1
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Elrys AS, Wang J, Meng L, Zhu Q, El-Sawy MM, Chen Z, Tu X, El-Saadony MT, Zhang Y, Zhang J, Cai Z, Müller C, Cheng Y. Integrative knowledge-based nitrogen management practices can provide positive effects on ecosystem nitrogen retention. NATURE FOOD 2023; 4:1075-1089. [PMID: 38053005 DOI: 10.1038/s43016-023-00888-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 11/03/2023] [Indexed: 12/07/2023]
Abstract
Knowledge-based nitrogen (N) management provides better synchronization of crop N demand with N supply to enhance crop production while reducing N losses. Yet, how these N management practices contribute to reducing N losses globally is unclear. Here we compiled 5,448 paired observations from 336 publications representing 286 sites to assess the impacts of four common knowledge-based N management practices, including balanced fertilization, organic fertilization, co-application of synthetic and organic fertilizers, and nitrification inhibitors, on global ecosystem N cycling. We found that organic and balanced fertilization rather than N-only fertilization stimulated soil nitrate retention by enhancing microbial biomass, but also stimulated soil N leaching and emissions relative to no fertilizer addition. Nitrification inhibitors, however, stimulated soil ammonium retention and plant N uptake while reducing N leaching and emissions. Therefore, integrative application of knowledge-based N management practices is imperative to stimulate ecosystem N retention and minimize the risk of N loss globally.
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Affiliation(s)
- Ahmed S Elrys
- College of Tropical Crops, Hainan University, Haikou, China
- Soil Science Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Jing Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Lei Meng
- College of Tropical Crops, Hainan University, Haikou, China
| | - Qilin Zhu
- College of Tropical Crops, Hainan University, Haikou, China
| | - Mostafa M El-Sawy
- Soil Science Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - ZhaoXiong Chen
- School of Geography, Nanjing Normal University, Nanjing, China
| | - XiaoShun Tu
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Mohamed T El-Saadony
- Department of Agricultural Microbiology, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - YanHui Zhang
- School of Geography, Nanjing Normal University, Nanjing, China
| | - JinBo Zhang
- College of Tropical Crops, Hainan University, Haikou, China
- School of Geography, Nanjing Normal University, Nanjing, China
- Liebig Centre of Agroecology and Climate Impact Research, Justus Liebig University, Giessen, Germany
| | - ZuCong Cai
- School of Geography, Nanjing Normal University, Nanjing, China
- Liebig Centre of Agroecology and Climate Impact Research, Justus Liebig University, Giessen, Germany
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
| | - Christoph Müller
- Liebig Centre of Agroecology and Climate Impact Research, Justus Liebig University, Giessen, Germany
- Institute of Plant Ecology, Justus Liebig University Giessen, Giessen, Germany
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Yi Cheng
- School of Geography, Nanjing Normal University, Nanjing, China.
- Liebig Centre of Agroecology and Climate Impact Research, Justus Liebig University, Giessen, Germany.
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China.
- Key Laboratory of Virtual Geographic Environment (Nanjing Normal University), Ministry of Education, Nanjing, China.
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2
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Yoon S, Heo H, Han H, Song DU, Bakken LR, Frostegård Å, Yoon S. Suggested role of NosZ in preventing N 2O inhibition of dissimilatory nitrite reduction to ammonium. mBio 2023; 14:e0154023. [PMID: 37737639 PMCID: PMC10653820 DOI: 10.1128/mbio.01540-23] [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: 06/23/2023] [Accepted: 07/31/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) is a microbial energy-conserving process that reduces NO3 - and/or NO2 - to NH4 +. Interestingly, DNRA-catalyzing microorganisms possessing nrfA genes are occasionally found harboring nosZ genes encoding nitrous oxide reductases, i.e., the only group of enzymes capable of removing the potent greenhouse gas N2O. Here, through a series of physiological experiments examining DNRA metabolism in one of such microorganisms, Bacillus sp. DNRA2, we have discovered that N2O may delay the transition to DNRA upon an oxic-to-anoxic transition, unless timely removed by the nitrous oxide reductases. These observations suggest a novel explanation as to why some nrfA-possessing microorganisms have retained nosZ genes: to remove N2O that may otherwise interfere with the transition from O2 respiration to DNRA.
