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Yang W, Cui H, Liu Q, Wang F, Liao H, Lu P, Qin S. Effect of nitrogen reduction by chemical fertilization with green manure (Vicia sativa L.) on soil microbial community, nitrogen metabolism and and yield of Uncaria rhynchophylla by metagenomics. Arch Microbiol 2024; 206:106. [PMID: 38363349 DOI: 10.1007/s00203-024-03839-2] [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: 11/23/2023] [Revised: 12/24/2023] [Accepted: 01/06/2024] [Indexed: 02/17/2024]
Abstract
Uncaria rhynchophylla is an important herbal medicine, and the predominant issues affecting its cultivation include a single method of fertilizer application and inappropriate chemical fertilizer application. To reduce the use of inorganic nitrogen fertilization and increase the yield of Uncaria rhynchophylla, field experiments in 2020-2021 were conducted. The experimental treatments included the following categories: S1, no fertilization; S2, application of chemical NPK fertilizer; and S3-S6, application of chemical fertilizers and green manures, featuring nitrogen fertilizers reductions of 0%, 15%, 30%, and 45%, respectively. The results showed that a moderate application of nitrogen fertilizer when combined with green manure, can help alleviate soil acidification and increase urease activity. Specifically, the treatment with green manure provided in a 14.71-66.67% increase in urease activity compared to S2. Metagenomics sequencing results showed a decrease in diversity in S3, S4, S5, and S6 compared to S2, but the application of chemical fertilizer with green manure promoted an increase in the relative abundance of Acidobacteria and Chloroflexi. In addition, the nitrification pathway displayed a progressive augmentation in tandem with the reduction in nitrogen fertilizer and application of green manure, reaching its zenith at S5. Conversely, other nitrogen metabolism pathways showed a decline in correlation with diminishing nitrogen fertilizer dosages. The rest of the treatments showed an increase in yield in comparison to S1, S5 showing significant differences (p < 0.05). In summary, although S2 demonstrate the ability to enhance soil microbial diversity, it is important to consider the long-term ecological impacts, and S5 may be a better choice.
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Affiliation(s)
- Wansheng Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - HongHao Cui
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
- Institute of Soil Fertilizer, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Qian Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Fang Wang
- Guizhou Industry Polytechnic College, Guiyang, 550008, China
| | - Heng Liao
- Institute of Soil Fertilizer, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Ping Lu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China.
| | - Song Qin
- Institute of Soil Fertilizer, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
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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: 1] [Impact Index Per Article: 1.0] [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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Chen Z, Huang Y, Shen Y, Zhang J, Deng J, Chen X. Denitrification shifted autotroph-heterotroph interactions in Microcystis aggregates. ENVIRONMENTAL RESEARCH 2023; 231:116269. [PMID: 37257745 DOI: 10.1016/j.envres.2023.116269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/13/2023] [Accepted: 05/27/2023] [Indexed: 06/02/2023]
Abstract
Denitrification is the most important process for nitrogen removal in eutrophic lakes and was mostly investigated in lake sediment. Denitrification could also be mediated by cyanobacterial aggregates, yet how this process impacts nitrogen (N) availability and the associated autotroph-heterotroph relationships within cyanobacterial aggregates has not been investigated. In this study, incubation experiments with nitrate amendment were conducted with Microcystis aggregates (MAs). Measurement of nitrogen contents, 16S rRNA-based microbial community profiling and metatranscriptomic sequencing were used to jointly assess nitrogen turnover dynamics, as well as changes in microbial composition and gene expression. Strong denitrification potential was revealed, and maximal N removal was achieved within two days, after which the communities entered a state of severe N limitation. Changes of active microbial communities were further promoted both with regard to taxonomic composition and transcriptive activities. Expression of transportation-related genes confirmed competition for N sources by Microcystis and phycospheric communities. Strong stress response to reactive oxygen species by Microcystis was revealed. Notably, interspecific relationships among Microcystis and phycospheric communities exhibited a shift toward antagonistic interactions, particularly evidenced by overall increased expression of genes related to cell lysis and utilization of cellular materials. Patterns of fatty acid and starch metabolism also suggested changes in carbon metabolism and cross-feeding patterns within MAs. Taken together, this study demonstrated substantial denitrification potential of MAs, which, importantly, further induced changes in both metabolic activities and autotroph-heterotroph interactions. These findings also highlight the key role of nutrient condition in shaping autotroph-heterotroph relationships.
