Jon Botthoff
- Center for Conservation Biology, University of California, Riverside, CA, USA
| | - James O Sickman
- Environmental Sciences, University of California, Riverside, CA, USA
| | - Emma L Aronson
- Microbiology and Plant Pathology, University of California, Riverside, CA, USA
| | - Peter M Homyak
- Environmental Sciences, University of California, Riverside, CA, USA
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11
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Crocker K, Lee KK, Chakraverti-Wuerthwein M, Li Z, Tikhonov M, Mani M, Gowda K, Kuehn S. Global patterns in gene content of soil microbiomes emerge from microbial interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.542950. [PMID: 38014336 PMCID: PMC10680560 DOI: 10.1101/2023.05.31.542950] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Microbial metabolism sustains life on Earth. Sequencing surveys of communities in hosts, oceans, and soils have revealed ubiquitous patterns linking the microbes present, the genes they possess, and local environmental conditions. One prominent explanation for these patterns is environmental filtering: local conditions select strains with particular traits. However, filtering assumes ecological interactions do not influence patterns, despite the fact that interactions can and do play an important role in structuring communities. Here, we demonstrate the insufficiency of the environmental filtering hypothesis for explaining global patterns in topsoil microbiomes. Using denitrification as a model system, we find that the abundances of two characteristic genotypes trade-off with pH; nar gene abundances increase while nap abundances decrease with declining pH. Contradicting the filtering hypothesis, we show that strains possessing the Nar genotype are enriched in low pH conditions but fail to grow alone. Instead, the dominance of Nar genotypes at low pH arises from an ecological interaction with Nap genotypes that alleviates nitrite toxicity. Our study provides a roadmap for dissecting how global associations between environmental variables and gene abundances arise from environmentally modulated community interactions.
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12
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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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13
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Zhang S, Pei L, Zhao Y, Shan J, Zheng X, Xu G, Sun Y, Wang F. Effects of microplastics and nitrogen deposition on soil multifunctionality, particularly C and N cycling. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131152. [PMID: 36934700 DOI: 10.1016/j.jhazmat.2023.131152] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/18/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Both nitrogen deposition (ND) and microplastics (MPs) pose global change challenges. The effects of MPs co-existing with ND on ecosystem functions are still largely unknown. Herein, we conducted a 10-month soil incubation experiment to explore the effects of polyethylene (PE) and polylactic acid (PLA) MPs on soil multifunctionality under different ND scenarios. We found that the interactions between ND and MPs affected soil multifucntionality. FAPROTAX function prediction indicated that both ND and MPs affected C and N cycling. ND increased some C-cycling processes, such as cellulolysis, ligninolysis, and plastic degradation. MPs also showed stimulating effects on these processes, particularly in the soil with ND. ND significantly decreased the abundance of functional genes NifH, amoA, and NirK, leading to inhibited N-fixation, nitrification, and denitrification. The addition of MPs also modified N-cycling processes: 0.1% PE enriched the bacterial groups for nitrate reduction, nitrate respiration, nitrite respiration, and nitrate ammonification, and 1% PLA MPs enriched N-fixation bacteria at all ND levels. We found that ND caused lower soil pH but higher soil N, decreased bacterial diversity and richness, and changed the composition and activity of functional bacteria, which explains why ND changed soil functions and regulated the impact of MPs.
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Affiliation(s)
- Shuwu Zhang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong Province 266042, PR China
| | - Lei Pei
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong Province 266042, PR China
| | - Yanxin Zhao
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong Province 266042, PR China
| | - Jun Shan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xuebo Zheng
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture and Rural Affairs, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Guangjian Xu
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong Province 266042, PR China
| | - Yuhuan Sun
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong Province 266042, PR China
| | - Fayuan Wang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong Province 266042, PR China.
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14
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Duan H, Wang H, Li S, Shen W, Zhuang Y, Zhang F, Li X, Zhai L, Liu H, Zhang L. Potential to mitigate nitrogen emissions from paddy runoff: A microbiological perspective. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161306. [PMID: 36592915 DOI: 10.1016/j.scitotenv.2022.161306] [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: 09/14/2022] [Revised: 12/06/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
Ditches and ponds are the basic units of agroecosystems that serve irrigation and drainage and also perform the natural ecological function of reducing nitrogen (N) emissions. To better enhance the design and advance management strategies in the paddy field ecosystem to minimize N emission, the N cycling microorganism in the paddy field ecosystem including interconnected fields with rice-wheat rotation, ditches, and ponds in central China was investigated by metagenomic techniques. Our results showed that ditches and ponds may be N removal hotspots by microorganisms in the rice and wheat seasons respectively. Given seasonal variation, the abundance of N-related microorganisms was high during the rice season. However, the Shannon and Simpson indices were lower and the microbial co-occurrence network was destabilized, which could make microbes in the rice season fragile and sensitive. Phytoplankton as key environmental factors affecting the N cycling microbial could promote more stable microbial communities through maintaining a good mutualistic symbiosis. While high algae concentration significantly promotes the abundance of norB than nosZ (P < 0.05), which may result in more N2O production. To trade off N removal and N2O emission, the algae concentration needs to be controlled. Our findings provide a systematic profile of N-related microorganisms in the paddy field ecosystem, and it would benefit in developing effective strategies for limiting N pollution in agriculture.
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Affiliation(s)
- He Duan
- Hubei Provincial Engineering Research Center of Non-Point Source Pollution Control, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Haodong Wang
- Hubei Provincial Engineering Research Center of Non-Point Source Pollution Control, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China; School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430078, China.
| | - Sisi Li
- Hubei Provincial Engineering Research Center of Non-Point Source Pollution Control, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Wangzheng Shen
- Hubei Provincial Engineering Research Center of Non-Point Source Pollution Control, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yanhua Zhuang
- Hubei Provincial Engineering Research Center of Non-Point Source Pollution Control, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Fulin Zhang
- Institute of Plant Protection, Soil and Fertilizer Sciences, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
| | - Xudong Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Limei Zhai
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Hongbin Liu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Liang Zhang
- Hubei Provincial Engineering Research Center of Non-Point Source Pollution Control, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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15
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Wu M, Zhang Z, Zhang X, Dong L, Liu C, Chen Y. Propionibacterium freudenreichii-Assisted Approach Reduces N 2O Emission and Improves Denitrification via Promoting Substrate Uptake and Metabolism. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:16895-16906. [PMID: 36366772 DOI: 10.1021/acs.est.2c05674] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
N2O emission is often encountered during biodenitrification. In this paper, a new approach of using microorganisms to promote substrate uptake and metabolism to reduce denitrification intermediate accumulation was reported. With the introduction of Propionibacterium freudenreichii to a biodenitrification system, N2O and nitrite accumulation was, respectively, decreased by 74 and 60% and the denitrification efficiency was increased by 150% at the time of 24 h with P. freudenreichii/groundwater denitrifier of 1/5 (OD600). Propionate, produced by P. freudenreichii, only accelerated nitrate removal and was not the main reason for the decreased intermediate accumulation. The proteomic and enzyme analyses revealed that P. freudenreichii stimulated biofilm formation by upregulating proteins involved in porin forming, putrescine biosynthesis, spermidine/putrescine transport, and quorum sensing and upregulated transport proteins, which facilitated the uptake of the carbon source, nitrate, and Fe and Mo (the required catalytic sites of denitrification enzymes). Further investigation revealed that P. freudenreichii activated the methylmalonyl-CoA pathway in the denitrifier and promoted it to synthesize heme/heme d1, the groups of denitrification enzymes and electron transfer proteins, which upregulated the expression of denitrifying enzyme proteins and enhanced the ratio of NosZ to NorB, resulting in the increase of generation, transfer, and consumption of electrons in biodenitrification. Therefore, a significant reduction in the denitrification intermediate accumulation and an improvement in the denitrification efficiency were observed.