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Affiliation(s)
- Sojung Yoon
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Hokwan Heo
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Heejoo Han
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Dong-Uk Song
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Lars R. Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Sukhwan Yoon
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
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3
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Zhang Y, Li J, Pang Y, Shu Y, Liu S, Sang P, Sun X, Liu J, Yang Y, Chen M, Hong P. Systematic investigation of simultaneous copper biosorption and nitrogen removal from wastewater by an aerobic denitrifying bacterium of auto-aggregation. ENVIRONMENTAL RESEARCH 2023; 235:116602. [PMID: 37429397 DOI: 10.1016/j.envres.2023.116602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 07/02/2023] [Accepted: 07/07/2023] [Indexed: 07/12/2023]
Abstract
Finding effective methods for simultaneous removal of eutrophic nutrients and heavy metals has attracted increasing concerns for the environmental remediation. Herein, a novel auto-aggregating aerobic denitrifying strain (Aeromonas veronii YL-41) was isolated with capacities for copper tolerance and biosorption. The denitrification efficiency and nitrogen removal pathway of the strain were investigated by nitrogen balance analysis and amplification of key denitrification functional genes. Moreover, the changes in the auto-aggregation properties of the strain caused by extracellular polymeric substances (EPS) production were focused on. The biosorption capacity and mechanisms of copper tolerance during denitrification were further explored by measuring changes in copper tolerance and adsorption indices, as well as by variations in extracellular functional groups. The strain showed extremely strong total nitrogen removal ability, with 67.5%, 82.08% and 78.48% of total nitrogen removal when NH4+-N, NO2--N, and NO3--N were used as the only initial nitrogen source, respectively. The successful amplification of napA, nirK, norR, and nosZ genes further demonstrated that the strain accomplished nitrate removal through a complete aerobic denitrification pathway. The production of protein-rich EPS of up to 23.31 mg/g and an auto-aggregation index of up to 76.42% may confer a strong biofilm-forming potential to the strain. Under the stress of 20 mg/L copper ions, the removal of nitrate-nitrogen was still as high as 71.4%. In addition, the strain could achieve an efficient removal of 96.9% of copper ions at an initial concentration of 80 mg/L. Scanning electron microscopy and deconvolution analysis of characteristic peaks confirmed that the strains encapsulate heavy metals by secreting EPS and, meanwhile, form strong hydrogen bonding structures to enhance intermolecular forces to resist copper ion stress. This study provides an innovative and effective biological approach for the synergistic bioaugmentation removal of eutrophic substances and heavy metals from aquatic environments.
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Affiliation(s)
- Yancheng Zhang
- College of Life Sciences, School of Ecology and Environment, Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded By Anhui Province and Ministry of Education, Anhui Normal University, Wuhu, 241002, China
| | - Jing Li
- College of Life Sciences, School of Ecology and Environment, Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded By Anhui Province and Ministry of Education, Anhui Normal University, Wuhu, 241002, China
| | - Yu Pang
- College of Life Sciences, School of Ecology and Environment, Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded By Anhui Province and Ministry of Education, Anhui Normal University, Wuhu, 241002, China
| | - Yilin Shu
- College of Life Sciences, School of Ecology and Environment, Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded By Anhui Province and Ministry of Education, Anhui Normal University, Wuhu, 241002, China
| | - Shu Liu
- College of Life Sciences, School of Ecology and Environment, Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded By Anhui Province and Ministry of Education, Anhui Normal University, Wuhu, 241002, China
| | - Pengcheng Sang
- College of Life Sciences, School of Ecology and Environment, Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded By Anhui Province and Ministry of Education, Anhui Normal University, Wuhu, 241002, China
| | - Xiaohui Sun
- College of Life Sciences, School of Ecology and Environment, Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded By Anhui Province and Ministry of Education, Anhui Normal University, Wuhu, 241002, China
| | - Jiexiu Liu
- College of Life Sciences, School of Ecology and Environment, Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded By Anhui Province and Ministry of Education, Anhui Normal University, Wuhu, 241002, China
| | - Yanfang Yang
- College of Life Sciences, School of Ecology and Environment, Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded By Anhui Province and Ministry of Education, Anhui Normal University, Wuhu, 241002, China
| | - Minglin Chen
- College of Life Sciences, School of Ecology and Environment, Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded By Anhui Province and Ministry of Education, Anhui Normal University, Wuhu, 241002, China.