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Affiliation(s)
- Zhijie Chen
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restorations, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Yingying Huang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restorations, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China; Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai, China.
| | - Yingshi Shen
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restorations, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Junyi Zhang
- Jiangsu Wuxi Environmental Monitoring Center, Jiangsu, China
| | - Jie Deng
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restorations, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China; Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai, China.
| | - Xuechu Chen
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restorations, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China; Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai, China
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Shi Z, Yang Y, Fan Y, He Y, Li T. Dynamic Responses of Rhizosphere Microorganisms to Biogas Slurry Combined with Chemical Fertilizer Application during the Whole Life Cycle of Rice Growth. Microorganisms 2023; 11:1755. [PMID: 37512927 PMCID: PMC10386682 DOI: 10.3390/microorganisms11071755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/14/2023] [Accepted: 07/01/2023] [Indexed: 07/30/2023] Open
Abstract
Biogas slurry combined with chemical fertilizer (BCF) is widely used as a fertilizer in paddy fields and rhizosphere microorganisms are key players in plant growth and reproduction. However, the dynamic responses of rhizosphere microorganisms of field-grown rice to BCF application still remain largely unknown. In this study, a field experiment was conducted in two proximate paddy fields in Chongming Island to study the impacts of BCF on the changes in rhizosphere microorganisms during the whole rice growth, including seedling, tillering, booting, and grain-filling stages, with solely chemical fertilizer (CF) treatment as control. The results showed BCF could increase the N-, P-, and C- levels in paddy water as well as the rhizosphere microbial abundance and diversity compared with control. In particular, the phosphate-solubilizing- and cellulose-decomposing-bacteria (e.g., Bacillus) and fungi (e.g., Mortierella) were more abundant in the rhizosphere of BCF than those of CF. Moreover, these microbes increased markedly at the booting and grain-filling stages in BCF, which could promote rice to obtain available nutrients (P and C). It was noted that denitrifying-like bacteria (e.g., Steroidobacteraceae) decreased and dissimilatory nitrate reduction to ammonia-related bacteria (e.g., Geobacter, Anaeromyxobacter, and Ignavibacterium) increased at the booting and filling stages, which could promote N-availability. TP in paddy water of BCF was most correlated to the bacteria, while COD was the most critical regulator for the fungi. Furthermore, correlation network analysis showed nutrient-cycling-related microorganisms were more closely interconnected in BCF than those in CF. These findings showed the application of biogas slurry plus chemical fertilizer could regulate rhizosphere microorganisms towards a beneficial fertilizer use for rice growth.
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Affiliation(s)
- Zhenbao Shi
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
| | - Yanmei Yang
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, Institute of Eco-Chongming, East China Normal University, Shanghai 200241, China
| | - Yehong Fan
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, Institute of Eco-Chongming, East China Normal University, Shanghai 200241, China
| | - Yan He
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, Institute of Eco-Chongming, East China Normal University, Shanghai 200241, China
| | - Tian Li
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
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Bose H, Sahu RP, Sar P. Impact of arsenic on microbial community structure and their metabolic potential from rice soils of West Bengal, India. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 841:156486. [PMID: 35667424 DOI: 10.1016/j.scitotenv.2022.156486] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 05/27/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Paddy soil is a heterogenous ecosystem that harbours diverse microbial communities critical for maintaining ecosystem sustainability and crop yield. Considering the importance of soil in crop production and recent reports on its contamination with arsenic (As) across the South East Asia, its microbial community composition and biogeochemical functions remained inadequately studied. We have characterized the microbial communities of rice soil from eleven paddy fields of As-contaminated sites from West Bengal (India), through metagenomics and amplicon sequencing. 16S rRNA gene sequencing showed considerable bacterial diversity [over 0.2 million Operational Taxonomic Units (OTUs)] and abundance (upto 1.6 × 107 gene copies/g soil). Existence of a core-microbiome (261 OTUs conserved out of a total 141,172 OTUs) across the samples was noted. Most of the core-microbiome members were also found to represent the abundant taxa of the soil. Statistical analyses suggested that the microbial communities were highly constrained by As, Fe K, N, PO43-, SO42- and organic carbon (OC). Members of Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Planctomycetes and Thaumarchaeota constituted the core-microbiome. Co-occurrence network analysis displayed significant interaction among diverse anaerobic, SO42- and NO3- reducing, cellulose and other organic matter or C1 compound utilizing, fermentative and aerobic/facultative anaerobic bacteria and archaea. Correlation analysis suggested that taxa which were positively linked with soil parameters that maintain soil health and productivity (e.g., N, K, PO43- and Fe) were adversely impacted by increasing As concentration. Shotgun metagenomics highlighted major metabolic pathways controlling the C (3-hydroxypropionate bicycle), N (Denitrification, dissimilatory NO3- reduction to ammonium), and S (assimilatory SO42- reduction and sulfide oxidation) cycling, As homeostasis (methylation and reduction) and plant growth promotion (polyphosphate hydrolysis and auxin biosynthesis). All these major biogeochemical processes were found to be catalyzed by the members of most abundant/core-community.