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Affiliation(s)
- Meirou Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Zhiqi Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xin Zhang
- Shanghai Municipal Engineering Design Institute (Group) Co. LTD, 901 Zhongshan North Second Road, Shanghai 200092, China
| | - Lei Dong
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
- Shanghai Municipal Engineering Design Institute (Group) Co. LTD, 901 Zhongshan North Second Road, Shanghai 200092, China
| | - Chao Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
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16
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Preparation for Denitrification and Phenotypic Diversification at the Cusp of Anoxia: a Purpose for N 2O Reductase Vis-à-Vis Multiple Roles of O 2. Appl Environ Microbiol 2022; 88:e0105322. [PMID: 36250705 PMCID: PMC9642011 DOI: 10.1128/aem.01053-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adaptation to anoxia by synthesizing a denitrification proteome costs metabolic energy, and the anaerobic respiration conserves less energy per electron than aerobic respiration. This implies a selective advantage of the stringent O2 repression of denitrification gene transcription, which is found in most denitrifying bacteria. In some bacteria, the metabolic burden of adaptation can be minimized further by phenotypic diversification, colloquially termed "bet-hedging," where all cells synthesize the N2O reductase (NosZ) but only a minority synthesize nitrite reductase (NirS), as demonstrated for the model strain Paracoccus denitrificans. We hypothesized that the cells lacking NirS would be entrapped in anoxia but with the possibility of escape if supplied with O2 or N2O. To test this, cells were exposed to gradual O2 depletion or sudden anoxia and subsequent spikes of O2 and N2O. The synthesis of NirS in single cells was monitored by using an mCherry-nirS fusion replacing the native nirS, and their growth was detected as dilution of green, fluorescent fluorescein isothiocyanate (FITC) stain. We demonstrate anoxic entrapment due to e--acceptor deprivation and show that O2 spiking leads to bet-hedging, while N2O spiking promotes NirS synthesis and growth in all cells carrying NosZ. The cells rescued by the N2O spike had much lower respiration rates than those rescued by the O2 spike, however, which could indicate that the well-known autocatalytic synthesis of NirS via NO production requires O2. Our results bring into relief a fitness advantage of pairing restrictive nirS expression with universal NosZ synthesis in energy-limited systems. IMPORTANCE Denitrifying bacteria have evolved elaborate regulatory networks securing their respiratory metabolism in environments with fluctuating oxygen concentrations. Here, we provide new insight regarding their bet-hedging in response to hypoxia, which minimizes their N2O emissions because all cells express NosZ, reducing N2O to N2, while a minority express NirS + Nor, reducing NO2- to N2O. We hypothesized that the cells without Nir were entrapped in anoxia, without energy to synthesize Nir, and that they could be rescued by short spikes of O2 or N2O. We confirm such entrapment and the rescue of all cells by an N2O spike but only a fraction by an O2 spike. The results shed light on the role of O2 repression in bet-hedging and generated a novel hypothesis regarding the autocatalytic nirS expression via NO production. Insight into the regulation of denitrification, including bet-hedging, holds a clue to understanding, and ultimately curbing, the escalating emissions of N2O, which contribute to anthropogenic climate forcing.
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17
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Liu H, Li Y, Pan B, Zheng X, Yu J, Ding H, Zhang Y. Pathways of soil N 2O uptake, consumption, and its driving factors: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:30850-30864. [PMID: 35092587 DOI: 10.1007/s11356-022-18619-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Nitrous oxide (N2O) is an important greenhouse gas that plays a significant role in atmospheric photochemical reactions and contributes to stratospheric ozone depletion. Soils are the main sources of N2O emissions. In recent years, it has been demonstrated that soil is not only a source but also a sink of N2O uptake and consumption. N2O emissions at the soil surface are the result of gross N2O production, uptake, and consumption, which are co-occurring processes. Soil N2O uptake and consumption are complex biological processes, and their mechanisms are still worth an in-depth systematic study. This paper aimed to systematically address the current research progress on soil N2O uptake and consumption. Based on a bibliometric perspective, this study has highlighted the pathways of soil N2O uptake and consumption and their driving factors and measurement techniques. This systematic review of N2O uptake and consumption will help to further understand N transformations and soil N2O emissions.
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Affiliation(s)
- Hongshan Liu
- College of Earth Sciences, Jilin University, Chao'yang, Changchun, 130061, Jilin, People's Republic of China
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China
| | - Yuefen Li
- College of Earth Sciences, Jilin University, Chao'yang, Changchun, 130061, Jilin, People's Republic of China.
| | - Baobao Pan
- School of Agriculture and Food, The University of Melbourne, Parkville, 3010, VIC, Australia
| | - Xiangzhou Zheng
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China
| | - Juhua Yu
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China
| | - Hong Ding
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China
| | - Yushu Zhang
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China.
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18
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Yuan J, Yan L, Li G, Sadiq M, Rahim N, Wu J, Ma W, Xu G, Du M. Effects of conservation tillage strategies on soil physicochemical indicators and N 2O emission under spring wheat monocropping system conditions. Sci Rep 2022; 12:7066. [PMID: 35487963 PMCID: PMC9054807 DOI: 10.1038/s41598-022-11391-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 04/20/2022] [Indexed: 11/16/2022] Open
Abstract
As one of the important greenhouse gas, nitrous oxide (N2O) has attracted much attention globally under climate change context. Agricultural practices are the main sources of greenhouse gas emissions. Nevertheless, scarcity of literature is available on the effects of different tillage measures on soil N2O emission under spring wheat (Triticum aestivum L.) ecosystem in the semi-arid area of the Loess Plateau. The main objective of the experimental study was to explore the influence of conservation tillage techniques on soil physicochemical properties, nitrous oxide emission and yield in the Northern semi-arid Dingxi region of China. Four treatments viz., conventional tillage (CT), no tillage (NT), straw mulch with conventional tillage (TS) and stubble-return with no-till (NTS) were evaluated under randomized complete block design with three replications. Our results depicted that compared with conventional tillage, bulk density and water content of topsoil was increased and soil pH value was reduced under conservation tillage techniques. Conservation tillage NT, TS and NTS increased organic carbon, TN, MBN and NH4+-N and reduced the accumulation of NO3–N. Additionally, although the N2O emission under NT, TS and NTS was 8.95, 41.90 and 21.05% respectively higher than under T treatment, the corresponding wheat yield was 15.40, 31.97 and 63.21% higher than T treatment. Moreover, correlation analysis showed that soil moisture and temperature were the most significant factors affecting soil N2O emission. The NTS treatment pointedly increased crop yield without significantly increasing soil N2O emission. Consequently, based on economic and environmental benefits and considering N2O emission and crop yield, we suggest that NTS technique is the best conservation tillage strategy in the semi-arid environmental zone of the Loess Plateau of Dingxi China.
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Affiliation(s)
- Jianyu Yuan
- College of Forestry, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lijuan Yan
- College of Agriculture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Guang Li
- College of Forestry, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Mahran Sadiq
- College of Forestry, Gansu Agricultural University, Lanzhou, 730070, China.,College of Agriculture, Gansu Agricultural University, Lanzhou, 730070, China.,Department of Soil and Environmental Sciences, University of Poonch Rawalakot, Rawalakot, 12350, AJK, Pakistan
| | - Nasir Rahim
- Department of Soil and Environmental Sciences, University of Poonch Rawalakot, Rawalakot, 12350, AJK, Pakistan
| | - Jiangqi Wu
- College of Forestry, Gansu Agricultural University, Lanzhou, 730070, China
| | - Weiwei Ma
- College of Forestry, Gansu Agricultural University, Lanzhou, 730070, China
| | - Guorong Xu
- College of Forestry, Gansu Agricultural University, Lanzhou, 730070, China
| | - Mengyin Du
- College of Forestry, Gansu Agricultural University, Lanzhou, 730070, China
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19
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Abalos D, Rittl TF, Recous S, Thiébeau P, Topp CFE, van Groenigen KJ, Butterbach-Bahl K, Thorman RE, Smith KE, Ahuja I, Olesen JE, Bleken MA, Rees RM, Hansen S. Predicting field N 2O emissions from crop residues based on their biochemical composition: A meta-analytical approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 812:152532. [PMID: 34952057 DOI: 10.1016/j.scitotenv.2021.152532] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/30/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Crop residue incorporation is a common practice to increase or restore organic matter stocks in agricultural soils. However, this practice often increases emissions of the powerful greenhouse gas nitrous oxide (N2O). Previous meta-analyses have linked various biochemical properties of crop residues to N2O emissions, but the relationships between these properties have been overlooked, hampering our ability to predict N2O emissions from specific residues. Here we combine comprehensive databases for N2O emissions from crop residues and crop residue biochemical characteristics with a random-meta-forest approach, to develop a predictive framework of crop residue effects on N2O emissions. On average, crop residue incorporation increased soil N2O emissions by 43% compared to residue removal, however crop residues led to both increases and reductions in N2O emissions. Crop residue effects on N2O emissions were best predicted by easily degradable fractions (i.e. water soluble carbon, soluble Van Soest fraction (NDS)), structural fractions and N returned with crop residues. The relationship between these biochemical properties and N2O emissions differed widely in terms of form and direction. However, due to the strong correlations among these properties, we were able to develop a simplified classification for crop residues based on the stage of physiological maturity of the plant at which the residue was generated. This maturity criteria provided the most robust and yet simple approach to categorize crop residues according to their potential to regulate N2O emissions. Immature residues (high water soluble carbon, soluble NDS and total N concentration, low relative cellulose, hemicellulose, lignin fractions, and low C:N ratio) strongly stimulated N2O emissions, whereas mature residues with opposite characteristics had marginal effects on N2O. The most important crop types belonging to the immature residue group - cover crops, grasslands and vegetables - are important for the delivery of multiple ecosystem services. Thus, these residues should be managed properly to avoid their potentially high N2O emissions.