| | - Pei Hong
- College of Life Sciences, School of Ecology and Environment, Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded By Anhui Province and Ministry of Education, Anhui Normal University, Wuhu, 241002, China.
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4
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Pizarro L, Magalhães C, Almeida CMR, Carvalho MDF, Semedo M. Cadmium effects on net N2O production by the deep-sea isolate Shewanella loihica PV-4. FEMS Microbiol Lett 2023; 370:fnad047. [PMID: 37279908 PMCID: PMC10337742 DOI: 10.1093/femsle/fnad047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/19/2023] [Accepted: 06/01/2023] [Indexed: 06/08/2023] Open
Abstract
Deep-sea mining may lead to the release of high concentrations of metals into the surrounding seabed, which can disturb important ecosystem functions provided by microbial communities. Among these, the production of N2O and its reduction to N2 is of great relevance since N2O is an important greenhouse gas. Metal impacts on net N2O production by deep-sea bacteria are, however, currently unexplored. Here, we evaluated the effects of cadmium (Cd) on net N2O production by a deep-sea isolate, Shewanella loihica PV-4. We performed a series of Cd exposure incubations in oxic conditions and determined N2O fluxes during induced anoxic conditions, as well as the relative expression of the nitrite reductase gene (nirK), preceding N2O production, and N2O reductase gene (nosZ), responsible for N2O reduction. Net N2O production by S. loihica PV-4 exposed to Cd was strongly inhibited when compared to the control treatment (no metal). Both nirK and nosZ gene expression were inhibited in reactors with Cd, but nirK inhibition was stronger, supporting the lower net N2O production observed with Cd. The Cd inhibition of net N2O production observed in this study poses the question whether other deep-sea bacteria would undergo the same effects. Future studies should address this question as well as its applicability to complex communities and other physicochemical conditions, which remain to be evaluated.
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Affiliation(s)
- Leonor Pizarro
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Faculty of Biotechnology, Catholic University of Portugal, Porto 4169-005, Portugal
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Department of Biology, Faculty of Sciences (FCUP), University of Porto, Porto 4169-007, Portugal
| | - C Marisa R Almeida
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Department of Chemistry and Biochemistry, Faculty of Sciences (FCUP), University of Porto, Porto 4169-007, Portugal
| | - Maria de Fátima Carvalho
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto 4050-313, Portugal
| | - Miguel Semedo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
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5
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Homology modeling and virtual characterization of cytochrome c nitrite reductase (NrfA) in three model bacteria responsible for short-circuit pathway, DNRA in the terrestrial nitrogen cycle. World J Microbiol Biotechnol 2022; 38:168. [DOI: 10.1007/s11274-022-03352-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/04/2022] [Indexed: 11/26/2022]
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6
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Li Y, Qian Y, Lou X, Hu Z, Hu Y, Zeng M, Liu Z. LuxS in Lactobacillus plantarum SS-128 Improves the Texture of Refrigerated Litopenaeus vannamei: Mechanism Exploration Using a Proteomics Approach. Front Microbiol 2022; 13:892788. [PMID: 35711745 PMCID: PMC9195002 DOI: 10.3389/fmicb.2022.892788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/29/2022] [Indexed: 11/17/2022] Open
Abstract