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Affiliation(s)
- Himadri Bose
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Rajendra Prasad Sahu
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Pinaki Sar
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India.
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Zheng Y, Liu X, Cai Y, Shao Q, Zhu W, Lin X. Combined intensive management of fertilization, tillage, and organic material mulching regulate soil bacterial communities and functional capacities by altering soil potassium and pH in a Moso bamboo forest. Front Microbiol 2022; 13:944874. [PMID: 36090117 PMCID: PMC9453820 DOI: 10.3389/fmicb.2022.944874] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/25/2022] [Indexed: 11/19/2022] Open
Abstract
Intensive management is a common practice in agricultural and forestry ecosystems to improve soil quality and crop yield by influencing nutrient supply and soil microbiota; however, the linkage between soil nutrients and bacterial community and functional capacities in intensively managed economic forests has not been well studied. In this study, we investigated the soil properties such as available potassium (AK), available nitrogen (AN), available phosphorus (AP), ammonium (NH4+), nitrate (NO3-), organic matter (OM), total nitrogen (TN), total phosphorus (TP), bacterial diversity and community composition, potential functions of rhizome roots, and soil microbiota across a chronosequence of intensively managed Moso bamboo (Phyllostachys edulis) forests. Our results demonstrated that the combined intensive management (deep tillage, fertilization, and organic material mulching) in this study caused a significant increase in the concentrations of AK, AN, AP, NH4+, NO3-, OM, TN, and TP (P < 0.05). However, they led to a remarkable decrease in pH (P < 0.05). Such changes lowered the Shannon diversity of the soil and rhizome root microbiota but did not significantly affect the community composition and functional capacity. Soil bacterial community variation was predominantly mediated by soil total potassium (TK) (15.02%), followed by pH (11.29%) and AK (11.13%). We further observed that Nitrospirae accounted for approximately 50% of the variation in soil pH, NO3-, NH4+, and AK, indicating its importance in soil nutrient cycling, especially nitrogen cycling. Accordingly, we propose that the management-induced changes in soil parameters reshaped the bacterial community structure and keystone bacterial assemblage, leading to the differentiation of microbial functions.
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Affiliation(s)
- Ying Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou, China
| | - Xinzhu Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Yanjiang Cai
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Qingsong Shao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou, China
| | - Wei Zhu
- Protection of Ecological Forestry Research Center in Huzhou, Huzhou, China
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- *Correspondence: Xinchun Lin
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Bose H, Saha A, Sahu RP, Dey AS, Sar P. Characterization of the rare microbiome of rice paddy soil from arsenic contaminated hotspot of West Bengal and their interrelation with arsenic and other geochemical parameters. World J Microbiol Biotechnol 2022; 38:171. [PMID: 35907093 DOI: 10.1007/s11274-022-03355-9] [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: 08/17/2021] [Accepted: 07/05/2022] [Indexed: 11/27/2022]
Abstract
Rare microbial taxa [bacterial and archaeal operational taxonomic units (OTUs) with mean relative abundance ≤ 0.001%] were critical for ecosystem function, yet, their identity and function remained incompletely understood, particularly in arsenic (As) contaminated rice soils. In the present study we have characterized the rare populations of the As-contaminated rice soil microbiomes from West Bengal (India) in terms of their identity, interaction and potential function. Major proportion of the OTUs (73% of total 38,289 OTUs) was represented by rare microbial taxa (henceforth mentioned as rare taxa), which covered 4.5-15.7% of the different communities. Taxonomic assignment of the rare taxa showed their affiliation to members of Gamma-, Alpha-, Delta- Proteobacteria, Actinobacteria, and Acidobacteria. SO42-, NO3-, NH4+and pH significantly impacted the distribution of rare taxa. Rare taxa positively correlated with As were found to be more frequent in relatively high As soil while the rare taxa negatively correlated with As were found to be more frequent in relatively low As soil. Co-occurrence-network analysis indicated that rare taxa whose abundance were correlated strongly (R > 0.8) with As also had strong association (R > 0.8) with PO42-, NO3-, and NH4+. Correlation analysis indicated that the rare taxa were likely to involved in two major guilds one, involved in N-metabolism and the second involved in As/Fe as well as other metabolisms. Role of the rare taxa in denitrification and dissimilatory NO3- reduction (DNRA), As biotransformation, S-, H-, C- and Fe-, metabolism was highlighted from 16S rRNA gene-based predictive analysis. Phylogenetic analysis of rare taxa indicated signatures of inhabitant rice soil microorganisms having significant roles in nitrogen (N) cycle and As-Fe metabolism. This study provided critical insights into the taxonomic identity, metabolic potentials and importance of the rare taxa in As biotransformation and biogeochemical cycling of essential nutrients in As-impacted rice soils.