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Affiliation(s)
- Diego Abalos
- Department of Agroecology, iCLIMATE, Aarhus University, Blichers Alle 20, 8830 Tjele, Denmark.
| | - Tatiana F Rittl
- NORSØK-Norwegian Centre for Organic Agriculture, Gunnars veg 6, 6630 Tingvoll, Norway
| | - Sylvie Recous
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, 51097 Reims, France
| | - Pascal Thiébeau
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, 51097 Reims, France
| | - Cairistiona F E Topp
- Scotland's Rural College, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK
| | - Kees Jan van Groenigen
- Department of Geography, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4 RJ, UK
| | - Klaus Butterbach-Bahl
- Institute of Meteorology and Climate Research (IMK-IFU), Karlsruhe Institute of Technology, Garmisch-Partenkirchen 82467, Germany
| | - Rachel E Thorman
- ADAS Boxworth, Battlegate Road, Boxworth, Cambridge CB23 4NN, UK
| | - Kate E Smith
- ADAS Boxworth, Battlegate Road, Boxworth, Cambridge CB23 4NN, UK
| | - Ishita Ahuja
- NORSØK-Norwegian Centre for Organic Agriculture, Gunnars veg 6, 6630 Tingvoll, Norway; Norwegian Institute of Bioeconomy Research, Skolegata 22, 7713 Steinkjer, Norway
| | - Jørgen E Olesen
- Department of Agroecology, iCLIMATE, Aarhus University, Blichers Alle 20, 8830 Tjele, Denmark
| | - Marina A Bleken
- Norwegian University of Life Sciences, Faculty of Environmental Sciences and Natural Resource Management, Elizabeth Stephensv. 13, 1433 Ås, Norway
| | - Robert M Rees
- Scotland's Rural College, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK
| | - Sissel Hansen
- NORSØK-Norwegian Centre for Organic Agriculture, Gunnars veg 6, 6630 Tingvoll, Norway
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20
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Dockx L, Caluwé M, Dobbeleers T, Dries J. Nitrous oxide formation during simultaneous phosphorus and nitrogen removal in aerobic granular sludge treating different carbon substrates. BIORESOURCE TECHNOLOGY 2022; 345:126542. [PMID: 34906707 DOI: 10.1016/j.biortech.2021.126542] [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: 10/25/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
The impact of different substrates on N2O dynamics and gene expression of marker enzymes (nirS, nirK and nosZ) involved in denitrifying enhanced biological phosphorus removal (d-EBPR) was investigated. Aerobic granular sludge fed with VFAs led to an anoxic P-uptake (27.7 ± 1.2 mg PO43--P.gVSS-1) and N2O emissions up to 80.7 ± 3.4% N2O-N. A decisive role of Accumulibacter in N2O formation was observed. Dosage of amino acids (12.0 ± 1.2 mg PO43--P.gVSS-1) and glucose (1.5 ± 0.9 mg PO43--P.gVSS-1) as sole substrate did not support d-EBPR activity. Presence of NO2- resulted in higher N2O formation in comparison to nitrate and a nosZ/(nirS + nirK) ratio lower than 0.3. A linear correlation (R2 > 0.95) between the nosZ/(nirS + nirK) ratio and the N2O reductase rate was found only when dosing the same type of substrate. This suggests an interplay between the microbial community composition and different polyhydroxyalkanoates derivatives, when dosing different substrates.
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Affiliation(s)
- Lennert Dockx
- BioWAVE, Biochemical Wastewater Valorization and Engineering, Faculty of Applied Engineering, University of Antwerp, Groenenborgerlaan 171, Antwerp 2020, Belgium
| | - Michel Caluwé
- BioWAVE, Biochemical Wastewater Valorization and Engineering, Faculty of Applied Engineering, University of Antwerp, Groenenborgerlaan 171, Antwerp 2020, Belgium
| | - Thomas Dobbeleers
- BioWAVE, Biochemical Wastewater Valorization and Engineering, Faculty of Applied Engineering, University of Antwerp, Groenenborgerlaan 171, Antwerp 2020, Belgium
| | - Jan Dries
- BioWAVE, Biochemical Wastewater Valorization and Engineering, Faculty of Applied Engineering, University of Antwerp, Groenenborgerlaan 171, Antwerp 2020, Belgium.
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21
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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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22
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Cao Y, Wang X, Zhang X, Misselbrook T, Bai Z, Ma L. Nitrifier denitrification dominates nitrous oxide production in composting and can be inhibited by a bioelectrochemical nitrification inhibitor. BIORESOURCE TECHNOLOGY 2021; 341:125851. [PMID: 34523577 DOI: 10.1016/j.biortech.2021.125851] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/22/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Targeted options to reduce nitrous oxide (N2O) emission from composting is scarce due to challenges in disentangling the complex N2O production pathways. Here, combined approaches of nitrogen form analysis, isotopocule mapping, quantitative PCR, and Illumina MiSeq sequencing were used to differentiate N2O production pathways and decipher the underlying biochemical mechanisms. Results suggested that most N2O was produced at the latter stage through nitrifier denitrification. The bioelectrochemical assistance through applying an electric potential reduced N2O emissions by 28.5-75.5%, and the underlying mitigation mechanism was ammonia oxidation repression, as evidenced by the observed reduction in the proportion of the amoA containing family Nitrosomonadaceae from 99% to 83% at the lower voltage and to a negligible level at the higher voltage assessed, which was attributed to their depressed competitiveness for oxygen with heterotrophs. The findings provide evidence that the bioelectrochemical assistance could function as a nitrification inhibitor to minimize compost derived N2O emissions.
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Affiliation(s)
- Yubo Cao
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Science, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, China; University of Chinese Academy of Science, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Xuan Wang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Science, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, China
| | - Xinyuan Zhang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Science, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, China
| | - Tom Misselbrook
- Sustainable Agricultural Sciences, Rothamsted Research, North Wyke, Okehampton EX20 2SB, UK
| | - Zhaohai Bai
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Science, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, China
| | - Lin Ma
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Science, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, China.