This study illustrated the texture changes of Shewanella baltica-inoculated Litopenaeus vannamei during refrigerated storage with the exogenous addition of Lactobacillus plantarum SS-128. The group inoculated with SS-128 had an improved texture compared with that inoculated with the luxS-mutant group (ΔluxS). Proteomics were conducted to analyze the protein alterations in L. vannamei and supernatant, respectively. During storage, many texture-related proteins, including myosin heavy chain and beta-actin, were maintained due to luxS. Some endogenous enzymes related to the energy metabolism and hydrolysis of L. vannamei were downregulated. The luxS-induced interaction with S. baltica showed significant changes in the expression of some critical enzymes and pathways. The ATP-dependent zinc metalloprotease FtsH and protease subunit HslV were downregulated, and the oxidative phosphorylation and glycosaminoglycan degradation pathways in S. baltica were inhibited, resulting in the slow deterioration of L. vannamei. By exploring the mechanism underlying SS-128-led manipulation of the metabolism of spoilage bacteria, we clarified the texture maintenance mechanism of luxS in SS-128, providing theoretical evidence for SS-128 application in food preservation.
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Affiliation(s)
- Yuan Li
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.,College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China.,Qingdao Engineering Research Center for Preservation Technology of Marine Foods, Qingdao, China
| | - Yilin Qian
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.,Qingdao Engineering Research Center for Preservation Technology of Marine Foods, Qingdao, China
| | - Xiaowei Lou
- Department of Food Science and Technology, National University of Singapore, Singapore, Singapore
| | - Zhiheng Hu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China.,College of Food Science and Technology, Hainan Tropical Ocean University, Sanya, China
| | - Yaqin Hu
- College of Food Science and Technology, Hainan Tropical Ocean University, Sanya, China
| | - Mingyong Zeng
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.,Qingdao Engineering Research Center for Preservation Technology of Marine Foods, Qingdao, China
| | - Zunying Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.,Qingdao Engineering Research Center for Preservation Technology of Marine Foods, Qingdao, China
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7
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Shi S, He L, Zhou Y, Fan X, Lin Z, He X, Zhou J. Response of nitrogen removal performance and microbial community to a wide range of pH in thermophilic denitrification system. BIORESOURCE TECHNOLOGY 2022; 352:127061. [PMID: 35351554 DOI: 10.1016/j.biortech.2022.127061] [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: 02/16/2022] [Revised: 03/20/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Thermophilic biological nitrogen removal would be a promising alternative to conventional approaches for the treatment of high-temperature wastewater. In this study, the response of thermophilic denitrification system (50 °C) to a wide range of pH (3-11) was investigated. The results showed that thermophilic denitrification could adapt to pH 5-11, but suffered from obvious nitrite and ammonia accumulation at pH 3. Microbial insights indicated that the enrichment of specific functional thermophiles has contributed to the tolerance towards unfavorable pH. Besides, the potential selecting advantage of nitrate reducing bacteria over nitrite reducing bacteria and the enrichment of dissimilatory nitrate reduction to ammonium (DNRA) bacteria could be responsible for the nitrite and ammonia accumulation at pH 3. Moreover, the functional gene prediction denoted higher narG/(nirK + nirS) and nrfA at pH 3, which could facilitate partial denitrification and DNRA. These findings could provide new insight into the application of thermophilic biological nitrogen removal.
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Affiliation(s)
- Shuohui Shi
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Lei He
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Ying Zhou
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Xing Fan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Ziyuan Lin
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Xuejie He
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Jian Zhou
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China.