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Affiliation(s)
- Himadri Bose
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Anumeha Saha
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Rajendra Prasad Sahu
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Anindya Sundar Dey
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Pinaki Sar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India.
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Ma X, Wang T, Shi Z, Chiariello NR, Docherty K, Field CB, Gutknecht J, Gao Q, Gu Y, Guo X, Hungate BA, Lei J, Niboyet A, Le Roux X, Yuan M, Yuan T, Zhou J, Yang Y. Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity. MICROBIOME 2022; 10:112. [PMID: 35902889 PMCID: PMC9330674 DOI: 10.1186/s40168-022-01309-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Anthropogenic activities have increased the inputs of atmospheric reactive nitrogen (N) into terrestrial ecosystems, affecting soil carbon stability and microbial communities. Previous studies have primarily examined the effects of nitrogen deposition on microbial taxonomy, enzymatic activities, and functional processes. Here, we examined various functional traits of soil microbial communities and how these traits are interrelated in a Mediterranean-type grassland administrated with 14 years of 7 g m-2 year-1 of N amendment, based on estimated atmospheric N deposition in areas within California, USA, by the end of the twenty-first century. RESULTS Soil microbial communities were significantly altered by N deposition. Consistent with higher aboveground plant biomass and litter, fast-growing bacteria, assessed by abundance-weighted average rRNA operon copy number, were favored in N deposited soils. The relative abundances of genes associated with labile carbon (C) degradation (e.g., amyA and cda) were also increased. In contrast, the relative abundances of functional genes associated with the degradation of more recalcitrant C (e.g., mannanase and chitinase) were either unchanged or decreased. Compared with the ambient control, N deposition significantly reduced network complexity, such as average degree and connectedness. The network for N deposited samples contained only genes associated with C degradation, suggesting that C degradation genes became more intensely connected under N deposition. CONCLUSIONS We propose a conceptual model to summarize the mechanisms of how changes in above- and belowground ecosystems by long-term N deposition collectively lead to more soil C accumulation. Video Abstract.
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Affiliation(s)
- Xingyu Ma
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
- China Urban Construction Design & Research Institute Co., Ltd, Beijing, 100120, China
| | - Tengxu Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
- North China Municipal Engineering Design & Research Institute Co., Ltd., the Beijing Branch, Beijing, 100081, China
| | - Zhou Shi
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Nona R Chiariello
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Kathryn Docherty
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, 49008, USA
| | - Christopher B Field
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Jessica Gutknecht
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, 06120, Halle, Germany
- Present address: Department of Soil, Water, and Climate, University of Minnesota, Twin Cities, Saint Paul, MN, 55104, USA
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yunfu Gu
- Department of Microbiology, College of Resource, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xue Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Jiesi Lei
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Audrey Niboyet
- Sorbonne Université, Université Paris Cité, UPEC, CNRS, INRAE, IRD, Institut d'Ecologie et des Sciences de l'Environnement de Paris, iEES-Paris, Paris, France
- AgroParisTech, Paris, France
| | - Xavier Le Roux
- Microbial Ecology Centre LEM, INRAE, CNRS, University of Lyon, University Lyon 1, VetAgroSup, UMR INRAE 1418, 43 boulevard du 11 novembre 1918, 69622, Villeurbanne, France
| | - Mengting Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Tong Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
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Weng R, He Y, Wang J, Zhang Z, Wei Z, Yang Y, Huang M, Zhou G. Quantitative characterization and genetic diversity associated with N-cycle pathways in urban rivers with different remediation techniques. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 804:150235. [PMID: 34798749 DOI: 10.1016/j.scitotenv.2021.150235] [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: 08/13/2021] [Revised: 09/04/2021] [Accepted: 09/05/2021] [Indexed: 06/13/2023]
Abstract
The nitrate reduction contributions of denitrification, anaerobic ammonium oxidation (anammox) and dissimilatory nitrate reduction to ammonium (DNRA) remain largely unknown especially in the context of river remediation. In this research, the quantitative differentiation of these three nitrate-reduction processes with different remediation conditions was done by the joint use of microbial analysis and nitrogen isotope-tracing. The experiments were done in simulated river systems with 100-day operations. The results of isotope-tracing showed that the respective N-removal contribution of denitrification was 85.88%-92.46% and 83.49%-84.73% in urban river with aeration and addition of Ca(NO3)2, whereas anammox became the same important (contribution of 49.35%-57.85%) with denitrification for nitrogen removal at a high C/N (Chemical oxygen demand/total nitrogen) ratio of 20. Besides, DNRA only occurred at a C/N ratio of 10 with high-level ammonium accumulation (11.20 ± 0.61 mg/L). Microbial analyses indicated that Ca(NO3)2 injection could promote not only the relative abundance of Proteobacteria (from 47.66% to 59.52%) but also the abundance of hzsB (from (4.66 ± 0.40) × 104 copies·g-1 to (2.66 ± 0.12) × 105 copies·g-1). Moreover, Ca(NO3)2 injection showed significantly positive correlation with Candidatus Jettenia of hzsB and Thiobacillus of all the denitrification functional genes including narG, norB, nosZ and nirS. The C/N ratio showed significantly positive correlation with Azoarcus of nirS (r = 0.941, p < 0.01) and Alloactinosynnema of hzsB (r = 0.941, p < 0.01). It was worth noting that Thiobacillus dominated in N-transformation processes, which underlined the need for the coupling of N transformation with other elements such as sulfur for better understanding and manipulating N cycling in urban rivers.