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23
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Gallarotti N, Barthel M, Verhoeven E, Pereira EIP, Bauters M, Baumgartner S, Drake TW, Boeckx P, Mohn J, Longepierre M, Mugula JK, Makelele IA, Ntaboba LC, Six J. In-depth analysis of N 2O fluxes in tropical forest soils of the Congo Basin combining isotope and functional gene analysis. THE ISME JOURNAL 2021; 15:3357-3374. [PMID: 34035444 PMCID: PMC8528805 DOI: 10.1038/s41396-021-01004-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 04/14/2021] [Accepted: 04/30/2021] [Indexed: 02/04/2023]
Abstract
Primary tropical forests generally exhibit large gaseous nitrogen (N) losses, occurring as nitric oxide (NO), nitrous oxide (N2O) or elemental nitrogen (N2). The release of N2O is of particular concern due to its high global warming potential and destruction of stratospheric ozone. Tropical forest soils are predicted to be among the largest natural sources of N2O; however, despite being the world's second-largest rainforest, measurements of gaseous N-losses from forest soils of the Congo Basin are scarce. In addition, long-term studies investigating N2O fluxes from different forest ecosystem types (lowland and montane forests) are scarce. In this study we show that fluxes measured in the Congo Basin were lower than fluxes measured in the Neotropics, and in the tropical forests of Australia and South East Asia. In addition, we show that despite different climatic conditions, average annual N2O fluxes in the Congo Basin's lowland forests (0.97 ± 0.53 kg N ha-1 year-1) were comparable to those in its montane forest (0.88 ± 0.97 kg N ha-1 year-1). Measurements of soil pore air N2O isotope data at multiple depths suggests that a microbial reduction of N2O to N2 within the soil may account for the observed low surface N2O fluxes and low soil pore N2O concentrations. The potential for microbial reduction is corroborated by a significant abundance and expression of the gene nosZ in soil samples from both study sites. Although isotopic and functional gene analyses indicate an enzymatic potential for complete denitrification, combined gaseous N-losses (N2O, N2) are unlikely to account for the missing N-sink in these forests. Other N-losses such as NO, N2 via Feammox or hydrological particulate organic nitrogen export could play an important role in soils of the Congo Basin and should be the focus of future research.
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Affiliation(s)
- Nora Gallarotti
- grid.5801.c0000 0001 2156 2780Department of Environmental Systems Science, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
| | - Matti Barthel
- grid.5801.c0000 0001 2156 2780Department of Environmental Systems Science, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
| | - Elizabeth Verhoeven
- grid.4391.f0000 0001 2112 1969College of Agricultural Sciences, Oregon State University, Corvallis, OR USA
| | - Engil Isadora Pujol Pereira
- grid.449717.80000 0004 5374 269XSchool of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Edinburg, TX USA
| | - Marijn Bauters
- grid.5342.00000 0001 2069 7798Isotope Bioscience Laboratory, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium ,grid.5342.00000 0001 2069 7798Computational and Applied Vegetation Ecology Lab, Department of Environment, Ghent University, Ghent, Belgium
| | - Simon Baumgartner
- grid.5801.c0000 0001 2156 2780Department of Environmental Systems Science, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland ,grid.7942.80000 0001 2294 713XEarth and Life Institute, Université Catholique de Louvain, Louvain, Belgium
| | - Travis W. Drake
- grid.5801.c0000 0001 2156 2780Department of Environmental Systems Science, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
| | - Pascal Boeckx
- grid.5342.00000 0001 2069 7798Isotope Bioscience Laboratory, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Joachim Mohn
- grid.7354.50000 0001 2331 3059Laboratory for Air Pollution/Environmental Technology, Swiss Federal Laboratories of Materials Science and Technology, Empa Dubendorf, Switzerland
| | - Manon Longepierre
- grid.5801.c0000 0001 2156 2780Department of Environmental Systems Science, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
| | - John Kalume Mugula
- grid.442836.f0000 0004 7477 7760Département de Biologie, Université Officielle de Bukavu, Bukavu, Democratic Republic of Congo
| | - Isaac Ahanamungu Makelele
- grid.442836.f0000 0004 7477 7760Département de Biologie, Université Officielle de Bukavu, Bukavu, Democratic Republic of Congo ,grid.5342.00000 0001 2069 7798Department of Green Chemistry and Technology, Ghent University, Ghent, Belgium
| | - Landry Cizungu Ntaboba
- grid.442834.d0000 0004 6011 4325Département d’ Agronomie, Université Catholique de Bukavu, Bukavu, Democratic Republic of Congo
| | - Johan Six
- grid.5801.c0000 0001 2156 2780Department of Environmental Systems Science, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
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24
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Zhang IH, Mullen S, Ciccarese D, Dumit D, Martocello DE, Toyofuku M, Nomura N, Smriga S, Babbin AR. Ratio of Electron Donor to Acceptor Influences Metabolic Specialization and Denitrification Dynamics in Pseudomonas aeruginosa in a Mixed Carbon Medium. Front Microbiol 2021; 12:711073. [PMID: 34566916 PMCID: PMC8461185 DOI: 10.3389/fmicb.2021.711073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/09/2021] [Indexed: 11/29/2022] Open
Abstract
Denitrifying microbes sequentially reduce nitrate (NO3 -) to nitrite (NO2 -), NO, N2O, and N2 through enzymes encoded by nar, nir, nor, and nos. Some denitrifiers maintain the whole four-gene pathway, but others possess partial pathways. Partial denitrifiers may evolve through metabolic specialization whereas complete denitrifiers may adapt toward greater metabolic flexibility in nitrogen oxide (NOx -) utilization. Both exist within natural environments, but we lack an understanding of selective pressures driving the evolution toward each lifestyle. Here we investigate differences in growth rate, growth yield, denitrification dynamics, and the extent of intermediate metabolite accumulation under varying nutrient conditions between the model complete denitrifier Pseudomonas aeruginosa and a community of engineered specialists with deletions in the denitrification genes nar or nir. Our results in a mixed carbon medium indicate a growth rate vs. yield tradeoff between complete and partial denitrifiers, which varies with total nutrient availability and ratios of organic carbon to NOx -. We found that the cultures of both complete and partial denitrifiers accumulated nitrite and that the metabolic lifestyle coupled with nutrient conditions are responsible for the extent of nitrite accumulation.
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Affiliation(s)
- Irene H. Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
- Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Susan Mullen
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Davide Ciccarese
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Diana Dumit
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Donald E. Martocello
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Masanori Toyofuku
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Steven Smriga
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Andrew R. Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
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25
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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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26
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Olaya-Abril A, Hidalgo-Carrillo J, Luque-Almagro VM, Fuentes-Almagro C, Urbano FJ, Moreno-Vivián C, Richardson DJ, Roldán MD. Effect of pH on the denitrification proteome of the soil bacterium Paracoccus denitrificans PD1222. Sci Rep 2021; 11:17276. [PMID: 34446760 PMCID: PMC8390676 DOI: 10.1038/s41598-021-96559-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 07/23/2021] [Indexed: 11/25/2022] Open
Abstract
Denitrification is a respiratory process by which nitrate is reduced to dinitrogen. Incomplete denitrification results in the emission of the greenhouse gas nitrous oxide and this is potentiated in acidic soils, which display reduced denitrification rates and high N2O/N2 ratios compared to alkaline soils. In this work, impact of pH on the proteome of the soil denitrifying bacterium Paracoccus denitrificans PD1222 was analysed with nitrate as sole energy and nitrogen source under anaerobic conditions at pH ranging from 6.5 to 7.5. Quantitative proteomic analysis revealed that the highest difference in protein representation was observed when the proteome at pH 6.5 was compared to the reference proteome at pH 7.2. However, this difference in the extracellular pH was not enough to produce modification of intracellular pH, which was maintained at 6.5 ± 0.1. The biosynthetic pathways of several cofactors relevant for denitrification and nitrogen assimilation like cobalamin, riboflavin, molybdopterin and nicotinamide were negatively affected at pH 6.5. In addition, peptide representation of reductases involved in nitrate assimilation and denitrification were reduced at pH 6.5. Data highlight the strong negative impact of pH on NosZ synthesis and intracellular copper content, thus impairing active NosZ assembly and, in turn, leading to elevated nitrous oxide emissions.
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Affiliation(s)
- Alfonso Olaya-Abril
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain
| | - Jesús Hidalgo-Carrillo
- Departamento de Química Orgánica, Universidad de Córdoba, Edificio Marie Curie, Campus de Rabanales, 14071, Córdoba, Spain
| | - Víctor M Luque-Almagro
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain
| | - Carlos Fuentes-Almagro
- Servicio Central de Apoyo a la Investigación (SCAI), Unidad de Proteómica, Universidad de Córdoba, Campus de Rabanales, 14071, Córdoba, Spain
| | - Francisco J Urbano
- Departamento de Química Orgánica, Universidad de Córdoba, Edificio Marie Curie, Campus de Rabanales, 14071, Córdoba, Spain
| | - Conrado Moreno-Vivián
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain
| | - David J Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - María Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain.