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8
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Meng T, Wei Q, Yang Y, Cai Z. The influences of soil sulfate content on the transformations of nitrate and sulfate during the reductive soil disinfestation (RSD) process. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151766. [PMID: 34801506 DOI: 10.1016/j.scitotenv.2021.151766] [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: 09/30/2021] [Revised: 11/02/2021] [Accepted: 11/13/2021] [Indexed: 06/13/2023]
Abstract
The transformations and products of sulfate (SO42-) and nitrate (NO3-), especially the influences of SO42- content on the transformations during RSD process, are unclear. In this study, a series of soil SO42- contents (from 333 to 3000 mg S kg-1) were prepared before RSD treatment. The results indicated that nearly all the cumulative NO3- (>98.6%) was removed and not affected by the soil SO42- content. The 15N recovery results showed that 0.57-1.24% and 2.94-4.59% of NO3- translated into ammonium (NH4+) and organic N, respectively, and high SO42- contents stimulated the processes of NO3- dissimilatory reduction and NO3- immobilization. The soluble SO42- contents decreased by 397-922 mg S kg-1, but the contents of total sulfur, sulfide, and sulfate precipitation varied slightly after RSD, indicating that the decreased SO42- was mainly immobilized into organic sulfur in all soils. In addition, a fraction of decreased SO42- was adsorbed to the soil with a relatively high SO42- content. The leaching of SO42- was high (42.9-602 mg S kg-1) during the RSD process, and the leaching amounts increased with increasing soil SO42- content. In terms of the gases emitted from the transformations of NO3- and SO42-, the cumulative emissions of nitrous oxide (N2O) and six sulfurous gases (hydrogen sulfide, carbonyl sulfide, carbon disulfide, methyl mercaptan, dimethyl sulfide, and dimethyl disulfide) were in the ranges of 17.1-21.2 mg N kg-1 and 7.78-23.5 μg S kg-1, respectively, during the whole RSD process. The emissions of sulfurous gases were inhibited by high soil SO42- content, but the N2O emissions were unaffected. In conclusion, the soil SO42- content influenced the transformations of NO3- and SO42- during RSD process, and the SO42- leaching and N2O emissions might threaten the environment which should be concerned.
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Affiliation(s)
- Tianzhu Meng
- College of Agriculture Science and Engineering, Hohai University, Nanjing 211106, China.
| | - Qi Wei
- College of Agriculture Science and Engineering, Hohai University, Nanjing 211106, China
| | - Yanju Yang
- School of Geography Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Zucong Cai
- School of Geography Sciences, Nanjing Normal University, Nanjing 210023, China; Zhongke Clean Soil (Guangzhou) Technology Service Co., Ltd., Guangzhou 510000, China.
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9
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Cheng Y, Elrys AS, Merwad ARM, Zhang H, Chen Z, Zhang J, Cai Z, Müller C. Global Patterns and Drivers of Soil Dissimilatory Nitrate Reduction to Ammonium. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:3791-3800. [PMID: 35226464 DOI: 10.1021/acs.est.1c07997] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Dissimilatory nitrate reduction to ammonium (DNRA), the nearly forgotten process in the terrestrial nitrogen (N) cycle, can conserve N by converting the mobile nitrate into non-mobile ammonium avoiding nitrate losses via denitrification, leaching, and runoff. However, global patterns and controlling factors of soil DNRA are still only rudimentarily known. By a meta-analysis of 231 observations from 85 published studies across terrestrial ecosystems, we find a global mean DNRA rate of 0.31 ± 0.05 mg N kg-1 day-1, being significantly greater in paddy soils (1.30 ± 0.59) than in forests (0.24 ± 0.03), grasslands (0.52 ± 0.15), and unfertilized croplands (0.18 ± 0.04). Soil DNRA was significantly enhanced at higher altitude and lower latitude. Soil DNRA was positively correlated with precipitation, temperature, pH, soil total carbon, and soil total N. Precipitation was the main stimulator for soil DNRA. Total carbon and pH were also important factors, but their effects were ecosystem-specific as total carbon stimulates DNRA in forest soils, whereas pH stimulates DNRA in unfertilized croplands and paddy soils. Higher temperatures inhibit soil DNRA via decreasing total carbon. Moreover, nitrous oxide (N2O) emissions were negatively related to soil DNRA. Thus, future changes in climate and land-use may interact with management practices that alter soil substrate availability and/or soil pH to enhance soil DNRA with positive effects on N conservation and lower N2O emissions.