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Affiliation(s)
- Rui Weng
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, Institute of Eco-Chongming, Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, East China Normal University, Shanghai 200241, China.
| | - Yan He
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, Institute of Eco-Chongming, Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, East China Normal University, Shanghai 200241, China.
| | - Jianhua Wang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, Institute of Eco-Chongming, Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, East China Normal University, Shanghai 200241, China.
| | - Zhen Zhang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, Institute of Eco-Chongming, Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, East China Normal University, Shanghai 200241, China.
| | - Zheng Wei
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, Institute of Eco-Chongming, Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, East China Normal University, Shanghai 200241, China.
| | - Yanmei Yang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, Institute of Eco-Chongming, Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, East China Normal University, Shanghai 200241, China.
| | - Minsheng Huang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, Institute of Eco-Chongming, Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, East China Normal University, Shanghai 200241, China.
| | - Gongming Zhou
- The State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China.
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10
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Too CC, Ong KS, Yule CM, Keller A. Putative roles of bacteria in the carbon and nitrogen cycles in a tropical peat swamp forest. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2020.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Rahman MM, Khanom A, Biswas SK. Effect of Pesticides and Chemical Fertilizers on the Nitrogen Cycle and Functional Microbial Communities in Paddy Soils: Bangladesh Perspective. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2021; 106:243-249. [PMID: 33452610 DOI: 10.1007/s00128-020-03092-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/20/2020] [Indexed: 06/12/2023]
Abstract
The concept of the Nitrogen (N) cycle has been modified over the years based on certain new pathways, including comammox, anammox, and DNRA (dissimilatory nitrate reduction to ammonium). Comammox, nitrification, anammox, denitrification, DNRA, and nitrogen fixation pathways play key roles in the N cycle in paddy soils. Pesticides and chemical fertilizers' effects on the N cycle in paddy soils together with the possible manifestation of these newly discovery pathways are the focus of this review. Both chemical fertilizers and pesticides' overuse affect nitrifying archaea/bacteria and denitrifying and anammox bacteria, while heavy metals affect the nitrification rates in paddy soils. To add extra value to this study, we quantified the comammox amoA single copy gene from the Nitrospira strain 'Nitrospira inopinata'. This review will help researchers access the latest information on the N cycle, particularly in the light of the most recent discoveries.
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Affiliation(s)
- M Mizanur Rahman
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, 7003, Bangladesh.
| | - Azmerry Khanom
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, 7003, Bangladesh
| | - Shudhangshu Kumar Biswas
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, 7003, Bangladesh
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12
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Nie WB, Ding J, Xie GJ, Yang L, Peng L, Tan X, Liu BF, Xing DF, Yuan Z, Ren NQ. Anaerobic Oxidation of Methane Coupled with Dissimilatory Nitrate Reduction to Ammonium Fuels Anaerobic Ammonium Oxidation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:1197-1208. [PMID: 33185425 DOI: 10.1021/acs.est.0c02664] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) is critical for mitigating methane emission and returning reactive nitrogen to the atmosphere. The genomes of n-DAMO archaea show that they have the potential to couple anaerobic oxidation of methane to dissimilatory nitrate reduction to ammonium (DNRA). However, physiological details of DNRA for n-DAMO archaea were not reported yet. This work demonstrated n-DAMO archaea coupling the anaerobic oxidation of methane to DNRA, which fueled Anammox in a methane-fed membrane biofilm reactor with nitrate as only electron acceptor. Microelectrode analysis revealed that ammonium accumulated where nitrite built up in the biofilm. Ammonium production and significant upregulation of gene expression for DNRA were detected in suspended n-DAMO culture with nitrite exposure, indicating that nitrite triggered DNRA by n-DAMO archaea. 15N-labeling batch experiments revealed that n-DAMO archaea produced ammonium from nitrate rather than from external nitrite. Localized gradients of nitrite produced by n-DAMO archaea in biofilms induced ammonium production via the DNRA process, which promoted nitrite consumption by Anammox bacteria and in turn helped n-DAMO archaea resist stress from nitrite. As biofilms predominate in various ecosystems, anaerobic oxidation of methane coupled with DNRA could be an important link between the global carbon and nitrogen cycles that should be investigated in future research.