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27
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Peng X, Ji Q, Angell JH, Kearns PJ, Bowen JL, Ward BB. Long-Term Fertilization Alters Nitrous Oxide Cycling Dynamics in Salt Marsh Sediments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:10832-10842. [PMID: 34291904 DOI: 10.1021/acs.est.1c01542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Salt marsh sediments are known hotspots for nitrogen cycling, including the production and consumption of nitrous oxide (N2O), a potent greenhouse gas and ozone-depleting agent. Coastal eutrophication, particularly elevated nitrogen loading from the application of fertilizers, is accelerating nitrogen cycling processes in salt marsh sediments. Here, we examine the impact of long-term fertilization on nitrogen cycling processes with a focus on N2O dynamics in a New England salt marsh. By combining 15N-tracer experiments with numerical modeling, we found that both nitrification and denitrification contribute to net N2O production in fertilized sediments. Long-term fertilization increased the relative importance of nitrification to N2O production, likely a result of increased oxygen penetration from nutrient-induced increases in marsh elevation. Substrate utilization rates of key nitrogen cycling processes revealed links between functions and the corresponding microbial communities. Higher specific substrate utilization rates leading to N2O production from nitrification in fertilized sediments indicate a shift in the community composition of ammonia oxidizers, whereas the lack of change in specific substrate utilization of N2O production from denitrification under long-term fertilization suggests resilience of the denitrifying communities. Both are consistent with previous studies on the functional gene community composition in these experimental plots.
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Affiliation(s)
- Xuefeng Peng
- Department of Geosciences, Princeton University, Princeton 08544, New Jersey, United States
| | - Qixing Ji
- Department of Geosciences, Princeton University, Princeton 08544, New Jersey, United States
| | - John H Angell
- Department of Biology, University of Massachusetts, Boston 02125-3300, Massachusetts, United States
| | - Patrick J Kearns
- Department of Biology, University of Massachusetts, Boston 02125-3300, Massachusetts, United States
| | - Jennifer L Bowen
- Department of Biology, University of Massachusetts, Boston 02125-3300, Massachusetts, United States
| | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton 08544, New Jersey, United States
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28
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Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N 2O emissions and nitrite accumulation in soil. ISME JOURNAL 2021; 16:26-37. [PMID: 34211102 PMCID: PMC8692524 DOI: 10.1038/s41396-021-01045-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [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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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: 1] [Impact Index Per Article: 0.3] [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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Duffner C, Holzapfel S, Wunderlich A, Einsiedl F, Schloter M, Schulz S. Dechloromonas and close relatives prevail during hydrogenotrophic denitrification in stimulated microcosms with oxic aquifer material. FEMS Microbiol Ecol 2021; 97:6081091. [PMID: 33428716 DOI: 10.1093/femsec/fiab004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 01/08/2021] [Indexed: 11/12/2022] Open
Abstract
Globally occurring nitrate pollution in groundwater is harming the environment and human health. In situ hydrogen addition to stimulate denitrification has been proposed as a remediation strategy. However, observed nitrite accumulation and incomplete denitrification are severe drawbacks that possibly stem from the specific microbial community composition. We set up a microcosm experiment comprising sediment and groundwater from a nitrate polluted oxic oligotrophic aquifer. After the microcosms were sparged with hydrogen gas, samples were taken regularly within 122 h for nitrate and nitrite measurements, community composition analysis via 16S rRNA gene amplicon sequencing and gene and transcript quantification via qPCR of reductase genes essential for complete denitrification. The highest nitrate reduction rates and greatest increase in bacterial abundance coincided with a 15.3-fold increase in relative abundance of Rhodocyclaceae, specifically six ASVs that are closely related to the genus Dechloromonas. The denitrification reductase genes napA, nirS and clade I nosZ also increased significantly over the observation period. We conclude that taxa of the genus Dechloromonas are the prevailing hydrogenotrophic denitrifiers in this nitrate polluted aquifer and the ability of hydrogenotrophic denitrification under the given conditions is species-specific.
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Affiliation(s)
- Clara Duffner
- Chair of Soil Science, TUM School of Life Sciences Weihenstephan, Technical University Munich, Emil-Ramann-Straße 2, 85354 Freising, Germany.,Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Sebastian Holzapfel
- Chair of Hydrogeology, Technical University Munich, Arcisstraße 21, 80333 Munich, Germany
| | - Anja Wunderlich
- Chair of Hydrogeology, Technical University Munich, Arcisstraße 21, 80333 Munich, Germany
| | - Florian Einsiedl
- Chair of Hydrogeology, Technical University Munich, Arcisstraße 21, 80333 Munich, Germany
| | - Michael Schloter
- Chair of Soil Science, TUM School of Life Sciences Weihenstephan, Technical University Munich, Emil-Ramann-Straße 2, 85354 Freising, Germany.,Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, 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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Huang Y, Jing J, Yan M, Hazard C, Chen Y, Guo C, Xiao X, Lin J. Contribution of pathogenic fungi to N 2O emissions increases temporally in intensively managed strawberry cropping soil. Appl Microbiol Biotechnol 2021; 105:2043-2056. [PMID: 33555364 DOI: 10.1007/s00253-021-11163-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 11/26/2022]
Abstract
Intensively managed agriculture land is a significant contributor to nitrous oxide (N2O) emissions, which adds to global warming and the depletion of the ozone layer. Recent studies have suggested that fungal dominant N2O production may be promoted by pathogenic fungi under high nitrogen fertilization and continuous cropping. Here, we measured the contribution of fungal communities to N2O production under intensively managed strawberry fields of three continuous cropping years (1, 5, and 10 years) and compared this adjacent bare soil. Higher N2O emission was observed from the 10-year field, of which fungi and prokaryotes accounted for 79.7% and 21.3%, respectively. Fungal population density in the 10-year field soil (4.25 × 105 colony forming units per g (CFU/g) of air-dried soil) was greater than the other cropping years. Illumina MiSeq sequencing of the nirK gene showed that long-term continuous cropping decreased the diversity of the fungal denitrifier community, but increased the abundance of Fusarium oxysporum. Additionally, F. oxysporum produced large amounts of N2O in culture and in sterile 10-year field soil. A systemic infection displayed by bioassay strawberry plants after inoculation demonstrated that F. oxysporum was a pathogenic fungus. Together, results suggest that long-term intensively managed monocropping significantly influenced the denitrifying fungal community and increased their biomass, which increased fungal contribution to N2O emissions and specifically by pathogenic fungi. KEY POINTS: • Distinguishing the role of fungi in long-term continuous cropping field. • Identifying the abundant fungal species with denitrifying ability.