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Affiliation(s)
- Yi Cheng
- School of Geography, Nanjing Normal University, Nanjing 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing 210023, China
- Jiangsu Engineering Research Center for Soil Utilization & Sustainable Agriculture, Nanjing 210023, China
| | - Ahmed S Elrys
- School of Geography, Nanjing Normal University, Nanjing 210023, China
- Soil Science Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Abdel-Rahman M Merwad
- Soil Science Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Huimin Zhang
- School of Geography, Nanjing Normal University, Nanjing 210023, China
| | - Zhaoxiong Chen
- School of Geography, Nanjing Normal University, Nanjing 210023, China
| | - Jinbo Zhang
- School of Geography, Nanjing Normal University, Nanjing 210023, China
| | - Zucong Cai
- School of Geography, Nanjing Normal University, Nanjing 210023, China
| | - Christoph Müller
- Institute of Plant Ecology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, Giessen 35392, Germany
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin 4, Ireland
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10
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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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Dissimilatory Nitrate Reduction to Ammonium (DNRA) and Denitrification Pathways Are Leveraged by Cyclic AMP Receptor Protein (CRP) Paralogues Based on Electron Donor/Acceptor Limitation in Shewanella loihica PV-4. Appl Environ Microbiol 2021; 87:AEM.01964-20. [PMID: 33158888 DOI: 10.1128/aem.01964-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
Under anoxic conditions, many bacteria, including Shewanella loihica strain PV-4, could use nitrate as an electron acceptor for dissimilatory nitrate reduction to ammonium (DNRA) and/or denitrification. Previous and current studies have shown that DNRA is favored under higher ambient carbon-to-nitrogen (C/N) ratios, whereas denitrification is upregulated under lower C/N ratios, which is consistent with our bioenergetics calculations. Interestingly, computational analyses indicate that the common cyclic AMP receptor protein (designated CRP1) and its paralogue CRP2 might both be involved in the regulation of two competing dissimilatory nitrate reduction pathways, DNRA and denitrification, in S. loihica PV-4 and several other denitrifying Shewanella species. To explore the regulatory mechanism underlying the dissimilatory nitrate reduction (DNR) pathways, nitrate reduction of a series of in-frame deletion mutants was analyzed under different C/N ratios. Deletion of crp1 could accelerate the reduction of nitrite to NO under both low and high C/N ratios. CRP1 is not required for denitrification and actually suppresses production of NO and N2O gases. Deletion of either of the NO-forming nitrite reductase genes nirK or crp2 blocked production of NO gas. Furthermore, real-time PCR and electrophoretic mobility shift assays (EMSAs) demonstrated that the transcription levels of DNRA-relevant genes such as nap-β (napDABGH), nrfA, and cymA were upregulated by CRP1, while nirK transcription was dependent on CRP2. There are tradeoffs between the different physiological roles of nitrate/lactate, as nitrogen nutrient/carbon source and electron acceptor/donor and CRPs may leverage dissimilatory nitrate reduction pathways for maximizing energy yield and bacterial survival under ambient environmental conditions.IMPORTANCE Some microbes utilize different dissimilatory nitrate reduction (DNR) pathways, including DNR to ammonia (DNRA) and denitrification pathways, for anaerobic respiration in response to ambient carbon/nitrogen ratio changes. Large-scale industrial nitrogen fixation and fertilizer application raise the concern of emission of N2O, a stable gas with potent global warming potential, as consequence of microbial respiration, thereby aggravating global warming and climate change. However, little is known about the molecular mechanism underlying the choice of two competing DNR pathways. We demonstrate that the global regulator CRP1, which is widely encoded in bacteria, is required for DNRA in S. loihica PV-4 strain, while the CRP2 paralogue is required for transcription of the nitrite reductase gene nirK for denitrification. Sufficient carbon source lead to the predominance of DNRA, while carbon source/electron donor deficiency may result in an incomplete denitrification process, raising the concern of high levels of N2O emission from nitrate-rich and carbon source-poor waters and soils.