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Affiliation(s)
- Wen-Bo Nie
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang, Harbin 150090, Heilongjiang, China
| | - Jie Ding
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang, Harbin 150090, Heilongjiang, China
| | - Guo-Jun Xie
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang, Harbin 150090, Heilongjiang, China
| | - Lu Yang
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551, Singapore
| | - Lai Peng
- School of Resources and Environmental Engineering, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Xin Tan
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang, Harbin 150090, Heilongjiang, China
| | - Bing-Feng Liu
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang, Harbin 150090, Heilongjiang, China
| | - De-Feng Xing
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang, Harbin 150090, Heilongjiang, China
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Nan-Qi Ren
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang, Harbin 150090, Heilongjiang, China
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13
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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: 113] [Impact Index Per Article: 28.3] [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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14
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Ding B, Luo W, Qin Y, Li Z. Effects of the addition of nitrogen and phosphorus on anaerobic ammonium oxidation coupled with iron reduction (Feammox) in the farmland soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 737:139849. [PMID: 32526563 DOI: 10.1016/j.scitotenv.2020.139849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/29/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
Anaerobic ammonium oxidation coupled with iron reduction is termed as Feammox, and is a new nitrogen removal process. However, there is a paucity of studies on the response of nutrient additions on Feammox process in farmland ecosystems. In this study, we investigated the shifts of Feammox and iron-reducers under nitrogen (N) and phosphorus (P) applications via isotopic tracing and high-throughput sequencing technology. In the isotopic tracing experiment, Feammox rates was significantly greater in the N and/or P applications soil (0.184-0.239 μg N g-1 day-1) than in the no fertilizer soil (0.172 μg N g-1 day-1). The results indicated that N and P applications could favor the Feammox reaction. Molecular analysis showed that five predominant iron-reducing bacteria, including Geobacter, Anaeromyxobacter, Pseudomonas, Thiobacillus and Bacillus, were detected. Their abundance in the soil with no fertilizer, N, P and N combined with P was 0.93%, 1.11%-1.71%, 0.99%, and 1.40%-1.75%, respectively. This implied that iron-reducing bacteria can be stimulated under N and P applications. Overall, the results of this study demonstrated that N and/or P applications could alter the activity of Feammox, and modulate the potential of IRB in the farmland soils.
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Affiliation(s)
- Bangjing Ding
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing 210023, China; School of the Environment, Nanjing University, Nanjing 210023, China
| | - Wenqi Luo
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing 210023, China; School of the Environment, Nanjing University, Nanjing 210023, China
| | - Yunbin Qin
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing 210023, China; School of the Environment, Nanjing University, Nanjing 210023, China
| | - Zhengkui Li
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing 210023, China; School of the Environment, Nanjing University, Nanjing 210023, China.