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Affiliation(s)
- Ying Huang
- Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, No. 6 Xianyin South Road, Qixia District, Nanjing, 210046, Jiangsu Province, China
| | - Jinquan Jing
- Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, No. 6 Xianyin South Road, Qixia District, Nanjing, 210046, Jiangsu Province, China
| | - Meiling Yan
- Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, No. 6 Xianyin South Road, Qixia District, Nanjing, 210046, Jiangsu Province, China
| | - Christina Hazard
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, 36 Avenue Guy de Collongue, 69134, Ecully, France
| | - Yuehong Chen
- Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, No. 6 Xianyin South Road, Qixia District, Nanjing, 210046, Jiangsu Province, China.
| | - Chengbao Guo
- Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, No. 6 Xianyin South Road, Qixia District, Nanjing, 210046, Jiangsu Province, China
| | - Xu Xiao
- Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, No. 6 Xianyin South Road, Qixia District, Nanjing, 210046, Jiangsu Province, China
| | - Jiujun Lin
- Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, No. 6 Xianyin South Road, Qixia District, Nanjing, 210046, Jiangsu Province, China
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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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Gao Y, Mania D, Mousavi SA, Lycus P, Arntzen MØ, Woliy K, Lindström K, Shapleigh JP, Bakken LR, Frostegård Å. Competition for electrons favours N 2 O reduction in denitrifying Bradyrhizobium isolates. Environ Microbiol 2021; 23:2244-2259. [PMID: 33463871 DOI: 10.1111/1462-2920.15404] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/21/2020] [Accepted: 01/15/2021] [Indexed: 11/28/2022]
Abstract
Bradyrhizobia are common members of soil microbiomes and known as N2 -fixing symbionts of economically important legumes. Many are also denitrifiers, which can act as sinks or sources for N2 O. Inoculation with compatible rhizobia is often needed for optimal N2 -fixation, but the choice of inoculant may have consequences for N2 O emission. Here, we determined the phylogeny and denitrification capacity of Bradyrhizobium strains, most of them isolated from peanut-nodules. Analyses of genomes and denitrification end-points showed that all were denitrifiers, but only ~1/3 could reduce N2 O. The N2 O-reducing isolates had strong preference for N2 O- over NO3 - -reduction. Such preference was also observed in a study of other bradyrhizobia and tentatively ascribed to competition between the electron pathways to Nap (periplasmic NO3 - reductase) and Nos (N2 O reductase). Another possible explanation is lower abundance of Nap than Nos. Here, proteomics revealed that Nap was instead more abundant than Nos, supporting the hypothesis that the electron pathway to Nos outcompetes that to Nap. In contrast, Paracoccus denitrificans, which has membrane-bond NO3 - reductase (Nar), reduced N2 O and NO3 - simultaneously. We propose that the control at the metabolic level, favouring N2 O reduction over NO3 - reduction, applies also to other denitrifiers carrying Nos and Nap but lacking Nar.
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Affiliation(s)
- Yuan Gao
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Daniel Mania
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Seyed Abdollah Mousavi
- Ecosystems and Environment Research programme, Faculty of Biological and Environmental Sciences, and Helsinki Institute of Sustainability Science (HELSUS), University of Helsinki, Finland
| | - Pawel Lycus
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Kedir Woliy
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Kristina Lindström
- Ecosystems and Environment Research programme, Faculty of Biological and Environmental Sciences, and Helsinki Institute of Sustainability Science (HELSUS), University of Helsinki, Finland
| | | | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
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Respiration characteristics and its responses to hydrothermal seasonal changes in reconstructed soils. Sci Rep 2021; 11:144. [PMID: 33420307 PMCID: PMC7794520 DOI: 10.1038/s41598-020-80623-4] [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: 08/17/2020] [Accepted: 12/17/2020] [Indexed: 01/29/2023] Open
Abstract
Seasonal changes in respiration and the components of four reconstructed soils (gravel + meteorite + lou; gravel + shale + lou; gravel + sand + lou; and gravel + soft rock + lou) in barren gravel land were monitored using the soil carbon flux measurement system. The results showed that (1) the monthly average respiration rate and the rates of the components in the four reconstructed soils were the highest in summer and lowest in winter. In winter, the monthly average respiration rates of the four reconstructed soils were not different (p > 0.05). In summer, the monthly average respiration rate of the sand or meteorite reconstructed soil was different from that of the other three (p < 0.05). (2) The heterotrophic and autotrophic respiration rates were different between the four reconstructed soils (p < 0.05). The contribution of heterotrophic respiration to total respiration in the four reconstructed soils was greater than that of autotrophic respiration throughout the year. In winter, autotrophic respiration accounts for the smallest proportion of total respiration. As the temperature rises, the proportion of autotrophic respiration to total respiration gradually increases and peaks in summer. In summer, the proportion of heterotrophic respiration in the total respiration is the smallest. With the decrease in temperature, the proportion of heterotrophic respiration in total respiration gradually increases and peaks in winter. (3) The maximum and minimum values of the monthly average respiration rate of the four reconstructed soils coincided with the months of maximum and minimum soil temperature. The soil volumetric water content changed with the amount of precipitation. The correlation between soil respiration and temperature was greater than that between soil respiration and volumetric water content. (4) The correlation in seasonal variation between respiration of the four remodelled soils and hydrothermal factors in the study area can be characterised by an exponential function and power-exponential function.
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Zhang L, Bill E, Kroneck PMH, Einsle O. Histidine-Gated Proton-Coupled Electron Transfer to the CuA Site of Nitrous Oxide Reductase. J Am Chem Soc 2020; 143:830-838. [DOI: 10.1021/jacs.0c10057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg im Breisgau, Germany
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | | | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg im Breisgau, Germany
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Wang S, Zhao J, Ding X, Li X. Nitric oxide and nitrous oxide production in anaerobic/anoxic nitrite-denitrifying phosphorus removal process: effect of phosphorus concentration. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:45925-45937. [PMID: 32808124 DOI: 10.1007/s11356-020-10499-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
Nitric oxide (NO) and nitrous oxide (N2O) production in biological nutrient removal has been studied widely due to the strong negative effects on the environment. Nitrite-denitrifying phosphorus removal (N-DPR), as a significant source of NO and N2O production, has received great attention. However, the mechanism of NO and N2O production at different phosphorus concentrations is not well understood. Therefore, this study was conducted to investigate the effect of phosphorus concentration on pollutant removal, as well as NO and N2O production during the N-DPR process. The results showed that the phosphorus removal efficiency was improved with the increase of phosphorus concentration, which is caused by the enrichment of denitrifying phosphorus accumulating organisms (DPAOs) at high phosphorus concentration. High NO production was observed at phosphorus concentration of 0.5 mg L-1, which is mainly attributed to the slow recovery of reductase activity and low abundance of DPAOs. The maximal N2O accumulation of 31.45 mg L-1 was also achieved at phosphorus concentration of 0.5 mg L-1. The possible reason is that fewer poly-β-hydroxyalkanoates (PHAs) were synthesized by glycogen accumulating organisms (GAOs) at low phosphorus concentration, which could intensify the electron competition among different reductases. In addition, free nitrous acid (FNA) inhibition was another significant reason for high N2O production.
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Affiliation(s)
- Sha Wang
- School of Water and Environment, Chang'an University, Xi'an, 710064, Shaanxi, China
| | - Jianqiang Zhao
- School of Water and Environment, 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.
| | - Xiaoqian Ding
- School of Architecture and Civil Engineering, Xi'an University of Science and Technology, Xi'an, 710054, Shaanxi, China
| | - Xiaoling Li
- School of Architectural Engineering Institute, Chang'an University, Xi'an, 710064, Shaanxi, China
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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: 106] [Impact Index Per Article: 26.5] [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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Fukushi M, Mino S, Tanaka H, Nakagawa S, Takai K, Sawabe T. Biogeochemical Implications of N 2O-Reducing Thermophilic Campylobacteria in Deep-Sea Vent Fields, and the Description of Nitratiruptor labii sp. nov. iScience 2020; 23:101462. [PMID: 32866828 PMCID: PMC7476070 DOI: 10.1016/j.isci.2020.101462] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/21/2020] [Accepted: 08/12/2020] [Indexed: 01/02/2023] Open
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas and has significantly increased in the atmosphere. Deep-sea hydrothermal fields are representative environments dominated by mesophilic to thermophilic members of the class Campylobacteria that possess clade II nosZ encoding nitrous oxide reductase. Here, we report a strain HRV44T representing the first thermophilic campylobacterium capable of growth by H2 oxidation coupled to N2O reduction. On the basis of physiological and genomic properties, it is proposed that strain HRV44T (=JCM 34002 = DSM 111345) represents a novel species of the genus Nitratiruptor, Nitratiruptor labii sp. nov. The comparison of the N2O consumption ability of strain HRV44T with those of additional Nitratiruptor and other campylobacterial strains revealed the highest level in strain HRV44T and suggests the N2O-respiring metabolism might be the common physiological trait for the genus Nitratiruptor. Our findings provide insights into contributions of thermophilic Campylobacteria to the N2O sink in deep-sea hydrothermal environments.