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12
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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: 90] [Impact Index Per Article: 22.5] [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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13
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Bornø ML, Rønn R, Ekelund F. Is wood ash amendment a suitable mitigation strategy for N 2O emissions from soil? THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 713:136581. [PMID: 31951843 DOI: 10.1016/j.scitotenv.2020.136581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/06/2020] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
Wood ash, the by-product of biomass combustion to energy, can return important nutrients back to the soil and counteract acidification. However, the application of wood ash may affect the emission of greenhouse gases. Here, the effect of wood ash application on nitrous oxide (N2O) emissions from different soil environments were investigated in a 40 days incubation experiment comprising ten different soil types amended with five different wood ash concentrations (0, 3, 9, 20, and 54 t ash ha-1). The emitted N2O was measured continuously, and initial soil properties without ash application (carbon (C), nitrogen (N), ammonium (NH4+), nitrate (NO3-), and pH) and resulting soil properties (pH, NH4+, and NO3-) were measured prior and after the incubation period, respectively. The Random Forests (RF) model was used to identify which factors (initial and resulting soil properties, vegetation, management, wood ash doze, and respiration rate) were the most important to predict the development of emitted N2O after ash application. Wood ash either increased, decreased, or had no effect on the amount of emitted N2O depending on soil type and ash dose. The RF model identified the final resulting pH as the most important factor for the prediction of emitted N2O. The results suggest that wood ash can mitigate N2O emissions from soil, however, this effect depends on soil type where a mitigating effect of wood ash application was observed mainly in low pH soils with high soil organic matter whereas an increase in N2O emissions was observed in mineral soils that had previously received N fertilization. This study emphasises the importance of pH manipulation in regards to N2O emissions from soil.
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Affiliation(s)
- Marie Louise Bornø
- University of Copenhagen, Department of Plant & Environmental Sciences, Højbakkegård allé 13, DK-2630 Tåstrup, Denmark; Sino-Danish Center for Education and Research (SDC), University of Chinese Academy of Sciences, 380 Huaibeizhuang, Huairou district, Beijing, China.
| | - Regin Rønn
- University of Copenhagen, Department of Biology, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark.
| | - Flemming Ekelund
- University of Copenhagen, Department of Biology, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark.
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14
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Han H, Song B, Song MJ, Yoon S. Enhanced Nitrous Oxide Production in Denitrifying Dechloromonas aromatica Strain RCB Under Salt or Alkaline Stress Conditions. Front Microbiol 2019; 10:1203. [PMID: 31275250 PMCID: PMC6593283 DOI: 10.3389/fmicb.2019.01203] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 05/13/2019] [Indexed: 11/25/2022] Open
Abstract
Salinity and pH have direct and indirect impacts on the growth and metabolic activities of microorganisms. In this study, the effects of salt and alkaline stresses on the kinetic balance between nitrous oxide (N2O) production and consumption in the denitrification pathway of Dechloromonas aromatica strain RCB were examined. N2O accumulated transiently only in insignificant amounts at low salinity (≤0.5% NaCl) and circumneutral pH (7.0 and 7.5). As compared to these control conditions, incubation at 0.7% salinity resulted in substantially longer lag phase and slower growth rate, along with the increase in the amounts of transiently accumulated N2O (15.8 ± 2.8 μmoles N2O-N/vessel). Incubation at pH 8.0 severely inhibited growth and resulted in permanent accumulation of 29.9 ± 1.3 μmoles N2O-N/vessel from reduction of 151 ± 20 μmoles NO3−/vessel. Monitoring of temporal