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15
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Involvement of NO 3 - in Ecophysiological Regulation of Dissimilatory Nitrate/Nitrite Reduction to Ammonium (DNRA) Is Implied by Physiological Characterization of Soil DNRA Bacteria Isolated via a Colorimetric Screening Method. Appl Environ Microbiol 2020; 86:AEM.01054-20. [PMID: 32631862 DOI: 10.1128/aem.01054-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/29/2020] [Indexed: 11/20/2022] Open
Abstract
Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) has recently regained attention as a nitrogen retention pathway that may potentially be harnessed to alleviate nitrogen loss resulting from denitrification. Until recently, the ecophysiology of DNRA bacteria inhabiting agricultural soils has remained largely unexplored, due to the difficulty in targeted enrichment and isolation of DNRA microorganisms. In this study, >100 DNRA bacteria were isolated from NO3 --reducing anoxic enrichment cultures established with rice paddy soils using a newly developed colorimetric screening method. Six of these isolates, each assigned to a different genus, were characterized to improve the understanding of DNRA physiology. All the isolates carried nrfA and/or nirB, and the Bacillus sp. strain possessed a clade II nosZ gene conferring the capacity for N2O reduction. A common prominent physiological feature observed in the isolates was NO2 - accumulation before NH4 + production, which was further examined with Citrobacter sp. strain DNRA3 (possessing nrfA and nirB) and Enterobacter sp. strain DNRA5 (possessing only nirB). Both isolates showed inhibition of NO2 --to-NH4 + reduction at submillimolar NO3 - concentrations and downregulation of nrfA or nirB transcription when NO3 - was being reduced to NO2 - In batch and chemostat experiments, both isolates produced NH4 + from NO3 - reduction when incubated with excess organic electron donors, while incubation with excess NO3 - resulted in NO2 - buildup but no substantial NH4 + production, presumably due to inhibitory NO3 - concentrations. This previously overlooked link between NO3 - repression of NO2 --to-NH4 + reduction and the C-to-N ratio regulation of DNRA activity may be a key mechanism underpinning denitrification-versus-DNRA competition in soil.IMPORTANCE Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) is an anaerobic microbial pathway that competes with denitrification for common substrates NO3 - and NO2 - Unlike denitrification, which leads to nitrogen loss and N2O emission, DNRA reduces NO3 - and NO2 - to NH4 +, a reactive nitrogen compound with a higher tendency to be retained in the soil matrix. Therefore, stimulation of DNRA has often been proposed as a strategy to improve fertilizer efficiency and reduce greenhouse gas emissions. Such attempts have been hampered by lack of insights into soil DNRA bacterial ecophysiology. Here, we have developed a new screening method for isolating DNRA-catalyzing organisms from agricultural soils without apparent DNRA activity. Physiological characteristics of six DNRA isolates were closely examined, disclosing a previously overlooked link between NO3 - repression of NO2 --to-NH4 + reduction and the C-to-N ratio regulation of DNRA activity, which may be a key to understanding why DNRA activity is rarely observed at substantial levels in nitrogen-rich agricultural soils.
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16
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Ding LJ, Cui HL, Nie SA, Long XE, Duan GL, Zhu YG. Microbiomes inhabiting rice roots and rhizosphere. FEMS Microbiol Ecol 2020; 95:5420819. [PMID: 30916760 DOI: 10.1093/femsec/fiz040] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 03/26/2019] [Indexed: 11/12/2022] Open
Abstract
Land plants directly contact soil through their roots. An enormous diversity of microbes dwelling in root-associated zones, including endosphere (inside root), rhizoplane (root surface) and rhizosphere (soil surrounding the root surface), play essential roles in ecosystem functioning and plant health. Rice is a staple food that feeds over 50% of the global population. Its root is a unique niche, which is often characterized by an oxic region (e.g. the rhizosphere) surrounded by anoxic bulk soil. This oxic-anoxic interface has been recognized as a pronounced hotspot that supports dynamic biogeochemical cycles mediated by various functional microbial groups. Considering the significance of rice production upon global food security and the methane budget, novel insights into how the overall microbial community (i.e. the microbiome) of the rice root system influences ecosystem functioning is the key to improving crop health and sustainable productivity of paddy ecosystems, and alleviating methane emissions. This mini-review summarizes the current understanding of microbial diversity of rice root-associated compartments to some extent, especially the rhizosphere, and makes a comparison of rhizosphere microbial community structures between rice and other crops/plants. Moreover, this paper describes the interactions between root-related microbiomes and rice plants, and further discusses the key factors shaping the rice root-related microbiomes.
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Affiliation(s)
- Long-Jun Ding
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hui-Ling Cui
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - San-An Nie
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China
| | - Xi-En Long
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, Fujian Province, China
| | - Gui-Lan Duan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, Fujian Province, China
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17
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Wan Y, Huang Z, Zhou L, Li T, Liao C, Yan X, Li N, Wang X. Bioelectrochemical Ammoniation Coupled with Microbial Electrolysis for Nitrogen Recovery from Nitrate in Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:3002-3011. [PMID: 31891257 DOI: 10.1021/acs.est.9b05290] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nitrate-N in wastewaters is hard to be recovered because it is difficult to volatilize with an opposite charge to ammonium. Here, we have proved the feasibility of dissimilatory nitrate reduction to ammonia (DNRA) by the easy-acclimated mixed electroactive bacteria, achieving the highest DNRA efficiency of 44%. It was then coupled with microbial electrolysis to concentrate ammonium by a factor of 4 in the catholyte for recovery. The abundance of electroactive bacteria in the biofilm before nitrate addition, especially Geobacter spp., was found to determine the DNRA efficiency. As the main competitors of DNRA bacteria, the growth of denitrifiers was more sensitive to C/N ratios. The DNRA microbial community contrarily showed a stable and recoverable ammoniation performance over C/N ratios ranging from 0.5 to 8.0. A strong competition of the electrode and nitrate on electron donors was observed at the early stage (15 d) of electroactive biofilm formation, which can be weakened when the biofilm was mature on 40 d. Quantitative PCR showed a significant increase in nirS and nrfA transcripts in the ammoniation process. nirS was inhibited significantly after nitrate depletion while nrfA was still upregulated. These findings provided a novel way to recover nitrate-N using organic wastes as both electron donor and power, which has broader implications on the sustainable wastewater treatment and the ecology of nitrogen cycling.