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Affiliation(s)
- Muneyuki Fukushi
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato-cho, Hakodate 041-8611, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato-cho, Hakodate 041-8611, Japan
| | - Hirohisa Tanaka
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato-cho, Hakodate 041-8611, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Japan
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato-cho, Hakodate 041-8611, Japan
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40
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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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41
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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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42
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Kim D, Nguyen LN, Oh S. Ecological impact of the antibiotic ciprofloxacin on microbial community of aerobic activated sludge. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2020; 42:1531-1541. [PMID: 31420762 DOI: 10.1007/s10653-019-00392-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 08/08/2019] [Indexed: 06/10/2023]
Abstract
This study investigated the effects and fate of the antibiotic ciprofloxacin (CIP) at environmentally relevant levels (50-500 µg/L) in activated sludge (AS) microbial communities under aerobic conditions. Exposure to 500 µg/L of CIP decreased species diversity by about 20% and significantly altered the phylogenetic structure of AS communities compared to those of control communities (no CIP exposure), while there were no significant changes upon exposure to 50 µg/L of CIP. Analysis of community composition revealed that exposure to 500 µg/L of CIP significantly reduced the relative abundance of Rhodobacteraceae and Nakamurellaceae by more than tenfold. These species frequently occur in AS communities across many full-scale wastewater treatment plants and are involved in key ecosystem functions (i.e., organic matter and nitrogen removal). Our analyses showed that 50-500 µg/L CIP was poorly removed in AS (about 20% removal), implying that the majority of CIP from AS processes may be released with either their effluents or waste sludge. We therefore strongly recommend further research on CIP residuals and/or post-treatment processes (e.g., anaerobic digestion) for waste streams that may cause ecological risks in receiving water bodies.
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Affiliation(s)
- Dogun Kim
- Department of Civil Engineering, Kyung Hee University, 1732 Deogyeong-daero, Giheung-Gu, Yongin-Si, Gyeonggi-do, 17104, Republic of Korea
| | - Luong N Nguyen
- Center for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Seungdae Oh
- Department of Civil Engineering, Kyung Hee University, 1732 Deogyeong-daero, Giheung-Gu, Yongin-Si, Gyeonggi-do, 17104, Republic of Korea.
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43
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Deng B, Shi Y, Zhang L, Fang H, Gao Y, Luo L, Feng W, Hu X, Wan S, Huang W, Guo X, Siemann E. Effects of spent mushroom substrate-derived biochar on soil CO 2 and N 2O emissions depend on pyrolysis temperature. CHEMOSPHERE 2020; 246:125608. [PMID: 31884231 DOI: 10.1016/j.chemosphere.2019.125608] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/03/2019] [Accepted: 12/07/2019] [Indexed: 06/10/2023]
Abstract
Edible mushroom cultivation is an important industry in intensively managed forest understories. However, proper disposal of spent mushroom substrate (SMS) presents a challenge to its sustainable development. Biochar derived from SMS could be used to improve soil quality while providing a solution for SMS disposal. But SMS biochar pyrolyzed at different temperatures may alter carbon dioxide (CO2) and nitrous oxide (N2O) emissions associated with global warming, especially under the context of nitrogen (N) addition and warming. We conducted a factorial incubation study to examine greenhouse gas emissions and N transformations in moso bamboo forest soil amended with SMS-biochar (control vs. pyrolyzed at 300, 450 or 600 °C) in different N-addition (0 or 100 mg N kg-1 soil) and temperature (20, 25 or 30 °C) treatments. Pyrolysis temperature affected pH, C and N of SMS-biochars. N-transformations depended on the interaction of pyrolysis temperature, N-addition, and incubation temperature but were generally lower with 450 °C biochar addition. Soil N2O emissions increased with N-addition and they were more sensitive to incubation temperatures without biochar. Soil CO2 emissions increased with incubation temperature or biochar pyrolyzed at lower temperatures. Pyrolysis temperature might have regulated the effects of SMS-derived biochar on N2O emissions via changes in dissolved C, N, pH and associated changes in soil microbial community compositions. Because of the importance of sustainable development of this understory industry, amending soils with biochar produced at higher temperatures may be the best strategy for both the disposal of SMS and the mitigation of greenhouse gas emissions.
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Affiliation(s)
- Bangliang Deng
- Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China; Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, 27695, USA
| | - Yanzhen Shi
- Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Ling Zhang
- Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Haifu Fang
- Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yu Gao
- Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Laicong Luo
- Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Weixun Feng
- Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaofei Hu
- School of Management, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Songze Wan
- Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Wei Huang
- Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaomin Guo
- Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Evan Siemann
- Department of Biosciences, Rice University, Houston, 77005, USA
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Bueno E, Pinedo V, Cava F. Adaptation of Vibrio cholerae to Hypoxic Environments. Front Microbiol 2020; 11:739. [PMID: 32425907 PMCID: PMC7212424 DOI: 10.3389/fmicb.2020.00739] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/30/2020] [Indexed: 01/02/2023] Open
Abstract
Bacteria can colonize virtually any environment on Earth due to their remarkable capacity to detect and respond quickly and adequately to environmental stressors. Vibrio cholerae is a cosmopolitan bacterium that inhabits a vast range of environments. The V. cholerae life cycle comprises diverse environmental and infective stages. The bacterium is found in aquatic ecosystems both under free-living conditions or associated with a wide range of aquatic organisms, and some strains are also capable of causing epidemics in humans. In order to adapt between environments, V. cholerae possesses a versatile metabolism characterized by the rapid cross-regulation of energy-producing pathways. Low oxygen concentration is a key environmental factor that governs V. cholerae physiology. This article reviews the metabolic plasticity that enables V. cholerae to thrive on low oxygen concentrations and its role in environmental and host adaptation.
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Affiliation(s)
- Emilio Bueno
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | | | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
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45
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Torregrosa-Crespo J, Pire C, Bergaust L, Martínez-Espinosa RM. Haloferax mediterranei, an Archaeal Model for Denitrification in Saline Systems, Characterized Through Integrated Physiological and Transcriptional Analyses. Front Microbiol 2020; 11:768. [PMID: 32390995 PMCID: PMC7188791 DOI: 10.3389/fmicb.2020.00768] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/31/2020] [Indexed: 11/13/2022] Open
Abstract
Haloferax mediterranei (R4) belongs to the group of halophilic archaea, one of the predominant microbial populations in hypersaline environments. In these ecosystems, the low availability of oxygen pushes the microbial inhabitants toward anaerobic pathways and the presence of N-oxyanions favor denitrification. In a recent study comparing three Haloferax species carrying dissimilatory N-oxide reductases, H. mediterranei showed promise as a future model for archaeal denitrification. This work further explores the respiratory physiology of this haloarchaeon when challenged with ranges of nitrite and nitrate concentrations and at neutral or sub-neutral pH during the transition to anoxia. Moreover, to begin to understand the transcriptional regulation of N-oxide reductases, detailed gas kinetics was combined with gene expression analyses at high resolution. The results show that H. mediterranei has an expression pattern similar to that observed in the bacterial Domain, well-coordinated at low concentrations of N-oxyanions. However, it could only sustain a few generations of exponential anaerobic growth, apparently requiring micro-oxic conditions for de novo synthesis of denitrification enzymes. This is the first integrated study within this field of knowledge in haloarchaea and Archaea in general, and it sheds lights on denitrification in salty environments.