changes in nirS1, nirS2, and nosZ transcription suggested that the nosZ/(nirS1+nirS2) ratios were indicative of whether N2O was produced or consumed at the time points where measurements were taken. The salt and alkaline stresses altered the N2O consumption kinetics of the resting D. aromatica cells with expressed nitrous oxide reductases. The N2O consumption rates of the cells subjected to the salt and alkaline stress conditions were significantly reduced from 0.84 ± 0.007 μmoles min−1 mg protein−1 of the control to 0.27 ± 0.02 μmoles min−1 mg protein−1 and 0.31 ± 0.03 μmoles min−1 mg protein−1, respectively, when the initial dissolved N2O concentration was 0.1 mM. As the rates of N2O production from NO2− reduction was not significantly affected by the stresses (0.45–0.55 μmoles min−1 mg protein−1), the N2O consumption rate was lower than the N2O production rate at the stress conditions, but not at the control condition. These results clearly indicate that the altered kinetics of expressed nitrous oxide reductase and the resultant disruption of kinetic balance between N2O production and consumption was another cause of enhanced N2O emission observed under the salt and alkaline stress conditions. These findings suggest that canonical denitrifiers may become a significant N2O source when faced with abrupt environmental changes.
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Affiliation(s)
- Heejoo Han
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Bongkeun Song
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Department of Biological Sciences, Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, VA, United States
| | - Min Joon Song
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Sukhwan Yoon
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
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15
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Yoon S, Song B, Phillips RL, Chang J, Song MJ. Ecological and physiological implications of nitrogen oxide reduction pathways on greenhouse gas emissions in agroecosystems. FEMS Microbiol Ecol 2019; 95:5488431. [DOI: 10.1093/femsec/fiz066] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 05/10/2019] [Indexed: 11/12/2022] Open
Abstract
ABSTRACT
Microbial reductive pathways of nitrogen (N) oxides are highly relevant to net emissions of greenhouse gases (GHG) from agroecosystems. Several biotic and abiotic N-oxide reductive pathways influence the N budget and net GHG production in soil. This review summarizes the recent findings of N-oxide reduction pathways and their implications to GHG emissions in agroecosystems and proposes several mitigation strategies. Denitrification is the primary N-oxide reductive pathway that results in direct N2O emissions and fixed N losses, which add to the net carbon footprint. We highlight how dissimilatory nitrate reduction to ammonium (DNRA), an alternative N-oxide reduction pathway, may be used to reduce N2O production and N losses via denitrification. Implications of nosZ abundance and diversity and expressed N2O reductase activity to soil N2O emissions are reviewed with focus on the role of the N2O-reducers as an important N2O sink. Non-prokaryotic N2O sources, e.g. fungal denitrification, codenitrification and chemodenitrification, are also summarized to emphasize their potential significance as modulators of soil N2O emissions. Through the extensive review of these recent scientific advancements, this study posits opportunities for GHG mitigation through manipulation of microbial N-oxide reductive pathways in soil.
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Affiliation(s)
- Sukhwan Yoon
- Department of Civil and Environmental Engineering, KAIST, 291 Daehakro, Yuseonggu, Daejeon 34141, South Korea
| | - Bongkeun Song
- Department of Biological Sciences, Virginia Institute of Marine Sciences, College of William and Mary, 1375 Greate Rd, Gloucester Point, VA 23062, USA
| | - Rebecca L Phillips
- Ecological Insights Corporation, 130 69th Street SE, Hazelton, ND 58544, USA
| | - Jin Chang
- Department of Civil and Environmental Engineering, KAIST, 291 Daehakro, Yuseonggu, Daejeon 34141, South Korea
| | - Min Joon Song
- Department of Civil and Environmental Engineering, KAIST, 291 Daehakro, Yuseonggu, Daejeon 34141, South Korea
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