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Affiliation(s)
- Yuxuan Wan
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Zongliang Huang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Lean Zhou
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Tian Li
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Chengmei Liao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Xuejun Yan
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Nan Li
- School of Environmental Science and Engineering, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Xin Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
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18
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Nojiri Y, Kaneko Y, Azegami Y, Shiratori Y, Ohte N, Senoo K, Otsuka S, Isobe K. Dissimilatory Nitrate Reduction to Ammonium and Responsible Microbes in Japanese Rice Paddy Soil. Microbes Environ 2020; 35:ME20069. [PMID: 33028782 PMCID: PMC7734399 DOI: 10.1264/jsme2.me20069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/14/2020] [Indexed: 11/29/2022] Open
Abstract
Nitrification-denitrification processes in the nitrogen cycle have been extensively examined in rice paddy soils. Nitrate is generally depleted in the reduced soil layer below the thin oxidized layer at the surface, and this may be attributed to high denitrification activity. In the present study, we investigated dissimilatory nitrate reduction to ammonium (DNRA), which competes with denitrification for nitrate, in order to challenge the conventional view of nitrogen cycling in paddy soils. We performed paddy soil microcosm experiments using 15N tracer analyses to assess DNRA and denitrification rates and conducted clone library analyses of transcripts of nitrite reductase genes (nrfA, nirS, and nirK) in order to identify the microbial populations carrying out these processes. The results obtained showed that DNRA occurred to a similar extent to denitrification and appeared to be enhanced by a nitrate limitation relative to organic carbon. We also demonstrated that different microbial taxa were responsible for these distinct processes. Based on these results and previous field observations, nitrate produced by nitrification within the surface oxidized layer may be reduced not only to gaseous N2 via denitrification, but also to NH4+ via DNRA, within the reduced layer. The present results also indicate that DNRA reduces N loss through denitrification and nitrate leaching and provides ammonium to rice roots in rice paddy fields.
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Affiliation(s)
- Yosuke Nojiri
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuka Kaneko
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yoichi Azegami
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Nobuhito Ohte
- Graduate School of Informatics, Kyoto University, Kyoto, Japan
| | - Keishi Senoo
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Shigeto Otsuka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Kazuo Isobe
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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19
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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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20
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Cannon J, Sanford RA, Connor L, Yang WH, Chee-Sanford J. Optimization of PCR primers to detect phylogenetically diverse nrfA genes associated with nitrite ammonification. J Microbiol Methods 2019; 160:49-59. [PMID: 30905502 DOI: 10.1016/j.mimet.2019.03.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/20/2019] [Accepted: 03/20/2019] [Indexed: 10/27/2022]
Abstract
Dissimilatory nitrate reduction to ammonium (DNRA) is now known to be a more prevalent process in terrestrial ecosystems than previously thought. The key enzyme, a pentaheme cytochrome c nitrite reductase NrfA associated with respiratory nitrite ammonification, is encoded by the nrfA gene in a broad phylogeny of bacteria. The lack of reliable and comprehensive molecular tools to detect diverse nrfA from environmental samples has hampered efforts to meaningfully characterize the genetic potential for DNRA in environmental systems. In this study, modifications were made to optimize the amplification efficiency of previously-designed PCR primers, targeting the diagnostic region of NrfA between the conserved third- and fourth heme binding domains, and to increase coverage to include detection of environmentally relevant Geobacteraceae-like nrfA. Using an alignment of the primers to >270 bacterial nrfA genes affiliated with 18 distinct clades, modifications to the primer sequences improved coverage, minimized amplification artifacts, and yielded the predicted product sizes from reference-, soil-, and groundwater DNA. Illumina sequencing of amplicons showed the successful recovery of nrfA gene fragments from environmental DNA based on alignments of the translated sequences. The new primers developed in this study are more efficient in PCR reactions, although gene targets with high GC content affect efficiency. Furthermore, the primers have a broader spectrum of detection and were validated rigorously for use in detecting nrfA from natural environments. These are suitable for conventional PCR, qPCR, and use in PCR access array technologies that allow multiplex gene amplification for downstream high throughput sequencing platforms.
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Affiliation(s)
- Jordan Cannon
- Dept. of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Robert A Sanford
- Dept. of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Wendy H Yang
- Dept. of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Dept. of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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