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Affiliation(s)
- Javier Torregrosa-Crespo
- Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, Alicante, Spain
| | - Carmen Pire
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Linda Bergaust
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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46
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Chee-Sanford J, Tian D, Sanford R. Consumption of N 2O and other N-cycle intermediates by Gemmatimonas aurantiaca strain T-27. MICROBIOLOGY-SGM 2020; 165:1345-1354. [PMID: 31580255 DOI: 10.1099/mic.0.000847] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Bacteria affiliated with the phylum Gemmatimonadetes are found in high abundance in many terrestrial and aquatic environments, yet little is known about their metabolic capabilities. Difficulty in their cultivation has prompted interest in identifying better growth conditions for metabolic studies, especially related to their ability to reduce N2O, a potent greenhouse gas. T-27 Gemmatimonas aurantiaca is one of few cultivated strains of Gemmatimonadetes available for physiological studies. Our objective was to test this organism's ability to use nitrite, nitrate, and N2O, and mineral forms of assimilable NH4 + at concentrations not typically used in tests for compound utilization. Cultures incubated under anaerobic conditions with nitrate, nitrite or N2O failed to grow or show depletion of these substrates. Nitrate and nitrite (1 mM) were not used even when cells were grown aerobically with the O2 allowed to deplete first. N2O reduction only commenced in the presence of O2 and continued to be depleted when refed to the culture under anaerobic, microaerobic and aerobic atmospheres. Carbon mineralization was coupled to the electron-accepting processes, with higher reducing equivalents needed for N2O utilization under aerobic atmospheres. N2O was reduced to N2 in the presence of 20% O2, however the rate of this reaction is reduced in the presence of high O2 concentration. This study demonstrated that G. aurantiaca T-27 possesses unique characteristics for assimilative and dissimilative N processes with new implications for cultivation strategies to better assess the metabolic abilities of Gemmatimonadetes.
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Affiliation(s)
| | - David Tian
- Department of Molecular and Cell Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Robert Sanford
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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47
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Avşar C, Aras ES. Quantification of denitrifier genes population size and its relationship with environmental factors. Arch Microbiol 2020; 202:1181-1192. [PMID: 32076734 DOI: 10.1007/s00203-020-01826-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 01/28/2020] [Accepted: 01/30/2020] [Indexed: 10/25/2022]
Abstract
The objectives of this study were to use real-time PCR for culture-independent quantification of the copy numbers of 16S rRNA and denitrification functional genes, and also the relationships between gene copy numbers and soil physicochemical properties. In this study, qPCR analysis of the soil samples showed 16S rRNA, nirS, nirK, nosZI and nosZII average densities of 3.0 × 108, 2.25 × 107, 2.9 × 105, 4.0 × 106 and 1.75 × 107 copies per gram of dry soil, respectively. In addition, the abundances of (nirS + nirK), nosZI and nosZII relative to 16S rRNA genes were 1.4-34.1%, 0.06-3.95% and 1.3-39%, respectively, confirming the low proportion of denitrifiers to total bacteria in soil. This showed that the non-denitrifying nosZII-type bacteria may contribute significantly to N2O consumption in the soil. Furthermore, the shifts in abundance and diversity of the total bacteria and denitrification functional gene copy numbers correlated significantly with the various soil factors. It is the first study in Turkey about the population size of denitrification functional genes in different soil samples. It also aims to draw attention to nitrous oxide-associated global warming.
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Affiliation(s)
- Cumhur Avşar
- Department of Biology, Faculty of Arts and Sciences, Sinop University, Sinop, Turkey.
| | - E Sümer Aras
- Department of Biology, Faculty of Science, Ankara University, Ankara, Turkey
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Audet J, Bastviken D, Bundschuh M, Buffam I, Feckler A, Klemedtsson L, Laudon H, Löfgren S, Natchimuthu S, Öquist M, Peacock M, Wallin MB. Forest streams are important sources for nitrous oxide emissions. GLOBAL CHANGE BIOLOGY 2020; 26:629-641. [PMID: 31465582 PMCID: PMC7027446 DOI: 10.1111/gcb.14812] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 08/15/2019] [Indexed: 05/28/2023]
Abstract
Streams and river networks are increasingly recognized as significant sources for the greenhouse gas nitrous oxide (N2 O). N2 O is a transformation product of nitrogenous compounds in soil, sediment and water. Agricultural areas are considered a particular hotspot for emissions because of the large input of nitrogen (N) fertilizers applied on arable land. However, there is little information on N2 O emissions from forest streams although they constitute a major part of the total stream network globally. Here, we compiled N2 O concentration data from low-order streams (~1,000 observations from 172 stream sites) covering a large geographical gradient in Sweden from the temperate to the boreal zone and representing catchments with various degrees of agriculture and forest coverage. Our results showed that agricultural and forest streams had comparable N2 O concentrations of 1.6 ± 2.1 and 1.3 ± 1.8 µg N/L, respectively (mean ± SD) despite higher total N (TN) concentrations in agricultural streams (1,520 ± 1,640 vs. 780 ± 600 µg N/L). Although clear patterns linking N2 O concentrations and environmental variables were difficult to discern, the percent saturation of N2 O in the streams was positively correlated with stream concentration of TN and negatively correlated with pH. We speculate that the apparent contradiction between lower TN concentration but similar N2 O concentrations in forest streams than in agricultural streams is due to the low pH (<6) in forest soils and streams which affects denitrification and yields higher N2 O emissions. An estimate of the N2 O emission from low-order streams at the national scale revealed that ~1.8 × 109 g N2 O-N are emitted annually in Sweden, with forest streams contributing about 80% of the total stream emission. Hence, our results provide evidence that forest streams can act as substantial N2 O sources in the landscape with 800 × 109 g CO2 -eq emitted annually in Sweden, equivalent to 25% of the total N2 O emissions from the Swedish agricultural sector.
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Affiliation(s)
- Joachim Audet
- Department of BioscienceAarhus UniversitySilkeborgDenmark
- Department of Aquatic Sciences and AssessmentSwedish University of Agricultural SciencesUppsalaSweden
| | - David Bastviken
- Department of Thematic Studies – Environmental ChangeLinköping UniversityLinköpingSweden
| | - Mirco Bundschuh
- Department of Aquatic Sciences and AssessmentSwedish University of Agricultural SciencesUppsalaSweden
- Institute for Environmental SciencesUniversity of Koblenz‐LandauLandauGermany
| | - Ishi Buffam
- Department of Biological SciencesUniversity of CincinnatiCincinnatiOHUSA
| | - Alexander Feckler
- Department of Aquatic Sciences and AssessmentSwedish University of Agricultural SciencesUppsalaSweden
| | - Leif Klemedtsson
- Department of Earth SciencesUniversity of GothenburgGothenburgSweden
| | - Hjalmar Laudon
- Department of Forest Ecology and ManagementSwedish University of Agricultural SciencesUmeåSweden
| | - Stefan Löfgren
- Department of Aquatic Sciences and AssessmentSwedish University of Agricultural SciencesUppsalaSweden
| | | | - Mats Öquist
- Department of Forest Ecology and ManagementSwedish University of Agricultural SciencesUmeåSweden
| | - Mike Peacock
- Department of Aquatic Sciences and AssessmentSwedish University of Agricultural SciencesUppsalaSweden
| | - Marcus B. Wallin
- Department of Earth Sciences, Air, Water and Landscape SciencesUppsala UniversityUppsalaSweden
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49
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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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INDISIM-Denitrification, an individual-based model for study the denitrification process. J Ind Microbiol Biotechnol 2019; 47:1-20. [PMID: 31691030 DOI: 10.1007/s10295-019-02245-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022]
Abstract
Denitrification is one of the key processes of the global nitrogen (N) cycle driven by bacteria. It has been widely known for more than 100 years as a process by which the biogeochemical N-cycle is balanced. To study this process, we develop an individual-based model called INDISIM-Denitrification. The model embeds a thermodynamic model for bacterial yield prediction inside the individual-based model INDISIM and is designed to simulate in aerobic and anaerobic conditions the cell growth kinetics of denitrifying bacteria. INDISIM-Denitrification simulates a bioreactor that contains a culture medium with succinate as a carbon source, ammonium as nitrogen source and various electron acceptors. To implement INDISIM-Denitrification, the individual-based model INDISIM was used to give sub-models for nutrient uptake, stirring and reproduction cycle. Using a thermodynamic approach, the denitrification pathway, cellular maintenance and individual mass degradation were modeled using microbial metabolic reactions. These equations are the basis of the sub-models for metabolic maintenance, individual mass synthesis and reducing internal cytotoxic products. The model was implemented in the open-access platform NetLogo. INDISIM-Denitrification is validated using a set of experimental data of two denitrifying bacteria in two different experimental conditions. This provides an interactive tool to study the denitrification process carried out by any denitrifying bacterium since INDISIM-Denitrification allows changes in the microbial empirical formula and in the energy-transfer-efficiency used to represent the metabolic pathways involved in the denitrification process. The simulator can be obtained from the authors on request.
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